--- /tmp/apbs-3.0.0+dfsg1-3ivgl96ul/debian/apbs-data_3.0.0+dfsg1-3_all.deb +++ apbs-data_3.0.0+dfsg1-3_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2020-07-23 09:35:23.000000 debian-binary │ --rw-r--r-- 0 0 0 13252 2020-07-23 09:35:23.000000 control.tar.xz │ --rw-r--r-- 0 0 0 226076816 2020-07-23 09:35:23.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 13260 2020-07-23 09:35:23.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 226075268 2020-07-23 09:35:23.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -80,15 +80,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 12137 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE5.out │ │ │ -rw-r--r-- 0 root (0) root (0) 1881 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE6.in │ │ │ -rw-r--r-- 0 root (0) root (0) 12139 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE6.out │ │ │ -rw-r--r-- 0 root (0) root (0) 1881 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE7.in │ │ │ -rw-r--r-- 0 root (0) root (0) 12132 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE7.out │ │ │ -rw-r--r-- 0 root (0) root (0) 1845 2020-05-30 01:47:30.000000 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in │ │ │ -rw-r--r-- 0 root (0) root (0) 799272 2020-05-30 01:47:30.000000 ./usr/share/apbs/examples/actin-dimer/complex.pqr │ │ │ --rw-r--r-- 0 root (0) root (0) 1323440 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/io.mc │ │ │ +-rw-r--r-- 0 root (0) root (0) 1323441 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/io.mc │ │ │ -rw-r--r-- 0 root (0) root (0) 1808 2020-05-30 01:47:30.000000 ./usr/share/apbs/examples/actin-dimer/mesh.m │ │ │ -rw-r--r-- 0 root (0) root (0) 399636 2020-05-30 01:47:30.000000 ./usr/share/apbs/examples/actin-dimer/mol1.pqr │ │ │ -rw-r--r-- 0 root (0) root (0) 399636 2020-05-30 01:47:30.000000 ./usr/share/apbs/examples/actin-dimer/mol2.pqr │ │ │ -rw-r--r-- 0 root (0) root (0) 7594185 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/actin-dimer/pot-PE0.dx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2020-07-23 09:35:23.000000 ./usr/share/apbs/examples/alkanes/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1221 2020-05-30 01:47:30.000000 ./usr/share/apbs/examples/alkanes/2-methylbutane.pdb │ │ │ -rw-r--r-- 0 root (0) root (0) 10276 2020-05-30 01:47:30.000000 ./usr/share/apbs/examples/alkanes/Makefile.in │ │ ├── ./usr/share/apbs/examples/FKBP/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:04:35 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 19:01:32 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr │ │ │ @@ -637,32 +637,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.826818 │ │ │ +Vacc_SASA: Time elapsed: 1.084597 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.303942e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.847125e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.592300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.870900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.346200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.269190e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.446434e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.177074e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.211746e-02 │ │ │ Vprtstp: contraction number = 6.211746e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -736,32 +736,32 @@ │ │ │ Vprtstp: contraction number = 6.956346e-01 │ │ │ Vprtstp: iteration = 25 │ │ │ Vprtstp: relative residual = 1.302234e-06 │ │ │ Vprtstp: contraction number = 6.974500e-01 │ │ │ Vprtstp: iteration = 26 │ │ │ Vprtstp: relative residual = 9.101840e-07 │ │ │ Vprtstp: contraction number = 6.989406e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.877710e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.092371e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.056942e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.079709e+02 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.506409949028E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.710000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.530000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -807,30 +807,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 7766.58 kT │ │ │ VPMG::extEnergy: extDiEnergy = 3755.14 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.805986 │ │ │ +Vacc_SASA: Time elapsed: 1.110994 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.023116e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.667264e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.739600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.044900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.646400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.278846e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.575866e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.159139e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.221522e-01 │ │ │ Vprtstp: contraction number = 1.221522e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -862,32 +862,32 @@ │ │ │ Vprtstp: contraction number = 4.471936e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.248629e-06 │ │ │ Vprtstp: contraction number = 4.746468e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 6.237535e-07 │ │ │ Vprtstp: contraction number = 4.995506e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.876330e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.918530e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.792509e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.028059e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.428963535142E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.100000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.921000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -908,32 +908,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.802347 │ │ │ +Vacc_SASA: Time elapsed: 1.024070 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.277975e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.681172e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.780800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.170000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.541300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.335205e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.457075e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.698787e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.215755e-02 │ │ │ Vprtstp: contraction number = 2.215755e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -947,32 +947,32 @@ │ │ │ Vprtstp: contraction number = 9.587608e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.603412e-06 │ │ │ Vprtstp: contraction number = 9.909475e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.626039e-07 │ │ │ Vprtstp: contraction number = 1.014112e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.438110e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.456390e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.550150e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.783109e+01 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.121921918409E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.490000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.200000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.708000e-03 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -1018,30 +1018,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 10309.9 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4985.22 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.805934 │ │ │ +Vacc_SASA: Time elapsed: 1.261526 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.001557e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.750992e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.920100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.843900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.652500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.332495e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.783603e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.995754e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.329182e-01 │ │ │ Vprtstp: contraction number = 1.329182e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1058,32 +1058,32 @@ │ │ │ Vprtstp: contraction number = 1.009933e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.280625e-06 │ │ │ Vprtstp: contraction number = 1.024328e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.326631e-07 │ │ │ Vprtstp: contraction number = 1.035924e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.816360e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.554820e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.983915e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.222471e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.696401888033E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.000000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.800000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -1104,32 +1104,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001734 │ │ │ +Vacc_SASA: Time elapsed: 0.006858 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.772500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.043040e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.342400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.350200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.808600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.268222e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.206640e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.320467e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.503042e-01 │ │ │ Vprtstp: contraction number = 1.503042e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1146,32 +1146,32 @@ │ │ │ Vprtstp: contraction number = 1.186135e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 3.304907e-06 │ │ │ Vprtstp: contraction number = 1.191339e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.951730e-07 │ │ │ Vprtstp: contraction number = 1.195716e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.021160e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.917850e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.910850e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.129564e+01 │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.176059394103E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.303500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -1217,30 +1217,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00535489 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001679 │ │ │ +Vacc_SASA: Time elapsed: 0.072125 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.898400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.641190e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.339200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.760000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.616700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.323534e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.612860e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.638853e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.268584e-01 │ │ │ Vprtstp: contraction number = 2.268584e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1269,32 +1269,32 @@ │ │ │ Vprtstp: contraction number = 3.027355e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.523815e-06 │ │ │ Vprtstp: contraction number = 3.032958e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.666858e-07 │ │ │ Vprtstp: contraction number = 3.037805e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.579920e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.248030e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.551611e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.791559e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.709734790786E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.700000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.300000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -1315,32 +1315,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.002310 │ │ │ +Vacc_SASA: Time elapsed: 0.012299 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.852900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.113400e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.887700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.679500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.025700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.504726e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020889e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.124328e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.197218e-01 │ │ │ Vprtstp: contraction number = 1.197218e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1357,32 +1357,32 @@ │ │ │ Vprtstp: contraction number = 1.080232e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.668171e-06 │ │ │ Vprtstp: contraction number = 1.086670e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.821545e-07 │ │ │ Vprtstp: contraction number = 1.091941e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.047700e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.025050e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.954618e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.202907e+01 │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.413483938867E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.000000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -1428,30 +1428,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0422608 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001658 │ │ │ +Vacc_SASA: Time elapsed: 0.011039 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.962200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.111030e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.706500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.729000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.231600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.517840e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062796e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.447616e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.511608e-01 │ │ │ Vprtstp: contraction number = 1.511608e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1468,32 +1468,32 @@ │ │ │ Vprtstp: contraction number = 1.062405e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.836009e-06 │ │ │ Vprtstp: contraction number = 1.072929e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.984242e-07 │ │ │ Vprtstp: contraction number = 1.080737e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.801770e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.579110e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.967040e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.220713e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.884571864356E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.128600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -1514,32 +1514,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.822972 │ │ │ +Vacc_SASA: Time elapsed: 1.154879 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.284140e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.667440e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.662000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.985500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.251600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.508531e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330269e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.807364e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.148454e-02 │ │ │ Vprtstp: contraction number = 6.148454e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1613,32 +1613,32 @@ │ │ │ Vprtstp: contraction number = 7.027151e-01 │ │ │ Vprtstp: iteration = 25 │ │ │ Vprtstp: relative residual = 1.401142e-06 │ │ │ Vprtstp: contraction number = 7.044026e-01 │ │ │ Vprtstp: iteration = 26 │ │ │ Vprtstp: relative residual = 9.889238e-07 │ │ │ Vprtstp: contraction number = 7.057985e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.679890e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.051776e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.057199e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.082879e+02 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.486452023042E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.750000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.320000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -1684,30 +1684,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 7766.05 kT │ │ │ VPMG::extEnergy: extDiEnergy = 3755.1 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.643738 │ │ │ +Vacc_SASA: Time elapsed: 1.185493 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.737870e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.676437e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.881600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.223100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 7.961000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.705524e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.526348e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.911375e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.211906e-01 │ │ │ Vprtstp: contraction number = 1.211906e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1739,32 +1739,32 @@ │ │ │ Vprtstp: contraction number = 4.581101e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.399352e-06 │ │ │ Vprtstp: contraction number = 4.836226e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.075712e-07 │ │ │ Vprtstp: contraction number = 5.056422e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.609000e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.679180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.242569e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.541779e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.371923967456E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.360000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -1785,32 +1785,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.645953 │ │ │ +Vacc_SASA: Time elapsed: 1.068298 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.055900e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.658775e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.255000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 7.563500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.187600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.466864e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.787771e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.497645e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.219671e-02 │ │ │ Vprtstp: contraction number = 2.219671e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1824,32 +1824,32 @@ │ │ │ Vprtstp: contraction number = 9.588702e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.611478e-06 │ │ │ Vprtstp: contraction number = 9.903019e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.632204e-07 │ │ │ Vprtstp: contraction number = 1.012861e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.513370e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.493850e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.309878e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.558901e+01 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.119297547416E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.790000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.730000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -1895,30 +1895,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 10305.9 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4984.29 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.808524 │ │ │ +Vacc_SASA: Time elapsed: 1.103447 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.932990e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.497550e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.692800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.498600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.604300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.330955e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.921747e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.766616e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.325279e-01 │ │ │ Vprtstp: contraction number = 1.325279e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1935,44 +1935,44 @@ │ │ │ Vprtstp: contraction number = 1.009444e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.272261e-06 │ │ │ Vprtstp: contraction number = 1.024006e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.317723e-07 │ │ │ Vprtstp: contraction number = 1.035733e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.272620e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.077860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.701610e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.929205e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.638817315582E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.250000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.957279e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.038033e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:04:47 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 19:14:27 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr │ │ │ @@ -2605,32 +2605,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.837299 │ │ │ +Vacc_SASA: Time elapsed: 1.368054 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.291176e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.456393e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.058700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.158500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.381600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.225990e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.424136e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.684196e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.251961e-02 │ │ │ Vprtstp: contraction number = 3.251961e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2647,32 +2647,32 @@ │ │ │ Vprtstp: contraction number = 1.569967e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.728368e-06 │ │ │ Vprtstp: contraction number = 1.692265e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.127259e-07 │ │ │ Vprtstp: contraction number = 1.809371e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.807220e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.679790e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.124692e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.340141e+01 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.619056487019E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.730000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.360000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -2718,30 +2718,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 7853.47 kT │ │ │ VPMG::extEnergy: extDiEnergy = 3800.32 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.804704 │ │ │ +Vacc_SASA: Time elapsed: 1.437705 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.073454e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.951546e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.786800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.602800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.315500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.538857e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.868843e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.249359e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.054672e-01 │ │ │ Vprtstp: contraction number = 1.054672e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2758,32 +2758,32 @@ │ │ │ Vprtstp: contraction number = 1.551340e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 4.573968e-06 │ │ │ Vprtstp: contraction number = 1.730130e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.440650e-07 │ │ │ Vprtstp: contraction number = 1.845367e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.957300e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.719560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.997386e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.251827e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.439357878013E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.000000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.040000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -2804,32 +2804,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.807905 │ │ │ +Vacc_SASA: Time elapsed: 1.285219 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.322845e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.419528e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.730700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.136200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.113900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.277408e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.584089e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.952077e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.215755e-02 │ │ │ Vprtstp: contraction number = 2.215755e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2843,32 +2843,32 @@ │ │ │ Vprtstp: contraction number = 9.587608e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.603412e-06 │ │ │ Vprtstp: contraction number = 9.909475e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.626039e-07 │ │ │ Vprtstp: contraction number = 1.014112e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.332400e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.202620e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.451332e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.705391e+01 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.121921918409E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.870000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.170000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -2914,30 +2914,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 10309.9 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4985.22 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.810103 │ │ │ +Vacc_SASA: Time elapsed: 1.603243 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.050581e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.081423e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.830800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.390400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.303100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.422172e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.968758e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085243e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.329182e-01 │ │ │ Vprtstp: contraction number = 1.329182e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2954,32 +2954,32 @@ │ │ │ Vprtstp: contraction number = 1.009933e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.280625e-06 │ │ │ Vprtstp: contraction number = 1.024328e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.326631e-07 │ │ │ Vprtstp: contraction number = 1.035924e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.639860e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.511100e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.242566e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.484659e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.696401888033E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.100000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.080000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -3000,32 +3000,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001712 │ │ │ +Vacc_SASA: Time elapsed: 0.063572 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.161040e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.122700e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.342100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.104400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.603700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.515934e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.542130e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.442190e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.464441e-01 │ │ │ Vprtstp: contraction number = 1.464441e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3042,32 +3042,32 @@ │ │ │ Vprtstp: contraction number = 1.083801e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.974607e-06 │ │ │ Vprtstp: contraction number = 1.096829e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.183173e-07 │ │ │ Vprtstp: contraction number = 1.105624e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.839630e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.627230e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.130011e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.394374e+01 │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.982504155807E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.100000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -3113,30 +3113,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0085798 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001705 │ │ │ +Vacc_SASA: Time elapsed: 0.011291 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.076680e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.271770e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.340800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.081400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.056700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.494694e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.005972e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.783493e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.791557e-01 │ │ │ Vprtstp: contraction number = 1.791557e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3156,32 +3156,32 @@ │ │ │ Vprtstp: contraction number = 1.764760e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.223991e-06 │ │ │ Vprtstp: contraction number = 1.794914e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.841505e-07 │ │ │ Vprtstp: contraction number = 1.811887e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.256590e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.863000e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.564569e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.807988e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.713502079454E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.410000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -3202,32 +3202,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001639 │ │ │ +Vacc_SASA: Time elapsed: 0.013927 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.894100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.778690e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.709700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.677300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.913500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.688212e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.505242e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.175746e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.197218e-01 │ │ │ Vprtstp: contraction number = 1.197218e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3244,32 +3244,32 @@ │ │ │ Vprtstp: contraction number = 1.080232e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.668171e-06 │ │ │ Vprtstp: contraction number = 1.086670e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.821545e-07 │ │ │ Vprtstp: contraction number = 1.091941e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.811110e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.729950e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.114535e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.433523e+01 │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.413483938867E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.640000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -3315,30 +3315,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0422608 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001655 │ │ │ +Vacc_SASA: Time elapsed: 0.020709 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.005300e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.667680e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.773800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.370400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.263700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.272110e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.957250e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.518386e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.511608e-01 │ │ │ Vprtstp: contraction number = 1.511608e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3355,32 +3355,32 @@ │ │ │ Vprtstp: contraction number = 1.062405e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.836009e-06 │ │ │ Vprtstp: contraction number = 1.072929e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.984242e-07 │ │ │ Vprtstp: contraction number = 1.080737e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.928440e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.787830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.345282e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.626185e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.884571864356E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.000000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.373000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -3401,32 +3401,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.857180 │ │ │ +Vacc_SASA: Time elapsed: 1.231666 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.386361e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.600109e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.662400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.250800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.975200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.612440e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.272397e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.927445e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.257199e-02 │ │ │ Vprtstp: contraction number = 3.257199e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3443,32 +3443,32 @@ │ │ │ Vprtstp: contraction number = 1.541269e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.608808e-06 │ │ │ Vprtstp: contraction number = 1.652212e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.820839e-07 │ │ │ Vprtstp: contraction number = 1.753372e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.767310e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.548560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.835185e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.123896e+01 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.592645225811E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.630000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.620000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -3514,30 +3514,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 7853.32 kT │ │ │ VPMG::extEnergy: extDiEnergy = 3800.2 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.802714 │ │ │ +Vacc_SASA: Time elapsed: 1.087093 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.063295e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.497692e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.660700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.825300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.835500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.196822e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.414793e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.248915e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051303e-01 │ │ │ Vprtstp: contraction number = 1.051303e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3554,32 +3554,32 @@ │ │ │ Vprtstp: contraction number = 1.566068e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 4.652962e-06 │ │ │ Vprtstp: contraction number = 1.751224e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.683754e-07 │ │ │ Vprtstp: contraction number = 1.866285e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.841570e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.626970e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.864636e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.087563e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.382181498242E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.330000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -3600,32 +3600,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.804100 │ │ │ +Vacc_SASA: Time elapsed: 1.243589 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.342330e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.045516e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.395300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.050400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.419000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.158040e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.686099e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.597841e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.219671e-02 │ │ │ Vprtstp: contraction number = 2.219671e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3639,32 +3639,32 @@ │ │ │ Vprtstp: contraction number = 9.588702e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.611478e-06 │ │ │ Vprtstp: contraction number = 9.903019e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.632204e-07 │ │ │ Vprtstp: contraction number = 1.012861e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.461490e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.178820e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.403521e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.622821e+01 │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.119297547416E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.500000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.245500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -3710,30 +3710,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 10305.9 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4984.29 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.805476 │ │ │ +Vacc_SASA: Time elapsed: 1.047692 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.032790e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.445586e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.661600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.744000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.264200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.184799e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.822993e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.874960e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.325279e-01 │ │ │ Vprtstp: contraction number = 1.325279e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3750,44 +3750,44 @@ │ │ │ Vprtstp: contraction number = 1.009444e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.272261e-06 │ │ │ Vprtstp: contraction number = 1.024006e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.317723e-07 │ │ │ Vprtstp: contraction number = 1.035733e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.825950e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.573060e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.006151e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.222018e+01 │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.638817315582E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.600000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.300000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.854116e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.175942e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:04:58 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 19:23:22 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr │ │ │ @@ -4420,32 +4420,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.824081 │ │ │ +Vacc_SASA: Time elapsed: 1.098174 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.301914e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.082492e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.667700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.476500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.030400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.353261e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.426136e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.475583e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.573903e-02 │ │ │ Vprtstp: contraction number = 6.573903e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4516,32 +4516,32 @@ │ │ │ Vprtstp: contraction number = 6.827181e-01 │ │ │ Vprtstp: iteration = 24 │ │ │ Vprtstp: relative residual = 1.259903e-06 │ │ │ Vprtstp: contraction number = 6.840214e-01 │ │ │ Vprtstp: iteration = 25 │ │ │ Vprtstp: relative residual = 8.633870e-07 │ │ │ Vprtstp: contraction number = 6.852808e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.020670e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.103985e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.051585e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.075155e+02 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.345051831139E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.560000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.380000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -4587,30 +4587,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 6529.57 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2987.06 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.810974 │ │ │ +Vacc_SASA: Time elapsed: 1.169580 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.017841e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.605163e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.722700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.449900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.379100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.384851e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.557233e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158100e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.216933e-01 │ │ │ Vprtstp: contraction number = 1.216933e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4639,32 +4639,32 @@ │ │ │ Vprtstp: contraction number = 3.953520e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.724728e-06 │ │ │ Vprtstp: contraction number = 4.218661e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.702114e-07 │ │ │ Vprtstp: contraction number = 4.465699e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.716080e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.508900e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.841035e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.089653e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.171725099545E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.470000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.501500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -4685,32 +4685,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.802643 │ │ │ +Vacc_SASA: Time elapsed: 1.117307 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.310468e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.966518e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.986100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.053100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.052100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.375585e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.448252e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.705523e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.208737e-02 │ │ │ Vprtstp: contraction number = 2.208737e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4724,32 +4724,32 @@ │ │ │ Vprtstp: contraction number = 9.525881e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.554352e-06 │ │ │ Vprtstp: contraction number = 9.854831e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.569345e-07 │ │ │ Vprtstp: contraction number = 1.009646e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.481020e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.438070e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.237205e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.472293e+01 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.014263549371E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.040000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.726000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -4795,30 +4795,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 9211.28 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4239.53 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.753998 │ │ │ +Vacc_SASA: Time elapsed: 1.014755 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.757910e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.434932e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.669600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.980100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.134900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.251302e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.763178e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.965213e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.291558e-01 │ │ │ Vprtstp: contraction number = 1.291558e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4835,32 +4835,32 @@ │ │ │ Vprtstp: contraction number = 1.003267e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.195888e-06 │ │ │ Vprtstp: contraction number = 1.018284e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.232544e-07 │ │ │ Vprtstp: contraction number = 1.030651e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.849370e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.614710e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.722909e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.935105e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.449231705544E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.100000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -4881,32 +4881,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008157 │ │ │ +Vacc_SASA: Time elapsed: 0.034378 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.711100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.732940e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.338400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.864700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.938900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.368097e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.183403e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.264770e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.937868e-02 │ │ │ Vprtstp: contraction number = 9.937868e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4923,32 +4923,32 @@ │ │ │ Vprtstp: contraction number = 1.252714e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.602930e-06 │ │ │ Vprtstp: contraction number = 1.287705e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.415857e-07 │ │ │ Vprtstp: contraction number = 1.312312e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.963500e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.837080e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.799777e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.028749e+01 │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.561986028141E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.600000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.910000e-04 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -4994,30 +4994,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00497505 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008658 │ │ │ +Vacc_SASA: Time elapsed: 0.013494 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.283200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.090030e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.346900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.030800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.119800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.193716e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.577224e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.569039e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.636290e-01 │ │ │ Vprtstp: contraction number = 2.636290e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5049,32 +5049,32 @@ │ │ │ Vprtstp: contraction number = 3.506954e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.726432e-06 │ │ │ Vprtstp: contraction number = 3.673674e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 6.664171e-07 │ │ │ Vprtstp: contraction number = 3.860084e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.061580e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.637270e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.525786e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.743587e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.344916094234E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.700000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -5095,32 +5095,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008195 │ │ │ +Vacc_SASA: Time elapsed: 0.013533 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.593000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.722260e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.445900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.052600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.345300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.282623e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020025e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.047812e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.352196e-02 │ │ │ Vprtstp: contraction number = 6.352196e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5134,32 +5134,32 @@ │ │ │ Vprtstp: contraction number = 1.012293e-01 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.271886e-06 │ │ │ Vprtstp: contraction number = 1.033361e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 6.595226e-07 │ │ │ Vprtstp: contraction number = 1.051554e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.638910e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.440740e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.399868e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.621030e+01 │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 9.389840581990E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.210000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -5205,30 +5205,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0518244 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008873 │ │ │ +Vacc_SASA: Time elapsed: 0.028457 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.989600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.796750e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.693000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.196700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.290700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.363885e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057790e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.312943e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.573900e-01 │ │ │ Vprtstp: contraction number = 1.573900e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5245,32 +5245,32 @@ │ │ │ Vprtstp: contraction number = 1.046499e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.765958e-06 │ │ │ Vprtstp: contraction number = 1.060018e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.889858e-07 │ │ │ Vprtstp: contraction number = 1.070160e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.906740e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.673710e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.788626e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.021282e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.361370594878E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.800000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.040000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -5291,32 +5291,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.770926 │ │ │ +Vacc_SASA: Time elapsed: 1.140444 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.205414e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.598959e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.650800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.157300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.148900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.295783e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.317718e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.650144e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.573435e-02 │ │ │ Vprtstp: contraction number = 6.573435e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5387,32 +5387,32 @@ │ │ │ Vprtstp: contraction number = 6.841463e-01 │ │ │ Vprtstp: iteration = 24 │ │ │ Vprtstp: relative residual = 1.230794e-06 │ │ │ Vprtstp: contraction number = 6.854643e-01 │ │ │ Vprtstp: iteration = 25 │ │ │ Vprtstp: relative residual = 8.453252e-07 │ │ │ Vprtstp: contraction number = 6.868128e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.178000e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.006330e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.843284e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.006583e+02 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.248457904492E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.480000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.015000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -5458,30 +5458,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 6529.31 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2986.91 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.798145 │ │ │ +Vacc_SASA: Time elapsed: 1.164909 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.015075e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.679448e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.731300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.123800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.830500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.366103e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.519661e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.675233e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.206113e-01 │ │ │ Vprtstp: contraction number = 1.206113e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5510,32 +5510,32 @@ │ │ │ Vprtstp: contraction number = 3.809962e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.385263e-06 │ │ │ Vprtstp: contraction number = 4.084139e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.028523e-07 │ │ │ Vprtstp: contraction number = 4.351898e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.443590e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.172780e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.352318e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.584584e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.037057682028E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.800000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.528000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -5556,32 +5556,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.788923 │ │ │ +Vacc_SASA: Time elapsed: 1.180971 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.332142e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.027933e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.636200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.481900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.511600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.251030e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.805638e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.173901e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.233304e-02 │ │ │ Vprtstp: contraction number = 2.233304e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5595,32 +5595,32 @@ │ │ │ Vprtstp: contraction number = 9.522390e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.574058e-06 │ │ │ Vprtstp: contraction number = 9.845638e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.587415e-07 │ │ │ Vprtstp: contraction number = 1.008486e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.515300e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.238130e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.422544e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.650088e+01 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.004264667397E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.440000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.350000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -5666,30 +5666,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 9208.92 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4238.63 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.797972 │ │ │ +Vacc_SASA: Time elapsed: 1.143984 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.868620e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.550776e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.721600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.237300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.639300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.214231e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.939107e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.454425e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.281343e-01 │ │ │ Vprtstp: contraction number = 1.281343e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5706,44 +5706,44 @@ │ │ │ Vprtstp: contraction number = 1.003059e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.185212e-06 │ │ │ Vprtstp: contraction number = 1.017952e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.220913e-07 │ │ │ Vprtstp: contraction number = 1.030122e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.827380e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.636140e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.925275e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.159969e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.314075450214E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.680000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.970010e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.748815e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:05:10 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 19:35:39 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr │ │ │ @@ -6376,32 +6376,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.824427 │ │ │ +Vacc_SASA: Time elapsed: 1.160130 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.382731e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.503900e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.659600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.685500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.222200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.639427e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.502691e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.264659e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.298567e-02 │ │ │ Vprtstp: contraction number = 3.298567e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6418,32 +6418,32 @@ │ │ │ Vprtstp: contraction number = 1.536726e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.666279e-06 │ │ │ Vprtstp: contraction number = 1.683668e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.055929e-07 │ │ │ Vprtstp: contraction number = 1.833984e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.832180e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.638600e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.858634e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.127035e+01 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.725356066403E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.430000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.770000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -6489,30 +6489,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 6899.51 kT │ │ │ VPMG::extEnergy: extDiEnergy = 3158.85 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.805878 │ │ │ +Vacc_SASA: Time elapsed: 1.021009 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.073698e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.606991e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.673400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.439900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.243400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.253842e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.945198e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.969225e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.032281e-01 │ │ │ Vprtstp: contraction number = 1.032281e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6529,32 +6529,32 @@ │ │ │ Vprtstp: contraction number = 1.485117e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 3.842446e-06 │ │ │ Vprtstp: contraction number = 1.674805e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 6.939533e-07 │ │ │ Vprtstp: contraction number = 1.806019e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.829790e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.577860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.133075e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.350796e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.209791610861E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.600000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.845300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.900000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -6575,32 +6575,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.797419 │ │ │ +Vacc_SASA: Time elapsed: 1.453299 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.324484e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.992990e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.909500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.067300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.114200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.594999e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648527e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.917894e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.208737e-02 │ │ │ Vprtstp: contraction number = 2.208737e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6614,32 +6614,32 @@ │ │ │ Vprtstp: contraction number = 9.525881e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.554352e-06 │ │ │ Vprtstp: contraction number = 9.854831e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.569345e-07 │ │ │ Vprtstp: contraction number = 1.009646e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.390640e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.196380e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.958372e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.272336e+01 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.014263549371E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.520000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.400000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -6685,30 +6685,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 9211.28 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4239.53 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.803119 │ │ │ +Vacc_SASA: Time elapsed: 1.232205 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.038994e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.929692e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.714300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.685300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.635800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.693687e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.007980e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137200e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.291558e-01 │ │ │ Vprtstp: contraction number = 1.291558e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6725,32 +6725,32 @@ │ │ │ Vprtstp: contraction number = 1.003267e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.195888e-06 │ │ │ Vprtstp: contraction number = 1.018284e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.232544e-07 │ │ │ Vprtstp: contraction number = 1.030651e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.887560e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.559400e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.555970e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.852885e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.449231705544E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.390000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -6771,32 +6771,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008199 │ │ │ +Vacc_SASA: Time elapsed: 0.057542 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.197240e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.862180e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.342100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.394200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.219300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.491921e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.499295e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.523147e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.464737e-02 │ │ │ Vprtstp: contraction number = 8.464737e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6813,32 +6813,32 @@ │ │ │ Vprtstp: contraction number = 1.071698e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.052787e-06 │ │ │ Vprtstp: contraction number = 1.084632e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.152581e-07 │ │ │ Vprtstp: contraction number = 1.094790e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.923500e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.681820e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.121174e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.358192e+01 │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 6.368169150406E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.080000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -6884,30 +6884,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00594757 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008619 │ │ │ +Vacc_SASA: Time elapsed: 0.019015 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.029660e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.018430e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.359900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.508200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.211700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.546114e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.962357e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.867010e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.027171e-01 │ │ │ Vprtstp: contraction number = 2.027171e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6927,32 +6927,32 @@ │ │ │ Vprtstp: contraction number = 1.717621e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.164324e-06 │ │ │ Vprtstp: contraction number = 1.754898e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.631488e-07 │ │ │ Vprtstp: contraction number = 1.779681e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.429440e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.016580e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.875725e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.144898e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.345277247759E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.130000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -6973,32 +6973,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008187 │ │ │ +Vacc_SASA: Time elapsed: 0.005962 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.267800e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.568660e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.466300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.053700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.442300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.510790e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.461097e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.287440e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.352196e-02 │ │ │ Vprtstp: contraction number = 6.352196e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7012,32 +7012,32 @@ │ │ │ Vprtstp: contraction number = 1.012293e-01 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.271886e-06 │ │ │ Vprtstp: contraction number = 1.033361e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 6.595226e-07 │ │ │ Vprtstp: contraction number = 1.051554e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.602880e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.352090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.782247e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.063853e+01 │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 9.389840581990E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.068000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -7083,30 +7083,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0518244 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.008641 │ │ │ +Vacc_SASA: Time elapsed: 0.035044 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.018400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.439690e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.719100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.050500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 7.597100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.231413e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.915222e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.591277e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.573900e-01 │ │ │ Vprtstp: contraction number = 1.573900e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7123,32 +7123,32 @@ │ │ │ Vprtstp: contraction number = 1.046499e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.765958e-06 │ │ │ Vprtstp: contraction number = 1.060018e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.889858e-07 │ │ │ Vprtstp: contraction number = 1.070160e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.963390e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.048390e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.141887e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.366414e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.361370594878E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.000000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.630000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -7169,32 +7169,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.802899 │ │ │ +Vacc_SASA: Time elapsed: 1.402354 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.373135e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.139170e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.763000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.031700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.946600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.854510e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.267200e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.991408e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.328224e-02 │ │ │ Vprtstp: contraction number = 3.328224e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7211,32 +7211,32 @@ │ │ │ Vprtstp: contraction number = 1.553323e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.764269e-06 │ │ │ Vprtstp: contraction number = 1.696908e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.244306e-07 │ │ │ Vprtstp: contraction number = 1.838895e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.821650e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.616880e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.470929e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.809428e+01 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.622871644072E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.640000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.210000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ @@ -7282,30 +7282,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 6899.11 kT │ │ │ VPMG::extEnergy: extDiEnergy = 3158.68 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.796367 │ │ │ +Vacc_SASA: Time elapsed: 1.023163 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.061031e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.463062e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.894700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.904100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.348600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.289518e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.410871e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.377836e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.025309e-01 │ │ │ Vprtstp: contraction number = 1.025309e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7322,32 +7322,32 @@ │ │ │ Vprtstp: contraction number = 1.507031e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 3.981847e-06 │ │ │ Vprtstp: contraction number = 1.699776e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.281025e-07 │ │ │ Vprtstp: contraction number = 1.828555e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.420130e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.206160e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.663961e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.914407e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.075005771448E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.600000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.780000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ @@ -7368,32 +7368,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.794674 │ │ │ +Vacc_SASA: Time elapsed: 1.684578 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.368882e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.035937e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.705400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 8.554800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.392000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.940014e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.689784e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.833218e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.233304e-02 │ │ │ Vprtstp: contraction number = 2.233304e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7407,30 +7407,30 @@ │ │ │ Vprtstp: contraction number = 9.522390e-02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.574058e-06 │ │ │ Vprtstp: contraction number = 9.845638e-02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.587415e-07 │ │ │ Vprtstp: contraction number = 1.008486e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.554340e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.271650e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.457040e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.834515e+01 │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.004264667397E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.600000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.340000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ @@ -7478,30 +7478,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 9208.92 kT │ │ │ VPMG::extEnergy: extDiEnergy = 4238.63 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.793106 │ │ │ +Vacc_SASA: Time elapsed: 1.611886 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.025122e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.138311e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.025900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.219900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.515200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.695139e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.826853e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.229605e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.281343e-01 │ │ │ Vprtstp: contraction number = 1.281343e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7518,34 +7518,34 @@ │ │ │ Vprtstp: contraction number = 1.003059e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.185212e-06 │ │ │ Vprtstp: contraction number = 1.017952e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.220913e-07 │ │ │ Vprtstp: contraction number = 1.030122e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.314100e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.128100e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.332833e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.625488e+01 │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.314075450214E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.900000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.610000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.862675e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.563610e+02 │ │ ├── ./usr/share/apbs/examples/actin-dimer/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:58 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:43:53 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -262,217 +262,217 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.270886 │ │ │ +Vacc_SASA: Time elapsed: 3.118918 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.890184e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.442539e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.799720e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 3.412500e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.407230e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.132474e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.391124e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.363364e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7775242.648804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.105322e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089827e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.252805e+05 │ │ │ Vprtstp: contraction number = 5.252805e+05 │ │ │ Vnewton: Attempting damping, relres = 0.062556 │ │ │ Vnewton: Attempting damping, relres = 0.525334 │ │ │ Vnewton: Damping accepted, relres = 0.062556 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.255619e-02 │ │ │ Vprtstp: contraction number = 6.255619e-02 │ │ │ Vnewton: Using errtol_s: 486389.547875 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.694400e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.504664e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.109788e+05 │ │ │ Vprtstp: contraction number = 1.109788e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.292368e-02 │ │ │ Vprtstp: contraction number = 2.065932e-01 │ │ │ Vnewton: Using errtol_s: 100484.762247 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.882327e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.730595e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.281526e+04 │ │ │ Vprtstp: contraction number = 3.281526e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.798952e-03 │ │ │ Vprtstp: contraction number = 2.939527e-01 │ │ │ Vnewton: Using errtol_s: 29537.770540 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.068279e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.005264e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.139405e+04 │ │ │ Vprtstp: contraction number = 1.139405e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.318894e-03 │ │ │ Vprtstp: contraction number = 3.471731e-01 │ │ │ Vnewton: Using errtol_s: 10254.719067 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026432e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035298e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.292845e+03 │ │ │ Vprtstp: contraction number = 4.292845e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.969084e-04 │ │ │ Vprtstp: contraction number = 3.767615e-01 │ │ │ Vnewton: Using errtol_s: 3863.583447 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.145552e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.274491e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.746643e+03 │ │ │ Vprtstp: contraction number = 1.746643e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.021786e-04 │ │ │ Vprtstp: contraction number = 4.068730e-01 │ │ │ Vnewton: Using errtol_s: 1571.987642 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.264354e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.513350e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.833563e+02 │ │ │ Vprtstp: contraction number = 7.833563e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 9.067555e-05 │ │ │ Vprtstp: contraction number = 4.484923e-01 │ │ │ Vnewton: Using errtol_s: 705.024393 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.385242e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.768069e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.880760e+02 │ │ │ Vprtstp: contraction number = 3.880760e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.492075e-05 │ │ │ Vprtstp: contraction number = 4.954009e-01 │ │ │ Vnewton: Using errtol_s: 349.269694 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.506228e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.034516e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.071891e+02 │ │ │ Vprtstp: contraction number = 2.071891e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.398262e-05 │ │ │ Vprtstp: contraction number = 5.338875e-01 │ │ │ Vnewton: Using errtol_s: 186.470725 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.626263e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.297027e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.168433e+02 │ │ │ Vprtstp: contraction number = 1.168433e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.352487e-05 │ │ │ Vprtstp: contraction number = 5.639446e-01 │ │ │ Vnewton: Using errtol_s: 105.159166 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.744607e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.556562e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.826136e+01 │ │ │ Vprtstp: contraction number = 6.826136e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.901399e-06 │ │ │ Vprtstp: contraction number = 5.842124e-01 │ │ │ Vnewton: Using errtol_s: 61.435293 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.864133e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.816155e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.091749e+01 │ │ │ Vprtstp: contraction number = 4.091749e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.736285e-06 │ │ │ Vprtstp: contraction number = 5.994236e-01 │ │ │ Vnewton: Using errtol_s: 36.825768 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.982594e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.056244e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.493482e+01 │ │ │ Vprtstp: contraction number = 2.493482e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 2.886257e-06 │ │ │ Vprtstp: contraction number = 6.093926e-01 │ │ │ Vnewton: Using errtol_s: 22.441349 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.100921e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.301662e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.538748e+01 │ │ │ Vprtstp: contraction number = 1.538748e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 1.781132e-06 │ │ │ Vprtstp: contraction number = 6.171079e-01 │ │ │ Vnewton: Using errtol_s: 13.848733 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.232808e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.539180e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.579209e+00 │ │ │ Vprtstp: contraction number = 9.579209e+00 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 1.108813e-06 │ │ │ Vprtstp: contraction number = 6.225327e-01 │ │ │ Vnewton: Using errtol_s: 8.621289 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.351578e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.818617e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.005674e+00 │ │ │ Vprtstp: contraction number = 6.005674e+00 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 6.951690e-07 │ │ │ Vprtstp: contraction number = 6.269489e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.999237e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.131008e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.995812e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.022166e+02 │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -481,17 +481,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.412172567798E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.232438411967E+05 kT │ │ │ Vpmg_energy: dielEnergy = 6.161638379331E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.104560e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.407150e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -537,193 +537,193 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.294338 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.266125 │ │ │ +Vacc_SASA: Time elapsed: 3.329506 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.467518e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.380239e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.518100e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 3.545140e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.095200e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.416609e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.935188e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.155030e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 9262588.477712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.007160e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.193755e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.740096e+05 │ │ │ Vprtstp: contraction number = 9.740096e+05 │ │ │ Vnewton: Attempting damping, relres = 0.096135 │ │ │ Vnewton: Attempting damping, relres = 0.545161 │ │ │ Vnewton: Damping accepted, relres = 0.096135 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.613536e-02 │ │ │ Vprtstp: contraction number = 9.613536e-02 │ │ │ Vnewton: Using errtol_s: 890462.283513 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.160527e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.472887e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.907605e+05 │ │ │ Vprtstp: contraction number = 1.907605e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.859794e-02 │ │ │ Vprtstp: contraction number = 1.934558e-01 │ │ │ Vnewton: Using errtol_s: 172265.062018 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.280129e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.758389e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.138633e+04 │ │ │ Vprtstp: contraction number = 5.138633e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.994948e-03 │ │ │ Vprtstp: contraction number = 2.685753e-01 │ │ │ Vnewton: Using errtol_s: 46266.149079 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.402960e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.086543e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.656736e+04 │ │ │ Vprtstp: contraction number = 1.656736e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.610090e-03 │ │ │ Vprtstp: contraction number = 3.223437e-01 │ │ │ Vnewton: Using errtol_s: 14913.601487 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.523591e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.417264e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.837272e+03 │ │ │ Vprtstp: contraction number = 5.837272e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.672493e-04 │ │ │ Vprtstp: contraction number = 3.523090e-01 │ │ │ Vnewton: Using errtol_s: 5254.196377 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.640553e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.748118e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.147141e+03 │ │ │ Vprtstp: contraction number = 2.147141e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.086390e-04 │ │ │ Vprtstp: contraction number = 3.678083e-01 │ │ │ Vnewton: Using errtol_s: 1932.536910 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.758331e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.076006e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.193498e+02 │ │ │ Vprtstp: contraction number = 8.193498e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.961379e-05 │ │ │ Vprtstp: contraction number = 3.815864e-01 │ │ │ Vnewton: Using errtol_s: 737.429804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.874709e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.394293e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352547e+02 │ │ │ Vprtstp: contraction number = 3.352547e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.257526e-05 │ │ │ Vprtstp: contraction number = 4.091660e-01 │ │ │ Vnewton: Using errtol_s: 301.731240 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.990940e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.714986e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.500666e+02 │ │ │ Vprtstp: contraction number = 1.500666e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.458127e-05 │ │ │ Vprtstp: contraction number = 4.476179e-01 │ │ │ Vnewton: Using errtol_s: 135.060298 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.107932e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.019866e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.280398e+01 │ │ │ Vprtstp: contraction number = 7.280398e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.074013e-06 │ │ │ Vprtstp: contraction number = 4.851438e-01 │ │ │ Vnewton: Using errtol_s: 65.523671 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.223748e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.323907e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.740960e+01 │ │ │ Vprtstp: contraction number = 3.740960e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.634908e-06 │ │ │ Vprtstp: contraction number = 5.138397e-01 │ │ │ Vnewton: Using errtol_s: 33.668661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.340672e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.648309e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.000118e+01 │ │ │ Vprtstp: contraction number = 2.000118e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.943416e-06 │ │ │ Vprtstp: contraction number = 5.346535e-01 │ │ │ Vnewton: Using errtol_s: 18.001066 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.454849e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.997770e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.094514e+01 │ │ │ Vprtstp: contraction number = 1.094514e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.063486e-06 │ │ │ Vprtstp: contraction number = 5.472249e-01 │ │ │ Vnewton: Using errtol_s: 9.850631 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.573530e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.323365e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.085292e+00 │ │ │ Vprtstp: contraction number = 6.085292e+00 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 5.912779e-07 │ │ │ Vprtstp: contraction number = 5.559810e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.722779e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.848450e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.461353e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.490200e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -732,17 +732,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.418972427545E+00 kT │ │ │ Vpmg_energy: qfEnergy = 2.355397093328E+05 kT │ │ │ Vpmg_energy: dielEnergy = 1.177642501639E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.051220e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.416160e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -763,217 +763,217 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.269206 │ │ │ +Vacc_SASA: Time elapsed: 4.370543 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.909096e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.934087e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.532940e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.967730e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 8.930410e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.710372e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.098528e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.713041e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7837779.438687 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.169669e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.762767e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.264175e+05 │ │ │ Vprtstp: contraction number = 5.264175e+05 │ │ │ Vnewton: Attempting damping, relres = 0.062206 │ │ │ Vnewton: Attempting damping, relres = 0.525499 │ │ │ Vnewton: Damping accepted, relres = 0.062206 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.220619e-02 │ │ │ Vprtstp: contraction number = 6.220619e-02 │ │ │ Vnewton: Using errtol_s: 487558.369599 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.325178e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.118744e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.104882e+05 │ │ │ Vprtstp: contraction number = 1.104882e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.277305e-02 │ │ │ Vprtstp: contraction number = 2.053340e-01 │ │ │ Vnewton: Using errtol_s: 100112.332342 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.441855e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.412265e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.234516e+04 │ │ │ Vprtstp: contraction number = 3.234516e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.716136e-03 │ │ │ Vprtstp: contraction number = 2.909357e-01 │ │ │ Vnewton: Using errtol_s: 29126.250452 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.557475e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.739235e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.113222e+04 │ │ │ Vprtstp: contraction number = 1.113222e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.278517e-03 │ │ │ Vprtstp: contraction number = 3.440448e-01 │ │ │ Vnewton: Using errtol_s: 10020.735856 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.675530e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.006511e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.146765e+03 │ │ │ Vprtstp: contraction number = 4.146765e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.761620e-04 │ │ │ Vprtstp: contraction number = 3.724330e-01 │ │ │ Vnewton: Using errtol_s: 3732.052866 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.792040e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039558e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.647764e+03 │ │ │ Vprtstp: contraction number = 1.647764e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.891857e-04 │ │ │ Vprtstp: contraction number = 3.973138e-01 │ │ │ Vnewton: Using errtol_s: 1482.795933 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.908731e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.071643e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.190477e+02 │ │ │ Vprtstp: contraction number = 7.190477e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.256252e-05 │ │ │ Vprtstp: contraction number = 4.364099e-01 │ │ │ Vnewton: Using errtol_s: 647.106851 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.026045e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.100728e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.514586e+02 │ │ │ Vprtstp: contraction number = 3.514586e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.035656e-05 │ │ │ Vprtstp: contraction number = 4.888000e-01 │ │ │ Vnewton: Using errtol_s: 316.305821 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.143988e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.129522e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.878144e+02 │ │ │ Vprtstp: contraction number = 1.878144e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.156625e-05 │ │ │ Vprtstp: contraction number = 5.343927e-01 │ │ │ Vnewton: Using errtol_s: 169.031531 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.261792e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155883e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.065907e+02 │ │ │ Vprtstp: contraction number = 1.065907e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.223961e-05 │ │ │ Vprtstp: contraction number = 5.675353e-01 │ │ │ Vnewton: Using errtol_s: 95.931363 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.381083e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.179637e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.270317e+01 │ │ │ Vprtstp: contraction number = 6.270317e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.200099e-06 │ │ │ Vprtstp: contraction number = 5.882621e-01 │ │ │ Vnewton: Using errtol_s: 56.432788 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.497323e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206415e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.774740e+01 │ │ │ Vprtstp: contraction number = 3.774740e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.334473e-06 │ │ │ Vprtstp: contraction number = 6.020019e-01 │ │ │ Vnewton: Using errtol_s: 33.972645 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.613634e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233143e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.304758e+01 │ │ │ Vprtstp: contraction number = 2.304758e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 2.646517e-06 │ │ │ Vprtstp: contraction number = 6.105742e-01 │ │ │ Vnewton: Using errtol_s: 20.742819 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.730581e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.261386e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.421587e+01 │ │ │ Vprtstp: contraction number = 1.421587e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 1.632386e-06 │ │ │ Vprtstp: contraction number = 6.168053e-01 │ │ │ Vnewton: Using errtol_s: 12.794282 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.847524e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.290944e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.829808e+00 │ │ │ Vprtstp: contraction number = 8.829808e+00 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 1.013913e-06 │ │ │ Vprtstp: contraction number = 6.211233e-01 │ │ │ Vnewton: Using errtol_s: 7.946827 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.967027e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320592e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.514712e+00 │ │ │ Vprtstp: contraction number = 5.514712e+00 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 6.332457e-07 │ │ │ Vprtstp: contraction number = 6.245562e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.954254e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.078283e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.746437e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.778701e+02 │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -982,17 +982,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.438982867308E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.232481159173E+05 kT │ │ │ Vpmg_energy: dielEnergy = 6.161845360142E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.100020e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.933030e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -1038,182 +1038,182 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.338388 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.298992 │ │ │ +Vacc_SASA: Time elapsed: 4.167172 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.475729e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.331885e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.546740e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.788150e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 8.998920e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.913783e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.549697e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.356351e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 9316156.472817 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.620734e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.361019e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.759901e+05 │ │ │ Vprtstp: contraction number = 9.759901e+05 │ │ │ Vnewton: Attempting damping, relres = 0.095792 │ │ │ Vnewton: Attempting damping, relres = 0.545068 │ │ │ Vnewton: Damping accepted, relres = 0.095792 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.579182e-02 │ │ │ Vprtstp: contraction number = 9.579182e-02 │ │ │ Vnewton: Using errtol_s: 892411.563062 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.774506e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.391409e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.903231e+05 │ │ │ Vprtstp: contraction number = 1.903231e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.845161e-02 │ │ │ Vprtstp: contraction number = 1.926220e-01 │ │ │ Vnewton: Using errtol_s: 171898.088650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.895294e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.420999e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.121980e+04 │ │ │ Vprtstp: contraction number = 5.121980e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.949951e-03 │ │ │ Vprtstp: contraction number = 2.682666e-01 │ │ │ Vnewton: Using errtol_s: 46114.513884 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.013055e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.446246e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.657747e+04 │ │ │ Vprtstp: contraction number = 1.657747e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.601844e-03 │ │ │ Vprtstp: contraction number = 3.236081e-01 │ │ │ Vnewton: Using errtol_s: 14923.031227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.132093e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.471270e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.880103e+03 │ │ │ Vprtstp: contraction number = 5.880103e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.681354e-04 │ │ │ Vprtstp: contraction number = 3.546758e-01 │ │ │ Vnewton: Using errtol_s: 5292.838197 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.249537e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.496173e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.176489e+03 │ │ │ Vprtstp: contraction number = 2.176489e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.102777e-04 │ │ │ Vprtstp: contraction number = 3.701190e-01 │ │ │ Vnewton: Using errtol_s: 1958.979878 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.367010e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.522088e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.247695e+02 │ │ │ Vprtstp: contraction number = 8.247695e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.968018e-05 │ │ │ Vprtstp: contraction number = 3.789284e-01 │ │ │ Vnewton: Using errtol_s: 742.313034 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.486677e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.549767e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.261401e+02 │ │ │ Vprtstp: contraction number = 3.261401e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.150750e-05 │ │ │ Vprtstp: contraction number = 3.954245e-01 │ │ │ Vnewton: Using errtol_s: 293.528762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.604321e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.576097e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.384546e+02 │ │ │ Vprtstp: contraction number = 1.384546e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.337564e-05 │ │ │ Vprtstp: contraction number = 4.245224e-01 │ │ │ Vnewton: Using errtol_s: 124.609538 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.722303e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.602493e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.300596e+01 │ │ │ Vprtstp: contraction number = 6.300596e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.086783e-06 │ │ │ Vprtstp: contraction number = 4.550649e-01 │ │ │ Vnewton: Using errtol_s: 56.705427 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.840286e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.631455e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.026431e+01 │ │ │ Vprtstp: contraction number = 3.026431e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.923726e-06 │ │ │ Vprtstp: contraction number = 4.803401e-01 │ │ │ Vnewton: Using errtol_s: 27.237888 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.958796e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.657531e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.506906e+01 │ │ │ Vprtstp: contraction number = 1.506906e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.455768e-06 │ │ │ Vprtstp: contraction number = 4.979152e-01 │ │ │ Vnewton: Using errtol_s: 13.562159 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.079308e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.683756e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.684345e+00 │ │ │ Vprtstp: contraction number = 7.684345e+00 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 7.423567e-07 │ │ │ Vprtstp: contraction number = 5.099418e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.617137e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.742041e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.523932e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.561311e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -1222,15 +1222,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.434662074417E+00 kT │ │ │ Vpmg_energy: qfEnergy = 2.352136568668E+05 kT │ │ │ Vpmg_energy: dielEnergy = 1.176012292477E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.060940e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.537300e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ @@ -1253,217 +1253,217 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.097944 │ │ │ +Vacc_SASA: Time elapsed: 8.229530 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.089012e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.075169e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.581610e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.710810e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.282980e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.592000e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.929754e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.723412e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 15819726.247791 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000295e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.727640e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.061014e+06 │ │ │ Vprtstp: contraction number = 1.061014e+06 │ │ │ Vnewton: Attempting damping, relres = 0.062452 │ │ │ Vnewton: Attempting damping, relres = 0.525397 │ │ │ Vnewton: Damping accepted, relres = 0.062452 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.245176e-02 │ │ │ Vprtstp: contraction number = 6.245176e-02 │ │ │ Vnewton: Using errtol_s: 987969.694273 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.015999e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.760421e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.221439e+05 │ │ │ Vprtstp: contraction number = 2.221439e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.274712e-02 │ │ │ Vprtstp: contraction number = 2.041114e-01 │ │ │ Vnewton: Using errtol_s: 201655.898404 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.027822e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.791929e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.509302e+04 │ │ │ Vprtstp: contraction number = 6.509302e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.704570e-03 │ │ │ Vprtstp: contraction number = 2.906202e-01 │ │ │ Vnewton: Using errtol_s: 58605.278995 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039533e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.823554e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.250351e+04 │ │ │ Vprtstp: contraction number = 2.250351e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.280353e-03 │ │ │ Vprtstp: contraction number = 3.456144e-01 │ │ │ Vnewton: Using errtol_s: 20254.828172 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051239e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.852788e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.447408e+03 │ │ │ Vprtstp: contraction number = 8.447408e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.805791e-04 │ │ │ Vprtstp: contraction number = 3.753490e-01 │ │ │ Vnewton: Using errtol_s: 7602.629655 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062788e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.884836e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.399185e+03 │ │ │ Vprtstp: contraction number = 3.399185e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.933739e-04 │ │ │ Vprtstp: contraction number = 4.023769e-01 │ │ │ Vnewton: Using errtol_s: 3059.122762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074525e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.919096e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.505025e+03 │ │ │ Vprtstp: contraction number = 1.505025e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.562081e-05 │ │ │ Vprtstp: contraction number = 4.427733e-01 │ │ │ Vnewton: Using errtol_s: 1354.497766 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086162e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.955521e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.407337e+02 │ │ │ Vprtstp: contraction number = 7.407337e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.214082e-05 │ │ │ Vprtstp: contraction number = 4.921797e-01 │ │ │ Vnewton: Using errtol_s: 666.656280 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.097789e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.986796e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955938e+02 │ │ │ Vprtstp: contraction number = 3.955938e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.250569e-05 │ │ │ Vprtstp: contraction number = 5.340591e-01 │ │ │ Vnewton: Using errtol_s: 356.033867 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109725e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.018083e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.238069e+02 │ │ │ Vprtstp: contraction number = 2.238069e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.273259e-05 │ │ │ Vprtstp: contraction number = 5.657500e-01 │ │ │ Vnewton: Using errtol_s: 201.426156 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121728e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048466e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.312226e+02 │ │ │ Vprtstp: contraction number = 1.312226e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.465385e-06 │ │ │ Vprtstp: contraction number = 5.863208e-01 │ │ │ Vnewton: Using errtol_s: 118.100345 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.133767e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.080873e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.886374e+01 │ │ │ Vprtstp: contraction number = 7.886374e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.486638e-06 │ │ │ Vprtstp: contraction number = 6.009922e-01 │ │ │ Vnewton: Using errtol_s: 70.977384 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.145694e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.109065e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.812776e+01 │ │ │ Vprtstp: contraction number = 4.812776e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 2.738037e-06 │ │ │ Vprtstp: contraction number = 6.102647e-01 │ │ │ Vnewton: Using errtol_s: 43.314994 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.157733e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.136631e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.971066e+01 │ │ │ Vprtstp: contraction number = 2.971066e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 1.690269e-06 │ │ │ Vprtstp: contraction number = 6.173289e-01 │ │ │ Vnewton: Using errtol_s: 26.739596 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.169533e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.164318e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.848360e+01 │ │ │ Vprtstp: contraction number = 1.848360e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 1.051550e-06 │ │ │ Vprtstp: contraction number = 6.221201e-01 │ │ │ Vnewton: Using errtol_s: 16.635240 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.181515e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.194002e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.157246e+01 │ │ │ Vprtstp: contraction number = 1.157246e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 6.583687e-07 │ │ │ Vprtstp: contraction number = 6.260933e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.973328e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.101631e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.966109e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.000704e+02 │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -1472,17 +1472,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.734614944651E+00 kT │ │ │ Vpmg_energy: qfEnergy = 2.465748372430E+05 kT │ │ │ Vpmg_energy: dielEnergy = 1.232753607231E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.704180e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.057140e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -1528,182 +1528,182 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.649873 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.803153 │ │ │ +Vacc_SASA: Time elapsed: 7.259786 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.664778e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.117904e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.287760e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 3.495250e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.037214e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.523889e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.272919e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.234667e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 18647566.992070 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.280336e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.239081e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.941752e+06 │ │ │ Vprtstp: contraction number = 1.941752e+06 │ │ │ Vnewton: Attempting damping, relres = 0.095497 │ │ │ Vnewton: Attempting damping, relres = 0.544786 │ │ │ Vnewton: Damping accepted, relres = 0.095497 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.549656e-02 │ │ │ Vprtstp: contraction number = 9.549656e-02 │ │ │ Vnewton: Using errtol_s: 1780778.449755 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.296335e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.268456e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.788571e+05 │ │ │ Vprtstp: contraction number = 3.788571e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.837082e-02 │ │ │ Vprtstp: contraction number = 1.923715e-01 │ │ │ Vnewton: Using errtol_s: 342571.038812 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.308579e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.296344e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.019639e+05 │ │ │ Vprtstp: contraction number = 1.019639e+05 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.923062e-03 │ │ │ Vprtstp: contraction number = 2.679828e-01 │ │ │ Vnewton: Using errtol_s: 91803.137006 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320647e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.323164e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.295911e+04 │ │ │ Vprtstp: contraction number = 3.295911e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.591047e-03 │ │ │ Vprtstp: contraction number = 3.231823e-01 │ │ │ Vnewton: Using errtol_s: 29669.150960 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.332808e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.350780e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.167703e+04 │ │ │ Vprtstp: contraction number = 1.167703e+04 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.636468e-04 │ │ │ Vprtstp: contraction number = 3.542616e-01 │ │ │ Vnewton: Using errtol_s: 10510.641014 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.345215e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.378427e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.318326e+03 │ │ │ Vprtstp: contraction number = 4.318326e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.084308e-04 │ │ │ Vprtstp: contraction number = 3.697898e-01 │ │ │ Vnewton: Using errtol_s: 3886.727604 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.357467e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.404661e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.645707e+03 │ │ │ Vprtstp: contraction number = 1.645707e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.942966e-05 │ │ │ Vprtstp: contraction number = 3.810841e-01 │ │ │ Vnewton: Using errtol_s: 1481.169947 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.369968e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.431330e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.631576e+02 │ │ │ Vprtstp: contraction number = 6.631576e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.200666e-05 │ │ │ Vprtstp: contraction number = 4.029560e-01 │ │ │ Vnewton: Using errtol_s: 596.846318 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.382359e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.458304e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.897130e+02 │ │ │ Vprtstp: contraction number = 2.897130e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.398265e-05 │ │ │ Vprtstp: contraction number = 4.368670e-01 │ │ │ Vnewton: Using errtol_s: 260.742452 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.394395e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.485525e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.365123e+02 │ │ │ Vprtstp: contraction number = 1.365123e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.588595e-06 │ │ │ Vprtstp: contraction number = 4.711978e-01 │ │ │ Vnewton: Using errtol_s: 122.861265 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.406488e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.511030e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.809649e+01 │ │ │ Vprtstp: contraction number = 6.809649e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.286589e-06 │ │ │ Vprtstp: contraction number = 4.988300e-01 │ │ │ Vnewton: Using errtol_s: 61.286879 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.418975e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.535704e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.533208e+01 │ │ │ Vprtstp: contraction number = 3.533208e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705256e-06 │ │ │ Vprtstp: contraction number = 5.188530e-01 │ │ │ Vnewton: Using errtol_s: 31.798881 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.430985e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.561395e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.878604e+01 │ │ │ Vprtstp: contraction number = 1.878604e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.066833e-07 │ │ │ Vprtstp: contraction number = 5.316991e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.669589e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.806157e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.495192e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.525261e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -1712,23 +1712,23 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.745937546040E+00 kT │ │ │ Vpmg_energy: qfEnergy = 4.708379041028E+05 kT │ │ │ Vpmg_energy: dielEnergy = 2.354068218640E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.627550e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.571200e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.442420e+02 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.584519e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:55:10 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 09:38:59 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -1986,140 +1986,140 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.300833 │ │ │ +Vacc_SASA: Time elapsed: 3.667639 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.091021e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.545874e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.529980e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.103910e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 8.804570e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.370379e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.480839e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.802793e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7775242.648804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.172852e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.414326e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.519208e+05 │ │ │ Vprtstp: contraction number = 4.519208e+05 │ │ │ Vnewton: Attempting damping, relres = 0.054343 │ │ │ Vnewton: Attempting damping, relres = 0.522411 │ │ │ Vnewton: Damping accepted, relres = 0.054343 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.434337e-02 │ │ │ Vprtstp: contraction number = 5.434337e-02 │ │ │ Vnewton: Using errtol_s: 422532.874830 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.666533e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.134740e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.825836e+04 │ │ │ Vprtstp: contraction number = 6.825836e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 8.031654e-03 │ │ │ Vprtstp: contraction number = 1.477946e-01 │ │ │ Vnewton: Using errtol_s: 62448.057923 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.795425e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.941943e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.274799e+04 │ │ │ Vprtstp: contraction number = 1.274799e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.476725e-03 │ │ │ Vprtstp: contraction number = 1.838631e-01 │ │ │ Vnewton: Using errtol_s: 11481.894443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.938143e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.751685e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.642149e+03 │ │ │ Vprtstp: contraction number = 2.642149e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.058466e-04 │ │ │ Vprtstp: contraction number = 2.071114e-01 │ │ │ Vnewton: Using errtol_s: 2378.031723 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107909e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.907005e+02 │ │ │ Vprtstp: contraction number = 5.907005e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.837606e-05 │ │ │ Vprtstp: contraction number = 2.235632e-01 │ │ │ Vnewton: Using errtol_s: 531.640431 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.223261e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.490109e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.434663e+02 │ │ │ Vprtstp: contraction number = 1.434663e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.660675e-05 │ │ │ Vprtstp: contraction number = 2.428738e-01 │ │ │ Vnewton: Using errtol_s: 129.121507 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.340057e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.783952e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.897369e+01 │ │ │ Vprtstp: contraction number = 3.897369e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.511300e-06 │ │ │ Vprtstp: contraction number = 2.716546e-01 │ │ │ Vnewton: Using errtol_s: 35.076449 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.454338e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.076185e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.167165e+01 │ │ │ Vprtstp: contraction number = 1.167165e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.351022e-06 │ │ │ Vprtstp: contraction number = 2.994751e-01 │ │ │ Vnewton: Using errtol_s: 10.504522 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568509e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.350961e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.750775e+00 │ │ │ Vprtstp: contraction number = 3.750775e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.341599e-07 │ │ │ Vprtstp: contraction number = 3.213567e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.104459e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.225307e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.477238e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.506923e+02 │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2128,17 +2128,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.649154177944E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.233253101346E+05 kT │ │ │ Vpmg_energy: dielEnergy = 6.165668863925E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.113370e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.798200e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -2184,138 +2184,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.297837 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.243720 │ │ │ +Vacc_SASA: Time elapsed: 2.861478 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.492750e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.179472e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.521390e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 3.175690e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.157800e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.360390e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.250613e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.667944e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 9261641.900268 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.320386e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.708295e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.279613e+05 │ │ │ Vprtstp: contraction number = 8.279613e+05 │ │ │ Vnewton: Attempting damping, relres = 0.082099 │ │ │ Vnewton: Attempting damping, relres = 0.538543 │ │ │ Vnewton: Damping accepted, relres = 0.082099 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.209891e-02 │ │ │ Vprtstp: contraction number = 8.209891e-02 │ │ │ Vnewton: Using errtol_s: 760370.715975 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.469785e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.981822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.156529e+05 │ │ │ Vprtstp: contraction number = 1.156529e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.133997e-02 │ │ │ Vprtstp: contraction number = 1.381257e-01 │ │ │ Vnewton: Using errtol_s: 105026.724448 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.583842e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.242499e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.966463e+04 │ │ │ Vprtstp: contraction number = 1.966463e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.911861e-03 │ │ │ Vprtstp: contraction number = 1.685949e-01 │ │ │ Vnewton: Using errtol_s: 17706.967510 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.697802e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.508467e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.721579e+03 │ │ │ Vprtstp: contraction number = 3.721579e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.617487e-04 │ │ │ Vprtstp: contraction number = 1.892129e-01 │ │ │ Vnewton: Using errtol_s: 3350.387034 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.813172e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.776817e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.320600e+02 │ │ │ Vprtstp: contraction number = 7.320600e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.114465e-05 │ │ │ Vprtstp: contraction number = 1.966687e-01 │ │ │ Vnewton: Using errtol_s: 658.916270 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.926708e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.037419e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.450384e+02 │ │ │ Vprtstp: contraction number = 1.450384e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.409447e-05 │ │ │ Vprtstp: contraction number = 1.981101e-01 │ │ │ Vnewton: Using errtol_s: 130.537961 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.041518e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.309386e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.437556e+01 │ │ │ Vprtstp: contraction number = 3.437556e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.340452e-06 │ │ │ Vprtstp: contraction number = 2.370044e-01 │ │ │ Vnewton: Using errtol_s: 30.938074 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.156529e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.571699e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.059415e+01 │ │ │ Vprtstp: contraction number = 1.059415e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.029507e-06 │ │ │ Vprtstp: contraction number = 3.081938e-01 │ │ │ Vnewton: Using errtol_s: 9.534923 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.273805e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.833493e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.916133e+00 │ │ │ Vprtstp: contraction number = 3.916133e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.805503e-07 │ │ │ Vprtstp: contraction number = 3.696433e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.106922e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.231276e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.432545e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.460212e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2324,17 +2324,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.591945419500E+00 kT │ │ │ Vpmg_energy: qfEnergy = 2.356288022123E+05 kT │ │ │ Vpmg_energy: dielEnergy = 1.178084778246E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.049150e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.959540e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -2355,140 +2355,140 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.274921 │ │ │ +Vacc_SASA: Time elapsed: 4.100996 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.028596e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.217697e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.534990e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.098000e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 8.911820e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.383963e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.907848e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.207463e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7837779.438687 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.976993e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.247905e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.514612e+05 │ │ │ Vprtstp: contraction number = 4.514612e+05 │ │ │ Vnewton: Attempting damping, relres = 0.053797 │ │ │ Vnewton: Attempting damping, relres = 0.522401 │ │ │ Vnewton: Damping accepted, relres = 0.053797 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.379672e-02 │ │ │ Vprtstp: contraction number = 5.379672e-02 │ │ │ Vnewton: Using errtol_s: 421646.851825 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.126854e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.529088e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.805281e+04 │ │ │ Vprtstp: contraction number = 6.805281e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 7.947357e-03 │ │ │ Vprtstp: contraction number = 1.477294e-01 │ │ │ Vnewton: Using errtol_s: 62289.628218 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.242081e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.767691e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.276985e+04 │ │ │ Vprtstp: contraction number = 1.276985e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.467975e-03 │ │ │ Vprtstp: contraction number = 1.847124e-01 │ │ │ Vnewton: Using errtol_s: 11505.665992 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.356488e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.020196e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.685314e+03 │ │ │ Vprtstp: contraction number = 2.685314e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.083318e-04 │ │ │ Vprtstp: contraction number = 2.100388e-01 │ │ │ Vnewton: Using errtol_s: 2416.636290 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.471770e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.279663e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.970818e+02 │ │ │ Vprtstp: contraction number = 5.970818e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.855221e-05 │ │ │ Vprtstp: contraction number = 2.223326e-01 │ │ │ Vnewton: Using errtol_s: 537.297133 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.586563e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.522833e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.381270e+02 │ │ │ Vprtstp: contraction number = 1.381270e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.586035e-05 │ │ │ Vprtstp: contraction number = 2.313616e-01 │ │ │ Vnewton: Using errtol_s: 124.309951 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.701678e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.782945e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.581259e+01 │ │ │ Vprtstp: contraction number = 3.581259e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.112278e-06 │ │ │ Vprtstp: contraction number = 2.592804e-01 │ │ │ Vnewton: Using errtol_s: 32.231131 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.817314e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.047845e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.075720e+01 │ │ │ Vprtstp: contraction number = 1.075720e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.235235e-06 │ │ │ Vprtstp: contraction number = 3.003774e-01 │ │ │ Vnewton: Using errtol_s: 9.681503 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.931370e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.330870e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.606387e+00 │ │ │ Vprtstp: contraction number = 3.606387e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.141158e-07 │ │ │ Vprtstp: contraction number = 3.352525e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.108186e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.230175e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.341759e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.372140e+02 │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2497,17 +2497,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.659237014157E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.233789041891E+05 kT │ │ │ Vpmg_energy: dielEnergy = 6.168342765954E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.094290e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.429800e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -2553,138 +2553,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.338577 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.272220 │ │ │ +Vacc_SASA: Time elapsed: 3.133781 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.530342e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.330579e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.529400e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 3.734750e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 8.845090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.434653e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.614684e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.644233e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 9315222.001185 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.683966e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.679966e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.310439e+05 │ │ │ Vprtstp: contraction number = 8.310439e+05 │ │ │ Vnewton: Attempting damping, relres = 0.081942 │ │ │ Vnewton: Attempting damping, relres = 0.538517 │ │ │ Vnewton: Damping accepted, relres = 0.081942 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.194219e-02 │ │ │ Vprtstp: contraction number = 8.194219e-02 │ │ │ Vnewton: Using errtol_s: 763309.735899 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.836171e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.936723e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.164941e+05 │ │ │ Vprtstp: contraction number = 1.164941e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.135719e-02 │ │ │ Vprtstp: contraction number = 1.386000e-01 │ │ │ Vnewton: Using errtol_s: 105794.756542 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.950891e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.190099e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.004035e+04 │ │ │ Vprtstp: contraction number = 2.004035e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.937352e-03 │ │ │ Vprtstp: contraction number = 1.705837e-01 │ │ │ Vnewton: Using errtol_s: 18046.864412 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.065092e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.453378e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.874509e+03 │ │ │ Vprtstp: contraction number = 3.874509e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.744478e-04 │ │ │ Vprtstp: contraction number = 1.932781e-01 │ │ │ Vnewton: Using errtol_s: 3488.064314 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.180870e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.708654e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.934449e+02 │ │ │ Vprtstp: contraction number = 7.934449e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.666874e-05 │ │ │ Vprtstp: contraction number = 2.047515e-01 │ │ │ Vnewton: Using errtol_s: 714.186341 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.295538e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.962285e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.631165e+02 │ │ │ Vprtstp: contraction number = 1.631165e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.576011e-05 │ │ │ Vprtstp: contraction number = 2.055611e-01 │ │ │ Vnewton: Using errtol_s: 146.808940 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.411020e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.241327e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.992341e+01 │ │ │ Vprtstp: contraction number = 3.992341e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.857249e-06 │ │ │ Vprtstp: contraction number = 2.447475e-01 │ │ │ Vnewton: Using errtol_s: 35.931127 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.527543e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.517641e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.373524e+01 │ │ │ Vprtstp: contraction number = 1.373524e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.327082e-06 │ │ │ Vprtstp: contraction number = 3.440488e-01 │ │ │ Vnewton: Using errtol_s: 12.362061 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.643495e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.798228e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.506580e+00 │ │ │ Vprtstp: contraction number = 5.506580e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.320241e-07 │ │ │ Vprtstp: contraction number = 4.008978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.115297e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.236609e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.408252e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.437150e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2693,17 +2693,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.613981699518E+00 kT │ │ │ Vpmg_energy: qfEnergy = 2.353039534047E+05 kT │ │ │ Vpmg_energy: dielEnergy = 1.176460315654E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.069620e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.840270e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -2724,140 +2724,140 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.015864 │ │ │ +Vacc_SASA: Time elapsed: 8.040187 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.115485e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.140553e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.574060e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 3.779640e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.164590e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.378487e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.592423e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019859e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 15819726.247791 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.662226e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023963e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.105286e+05 │ │ │ Vprtstp: contraction number = 9.105286e+05 │ │ │ Vnewton: Attempting damping, relres = 0.054151 │ │ │ Vnewton: Attempting damping, relres = 0.522361 │ │ │ Vnewton: Damping accepted, relres = 0.054151 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.415081e-02 │ │ │ Vprtstp: contraction number = 5.415081e-02 │ │ │ Vnewton: Using errtol_s: 856650.988867 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.812542e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052030e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.365159e+05 │ │ │ Vprtstp: contraction number = 1.365159e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 7.938600e-03 │ │ │ Vprtstp: contraction number = 1.466017e-01 │ │ │ Vnewton: Using errtol_s: 125586.474947 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.928792e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.078588e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.543138e+04 │ │ │ Vprtstp: contraction number = 2.543138e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.449191e-03 │ │ │ Vprtstp: contraction number = 1.825500e-01 │ │ │ Vnewton: Using errtol_s: 22925.804865 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.043603e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.106071e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.291506e+03 │ │ │ Vprtstp: contraction number = 5.291506e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.010412e-04 │ │ │ Vprtstp: contraction number = 2.077305e-01 │ │ │ Vnewton: Using errtol_s: 4762.388621 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.159979e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.130363e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.180651e+03 │ │ │ Vprtstp: contraction number = 1.180651e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.716597e-05 │ │ │ Vprtstp: contraction number = 2.231123e-01 │ │ │ Vnewton: Using errtol_s: 1062.547289 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.275959e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.157071e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.813654e+02 │ │ │ Vprtstp: contraction number = 2.813654e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.600723e-05 │ │ │ Vprtstp: contraction number = 2.383235e-01 │ │ │ Vnewton: Using errtol_s: 253.229951 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.392933e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183436e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.533652e+01 │ │ │ Vprtstp: contraction number = 7.533652e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.285970e-06 │ │ │ Vprtstp: contraction number = 2.677522e-01 │ │ │ Vnewton: Using errtol_s: 67.802871 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.508393e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.210848e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.308540e+01 │ │ │ Vprtstp: contraction number = 2.308540e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.313362e-06 │ │ │ Vprtstp: contraction number = 3.064328e-01 │ │ │ Vnewton: Using errtol_s: 20.777024 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.623692e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.239301e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.670717e+00 │ │ │ Vprtstp: contraction number = 7.670717e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.363948e-07 │ │ │ Vprtstp: contraction number = 3.322731e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.115102e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.240249e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.450578e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.479212e+02 │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2866,17 +2866,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.013375850535E+01 kT │ │ │ Vpmg_energy: qfEnergy = 2.468101698845E+05 kT │ │ │ Vpmg_energy: dielEnergy = 1.233922430579E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.070550e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.135050e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ @@ -2922,138 +2922,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.652629 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.948749 │ │ │ +Vacc_SASA: Time elapsed: 7.497432 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.829069e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.277764e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.531180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 3.873570e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.035540e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.434385e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.640067e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.280974e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 18644287.879827 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.711033e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.285238e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.651555e+06 │ │ │ Vprtstp: contraction number = 1.651555e+06 │ │ │ Vnewton: Attempting damping, relres = 0.081643 │ │ │ Vnewton: Attempting damping, relres = 0.538237 │ │ │ Vnewton: Damping accepted, relres = 0.081643 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164291e-02 │ │ │ Vprtstp: contraction number = 8.164291e-02 │ │ │ Vnewton: Using errtol_s: 1522173.863324 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.863086e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.315166e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.305601e+05 │ │ │ Vprtstp: contraction number = 2.305601e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.125644e-02 │ │ │ Vprtstp: contraction number = 1.378740e-01 │ │ │ Vnewton: Using errtol_s: 209868.227405 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.984916e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.344281e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.940032e+04 │ │ │ Vprtstp: contraction number = 3.940032e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.903339e-03 │ │ │ Vprtstp: contraction number = 1.690890e-01 │ │ │ Vnewton: Using errtol_s: 35486.402387 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010911e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.373324e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.544305e+03 │ │ │ Vprtstp: contraction number = 7.544305e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.642891e-04 │ │ │ Vprtstp: contraction number = 1.913948e-01 │ │ │ Vnewton: Using errtol_s: 6791.911566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022525e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.400993e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.522155e+03 │ │ │ Vprtstp: contraction number = 1.522155e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.348563e-05 │ │ │ Vprtstp: contraction number = 2.017234e-01 │ │ │ Vnewton: Using errtol_s: 1370.087193 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034663e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427346e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.106660e+02 │ │ │ Vprtstp: contraction number = 3.106660e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.499708e-05 │ │ │ Vprtstp: contraction number = 2.040818e-01 │ │ │ Vnewton: Using errtol_s: 279.609899 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047043e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457790e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.690225e+01 │ │ │ Vprtstp: contraction number = 7.690225e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.712245e-06 │ │ │ Vprtstp: contraction number = 2.475312e-01 │ │ │ Vnewton: Using errtol_s: 69.212171 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.059396e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.488504e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.600764e+01 │ │ │ Vprtstp: contraction number = 2.600764e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.255497e-06 │ │ │ Vprtstp: contraction number = 3.382042e-01 │ │ │ Vnewton: Using errtol_s: 23.407850 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.071956e+02 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.516351e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011646e+01 │ │ │ Vprtstp: contraction number = 1.011646e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.883437e-07 │ │ │ Vprtstp: contraction number = 3.889644e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.173692e+01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.297476e+01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.620879e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.650050e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -3062,23 +3062,23 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.005009553015E+01 kT │ │ │ Vpmg_energy: qfEnergy = 4.710211065569E+05 kT │ │ │ Vpmg_energy: dielEnergy = 2.354978106920E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.607480e-01 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.393420e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.083983e+02 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.543640e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:56:12 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 10:11:51 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -3431,250 +3431,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.252868 │ │ │ +Vacc_SASA: Time elapsed: 3.838351 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.611739e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.002303e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.629700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.024930e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.578850e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.385526e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.047327e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.008470e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.210922e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.071126e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.595609e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.522365e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.900253e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.577855e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.182484e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.697677e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.464447e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.982233e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.747455e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.204920e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.028998e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.419285e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.318092e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.606479e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.599952e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.815238e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.881158e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.024216e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.162201e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219509e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.454293e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.420506e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.734148e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.609856e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.014256e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.793058e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.307302e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.982111e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.588951e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.180396e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.870846e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.394563e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.140743e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.610867e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.435993e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.819228e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.602284e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.854558e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.928004e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.944440e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -3683,15 +3683,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.479770161201E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.169401599673E+03 kT │ │ │ Vpmg_energy: dielEnergy = 6.300507194512E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.550200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.777200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -3739,171 +3739,171 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00578902 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.271295 │ │ │ +Vacc_SASA: Time elapsed: 3.779464 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.841528e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.078111e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.630200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.278220e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.696660e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.440177e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.177953e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.065573e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3431662.159805 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.197525e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.099117e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.373293e+05 │ │ │ Vprtstp: contraction number = 3.373293e+05 │ │ │ Vnewton: Attempting damping, relres = 0.089626 │ │ │ Vnewton: Attempting damping, relres = 0.541581 │ │ │ Vnewton: Damping accepted, relres = 0.089626 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.962597e-02 │ │ │ Vprtstp: contraction number = 8.962597e-02 │ │ │ Vnewton: Using errtol_s: 307566.035257 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237440e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.407329e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.223173e+04 │ │ │ Vprtstp: contraction number = 6.223173e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.639798e-02 │ │ │ Vprtstp: contraction number = 1.829601e-01 │ │ │ Vnewton: Using errtol_s: 56272.319668 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.267713e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.709251e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.604081e+04 │ │ │ Vprtstp: contraction number = 1.604081e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.208259e-03 │ │ │ Vprtstp: contraction number = 2.566328e-01 │ │ │ Vnewton: Using errtol_s: 14441.323490 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.299214e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.036318e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.994316e+03 │ │ │ Vprtstp: contraction number = 4.994316e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.309837e-03 │ │ │ Vprtstp: contraction number = 3.112539e-01 │ │ │ Vnewton: Using errtol_s: 4494.917566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329549e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.326348e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.695194e+03 │ │ │ Vprtstp: contraction number = 1.695194e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.445882e-04 │ │ │ Vprtstp: contraction number = 3.394226e-01 │ │ │ Vnewton: Using errtol_s: 1525.676669 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.360986e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.589737e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.988429e+02 │ │ │ Vprtstp: contraction number = 5.988429e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.570548e-04 │ │ │ Vprtstp: contraction number = 3.532589e-01 │ │ │ Vnewton: Using errtol_s: 538.958849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.391084e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.906499e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.157694e+02 │ │ │ Vprtstp: contraction number = 2.157694e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.658847e-05 │ │ │ Vprtstp: contraction number = 3.603104e-01 │ │ │ Vnewton: Using errtol_s: 194.192499 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.421356e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.194042e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.859364e+01 │ │ │ Vprtstp: contraction number = 7.859364e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.061225e-05 │ │ │ Vprtstp: contraction number = 3.642483e-01 │ │ │ Vnewton: Using errtol_s: 70.734280 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.451489e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.473762e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.887021e+01 │ │ │ Vprtstp: contraction number = 2.887021e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.571604e-06 │ │ │ Vprtstp: contraction number = 3.673351e-01 │ │ │ Vnewton: Using errtol_s: 25.983185 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.481745e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.760114e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.070116e+01 │ │ │ Vprtstp: contraction number = 1.070116e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.806524e-06 │ │ │ Vprtstp: contraction number = 3.706644e-01 │ │ │ Vnewton: Using errtol_s: 9.631041 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.513049e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.068291e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.050515e+00 │ │ │ Vprtstp: contraction number = 4.050515e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.062302e-06 │ │ │ Vprtstp: contraction number = 3.785119e-01 │ │ │ Vnewton: Using errtol_s: 3.645463 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.545277e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.389506e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.586893e+00 │ │ │ Vprtstp: contraction number = 1.586893e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.161843e-07 │ │ │ Vprtstp: contraction number = 3.917757e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.909874e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.173388e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.629388e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.645770e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -3912,17 +3912,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.504529533890E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.061382616797E+04 kT │ │ │ Vpmg_energy: dielEnergy = 5.339258817013E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.247300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.006300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -3943,272 +3943,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.318198 │ │ │ +Vacc_SASA: Time elapsed: 4.541521 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.725214e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.751225e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.640000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.237370e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.727310e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.942982e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.869728e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.775504e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.888559e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.817915e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.929912e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.119327e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.958741e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.367337e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.987526e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.596179e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.014992e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.800335e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.043611e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.011535e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.070908e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.237474e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.099489e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.470287e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.128162e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.681011e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.155634e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.911097e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.183028e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013818e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.211519e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.037698e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.240215e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.063649e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.267743e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089082e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.298259e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112523e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.325863e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.133750e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.354516e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155768e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.381953e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.179027e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.409528e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.201747e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.438179e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.223425e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.465518e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.244311e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.168980e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.412414e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.854296e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.876123e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -4217,17 +4217,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.521116242377E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.321247419853E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.153524159473E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.509000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.064900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -4273,193 +4273,193 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0721278 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.259861 │ │ │ +Vacc_SASA: Time elapsed: 3.741018 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.797819e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.469749e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.501800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.790800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.600830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.050905e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.793084e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.269654e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3863048.260999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.808660e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.273105e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.079329e+05 │ │ │ Vprtstp: contraction number = 4.079329e+05 │ │ │ Vnewton: Attempting damping, relres = 0.096763 │ │ │ Vnewton: Attempting damping, relres = 0.545251 │ │ │ Vnewton: Damping accepted, relres = 0.096763 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.676296e-02 │ │ │ Vprtstp: contraction number = 9.676296e-02 │ │ │ Vnewton: Using errtol_s: 373799.984181 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.845195e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.302275e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.732785e+04 │ │ │ Vprtstp: contraction number = 7.732785e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.807372e-02 │ │ │ Vprtstp: contraction number = 1.867834e-01 │ │ │ Vnewton: Using errtol_s: 69819.644697 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.872195e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330841e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.985652e+04 │ │ │ Vprtstp: contraction number = 1.985652e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.627077e-03 │ │ │ Vprtstp: contraction number = 2.560113e-01 │ │ │ Vnewton: Using errtol_s: 17874.621452 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.899119e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.359607e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.114622e+03 │ │ │ Vprtstp: contraction number = 6.114622e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.424617e-03 │ │ │ Vprtstp: contraction number = 3.078870e-01 │ │ │ Vnewton: Using errtol_s: 5503.364448 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.926107e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.387304e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.092890e+03 │ │ │ Vprtstp: contraction number = 2.092890e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.875987e-04 │ │ │ Vprtstp: contraction number = 3.422665e-01 │ │ │ Vnewton: Using errtol_s: 1883.617345 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.953165e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.419155e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.574998e+02 │ │ │ Vprtstp: contraction number = 7.574998e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.764801e-04 │ │ │ Vprtstp: contraction number = 3.619372e-01 │ │ │ Vnewton: Using errtol_s: 681.751152 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.980289e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.448356e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.922283e+02 │ │ │ Vprtstp: contraction number = 2.922283e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 6.808241e-05 │ │ │ Vprtstp: contraction number = 3.857795e-01 │ │ │ Vnewton: Using errtol_s: 263.005621 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.008053e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.475714e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.230857e+02 │ │ │ Vprtstp: contraction number = 1.230857e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.867611e-05 │ │ │ Vprtstp: contraction number = 4.211970e-01 │ │ │ Vnewton: Using errtol_s: 110.777182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.034957e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.503178e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.644162e+01 │ │ │ Vprtstp: contraction number = 5.644162e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.314958e-05 │ │ │ Vprtstp: contraction number = 4.585554e-01 │ │ │ Vnewton: Using errtol_s: 50.797474 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.061953e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.529416e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.814912e+01 │ │ │ Vprtstp: contraction number = 2.814912e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.558089e-06 │ │ │ Vprtstp: contraction number = 4.987298e-01 │ │ │ Vnewton: Using errtol_s: 25.334216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.089035e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.556238e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.477957e+01 │ │ │ Vprtstp: contraction number = 1.477957e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.443295e-06 │ │ │ Vprtstp: contraction number = 5.250454e-01 │ │ │ Vnewton: Using errtol_s: 13.301614 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.116953e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.584068e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.444333e+00 │ │ │ Vprtstp: contraction number = 8.444333e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.967333e-06 │ │ │ Vprtstp: contraction number = 5.713519e-01 │ │ │ Vnewton: Using errtol_s: 7.599902 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.143937e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.611875e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.056221e+00 │ │ │ Vprtstp: contraction number = 5.056221e+00 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.177982e-06 │ │ │ Vprtstp: contraction number = 5.987712e-01 │ │ │ Vnewton: Using errtol_s: 4.550602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.170989e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.642575e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.242153e+00 │ │ │ Vprtstp: contraction number = 3.242153e+00 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.553462e-07 │ │ │ Vprtstp: contraction number = 6.412203e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.992052e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.230506e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.990621e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.002307e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -4468,17 +4468,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.360671447276E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.843358669820E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.205607078702E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.185400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.780700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -4499,261 +4499,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.962484 │ │ │ +Vacc_SASA: Time elapsed: 8.159221 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.516042e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.652477e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.606400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.068740e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.632670e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.402054e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.770743e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.679976e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.786079e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682891e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.823252e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.706642e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.850621e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.727105e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.877998e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.749378e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.905355e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.769921e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.932653e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.790570e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.959997e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.814291e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.988570e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.838835e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.017233e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.864209e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.044567e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.889195e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.071898e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.915754e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.100454e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.942929e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.127829e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.968690e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.155215e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.995300e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.182574e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.020968e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.209956e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.046561e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.237359e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.071144e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.264685e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.096641e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.293162e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.122840e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.320531e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.148073e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.706313e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.935708e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.906872e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.922115e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -4762,17 +4762,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.970329890600E+00 kT │ │ │ Vpmg_energy: qfEnergy = 3.499206035649E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.787861710155E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.530300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.326500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -4818,182 +4818,182 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.081031 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.941672 │ │ │ +Vacc_SASA: Time elapsed: 10.094157 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.743462e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.225525e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.451700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.143630e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.614280e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.857076e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.942536e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.185005e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7257742.969900 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.958093e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.189252e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.332655e+05 │ │ │ Vprtstp: contraction number = 7.332655e+05 │ │ │ Vnewton: Attempting damping, relres = 0.092954 │ │ │ Vnewton: Attempting damping, relres = 0.543087 │ │ │ Vnewton: Damping accepted, relres = 0.092954 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.295377e-02 │ │ │ Vprtstp: contraction number = 9.295377e-02 │ │ │ Vnewton: Using errtol_s: 674634.557796 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.993235e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.223760e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.375383e+05 │ │ │ Vprtstp: contraction number = 1.375383e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.716852e-02 │ │ │ Vprtstp: contraction number = 1.846995e-01 │ │ │ Vnewton: Using errtol_s: 124604.673279 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.020174e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.253793e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.550512e+04 │ │ │ Vprtstp: contraction number = 3.550512e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.404594e-03 │ │ │ Vprtstp: contraction number = 2.565507e-01 │ │ │ Vnewton: Using errtol_s: 31967.413641 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.047003e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.282903e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.099641e+04 │ │ │ Vprtstp: contraction number = 1.099641e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.363650e-03 │ │ │ Vprtstp: contraction number = 3.095972e-01 │ │ │ Vnewton: Using errtol_s: 9897.022727 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.073909e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.311281e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.730401e+03 │ │ │ Vprtstp: contraction number = 3.730401e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.625937e-04 │ │ │ Vprtstp: contraction number = 3.392320e-01 │ │ │ Vnewton: Using errtol_s: 3357.386399 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.102114e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.339839e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.301607e+03 │ │ │ Vprtstp: contraction number = 1.301607e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.614068e-04 │ │ │ Vprtstp: contraction number = 3.489169e-01 │ │ │ Vnewton: Using errtol_s: 1171.448936 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.129684e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.372211e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.645153e+02 │ │ │ Vprtstp: contraction number = 4.645153e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.760250e-05 │ │ │ Vprtstp: contraction number = 3.568778e-01 │ │ │ Vnewton: Using errtol_s: 418.064161 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.156677e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.399925e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.772219e+02 │ │ │ Vprtstp: contraction number = 1.772219e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.197650e-05 │ │ │ Vprtstp: contraction number = 3.815199e-01 │ │ │ Vnewton: Using errtol_s: 159.499808 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.183602e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.427906e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.471028e+01 │ │ │ Vprtstp: contraction number = 7.471028e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 9.264488e-06 │ │ │ Vprtstp: contraction number = 4.215634e-01 │ │ │ Vnewton: Using errtol_s: 67.239276 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.211533e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.455621e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.443502e+01 │ │ │ Vprtstp: contraction number = 3.443502e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 4.270137e-06 │ │ │ Vprtstp: contraction number = 4.609145e-01 │ │ │ Vnewton: Using errtol_s: 30.991559 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.238477e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.482409e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.720700e+01 │ │ │ Vprtstp: contraction number = 1.720700e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.133763e-06 │ │ │ Vprtstp: contraction number = 4.996942e-01 │ │ │ Vnewton: Using errtol_s: 15.486302 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.265412e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.508251e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.259710e+00 │ │ │ Vprtstp: contraction number = 9.259710e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.148258e-06 │ │ │ Vprtstp: contraction number = 5.381377e-01 │ │ │ Vnewton: Using errtol_s: 8.333763 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.292255e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.534354e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.358358e+00 │ │ │ Vprtstp: contraction number = 5.358358e+00 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 6.644658e-07 │ │ │ Vprtstp: contraction number = 5.786728e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.703765e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.942927e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.736704e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.756838e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -5002,27 +5002,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.140717793128E+00 kT │ │ │ Vpmg_energy: qfEnergy = 2.905500135129E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.454863407382E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.140000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.476700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.345458e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.559284e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:56:45 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 11:06:31 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -5375,250 +5375,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.256268 │ │ │ +Vacc_SASA: Time elapsed: 3.687800 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.611142e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.529737e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.588400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.983300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.749190e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.227769e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.056829e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.115065e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.245684e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.955985e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.669761e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.914729e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.982343e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.606993e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.296949e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648646e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.610764e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.522211e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.924081e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039357e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.224949e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238060e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.536650e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.416969e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.849687e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.610739e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.164676e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.829515e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.478681e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.044661e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.793159e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.237822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.107217e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.444912e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.409029e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.626456e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.733389e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.816996e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.035175e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.009497e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.349899e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.202831e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.650099e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.402685e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.950668e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.603959e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.132347e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.398606e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.717863e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.731560e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -5627,17 +5627,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.939690296929E-01 kT │ │ │ Vpmg_energy: qfEnergy = 9.376673747482E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.692177592704E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.526400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.922300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -5683,171 +5683,171 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0309075 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.226459 │ │ │ +Vacc_SASA: Time elapsed: 4.311686 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.866995e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.758101e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.615200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.611200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.595020e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.442866e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233564e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.853004e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6495765.822087 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.249225e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.883457e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.362765e+05 │ │ │ Vprtstp: contraction number = 6.362765e+05 │ │ │ Vnewton: Attempting damping, relres = 0.088746 │ │ │ Vnewton: Attempting damping, relres = 0.541895 │ │ │ Vnewton: Damping accepted, relres = 0.088746 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.874646e-02 │ │ │ Vprtstp: contraction number = 8.874646e-02 │ │ │ Vnewton: Using errtol_s: 576476.204773 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.288132e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.159658e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.170231e+05 │ │ │ Vprtstp: contraction number = 1.170231e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.623146e-02 │ │ │ Vprtstp: contraction number = 1.828970e-01 │ │ │ Vnewton: Using errtol_s: 105435.741217 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.317727e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.433400e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.955662e+04 │ │ │ Vprtstp: contraction number = 2.955662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.095304e-03 │ │ │ Vprtstp: contraction number = 2.523066e-01 │ │ │ Vnewton: Using errtol_s: 26602.134295 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.346042e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.710628e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.995691e+03 │ │ │ Vprtstp: contraction number = 8.995691e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.246378e-03 │ │ │ Vprtstp: contraction number = 3.043434e-01 │ │ │ Vnewton: Using errtol_s: 8096.182717 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.375615e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.988680e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.013650e+03 │ │ │ Vprtstp: contraction number = 3.013650e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.175484e-04 │ │ │ Vprtstp: contraction number = 3.350093e-01 │ │ │ Vnewton: Using errtol_s: 2712.296685 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.404024e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.275225e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.048604e+03 │ │ │ Vprtstp: contraction number = 1.048604e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.452864e-04 │ │ │ Vprtstp: contraction number = 3.479510e-01 │ │ │ Vnewton: Using errtol_s: 943.746446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.433610e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.528119e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.603662e+02 │ │ │ Vprtstp: contraction number = 3.603662e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.992953e-05 │ │ │ Vprtstp: contraction number = 3.436628e-01 │ │ │ Vnewton: Using errtol_s: 324.330531 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.463218e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.766692e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.297355e+02 │ │ │ Vprtstp: contraction number = 1.297355e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.797512e-05 │ │ │ Vprtstp: contraction number = 3.600099e-01 │ │ │ Vnewton: Using errtol_s: 116.762190 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.491629e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.030385e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.314764e+01 │ │ │ Vprtstp: contraction number = 5.314764e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.363712e-06 │ │ │ Vprtstp: contraction number = 4.096613e-01 │ │ │ Vnewton: Using errtol_s: 47.832946 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521177e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.303871e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.432172e+01 │ │ │ Vprtstp: contraction number = 2.432172e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.369821e-06 │ │ │ Vprtstp: contraction number = 4.576253e-01 │ │ │ Vnewton: Using errtol_s: 21.889567 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.550713e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.583459e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.198142e+01 │ │ │ Vprtstp: contraction number = 1.198142e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.660048e-06 │ │ │ Vprtstp: contraction number = 4.926220e-01 │ │ │ Vnewton: Using errtol_s: 10.783282 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.579008e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.835822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.178209e+00 │ │ │ Vprtstp: contraction number = 6.178209e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 8.560021e-07 │ │ │ Vprtstp: contraction number = 5.156491e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.682747e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.934173e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.200706e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.216785e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -5856,17 +5856,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.088785414018E-01 kT │ │ │ Vpmg_energy: qfEnergy = 7.513083652575E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.773034744692E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.090200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.551100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -5887,272 +5887,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.275705 │ │ │ +Vacc_SASA: Time elapsed: 3.425204 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.645322e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.261848e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.676000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.352600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.685890e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.150782e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.894779e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.109499e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.912894e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.137524e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.949987e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.321220e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.978743e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.490584e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.006108e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.657679e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.034502e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.821895e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.062928e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.987139e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.091734e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.162749e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.120438e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.338940e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.147672e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.503382e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.176300e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.673039e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.203632e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.824690e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.233387e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.984448e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.262231e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.149339e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.289475e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.312945e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.318106e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.478387e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.346704e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.642052e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.375096e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.801776e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.403512e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.957917e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.432107e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.011816e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.460621e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028222e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.487555e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.044284e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.137385e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.384528e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.486031e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.498554e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -6161,17 +6161,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.529259077785E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 3.922111986755E-02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.569400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.156600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -6217,149 +6217,149 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00111335 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.269327 │ │ │ +Vacc_SASA: Time elapsed: 3.288655 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.668069e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.113614e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.678600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.753700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.649420e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.229694e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.802846e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065112e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 659220.576503 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.820962e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067972e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.405229e+04 │ │ │ Vprtstp: contraction number = 7.405229e+04 │ │ │ Vnewton: Attempting damping, relres = 0.101194 │ │ │ Vnewton: Attempting damping, relres = 0.547249 │ │ │ Vnewton: Damping accepted, relres = 0.101194 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011936e-01 │ │ │ Vprtstp: contraction number = 1.011936e-01 │ │ │ Vnewton: Using errtol_s: 66708.882844 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.858120e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085784e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.227539e+04 │ │ │ Vprtstp: contraction number = 1.227539e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.676045e-02 │ │ │ Vprtstp: contraction number = 1.656277e-01 │ │ │ Vnewton: Using errtol_s: 11048.836228 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.886699e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102263e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.508807e+03 │ │ │ Vprtstp: contraction number = 2.508807e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.425225e-03 │ │ │ Vprtstp: contraction number = 2.043635e-01 │ │ │ Vnewton: Using errtol_s: 2257.978588 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.915302e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.118149e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.967621e+02 │ │ │ Vprtstp: contraction number = 5.967621e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 8.147347e-04 │ │ │ Vprtstp: contraction number = 2.378632e-01 │ │ │ Vnewton: Using errtol_s: 537.089910 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.944050e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.133750e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.589401e+02 │ │ │ Vprtstp: contraction number = 1.589401e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 2.169933e-04 │ │ │ Vprtstp: contraction number = 2.663361e-01 │ │ │ Vnewton: Using errtol_s: 143.046443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.971202e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.148267e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.567685e+01 │ │ │ Vprtstp: contraction number = 4.567685e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 6.236027e-05 │ │ │ Vprtstp: contraction number = 2.873834e-01 │ │ │ Vnewton: Using errtol_s: 41.109175 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.999627e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.164376e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.380678e+01 │ │ │ Vprtstp: contraction number = 1.380678e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.884969e-05 │ │ │ Vprtstp: contraction number = 3.022708e-01 │ │ │ Vnewton: Using errtol_s: 12.426102 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.028097e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180988e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.334509e+00 │ │ │ Vprtstp: contraction number = 4.334509e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.917683e-06 │ │ │ Vprtstp: contraction number = 3.139406e-01 │ │ │ Vnewton: Using errtol_s: 3.901058 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.056880e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.195907e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.401869e+00 │ │ │ Vprtstp: contraction number = 1.401869e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.913900e-06 │ │ │ Vprtstp: contraction number = 3.234205e-01 │ │ │ Vnewton: Using errtol_s: 1.261682 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.085596e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.210931e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.640279e-01 │ │ │ Vprtstp: contraction number = 4.640279e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.335135e-07 │ │ │ Vprtstp: contraction number = 3.310066e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.039059e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.285988e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.594369e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.608243e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -6368,17 +6368,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.628092645566E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 3.231942662448E-02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.476800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.470400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -6399,261 +6399,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.033531 │ │ │ +Vacc_SASA: Time elapsed: 6.874350 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.631051e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.040233e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.757800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.160580e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.794040e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.463629e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.698688e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.234249e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.716177e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237422e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.753391e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.258777e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.781811e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.279426e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.810500e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.300245e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.837662e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320748e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.866011e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.340491e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.894537e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.361373e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.922960e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.383658e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.951314e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.403860e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.980018e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.425343e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.008637e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.447211e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.040980e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.468806e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.069548e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.490590e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.098163e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.513761e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.126488e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.534855e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.153660e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.555769e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.183230e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.576878e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.211688e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.598972e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.242115e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.618249e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.272810e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.636921e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.956354e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.203651e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.186175e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.202151e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -6662,17 +6662,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.345658970657E-01 kT │ │ │ Vpmg_energy: qfEnergy = 9.376279132276E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.692311982408E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.572500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.377900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -6718,171 +6718,171 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0354778 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.943085 │ │ │ +Vacc_SASA: Time elapsed: 6.605058 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.752450e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.048709e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.549300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.065500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.673120e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.139006e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.896858e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.662241e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7084866.598925 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.912914e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.664806e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.984768e+05 │ │ │ Vprtstp: contraction number = 6.984768e+05 │ │ │ Vnewton: Attempting damping, relres = 0.089369 │ │ │ Vnewton: Attempting damping, relres = 0.542089 │ │ │ Vnewton: Damping accepted, relres = 0.089369 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.936880e-02 │ │ │ Vprtstp: contraction number = 8.936880e-02 │ │ │ Vnewton: Using errtol_s: 633166.041219 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.948775e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.687703e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.273163e+05 │ │ │ Vprtstp: contraction number = 1.273163e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.619364e-02 │ │ │ Vprtstp: contraction number = 1.812001e-01 │ │ │ Vnewton: Using errtol_s: 114729.758442 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.975882e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.709314e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.151737e+04 │ │ │ Vprtstp: contraction number = 3.151737e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.003932e-03 │ │ │ Vprtstp: contraction number = 2.472534e-01 │ │ │ Vnewton: Using errtol_s: 28367.322157 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.003233e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.731898e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.393741e+03 │ │ │ Vprtstp: contraction number = 9.393741e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.193311e-03 │ │ │ Vprtstp: contraction number = 2.980349e-01 │ │ │ Vnewton: Using errtol_s: 8454.451884 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.030528e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.754911e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.092776e+03 │ │ │ Vprtstp: contraction number = 3.092776e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.928814e-04 │ │ │ Vprtstp: contraction number = 3.292363e-01 │ │ │ Vnewton: Using errtol_s: 2783.512220 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.057813e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.776233e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.061371e+03 │ │ │ Vprtstp: contraction number = 1.061371e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.348278e-04 │ │ │ Vprtstp: contraction number = 3.431770e-01 │ │ │ Vnewton: Using errtol_s: 955.237298 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.085143e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.797884e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.607964e+02 │ │ │ Vprtstp: contraction number = 3.607964e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.583260e-05 │ │ │ Vprtstp: contraction number = 3.399342e-01 │ │ │ Vnewton: Using errtol_s: 324.717847 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.112728e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.820145e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.293597e+02 │ │ │ Vprtstp: contraction number = 1.293597e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.643277e-05 │ │ │ Vprtstp: contraction number = 3.585389e-01 │ │ │ Vnewton: Using errtol_s: 116.423976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.141481e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.842253e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.299042e+01 │ │ │ Vprtstp: contraction number = 5.299042e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 6.731454e-06 │ │ │ Vprtstp: contraction number = 4.096360e-01 │ │ │ Vnewton: Using errtol_s: 47.691450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.169822e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.864679e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.428459e+01 │ │ │ Vprtstp: contraction number = 2.428459e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.084907e-06 │ │ │ Vprtstp: contraction number = 4.582824e-01 │ │ │ Vnewton: Using errtol_s: 21.856153 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.197137e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.886278e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.197548e+01 │ │ │ Vprtstp: contraction number = 1.197548e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.521262e-06 │ │ │ Vprtstp: contraction number = 4.931307e-01 │ │ │ Vnewton: Using errtol_s: 10.777941 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.224435e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.908776e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.181341e+00 │ │ │ Vprtstp: contraction number = 6.181341e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.852242e-07 │ │ │ Vprtstp: contraction number = 5.161662e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.490856e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.737574e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.659755e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.672062e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -6891,27 +6891,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.684722914233E-01 kT │ │ │ Vpmg_energy: qfEnergy = 7.513063949705E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.773049125938E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.110500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.200400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.278953e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.928634e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:57:17 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 11:47:30 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -7264,250 +7264,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.249886 │ │ │ +Vacc_SASA: Time elapsed: 2.850121 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.595857e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.677551e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.615600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.756700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.590860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.055360e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.025185e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.105088e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.179667e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.593829e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.572013e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.455305e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.869364e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.080694e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.153782e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.742632e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.437911e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.369192e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.732409e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.959431e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.016678e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060498e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.300727e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.219097e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.594865e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.381252e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.889760e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.545226e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.188091e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.702535e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.485211e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.860112e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.771519e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.010129e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.068764e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.163043e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.353235e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.319733e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.638185e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.472647e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.936306e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.631903e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.234060e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.791395e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.517641e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.956290e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.720847e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.973823e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.053158e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.065211e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -7516,17 +7516,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.966602122039E-02 kT │ │ │ Vpmg_energy: qfEnergy = 3.975619983960E+01 kT │ │ │ Vpmg_energy: dielEnergy = 4.589187237063E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.535600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.908400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -7572,160 +7572,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00234933 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.237435 │ │ │ +Vacc_SASA: Time elapsed: 3.081064 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.691428e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.183339e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.517400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.486500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.606510e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.165520e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.171685e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.159727e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2418328.609890 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.187789e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.185717e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.297991e+05 │ │ │ Vprtstp: contraction number = 2.297991e+05 │ │ │ Vnewton: Attempting damping, relres = 0.085636 │ │ │ Vnewton: Attempting damping, relres = 0.540011 │ │ │ Vnewton: Damping accepted, relres = 0.085636 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.563556e-02 │ │ │ Vprtstp: contraction number = 8.563556e-02 │ │ │ Vnewton: Using errtol_s: 207094.936691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.226194e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.417318e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.943259e+04 │ │ │ Vprtstp: contraction number = 3.943259e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.467770e-02 │ │ │ Vprtstp: contraction number = 1.713972e-01 │ │ │ Vnewton: Using errtol_s: 35495.493076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.256009e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.660164e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.192651e+03 │ │ │ Vprtstp: contraction number = 9.192651e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.421180e-03 │ │ │ Vprtstp: contraction number = 2.330870e-01 │ │ │ Vnewton: Using errtol_s: 8273.537556 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.285526e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.884967e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.625902e+03 │ │ │ Vprtstp: contraction number = 2.625902e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 9.772537e-04 │ │ │ Vprtstp: contraction number = 2.856481e-01 │ │ │ Vnewton: Using errtol_s: 2363.320499 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.313834e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.095344e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.336695e+02 │ │ │ Vprtstp: contraction number = 8.336695e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.102569e-04 │ │ │ Vprtstp: contraction number = 3.174784e-01 │ │ │ Vnewton: Using errtol_s: 750.303246 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.343313e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.307188e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.790113e+02 │ │ │ Vprtstp: contraction number = 2.790113e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.038363e-04 │ │ │ Vprtstp: contraction number = 3.346783e-01 │ │ │ Vnewton: Using errtol_s: 251.110249 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.371588e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.523461e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.595120e+01 │ │ │ Vprtstp: contraction number = 9.595120e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.570900e-05 │ │ │ Vprtstp: contraction number = 3.438971e-01 │ │ │ Vnewton: Using errtol_s: 86.356086 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.399942e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.745100e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.363636e+01 │ │ │ Vprtstp: contraction number = 3.363636e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.251804e-05 │ │ │ Vprtstp: contraction number = 3.505570e-01 │ │ │ Vnewton: Using errtol_s: 30.272729 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.429439e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.962468e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.212621e+01 │ │ │ Vprtstp: contraction number = 1.212621e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.512865e-06 │ │ │ Vprtstp: contraction number = 3.605089e-01 │ │ │ Vnewton: Using errtol_s: 10.913589 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457614e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.181967e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.547757e+00 │ │ │ Vprtstp: contraction number = 4.547757e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.692484e-06 │ │ │ Vprtstp: contraction number = 3.750353e-01 │ │ │ Vnewton: Using errtol_s: 4.092981 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.485777e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.397653e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.787566e+00 │ │ │ Vprtstp: contraction number = 1.787566e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.652567e-07 │ │ │ Vprtstp: contraction number = 3.930654e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.364302e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.616419e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.439826e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.452963e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -7734,17 +7734,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.201138998655E-02 kT │ │ │ Vpmg_energy: qfEnergy = 4.154611536454E+02 kT │ │ │ Vpmg_energy: dielEnergy = 2.802895931375E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.324100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.617300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -7765,272 +7765,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.259019 │ │ │ +Vacc_SASA: Time elapsed: 2.867805 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.614002e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.620904e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.447400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.791100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.583700e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.158044e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.797220e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.649257e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.812875e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.674495e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.848172e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.848001e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.875232e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.003336e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.902333e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.157724e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.930542e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.308499e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.957390e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.460331e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.985558e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.612170e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.012614e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.768215e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.039680e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.924542e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.066759e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.077235e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.093830e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.233392e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.120876e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.385892e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.147987e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.543644e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.174990e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.698507e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.203262e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.857141e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.230357e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.016631e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.257555e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.179267e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.284522e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.337728e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.311551e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.492529e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.338724e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.655397e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.365684e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.820978e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.895069e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.132052e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.329430e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.342191e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8039,15 +8039,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.651047489982E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.716292902858E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.798539842617E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.524600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.307300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -8095,160 +8095,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00429089 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.251478 │ │ │ +Vacc_SASA: Time elapsed: 3.374080 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.767231e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.519985e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.463900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.334500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.591110e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.286271e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.690171e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.038500e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3456404.072365 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.704866e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.067517e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.424168e+05 │ │ │ Vprtstp: contraction number = 3.424168e+05 │ │ │ Vnewton: Attempting damping, relres = 0.089811 │ │ │ Vnewton: Attempting damping, relres = 0.542258 │ │ │ Vnewton: Damping accepted, relres = 0.089811 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.981102e-02 │ │ │ Vprtstp: contraction number = 8.981102e-02 │ │ │ Vnewton: Using errtol_s: 310423.190924 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.740310e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.310408e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.148381e+04 │ │ │ Vprtstp: contraction number = 6.148381e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.602901e-02 │ │ │ Vprtstp: contraction number = 1.784748e-01 │ │ │ Vnewton: Using errtol_s: 55402.729239 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.767391e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.544130e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.483491e+04 │ │ │ Vprtstp: contraction number = 1.483491e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.863008e-03 │ │ │ Vprtstp: contraction number = 2.410011e-01 │ │ │ Vnewton: Using errtol_s: 13352.116026 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.795617e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.768882e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.268024e+03 │ │ │ Vprtstp: contraction number = 4.268024e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111340e-03 │ │ │ Vprtstp: contraction number = 2.876878e-01 │ │ │ Vnewton: Using errtol_s: 3841.240882 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.822726e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.977710e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.355750e+03 │ │ │ Vprtstp: contraction number = 1.355750e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.530190e-04 │ │ │ Vprtstp: contraction number = 3.176516e-01 │ │ │ Vnewton: Using errtol_s: 1220.176206 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.849797e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018922e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.554936e+02 │ │ │ Vprtstp: contraction number = 4.554936e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.186043e-04 │ │ │ Vprtstp: contraction number = 3.359715e-01 │ │ │ Vnewton: Using errtol_s: 409.944430 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.876857e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040499e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.577730e+02 │ │ │ Vprtstp: contraction number = 1.577730e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.108191e-05 │ │ │ Vprtstp: contraction number = 3.463779e-01 │ │ │ Vnewton: Using errtol_s: 141.995679 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.903993e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.061509e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.547816e+01 │ │ │ Vprtstp: contraction number = 5.547816e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.444575e-05 │ │ │ Vprtstp: contraction number = 3.516328e-01 │ │ │ Vnewton: Using errtol_s: 49.930345 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.931124e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082092e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.964653e+01 │ │ │ Vprtstp: contraction number = 1.964653e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.115686e-06 │ │ │ Vprtstp: contraction number = 3.541309e-01 │ │ │ Vnewton: Using errtol_s: 17.681880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.959304e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102686e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.015901e+00 │ │ │ Vprtstp: contraction number = 7.015901e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.826844e-06 │ │ │ Vprtstp: contraction number = 3.571063e-01 │ │ │ Vnewton: Using errtol_s: 6.314311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.986432e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123947e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.553268e+00 │ │ │ Vprtstp: contraction number = 2.553268e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.648357e-07 │ │ │ Vprtstp: contraction number = 3.639258e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.167688e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.407134e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.408409e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.422494e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8257,17 +8257,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.579314308709E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.986093532858E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.486705407480E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.166600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.184900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -8288,261 +8288,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.934853 │ │ │ +Vacc_SASA: Time elapsed: 6.999808 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.503869e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.080959e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.640700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.357200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.781480e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.081254e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.585612e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.154005e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.603398e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156575e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.640764e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.177343e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.669208e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.194695e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.696605e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.212081e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.725341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229669e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.754050e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.247407e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.782552e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.265472e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.809732e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.283953e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.838374e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.302282e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.865677e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320300e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.894338e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.337861e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.921994e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355297e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.950593e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.372931e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.977899e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.390826e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.005263e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.408119e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.033767e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.426458e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.061175e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.444574e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.088553e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.463143e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.115931e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.481395e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.145425e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.500726e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.806920e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.051689e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.643910e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.655675e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8551,17 +8551,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.659936219773E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.771591154168E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.850889250612E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.549300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.157300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -8607,160 +8607,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0122306 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.942683 │ │ │ +Vacc_SASA: Time elapsed: 7.783577 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.678641e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.210649e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.453700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.250100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.601820e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.264823e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.761138e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.529020e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 5774426.010351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.776326e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.531862e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.536200e+05 │ │ │ Vprtstp: contraction number = 5.536200e+05 │ │ │ Vnewton: Attempting damping, relres = 0.086816 │ │ │ Vnewton: Attempting damping, relres = 0.540697 │ │ │ Vnewton: Damping accepted, relres = 0.086816 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.681646e-02 │ │ │ Vprtstp: contraction number = 8.681646e-02 │ │ │ Vnewton: Using errtol_s: 501315.229123 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.811683e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.554753e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.813919e+04 │ │ │ Vprtstp: contraction number = 9.813919e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.530865e-02 │ │ │ Vprtstp: contraction number = 1.763335e-01 │ │ │ Vnewton: Using errtol_s: 88398.668796 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.838719e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.575582e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.359807e+04 │ │ │ Vprtstp: contraction number = 2.359807e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.678183e-03 │ │ │ Vprtstp: contraction number = 2.402683e-01 │ │ │ Vnewton: Using errtol_s: 21239.395305 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.865721e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.595900e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.835940e+03 │ │ │ Vprtstp: contraction number = 6.835940e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.065460e-03 │ │ │ Vprtstp: contraction number = 2.896703e-01 │ │ │ Vnewton: Using errtol_s: 6152.421286 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.892760e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.616523e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.186690e+03 │ │ │ Vprtstp: contraction number = 2.186690e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.408183e-04 │ │ │ Vprtstp: contraction number = 3.198790e-01 │ │ │ Vnewton: Using errtol_s: 1968.030266 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.919780e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.637489e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.369221e+02 │ │ │ Vprtstp: contraction number = 7.369221e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.148566e-04 │ │ │ Vprtstp: contraction number = 3.370025e-01 │ │ │ Vnewton: Using errtol_s: 663.231119 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.946832e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.660575e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.557331e+02 │ │ │ Vprtstp: contraction number = 2.557331e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.985850e-05 │ │ │ Vprtstp: contraction number = 3.470283e-01 │ │ │ Vnewton: Using errtol_s: 230.159953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.973893e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.687210e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.020719e+01 │ │ │ Vprtstp: contraction number = 9.020719e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.405966e-05 │ │ │ Vprtstp: contraction number = 3.527394e-01 │ │ │ Vnewton: Using errtol_s: 81.186485 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.000907e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.713163e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.225420e+01 │ │ │ Vprtstp: contraction number = 3.225420e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.027128e-06 │ │ │ Vprtstp: contraction number = 3.575568e-01 │ │ │ Vnewton: Using errtol_s: 29.028780 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.027957e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.740461e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.171930e+01 │ │ │ Vprtstp: contraction number = 1.171930e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.826566e-06 │ │ │ Vprtstp: contraction number = 3.633419e-01 │ │ │ Vnewton: Using errtol_s: 10.547373 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.055001e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.767060e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.353564e+00 │ │ │ Vprtstp: contraction number = 4.353564e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.785449e-07 │ │ │ Vprtstp: contraction number = 3.714865e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.142283e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.386941e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.631658e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.645533e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8769,27 +8769,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.126180200466E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.029835397910E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.515709858498E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.201100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.892700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.107557e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.792921e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:57:48 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 12:25:34 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -9142,250 +9142,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.248281 │ │ │ +Vacc_SASA: Time elapsed: 3.449904 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.590142e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.494886e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.520500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.166580e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.585780e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.541640e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.015925e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.473217e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.173959e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.762760e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.564888e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.969247e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.849638e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.734168e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.147136e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.543499e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.458159e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.461833e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.742173e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.041727e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.025631e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.241407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.309979e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.448530e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.595663e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.647654e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.879889e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.851226e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.164831e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.053415e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.449431e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.244579e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.734242e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.436105e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.018946e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.626822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.312687e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.832320e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.597684e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.031394e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.882948e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.219998e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.175619e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.426410e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.459556e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.648122e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.661785e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.913694e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.767792e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.785372e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -9394,17 +9394,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.475399192616E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.444578731292E+04 kT │ │ │ Vpmg_energy: dielEnergy = 7.168962891577E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.511800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.282100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -9450,171 +9450,171 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.244357 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.226210 │ │ │ +Vacc_SASA: Time elapsed: 3.852438 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.893550e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.720663e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.506100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.129600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.601830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.397063e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.184809e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.906364e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7151537.194828 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200836e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.937531e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.220296e+05 │ │ │ Vprtstp: contraction number = 7.220296e+05 │ │ │ Vnewton: Attempting damping, relres = 0.092215 │ │ │ Vnewton: Attempting damping, relres = 0.543248 │ │ │ Vnewton: Damping accepted, relres = 0.092215 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.221458e-02 │ │ │ Vprtstp: contraction number = 9.221458e-02 │ │ │ Vnewton: Using errtol_s: 659475.973035 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.239940e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.269763e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.360213e+05 │ │ │ Vprtstp: contraction number = 1.360213e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.716437e-02 │ │ │ Vprtstp: contraction number = 1.861351e-01 │ │ │ Vnewton: Using errtol_s: 122751.620274 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.269008e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.584499e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.560242e+04 │ │ │ Vprtstp: contraction number = 3.560242e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.482910e-03 │ │ │ Vprtstp: contraction number = 2.611753e-01 │ │ │ Vnewton: Using errtol_s: 32059.695083 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.297467e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.912452e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.131656e+04 │ │ │ Vprtstp: contraction number = 1.131656e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.424570e-03 │ │ │ Vprtstp: contraction number = 3.177779e-01 │ │ │ Vnewton: Using errtol_s: 10187.862459 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.327103e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.203439e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.913208e+03 │ │ │ Vprtstp: contraction number = 3.913208e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.925362e-04 │ │ │ Vprtstp: contraction number = 3.457439e-01 │ │ │ Vnewton: Using errtol_s: 3522.390814 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.356755e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.482380e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.383064e+03 │ │ │ Vprtstp: contraction number = 1.383064e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.740621e-04 │ │ │ Vprtstp: contraction number = 3.533996e-01 │ │ │ Vnewton: Using errtol_s: 1244.811552 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.385125e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.770346e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.895564e+02 │ │ │ Vprtstp: contraction number = 4.895564e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 6.160970e-05 │ │ │ Vprtstp: contraction number = 3.539524e-01 │ │ │ Vnewton: Using errtol_s: 440.604077 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.414761e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.045481e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.817812e+02 │ │ │ Vprtstp: contraction number = 1.817812e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.287666e-05 │ │ │ Vprtstp: contraction number = 3.713159e-01 │ │ │ Vnewton: Using errtol_s: 163.603290 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.444106e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.308301e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.297744e+01 │ │ │ Vprtstp: contraction number = 7.297744e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 9.184003e-06 │ │ │ Vprtstp: contraction number = 4.014573e-01 │ │ │ Vnewton: Using errtol_s: 65.679739 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.473845e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.580991e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.147662e+01 │ │ │ Vprtstp: contraction number = 3.147662e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.961242e-06 │ │ │ Vprtstp: contraction number = 4.313197e-01 │ │ │ Vnewton: Using errtol_s: 28.328967 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.502120e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.880057e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.429069e+01 │ │ │ Vprtstp: contraction number = 1.429069e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.798442e-06 │ │ │ Vprtstp: contraction number = 4.540096e-01 │ │ │ Vnewton: Using errtol_s: 12.861624 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.531671e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.176113e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.773546e+00 │ │ │ Vprtstp: contraction number = 6.773546e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 8.524311e-07 │ │ │ Vprtstp: contraction number = 4.739831e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.690961e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.942906e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.543117e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.559148e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -9623,17 +9623,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.623170000406E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.125246141954E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.603584772163E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.850200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.390500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.600000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -9654,272 +9654,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.252280 │ │ │ +Vacc_SASA: Time elapsed: 4.403557 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.606272e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.734462e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.497600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.517540e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.577350e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.317076e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.841842e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.523461e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.856328e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.558411e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.892829e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.799846e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.919791e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.024660e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.946783e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.256343e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.974499e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.483917e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.001346e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.708428e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.028357e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.930332e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.055179e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.135486e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.080761e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.336975e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.107657e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.533699e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.133270e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.723602e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.160108e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.911405e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.185794e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.009969e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.212609e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028304e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.238315e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047892e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.265298e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066862e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.299867e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087119e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.405334e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107692e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.432302e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126493e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.459165e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.144606e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.484842e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.162397e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.633741e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.871599e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.260931e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.276890e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -9928,17 +9928,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.730884767842E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 2.814808503921E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.555800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.272300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -9984,160 +9984,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.000691975 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.030973 │ │ │ +Vacc_SASA: Time elapsed: 3.470590 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.417535e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.392846e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.546400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.037060e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.639450e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.244276e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.773349e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.184294e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 951047.684475 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.789338e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.186964e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.162547e+05 │ │ │ Vprtstp: contraction number = 1.162547e+05 │ │ │ Vnewton: Attempting damping, relres = 0.112161 │ │ │ Vnewton: Attempting damping, relres = 0.552182 │ │ │ Vnewton: Damping accepted, relres = 0.112161 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.121606e-01 │ │ │ Vprtstp: contraction number = 1.121606e-01 │ │ │ Vnewton: Using errtol_s: 106670.078940 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.823343e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.205066e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.126153e+04 │ │ │ Vprtstp: contraction number = 2.126153e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.016407e-02 │ │ │ Vprtstp: contraction number = 1.797785e-01 │ │ │ Vnewton: Using errtol_s: 19176.991465 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.848944e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.221763e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.910429e+03 │ │ │ Vprtstp: contraction number = 4.910429e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.647657e-03 │ │ │ Vprtstp: contraction number = 2.304920e-01 │ │ │ Vnewton: Using errtol_s: 4420.143642 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.875688e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238752e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.327403e+03 │ │ │ Vprtstp: contraction number = 1.327403e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.256188e-03 │ │ │ Vprtstp: contraction number = 2.702841e-01 │ │ │ Vnewton: Using errtol_s: 1194.694354 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.901165e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.255487e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.951603e+02 │ │ │ Vprtstp: contraction number = 3.951603e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.739525e-04 │ │ │ Vprtstp: contraction number = 2.976884e-01 │ │ │ Vnewton: Using errtol_s: 355.646671 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.927905e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.271497e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.251397e+02 │ │ │ Vprtstp: contraction number = 1.251397e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.184231e-04 │ │ │ Vprtstp: contraction number = 3.166794e-01 │ │ │ Vnewton: Using errtol_s: 112.625980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.953417e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.287399e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.114263e+01 │ │ │ Vprtstp: contraction number = 4.114263e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.893431e-05 │ │ │ Vprtstp: contraction number = 3.287731e-01 │ │ │ Vnewton: Using errtol_s: 37.028389 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.980286e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305077e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.383573e+01 │ │ │ Vprtstp: contraction number = 1.383573e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.309310e-05 │ │ │ Vprtstp: contraction number = 3.362869e-01 │ │ │ Vnewton: Using errtol_s: 12.452161 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.005919e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321381e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725230e+00 │ │ │ Vprtstp: contraction number = 4.725230e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.471602e-06 │ │ │ Vprtstp: contraction number = 3.415236e-01 │ │ │ Vnewton: Using errtol_s: 4.252707 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.032686e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.338324e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.633794e+00 │ │ │ Vprtstp: contraction number = 1.633794e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.546100e-06 │ │ │ Vprtstp: contraction number = 3.457598e-01 │ │ │ Vnewton: Using errtol_s: 1.470415 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.058302e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355862e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.703633e-01 │ │ │ Vprtstp: contraction number = 5.703633e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.397489e-07 │ │ │ Vprtstp: contraction number = 3.491035e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.048048e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.287948e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.874469e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.888393e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -10146,17 +10146,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.677193160789E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 2.890717240309E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.367000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.965300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -10177,261 +10177,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.008987 │ │ │ +Vacc_SASA: Time elapsed: 7.946369 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.558457e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.314371e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.542500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.992500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.685280e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.366998e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.661442e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.382610e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.676671e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.385389e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.713702e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.408210e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.740910e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.429563e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.769334e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452586e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.795021e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.475242e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.821910e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.498350e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.850948e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521344e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.878195e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.543724e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.905423e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.562824e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.933857e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581281e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.961017e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.599979e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.989677e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.618220e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.016966e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.637292e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.045423e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.655556e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.072739e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.674485e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.101193e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.693841e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.128373e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.711743e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.156851e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.729657e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.184218e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.749796e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.212725e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.769727e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.724591e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.959080e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.047359e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.062039e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -10440,17 +10440,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.633470349209E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.444874244202E+04 kT │ │ │ Vpmg_energy: dielEnergy = 7.168739971796E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.682700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.392900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -10496,171 +10496,171 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.23862 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.023189 │ │ │ +Vacc_SASA: Time elapsed: 7.397020 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.878487e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.932267e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.612200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.883700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.616870e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.101942e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.848985e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.797555e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8022421.271471 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.864713e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.800443e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.182694e+05 │ │ │ Vprtstp: contraction number = 8.182694e+05 │ │ │ Vnewton: Attempting damping, relres = 0.093297 │ │ │ Vnewton: Attempting damping, relres = 0.543649 │ │ │ Vnewton: Damping accepted, relres = 0.093297 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.329693e-02 │ │ │ Vprtstp: contraction number = 9.329693e-02 │ │ │ Vnewton: Using errtol_s: 748467.258105 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.901908e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.824467e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.535104e+05 │ │ │ Vprtstp: contraction number = 1.535104e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.727080e-02 │ │ │ Vprtstp: contraction number = 1.851165e-01 │ │ │ Vnewton: Using errtol_s: 138553.663149 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.929057e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.847663e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.960039e+04 │ │ │ Vprtstp: contraction number = 3.960039e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.444863e-03 │ │ │ Vprtstp: contraction number = 2.573628e-01 │ │ │ Vnewton: Using errtol_s: 35658.564568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.956142e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.872200e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.238461e+04 │ │ │ Vprtstp: contraction number = 1.238461e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.389740e-03 │ │ │ Vprtstp: contraction number = 3.126620e-01 │ │ │ Vnewton: Using errtol_s: 11149.079578 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.983358e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.896053e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.220923e+03 │ │ │ Vprtstp: contraction number = 4.220923e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.735885e-04 │ │ │ Vprtstp: contraction number = 3.407749e-01 │ │ │ Vnewton: Using errtol_s: 3799.326730 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.011163e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.919266e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.473378e+03 │ │ │ Vprtstp: contraction number = 1.473378e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.652984e-04 │ │ │ Vprtstp: contraction number = 3.490339e-01 │ │ │ Vnewton: Using errtol_s: 1326.093695 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.038390e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.941148e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.152403e+02 │ │ │ Vprtstp: contraction number = 5.152403e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.780294e-05 │ │ │ Vprtstp: contraction number = 3.496884e-01 │ │ │ Vnewton: Using errtol_s: 463.719535 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.065562e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.963892e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.890344e+02 │ │ │ Vprtstp: contraction number = 1.890344e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.120696e-05 │ │ │ Vprtstp: contraction number = 3.668838e-01 │ │ │ Vnewton: Using errtol_s: 170.131203 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.092701e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.988114e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.514797e+01 │ │ │ Vprtstp: contraction number = 7.514797e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 8.430525e-06 │ │ │ Vprtstp: contraction number = 3.975357e-01 │ │ │ Vnewton: Using errtol_s: 67.633227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.119902e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.013737e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.220080e+01 │ │ │ Vprtstp: contraction number = 3.220080e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.612467e-06 │ │ │ Vprtstp: contraction number = 4.284985e-01 │ │ │ Vnewton: Using errtol_s: 28.980733 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.147087e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.038395e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.453992e+01 │ │ │ Vprtstp: contraction number = 1.453992e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.631169e-06 │ │ │ Vprtstp: contraction number = 4.515389e-01 │ │ │ Vnewton: Using errtol_s: 13.085928 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.174463e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.063480e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.875948e+00 │ │ │ Vprtstp: contraction number = 6.875948e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.713824e-07 │ │ │ Vprtstp: contraction number = 4.729015e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.460253e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.701963e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.905400e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.917778e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -10669,27 +10669,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.853787896122E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.125276033199E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.603543842121E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.847300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.032780e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.227729e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.088751e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:58:19 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 13:10:05 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -11042,250 +11042,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.275446 │ │ │ +Vacc_SASA: Time elapsed: 3.532230 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.641440e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.585187e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.578000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.407800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.588540e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.184855e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.077803e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.285133e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.234585e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.855903e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.628468e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.987524e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.913901e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.760451e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.212282e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.515614e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.496337e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.354682e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.793690e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018061e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.079437e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.196981e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.378046e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.376781e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.664103e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.558007e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.949929e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.724578e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.247421e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.894317e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.533554e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.065021e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.831025e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.231840e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.115954e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.402949e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.401818e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.572405e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.697771e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.737007e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.982955e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.923772e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.280902e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.127736e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.566946e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.295517e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.711432e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.972271e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.388236e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.401950e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11294,17 +11294,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.108926489514E-02 kT │ │ │ Vpmg_energy: qfEnergy = 2.835800313442E+02 kT │ │ │ Vpmg_energy: dielEnergy = 1.215330905259E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.565000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.080500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -11350,160 +11350,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.001948 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.238955 │ │ │ +Vacc_SASA: Time elapsed: 3.460673 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.720807e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.314008e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.501600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.045390e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.868690e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.078465e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.181650e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.506912e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1613641.621006 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.197380e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.535608e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.672701e+05 │ │ │ Vprtstp: contraction number = 1.672701e+05 │ │ │ Vnewton: Attempting damping, relres = 0.093643 │ │ │ Vnewton: Attempting damping, relres = 0.544180 │ │ │ Vnewton: Damping accepted, relres = 0.093643 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.364296e-02 │ │ │ Vprtstp: contraction number = 9.364296e-02 │ │ │ Vnewton: Using errtol_s: 151106.180064 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237012e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.787633e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.923422e+04 │ │ │ Vprtstp: contraction number = 2.923422e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.630658e-02 │ │ │ Vprtstp: contraction number = 1.741357e-01 │ │ │ Vnewton: Using errtol_s: 26312.974291 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.266828e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.014603e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.609437e+03 │ │ │ Vprtstp: contraction number = 6.609437e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.686501e-03 │ │ │ Vprtstp: contraction number = 2.260744e-01 │ │ │ Vnewton: Using errtol_s: 5948.690797 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.296822e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.245039e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.798444e+03 │ │ │ Vprtstp: contraction number = 1.798444e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.003087e-03 │ │ │ Vprtstp: contraction number = 2.720974e-01 │ │ │ Vnewton: Using errtol_s: 1618.623129 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.325584e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.470690e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.516770e+02 │ │ │ Vprtstp: contraction number = 5.516770e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.076965e-04 │ │ │ Vprtstp: contraction number = 3.067495e-01 │ │ │ Vnewton: Using errtol_s: 496.511822 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355368e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.684818e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.808462e+02 │ │ │ Vprtstp: contraction number = 1.808462e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.008662e-04 │ │ │ Vprtstp: contraction number = 3.278106e-01 │ │ │ Vnewton: Using errtol_s: 162.761828 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.384022e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.902058e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.118139e+01 │ │ │ Vprtstp: contraction number = 6.118139e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.412361e-05 │ │ │ Vprtstp: contraction number = 3.383059e-01 │ │ │ Vnewton: Using errtol_s: 55.063279 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.413919e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.131636e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.100954e+01 │ │ │ Vprtstp: contraction number = 2.100954e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.171796e-05 │ │ │ Vprtstp: contraction number = 3.433974e-01 │ │ │ Vnewton: Using errtol_s: 18.908586 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.442650e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.364158e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.287024e+00 │ │ │ Vprtstp: contraction number = 7.287024e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.064299e-06 │ │ │ Vprtstp: contraction number = 3.468436e-01 │ │ │ Vnewton: Using errtol_s: 6.558322 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472519e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.584117e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.550680e+00 │ │ │ Vprtstp: contraction number = 2.550680e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.422628e-06 │ │ │ Vprtstp: contraction number = 3.500304e-01 │ │ │ Vnewton: Using errtol_s: 2.295612 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.502427e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.828314e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.008406e-01 │ │ │ Vprtstp: contraction number = 9.008406e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.024390e-07 │ │ │ Vprtstp: contraction number = 3.531767e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.436387e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.715939e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.523619e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.535959e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11512,17 +11512,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.604850020008E-02 kT │ │ │ Vpmg_energy: qfEnergy = 2.451766100693E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.154345982163E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.552200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -11543,272 +11543,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.293882 │ │ │ +Vacc_SASA: Time elapsed: 2.936927 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.667627e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.860560e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.502100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.235000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.612090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.216672e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.820174e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.083925e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.836118e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.111086e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.871989e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.301944e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.899237e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.464883e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.926419e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.629045e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.953647e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.799082e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.980909e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.973969e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.008094e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.145276e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.035276e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.321571e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.062517e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.491671e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.089794e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.655806e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.116939e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.838030e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.144233e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.018944e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.172711e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.213241e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.200585e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.408572e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.227861e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.595982e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.255095e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.790305e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.282395e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.993343e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.309534e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.211091e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.336760e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.395849e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.363914e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.608993e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.391155e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.800612e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.915611e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.157237e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.887112e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.901088e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11817,17 +11817,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.931678298316E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.306896751937E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.531231404824E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.542800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.746500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -11873,193 +11873,193 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.211097 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.292430 │ │ │ +Vacc_SASA: Time elapsed: 3.170006 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.991490e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.572653e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.603300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.534900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.619910e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.291552e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.738236e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003096e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6738070.309592 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.753824e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.006090e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.878637e+05 │ │ │ Vprtstp: contraction number = 6.878637e+05 │ │ │ Vnewton: Attempting damping, relres = 0.093216 │ │ │ Vnewton: Attempting damping, relres = 0.543864 │ │ │ Vnewton: Damping accepted, relres = 0.093216 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.321581e-02 │ │ │ Vprtstp: contraction number = 9.321581e-02 │ │ │ Vnewton: Using errtol_s: 628094.651911 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.789800e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033025e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.296036e+05 │ │ │ Vprtstp: contraction number = 1.296036e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.735879e-02 │ │ │ Vprtstp: contraction number = 1.862215e-01 │ │ │ Vnewton: Using errtol_s: 116964.740632 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.818175e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056636e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.402622e+04 │ │ │ Vprtstp: contraction number = 3.402622e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.547490e-03 │ │ │ Vprtstp: contraction number = 2.619705e-01 │ │ │ Vnewton: Using errtol_s: 30641.306038 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.845519e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079800e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.090470e+04 │ │ │ Vprtstp: contraction number = 1.090470e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.456938e-03 │ │ │ Vprtstp: contraction number = 3.203829e-01 │ │ │ Vnewton: Using errtol_s: 9816.950613 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.872869e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102509e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.894978e+03 │ │ │ Vprtstp: contraction number = 3.894978e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.203198e-04 │ │ │ Vprtstp: contraction number = 3.571324e-01 │ │ │ Vnewton: Using errtol_s: 3505.951173 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.900239e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.125995e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.485775e+03 │ │ │ Vprtstp: contraction number = 1.485775e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.984627e-04 │ │ │ Vprtstp: contraction number = 3.814246e-01 │ │ │ Vnewton: Using errtol_s: 1337.255961 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.927529e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.150355e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.014858e+02 │ │ │ Vprtstp: contraction number = 6.014858e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.034105e-05 │ │ │ Vprtstp: contraction number = 4.048168e-01 │ │ │ Vnewton: Using errtol_s: 541.343626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.954632e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.176218e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.638957e+02 │ │ │ Vprtstp: contraction number = 2.638957e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.524853e-05 │ │ │ Vprtstp: contraction number = 4.387363e-01 │ │ │ Vnewton: Using errtol_s: 237.507104 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.981979e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.205504e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.262556e+02 │ │ │ Vprtstp: contraction number = 1.262556e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.686391e-05 │ │ │ Vprtstp: contraction number = 4.784287e-01 │ │ │ Vnewton: Using errtol_s: 113.630225 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.009253e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232631e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.580661e+01 │ │ │ Vprtstp: contraction number = 6.580661e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.789758e-06 │ │ │ Vprtstp: contraction number = 5.212170e-01 │ │ │ Vnewton: Using errtol_s: 59.226009 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.035339e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.262770e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.615710e+01 │ │ │ Vprtstp: contraction number = 3.615710e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.829486e-06 │ │ │ Vprtstp: contraction number = 5.494446e-01 │ │ │ Vnewton: Using errtol_s: 32.541413 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.064100e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.293091e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.063008e+01 │ │ │ Vprtstp: contraction number = 2.063008e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 2.755549e-06 │ │ │ Vprtstp: contraction number = 5.705677e-01 │ │ │ Vnewton: Using errtol_s: 18.567080 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.091382e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322219e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.211023e+01 │ │ │ Vprtstp: contraction number = 1.211023e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.617557e-06 │ │ │ Vprtstp: contraction number = 5.870182e-01 │ │ │ Vnewton: Using errtol_s: 10.899214 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.118547e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.353656e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.261707e+00 │ │ │ Vprtstp: contraction number = 7.261707e+00 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 9.699420e-07 │ │ │ Vprtstp: contraction number = 5.996338e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.009868e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.255376e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.774046e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.787887e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -12068,17 +12068,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.021244083579E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.026826573171E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.129339951363E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.887400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.615700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -12099,261 +12099,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.995818 │ │ │ +Vacc_SASA: Time elapsed: 7.359796 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.567231e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.723219e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.687000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.468500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.725750e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.179007e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.723588e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.390595e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.739176e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.393302e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.776220e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.415803e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.803485e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.436564e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.830615e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.458054e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.857734e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.477812e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.884673e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.499309e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.910605e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.522109e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.937664e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.545943e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.964736e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568939e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.991959e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.593040e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.018998e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.617913e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.044785e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.640294e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.071818e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.661093e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.098991e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682725e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.126144e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.708030e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.153419e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.732697e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.181909e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.758154e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.208980e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.783800e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.236250e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.807251e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.264666e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.830900e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.612441e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.853231e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.610791e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.623596e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -12362,17 +12362,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.165566732606E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.340422491969E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.679021613149E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.546700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.649800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -12418,193 +12418,193 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.211587 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.098671 │ │ │ +Vacc_SASA: Time elapsed: 8.559461 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.993197e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.071362e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.676600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.192100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.702950e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.740193e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.912339e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.864344e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8285587.408912 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.928377e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.867799e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.439767e+05 │ │ │ Vprtstp: contraction number = 8.439767e+05 │ │ │ Vnewton: Attempting damping, relres = 0.093056 │ │ │ Vnewton: Attempting damping, relres = 0.543707 │ │ │ Vnewton: Damping accepted, relres = 0.093056 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.305605e-02 │ │ │ Vprtstp: contraction number = 9.305605e-02 │ │ │ Vnewton: Using errtol_s: 771024.060477 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.965529e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.898364e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.575262e+05 │ │ │ Vprtstp: contraction number = 1.575262e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.715846e-02 │ │ │ Vprtstp: contraction number = 1.843885e-01 │ │ │ Vnewton: Using errtol_s: 142167.953902 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.995446e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.927092e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.047316e+04 │ │ │ Vprtstp: contraction number = 4.047316e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.398299e-03 │ │ │ Vprtstp: contraction number = 2.563341e-01 │ │ │ Vnewton: Using errtol_s: 36442.493025 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.025947e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.952728e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.265955e+04 │ │ │ Vprtstp: contraction number = 1.265955e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.375423e-03 │ │ │ Vprtstp: contraction number = 3.127169e-01 │ │ │ Vnewton: Using errtol_s: 11396.183497 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.054627e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.975918e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.418878e+03 │ │ │ Vprtstp: contraction number = 4.418878e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.800426e-04 │ │ │ Vprtstp: contraction number = 3.490147e-01 │ │ │ Vnewton: Using errtol_s: 3977.435333 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.085538e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.000119e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.644482e+03 │ │ │ Vprtstp: contraction number = 1.644482e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.786343e-04 │ │ │ Vprtstp: contraction number = 3.721217e-01 │ │ │ Vnewton: Using errtol_s: 1480.089823 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.113056e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.024281e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.478261e+02 │ │ │ Vprtstp: contraction number = 6.478261e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.036914e-05 │ │ │ Vprtstp: contraction number = 3.939286e-01 │ │ │ Vnewton: Using errtol_s: 583.049663 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.143193e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048466e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.772344e+02 │ │ │ Vprtstp: contraction number = 2.772344e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.011396e-05 │ │ │ Vprtstp: contraction number = 4.279428e-01 │ │ │ Vnewton: Using errtol_s: 249.511882 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.172164e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.074708e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.301479e+02 │ │ │ Vprtstp: contraction number = 1.301479e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.413700e-05 │ │ │ Vprtstp: contraction number = 4.694500e-01 │ │ │ Vnewton: Using errtol_s: 117.133345 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.200895e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.101837e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.695205e+01 │ │ │ Vprtstp: contraction number = 6.695205e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.272497e-06 │ │ │ Vprtstp: contraction number = 5.144300e-01 │ │ │ Vnewton: Using errtol_s: 60.256908 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.229311e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.127227e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.650946e+01 │ │ │ Vprtstp: contraction number = 3.650946e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.965746e-06 │ │ │ Vprtstp: contraction number = 5.453073e-01 │ │ │ Vnewton: Using errtol_s: 32.858531 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.257439e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.154366e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.073747e+01 │ │ │ Vprtstp: contraction number = 2.073747e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 2.252553e-06 │ │ │ Vprtstp: contraction number = 5.680025e-01 │ │ │ Vnewton: Using errtol_s: 18.663727 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.284737e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.182763e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.213300e+01 │ │ │ Vprtstp: contraction number = 1.213300e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.317915e-06 │ │ │ Vprtstp: contraction number = 5.850760e-01 │ │ │ Vnewton: Using errtol_s: 10.919699 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.311886e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.210034e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.261261e+00 │ │ │ Vprtstp: contraction number = 7.261261e+00 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.887354e-07 │ │ │ Vprtstp: contraction number = 5.984722e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.208619e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.464851e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.717471e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.736172e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -12613,27 +12613,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.328637769519E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.051514241768E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.245601958271E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.969900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.826400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.367572e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.236643e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:58:52 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 13:57:41 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -12986,250 +12986,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.254268 │ │ │ +Vacc_SASA: Time elapsed: 3.677815 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.657591e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.760674e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.536300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.423400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.656050e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.408516e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.100973e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.664625e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.256609e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010356e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.641639e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.462534e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.941847e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.566480e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.230063e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.422141e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.516736e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.365091e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.815703e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.118691e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.103638e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.298161e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.391323e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.481745e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.679650e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.653753e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.968129e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.831037e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.255961e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.017219e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.540212e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.190919e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.822900e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.376584e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.107366e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.562817e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.391930e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.739624e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.674053e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.923756e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.957306e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.113704e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.255092e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.289509e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.542152e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.475952e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.662468e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.921115e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.578530e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.593869e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -13238,15 +13238,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.135373636445E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.691003222948E+03 kT │ │ │ Vpmg_energy: dielEnergy = 8.436188542984E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.526700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.716000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -13294,160 +13294,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00329728 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.235430 │ │ │ +Vacc_SASA: Time elapsed: 3.123258 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.786798e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.185207e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.568600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.283980e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.664500e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.454349e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183570e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.704243e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2672785.067134 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200132e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.737393e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.848718e+05 │ │ │ Vprtstp: contraction number = 2.848718e+05 │ │ │ Vnewton: Attempting damping, relres = 0.096187 │ │ │ Vnewton: Attempting damping, relres = 0.545650 │ │ │ Vnewton: Damping accepted, relres = 0.096187 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.618699e-02 │ │ │ Vprtstp: contraction number = 9.618699e-02 │ │ │ Vnewton: Using errtol_s: 257087.160547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238387e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.043770e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.201088e+04 │ │ │ Vprtstp: contraction number = 5.201088e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.751490e-02 │ │ │ Vprtstp: contraction number = 1.820922e-01 │ │ │ Vnewton: Using errtol_s: 46813.558642 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.268154e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.305683e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.230808e+04 │ │ │ Vprtstp: contraction number = 1.230808e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.144590e-03 │ │ │ Vprtstp: contraction number = 2.366322e-01 │ │ │ Vnewton: Using errtol_s: 11077.597147 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.296841e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.573047e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.460119e+03 │ │ │ Vprtstp: contraction number = 3.460119e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.165151e-03 │ │ │ Vprtstp: contraction number = 2.811258e-01 │ │ │ Vnewton: Using errtol_s: 3114.198540 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.325502e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.828437e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.085640e+03 │ │ │ Vprtstp: contraction number = 1.085640e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.655733e-04 │ │ │ Vprtstp: contraction number = 3.137561e-01 │ │ │ Vnewton: Using errtol_s: 977.098856 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.354127e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.109861e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.609545e+02 │ │ │ Vprtstp: contraction number = 3.609545e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.215452e-04 │ │ │ Vprtstp: contraction number = 3.324784e-01 │ │ │ Vnewton: Using errtol_s: 324.864231 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.383948e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.419985e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.235133e+02 │ │ │ Vprtstp: contraction number = 1.235133e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.159074e-05 │ │ │ Vprtstp: contraction number = 3.421833e-01 │ │ │ Vnewton: Using errtol_s: 111.163117 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.413888e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.698390e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.301270e+01 │ │ │ Vprtstp: contraction number = 4.301270e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.448364e-05 │ │ │ Vprtstp: contraction number = 3.482419e-01 │ │ │ Vnewton: Using errtol_s: 38.711660 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.443777e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.945610e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.517421e+01 │ │ │ Vprtstp: contraction number = 1.517421e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.109589e-06 │ │ │ Vprtstp: contraction number = 3.527835e-01 │ │ │ Vnewton: Using errtol_s: 13.656834 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472375e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.183061e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.423218e+00 │ │ │ Vprtstp: contraction number = 5.423218e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.826149e-06 │ │ │ Vprtstp: contraction number = 3.573964e-01 │ │ │ Vnewton: Using errtol_s: 4.880904 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.503554e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.434912e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.968727e+00 │ │ │ Vprtstp: contraction number = 1.968727e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.629250e-07 │ │ │ Vprtstp: contraction number = 3.630180e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.437299e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.697221e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.964774e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.981667e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -13456,17 +13456,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.950394306049E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.339241623976E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.685521460249E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.332000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.196800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -13487,272 +13487,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.261355 │ │ │ +Vacc_SASA: Time elapsed: 3.217751 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.656081e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.340024e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.499700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.104660e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.887080e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.349234e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.824045e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.729194e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.839092e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.761726e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.876275e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.970003e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.903566e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.152215e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.930784e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.343452e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.958087e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.519992e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.985371e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.700810e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.015595e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.886022e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.047421e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.062328e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.074658e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.255266e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.101846e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.444984e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.129149e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.629587e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.156435e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.840889e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.183625e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.048589e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.210924e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.262516e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.238183e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.462862e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.265378e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.651170e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.292684e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.828110e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.319961e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000184e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.348114e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016647e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.375324e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033445e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.402691e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049847e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.995265e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.265479e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.913787e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.929575e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -13761,17 +13761,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.295996694910E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 1.633599871123E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.542500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.662000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -13817,149 +13817,149 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00296493 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.297706 │ │ │ +Vacc_SASA: Time elapsed: 2.933343 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.715687e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.841381e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.643300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.450300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.634180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.068792e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.721383e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.069375e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1184087.054280 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.736918e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.072089e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.354114e+05 │ │ │ Vprtstp: contraction number = 1.354114e+05 │ │ │ Vnewton: Attempting damping, relres = 0.103158 │ │ │ Vnewton: Attempting damping, relres = 0.548288 │ │ │ Vnewton: Damping accepted, relres = 0.103158 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.031582e-01 │ │ │ Vprtstp: contraction number = 1.031582e-01 │ │ │ Vnewton: Using errtol_s: 122148.348169 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.772633e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088248e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.326538e+04 │ │ │ Vprtstp: contraction number = 2.326538e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.769124e-02 │ │ │ Vprtstp: contraction number = 1.714961e-01 │ │ │ Vnewton: Using errtol_s: 20947.970777 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.799808e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104024e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.939304e+03 │ │ │ Vprtstp: contraction number = 4.939304e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.754561e-03 │ │ │ Vprtstp: contraction number = 2.122271e-01 │ │ │ Vnewton: Using errtol_s: 4445.727289 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.827114e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120738e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.225369e+03 │ │ │ Vprtstp: contraction number = 1.225369e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 9.313919e-04 │ │ │ Vprtstp: contraction number = 2.480695e-01 │ │ │ Vnewton: Using errtol_s: 1102.849143 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.854329e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.138007e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.425596e+02 │ │ │ Vprtstp: contraction number = 3.425596e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 2.603732e-04 │ │ │ Vprtstp: contraction number = 2.795528e-01 │ │ │ Vnewton: Using errtol_s: 308.304585 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.881496e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156631e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.033702e+02 │ │ │ Vprtstp: contraction number = 1.033702e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 7.856958e-05 │ │ │ Vprtstp: contraction number = 3.017575e-01 │ │ │ Vnewton: Using errtol_s: 93.033224 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.908659e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.175295e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.261191e+01 │ │ │ Vprtstp: contraction number = 3.261191e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.478764e-05 │ │ │ Vprtstp: contraction number = 3.154865e-01 │ │ │ Vnewton: Using errtol_s: 29.350728 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.935904e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193404e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.060426e+01 │ │ │ Vprtstp: contraction number = 1.060426e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.060077e-06 │ │ │ Vprtstp: contraction number = 3.251651e-01 │ │ │ Vnewton: Using errtol_s: 9.543833 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.963092e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.211619e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.527652e+00 │ │ │ Vprtstp: contraction number = 3.527652e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.681295e-06 │ │ │ Vprtstp: contraction number = 3.326637e-01 │ │ │ Vnewton: Using errtol_s: 3.174887 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.992361e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229027e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.192253e+00 │ │ │ Vprtstp: contraction number = 1.192253e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.062069e-07 │ │ │ Vprtstp: contraction number = 3.379736e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.914035e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.148397e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.744567e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.756294e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -13968,17 +13968,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.599961867885E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 1.358968211460E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.503200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.324500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -13999,261 +13999,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.987794 │ │ │ +Vacc_SASA: Time elapsed: 7.001044 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.561514e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.040611e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.763300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.238470e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.700760e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.185437e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.596899e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.253274e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.612064e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.256280e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.648948e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.277714e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.677304e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.296800e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.704558e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.316643e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.732986e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.335792e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.760244e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.356290e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.788654e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.376224e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.815986e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.395783e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.843328e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.416509e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.870706e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.436087e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.898012e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.455090e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.925227e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.474730e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.953777e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.493821e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.981035e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.514255e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.008286e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.534637e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.036665e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.554486e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.063955e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.575474e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.092410e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.596361e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.119454e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.620008e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.146644e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.646383e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.706527e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.944282e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.159069e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.172410e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -14262,17 +14262,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.987808702613E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.699917781088E+03 kT │ │ │ Vpmg_energy: dielEnergy = 8.464002723965E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.536700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.632400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -14318,160 +14318,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0125918 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.963734 │ │ │ +Vacc_SASA: Time elapsed: 9.569395 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.673387e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.139496e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.478000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.462400e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.626860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.956975e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.760837e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682833e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3745818.555400 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.776264e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.686654e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.036148e+05 │ │ │ Vprtstp: contraction number = 4.036148e+05 │ │ │ Vnewton: Attempting damping, relres = 0.097470 │ │ │ Vnewton: Attempting damping, relres = 0.545903 │ │ │ Vnewton: Damping accepted, relres = 0.097470 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.746961e-02 │ │ │ Vprtstp: contraction number = 9.746961e-02 │ │ │ Vnewton: Using errtol_s: 365103.476411 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.813445e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.719563e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.291408e+04 │ │ │ Vprtstp: contraction number = 7.291408e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.752435e-02 │ │ │ Vprtstp: contraction number = 1.797929e-01 │ │ │ Vnewton: Using errtol_s: 65643.018240 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.840700e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.751236e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.675888e+04 │ │ │ Vprtstp: contraction number = 1.675888e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.026892e-03 │ │ │ Vprtstp: contraction number = 2.297884e-01 │ │ │ Vnewton: Using errtol_s: 15084.007144 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.866868e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.780505e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.533188e+03 │ │ │ Vprtstp: contraction number = 4.533188e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.089215e-03 │ │ │ Vprtstp: contraction number = 2.704853e-01 │ │ │ Vnewton: Using errtol_s: 4080.002297 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.894224e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.811780e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.369611e+03 │ │ │ Vprtstp: contraction number = 1.369611e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.290808e-04 │ │ │ Vprtstp: contraction number = 3.021265e-01 │ │ │ Vnewton: Using errtol_s: 1232.676861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.921545e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.838316e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.398009e+02 │ │ │ Vprtstp: contraction number = 4.398009e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.056716e-04 │ │ │ Vprtstp: contraction number = 3.211115e-01 │ │ │ Vnewton: Using errtol_s: 395.826722 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.948877e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.865335e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.460593e+02 │ │ │ Vprtstp: contraction number = 1.460593e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.509370e-05 │ │ │ Vprtstp: contraction number = 3.321014e-01 │ │ │ Vnewton: Using errtol_s: 131.454614 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.976297e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.893557e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.960244e+01 │ │ │ Vprtstp: contraction number = 4.960244e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.191794e-05 │ │ │ Vprtstp: contraction number = 3.396035e-01 │ │ │ Vnewton: Using errtol_s: 44.642449 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.003489e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.921890e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.713194e+01 │ │ │ Vprtstp: contraction number = 1.713194e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.116267e-06 │ │ │ Vprtstp: contraction number = 3.453841e-01 │ │ │ Vnewton: Using errtol_s: 15.418791 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.030799e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.952236e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.017264e+00 │ │ │ Vprtstp: contraction number = 6.017264e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.445758e-06 │ │ │ Vprtstp: contraction number = 3.512303e-01 │ │ │ Vnewton: Using errtol_s: 5.415546 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.056859e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.985427e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.154066e+00 │ │ │ Vprtstp: contraction number = 2.154066e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.175534e-07 │ │ │ Vprtstp: contraction number = 3.579807e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.167762e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.398989e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.318790e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.340791e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -14480,27 +14480,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.620792182088E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.339466431031E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.686807644409E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.231500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.943800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.109916e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.015400e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:59:23 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 14:40:36 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -14853,250 +14853,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.246541 │ │ │ +Vacc_SASA: Time elapsed: 3.985941 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.642298e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.179374e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.548700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.970600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.634260e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.626136e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.073045e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.426574e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.236825e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.154398e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.620446e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.745614e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.918897e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.967508e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.205151e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.087339e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.492621e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.011694e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.792955e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.223815e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.078447e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.432360e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.377550e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.634828e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.665102e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.853294e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.952067e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.061102e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.251566e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.264098e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.538824e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.442266e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.825923e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.639407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.124846e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.816729e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.412253e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.984375e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.699705e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.164192e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.998809e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.346793e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.286318e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.534297e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.571082e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.735666e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.725949e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.980832e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.827282e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.845830e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15105,15 +15105,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.410514495807E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 1.129100557647E+00 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.525200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.289900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -15161,160 +15161,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.000190853 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.273841 │ │ │ +Vacc_SASA: Time elapsed: 3.449539 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.662500e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.349632e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.582400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.039000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.663530e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.265322e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174510e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.959442e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1032634.725607 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.192265e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.996117e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.090058e+05 │ │ │ Vprtstp: contraction number = 1.090058e+05 │ │ │ Vnewton: Attempting damping, relres = 0.095383 │ │ │ Vnewton: Attempting damping, relres = 0.544753 │ │ │ Vnewton: Damping accepted, relres = 0.095383 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.538325e-02 │ │ │ Vprtstp: contraction number = 9.538325e-02 │ │ │ Vnewton: Using errtol_s: 98496.056858 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.230518e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.214034e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.829312e+04 │ │ │ Vprtstp: contraction number = 1.829312e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.595089e-02 │ │ │ Vprtstp: contraction number = 1.672295e-01 │ │ │ Vnewton: Using errtol_s: 16471.442714 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.259123e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.407916e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.867524e+03 │ │ │ Vprtstp: contraction number = 3.867524e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.370960e-03 │ │ │ Vprtstp: contraction number = 2.113337e-01 │ │ │ Vnewton: Using errtol_s: 3480.970171 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.291226e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.586960e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.812010e+02 │ │ │ Vprtstp: contraction number = 9.812010e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 8.551815e-04 │ │ │ Vprtstp: contraction number = 2.536908e-01 │ │ │ Vnewton: Using errtol_s: 883.090100 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320323e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.782695e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.836594e+02 │ │ │ Vprtstp: contraction number = 2.836594e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 2.472259e-04 │ │ │ Vprtstp: contraction number = 2.890917e-01 │ │ │ Vnewton: Using errtol_s: 255.294034 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.350234e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.989570e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.927772e+01 │ │ │ Vprtstp: contraction number = 8.927772e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 7.781068e-05 │ │ │ Vprtstp: contraction number = 3.147352e-01 │ │ │ Vnewton: Using errtol_s: 80.350015 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.378863e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.182906e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.937189e+01 │ │ │ Vprtstp: contraction number = 2.937189e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.559929e-05 │ │ │ Vprtstp: contraction number = 3.289945e-01 │ │ │ Vnewton: Using errtol_s: 26.434712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.408643e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.364040e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.890447e+00 │ │ │ Vprtstp: contraction number = 9.890447e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.620089e-06 │ │ │ Vprtstp: contraction number = 3.367316e-01 │ │ │ Vnewton: Using errtol_s: 8.901403 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.441240e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.565061e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.377400e+00 │ │ │ Vprtstp: contraction number = 3.377400e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.943597e-06 │ │ │ Vprtstp: contraction number = 3.414810e-01 │ │ │ Vnewton: Using errtol_s: 3.039660 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472097e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.761558e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.164729e+00 │ │ │ Vprtstp: contraction number = 1.164729e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.015127e-06 │ │ │ Vprtstp: contraction number = 3.448595e-01 │ │ │ Vnewton: Using errtol_s: 1.048256 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.500693e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.970768e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.047354e-01 │ │ │ Vprtstp: contraction number = 4.047354e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.527500e-07 │ │ │ Vprtstp: contraction number = 3.474933e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.491216e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.749956e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.195890e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.209881e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15323,17 +15323,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.262250874476E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 7.842003689004E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.710900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -15354,272 +15354,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.264519 │ │ │ +Vacc_SASA: Time elapsed: 3.585157 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.643928e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.563890e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.600300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.237750e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.638560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.471587e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.816486e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.218320e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.832571e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.249639e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.868281e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.468628e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.895489e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.680906e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.923741e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.890203e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.950864e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.091682e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.977955e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.286285e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.006033e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.482169e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.033192e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.689144e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.060375e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.911992e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.087633e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.128368e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.116055e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.360218e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.144788e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.574867e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.173842e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.793307e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.202927e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.030739e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.229682e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.269308e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.257017e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.513120e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.284252e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.739519e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.311533e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.976870e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.337905e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022629e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.365283e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047089e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.393994e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.070971e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.984748e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.230012e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.702268e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.718701e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15628,17 +15628,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.028844380467E+00 kT │ │ │ Vpmg_energy: qfEnergy = 9.611210700866E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.863079386675E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.343700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.856600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.200000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -15684,171 +15684,171 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0377574 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.265201 │ │ │ +Vacc_SASA: Time elapsed: 4.179905 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.965287e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.119741e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.562400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.638290e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.694710e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.665908e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.739266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.100142e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6079198.405761 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.754719e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104470e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.898758e+05 │ │ │ Vprtstp: contraction number = 5.898758e+05 │ │ │ Vnewton: Attempting damping, relres = 0.088148 │ │ │ Vnewton: Attempting damping, relres = 0.541560 │ │ │ Vnewton: Damping accepted, relres = 0.088148 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.814828e-02 │ │ │ Vprtstp: contraction number = 8.814828e-02 │ │ │ Vnewton: Using errtol_s: 535870.896065 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.791730e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140917e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.077049e+05 │ │ │ Vprtstp: contraction number = 1.077049e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.598309e-02 │ │ │ Vprtstp: contraction number = 1.813205e-01 │ │ │ Vnewton: Using errtol_s: 97164.364787 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.821785e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.172826e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.746148e+04 │ │ │ Vprtstp: contraction number = 2.746148e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.065921e-03 │ │ │ Vprtstp: contraction number = 2.543889e-01 │ │ │ Vnewton: Using errtol_s: 24717.539236 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.850882e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.203083e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.490060e+03 │ │ │ Vprtstp: contraction number = 8.490060e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.256932e-03 │ │ │ Vprtstp: contraction number = 3.091382e-01 │ │ │ Vnewton: Using errtol_s: 7641.136045 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.879092e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233747e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.906153e+03 │ │ │ Vprtstp: contraction number = 2.906153e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.302464e-04 │ │ │ Vprtstp: contraction number = 3.422990e-01 │ │ │ Vnewton: Using errtol_s: 2615.553137 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.907080e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.262914e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.038756e+03 │ │ │ Vprtstp: contraction number = 1.038756e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.537840e-04 │ │ │ Vprtstp: contraction number = 3.574324e-01 │ │ │ Vnewton: Using errtol_s: 934.883311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.933144e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292423e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.756989e+02 │ │ │ Vprtstp: contraction number = 3.756989e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.562081e-05 │ │ │ Vprtstp: contraction number = 3.616814e-01 │ │ │ Vnewton: Using errtol_s: 338.129920 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.959400e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322378e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.372077e+02 │ │ │ Vprtstp: contraction number = 1.372077e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.031307e-05 │ │ │ Vprtstp: contraction number = 3.652064e-01 │ │ │ Vnewton: Using errtol_s: 123.487196 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.986982e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.351405e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.308624e+01 │ │ │ Vprtstp: contraction number = 5.308624e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.859206e-06 │ │ │ Vprtstp: contraction number = 3.869039e-01 │ │ │ Vnewton: Using errtol_s: 47.777672 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.014689e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.380520e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.247149e+01 │ │ │ Vprtstp: contraction number = 2.247149e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.326814e-06 │ │ │ Vprtstp: contraction number = 4.233015e-01 │ │ │ Vnewton: Using errtol_s: 20.224360 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.042250e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.409928e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.031380e+01 │ │ │ Vprtstp: contraction number = 1.031380e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.526916e-06 │ │ │ Vprtstp: contraction number = 4.589724e-01 │ │ │ Vnewton: Using errtol_s: 9.282423 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.071187e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.438350e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.018395e+00 │ │ │ Vprtstp: contraction number = 5.018395e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.429527e-07 │ │ │ Vprtstp: contraction number = 4.865709e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.525822e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.780063e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.637509e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.656651e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15857,15 +15857,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.101910647011E+00 kT │ │ │ Vpmg_energy: qfEnergy = 7.806992325165E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.916747531828E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.590500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.819100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ @@ -15888,261 +15888,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.397615 │ │ │ +Vacc_SASA: Time elapsed: 6.761665 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.025407e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.057920e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.141300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.417800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.107230e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.167500e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.626082e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.473312e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.644473e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.475982e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.680520e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.499417e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.708063e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.522731e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.735511e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.546120e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.763049e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.566608e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.790652e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.586410e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.817337e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.605865e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.845955e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.627042e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.873534e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.647066e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.901039e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.667696e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.927396e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.687104e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.956318e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.705758e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.983991e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.725667e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.011635e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.748296e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.039153e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.767338e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.066832e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.786457e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.094430e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.804877e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.122017e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.824792e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.148412e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.847912e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.175987e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.868872e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.701873e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.987316e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.117452e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.130174e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -16151,17 +16151,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.017893422646E+00 kT │ │ │ Vpmg_energy: qfEnergy = 9.611562953522E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.865716990042E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.362000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.632400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -16207,171 +16207,171 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0371069 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 3.925225 │ │ │ +Vacc_SASA: Time elapsed: 7.114956 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.800619e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.570603e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.878700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.952900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.022260e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.061289e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.707366e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.894930e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6935084.404705 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.724058e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.897633e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.727592e+05 │ │ │ Vprtstp: contraction number = 6.727592e+05 │ │ │ Vnewton: Attempting damping, relres = 0.088102 │ │ │ Vnewton: Attempting damping, relres = 0.541455 │ │ │ Vnewton: Damping accepted, relres = 0.088102 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.810224e-02 │ │ │ Vprtstp: contraction number = 8.810224e-02 │ │ │ Vnewton: Using errtol_s: 610996.445538 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.760507e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.921068e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.225330e+05 │ │ │ Vprtstp: contraction number = 1.225330e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.593368e-02 │ │ │ Vprtstp: contraction number = 1.808544e-01 │ │ │ Vnewton: Using errtol_s: 110501.406789 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.787922e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.941916e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.085731e+04 │ │ │ Vprtstp: contraction number = 3.085731e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.004954e-03 │ │ │ Vprtstp: contraction number = 2.513515e-01 │ │ │ Vnewton: Using errtol_s: 27774.696268 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.815297e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.963617e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.402021e+03 │ │ │ Vprtstp: contraction number = 9.402021e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.220185e-03 │ │ │ Vprtstp: contraction number = 3.046688e-01 │ │ │ Vnewton: Using errtol_s: 8462.082872 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.842664e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.985160e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.175895e+03 │ │ │ Vprtstp: contraction number = 3.175895e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.121575e-04 │ │ │ Vprtstp: contraction number = 3.377829e-01 │ │ │ Vnewton: Using errtol_s: 2858.347084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.870100e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.005834e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.121720e+03 │ │ │ Vprtstp: contraction number = 1.121720e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.455722e-04 │ │ │ Vprtstp: contraction number = 3.531955e-01 │ │ │ Vnewton: Using errtol_s: 1009.555317 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.897637e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.026803e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.008316e+02 │ │ │ Vprtstp: contraction number = 4.008316e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.201806e-05 │ │ │ Vprtstp: contraction number = 3.573352e-01 │ │ │ Vnewton: Using errtol_s: 360.749636 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.924976e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048249e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.444166e+02 │ │ │ Vprtstp: contraction number = 1.444166e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.874168e-05 │ │ │ Vprtstp: contraction number = 3.602918e-01 │ │ │ Vnewton: Using errtol_s: 129.975153 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.952308e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.070022e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.512662e+01 │ │ │ Vprtstp: contraction number = 5.512662e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.154062e-06 │ │ │ Vprtstp: contraction number = 3.817193e-01 │ │ │ Vnewton: Using errtol_s: 49.614025 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.979679e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.092015e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.308362e+01 │ │ │ Vprtstp: contraction number = 2.308362e+01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.995677e-06 │ │ │ Vprtstp: contraction number = 4.187379e-01 │ │ │ Vnewton: Using errtol_s: 20.775274 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.006977e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.112912e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051871e+01 │ │ │ Vprtstp: contraction number = 1.051871e+01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.365066e-06 │ │ │ Vprtstp: contraction number = 4.556784e-01 │ │ │ Vnewton: Using errtol_s: 9.466845 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.034341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.134161e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.098076e+00 │ │ │ Vprtstp: contraction number = 5.098076e+00 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 6.616025e-07 │ │ │ Vprtstp: contraction number = 4.846672e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.473647e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.761522e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.584793e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.597361e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -16380,27 +16380,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.129100275217E+00 kT │ │ │ Vpmg_energy: qfEnergy = 7.806947604587E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.916855498576E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.601600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.263700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.082270e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.153992e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:59:53 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 15:26:38 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -16753,250 +16753,250 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.785905 │ │ │ +Vacc_SASA: Time elapsed: 3.238322 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.183523e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.084904e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.025300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.081870e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.996130e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.225155e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.620404e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.742057e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.805572e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.437488e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.185199e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.581593e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.494918e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.098363e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.798504e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.609410e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.090970e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.237648e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.381003e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.988102e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.671555e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066765e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.950583e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233501e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.253124e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.422174e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.544447e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.606911e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.835464e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.808449e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.127255e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.021016e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.408163e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.233967e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.690003e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.432978e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.969829e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.609089e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.275567e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.780549e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.566502e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.947025e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.867282e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.108727e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.159325e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.276313e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.760765e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.055029e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.371636e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.385660e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -17005,17 +17005,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.751162440734E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.947112425311E+03 kT │ │ │ Vpmg_energy: dielEnergy = 9.674060402300E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.309200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.409500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -17061,160 +17061,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0113169 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.991147 │ │ │ +Vacc_SASA: Time elapsed: 3.436663 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.563238e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.744545e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.572500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.609470e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.631190e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.605236e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.122441e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.496345e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2854416.159669 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.138343e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.524005e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.073946e+05 │ │ │ Vprtstp: contraction number = 3.073946e+05 │ │ │ Vnewton: Attempting damping, relres = 0.097301 │ │ │ Vnewton: Attempting damping, relres = 0.546102 │ │ │ Vnewton: Damping accepted, relres = 0.097301 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.730086e-02 │ │ │ Vprtstp: contraction number = 9.730086e-02 │ │ │ Vnewton: Using errtol_s: 277737.152012 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.179043e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.751485e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.422127e+04 │ │ │ Vprtstp: contraction number = 5.422127e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.709795e-02 │ │ │ Vprtstp: contraction number = 1.757225e-01 │ │ │ Vnewton: Using errtol_s: 48804.661136 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.213575e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.968316e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.206353e+04 │ │ │ Vprtstp: contraction number = 1.206353e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 3.803701e-03 │ │ │ Vprtstp: contraction number = 2.224653e-01 │ │ │ Vnewton: Using errtol_s: 10857.344468 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.249465e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.190729e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.177380e+03 │ │ │ Vprtstp: contraction number = 3.177380e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.001847e-03 │ │ │ Vprtstp: contraction number = 2.633874e-01 │ │ │ Vnewton: Using errtol_s: 2859.687867 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.278149e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.426756e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.523572e+02 │ │ │ Vprtstp: contraction number = 9.523572e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.002837e-04 │ │ │ Vprtstp: contraction number = 2.997301e-01 │ │ │ Vnewton: Using errtol_s: 857.134538 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.307843e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.654444e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.079890e+02 │ │ │ Vprtstp: contraction number = 3.079890e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.711021e-05 │ │ │ Vprtstp: contraction number = 3.233949e-01 │ │ │ Vnewton: Using errtol_s: 277.192960 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.337821e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.884595e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.041211e+02 │ │ │ Vprtstp: contraction number = 1.041211e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.282966e-05 │ │ │ Vprtstp: contraction number = 3.380660e-01 │ │ │ Vnewton: Using errtol_s: 93.709510 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.367783e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.111326e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.682551e+01 │ │ │ Vprtstp: contraction number = 3.682551e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.161114e-05 │ │ │ Vprtstp: contraction number = 3.536784e-01 │ │ │ Vnewton: Using errtol_s: 33.143025 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.397660e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.334244e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.414772e+01 │ │ │ Vprtstp: contraction number = 1.414772e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.460791e-06 │ │ │ Vprtstp: contraction number = 3.841820e-01 │ │ │ Vnewton: Using errtol_s: 12.732955 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427511e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.551797e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.014294e+00 │ │ │ Vprtstp: contraction number = 6.014294e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.896313e-06 │ │ │ Vprtstp: contraction number = 4.251068e-01 │ │ │ Vnewton: Using errtol_s: 5.412865 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.458489e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.763792e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.770154e+00 │ │ │ Vprtstp: contraction number = 2.770154e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.734323e-07 │ │ │ Vprtstp: contraction number = 4.605951e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.656416e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.914618e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.464544e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.484006e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -17223,17 +17223,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.831261294961E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.781344550664E+04 kT │ │ │ Vpmg_energy: dielEnergy = 8.939288545980E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.455500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.731500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -17254,272 +17254,272 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.292864 │ │ │ +Vacc_SASA: Time elapsed: 3.235757 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.729807e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.143655e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.571000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.065940e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.675680e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.118799e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.790365e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.015951e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.807458e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.040075e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.846441e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.218751e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.877950e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.381890e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.908085e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.538846e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.936749e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.691153e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.964007e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.850937e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.991180e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.011477e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.018376e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.168073e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048042e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.359031e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.076815e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.540261e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105293e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.729578e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.134159e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.907023e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.162902e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.070015e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.193294e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.228440e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.222134e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.386116e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.250749e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.541084e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.279076e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.693432e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.308955e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.844873e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.337691e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.998928e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.366502e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.151632e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.393821e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.303828e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.257266e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.508413e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.424689e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.437747e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -17528,17 +17528,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.114658040660E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.255454137160E+02 kT │ │ │ Vpmg_energy: dielEnergy = 1.687649926413E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.243300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.040600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -17584,160 +17584,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00476673 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.305159 │ │ │ +Vacc_SASA: Time elapsed: 2.728678 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.770245e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.641987e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.581500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.704800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.669850e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.125476e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.721521e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.490280e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1723088.414735 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.738841e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.514306e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.042446e+05 │ │ │ Vprtstp: contraction number = 2.042446e+05 │ │ │ Vnewton: Attempting damping, relres = 0.108739 │ │ │ Vnewton: Attempting damping, relres = 0.550663 │ │ │ Vnewton: Damping accepted, relres = 0.108739 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.087385e-01 │ │ │ Vprtstp: contraction number = 1.087385e-01 │ │ │ Vnewton: Using errtol_s: 187366.060856 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.775746e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.677412e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.786866e+04 │ │ │ Vprtstp: contraction number = 3.786866e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.981324e-02 │ │ │ Vprtstp: contraction number = 1.822100e-01 │ │ │ Vnewton: Using errtol_s: 34139.969757 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.802932e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.820029e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.828513e+03 │ │ │ Vprtstp: contraction number = 8.828513e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.612234e-03 │ │ │ Vprtstp: contraction number = 2.327854e-01 │ │ │ Vnewton: Using errtol_s: 7947.287090 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.829954e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.961994e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.384276e+03 │ │ │ Vprtstp: contraction number = 2.384276e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.245382e-03 │ │ │ Vprtstp: contraction number = 2.700171e-01 │ │ │ Vnewton: Using errtol_s: 2145.903122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.857128e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010490e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.047320e+02 │ │ │ Vprtstp: contraction number = 7.047320e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.680970e-04 │ │ │ Vprtstp: contraction number = 2.955696e-01 │ │ │ Vnewton: Using errtol_s: 634.263634 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.885691e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024710e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.207559e+02 │ │ │ Vprtstp: contraction number = 2.207559e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.153050e-04 │ │ │ Vprtstp: contraction number = 3.132463e-01 │ │ │ Vnewton: Using errtol_s: 198.680750 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.912617e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038857e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.166503e+01 │ │ │ Vprtstp: contraction number = 7.166503e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.743196e-05 │ │ │ Vprtstp: contraction number = 3.246343e-01 │ │ │ Vnewton: Using errtol_s: 64.498581 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.941110e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052934e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.385676e+01 │ │ │ Vprtstp: contraction number = 2.385676e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.246082e-05 │ │ │ Vprtstp: contraction number = 3.328924e-01 │ │ │ Vnewton: Using errtol_s: 21.471088 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.967952e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067221e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.086151e+00 │ │ │ Vprtstp: contraction number = 8.086151e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.223542e-06 │ │ │ Vprtstp: contraction number = 3.389459e-01 │ │ │ Vnewton: Using errtol_s: 7.277537 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.996053e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081509e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.777094e+00 │ │ │ Vprtstp: contraction number = 2.777094e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.450526e-06 │ │ │ Vprtstp: contraction number = 3.434383e-01 │ │ │ Vnewton: Using errtol_s: 2.499385 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.027463e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.095551e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.633001e-01 │ │ │ Vprtstp: contraction number = 9.633001e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.031489e-07 │ │ │ Vprtstp: contraction number = 3.468734e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.269783e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.518931e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.591577e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.604228e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -17746,17 +17746,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.878540629655E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.319538441543E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.644040185021E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.288500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.454200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -17777,261 +17777,261 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.985766 │ │ │ +Vacc_SASA: Time elapsed: 6.166691 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.585965e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.191642e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.512500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.588500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.832930e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.091666e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.636032e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.116645e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.656035e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119031e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.691795e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137497e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.719024e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.153820e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.746046e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.170463e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.773130e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.187167e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.800846e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.204152e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.828102e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.220819e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.855162e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237412e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.882218e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.254586e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.909379e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.271560e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.936548e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.288769e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.965032e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305916e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.992214e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322740e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.019288e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.339300e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.046459e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355997e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.073589e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.373015e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ Vprtstp: iteration = 16 │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.100665e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.389858e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ Vprtstp: iteration = 17 │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.127908e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.407286e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.155055e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.425381e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.185700e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.442468e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ Vprtstp: iteration = 20 │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 5.706876e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.956141e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.418096e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.430117e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -18040,17 +18040,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.211144338750E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.301973448783E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.153004707320E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.581200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.710400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -18096,160 +18096,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0260263 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.958280 │ │ │ +Vacc_SASA: Time elapsed: 6.515923 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.751190e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.831506e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.539700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.656100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.646160e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.163706e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.808975e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.467665e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4514465.797290 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.824996e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.470137e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.961912e+05 │ │ │ Vprtstp: contraction number = 4.961912e+05 │ │ │ Vnewton: Attempting damping, relres = 0.099852 │ │ │ Vnewton: Attempting damping, relres = 0.546981 │ │ │ Vnewton: Damping accepted, relres = 0.099852 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.985216e-02 │ │ │ Vprtstp: contraction number = 9.985216e-02 │ │ │ Vnewton: Using errtol_s: 450779.157003 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.860843e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.492491e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.942393e+04 │ │ │ Vprtstp: contraction number = 8.942393e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.783565e-02 │ │ │ Vprtstp: contraction number = 1.786206e-01 │ │ │ Vnewton: Using errtol_s: 80518.432475 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.888100e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.513603e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.031115e+04 │ │ │ Vprtstp: contraction number = 2.031115e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.049611e-03 │ │ │ Vprtstp: contraction number = 2.270515e-01 │ │ │ Vnewton: Using errtol_s: 18281.831872 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.915073e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.535970e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.419185e+03 │ │ │ Vprtstp: contraction number = 5.419185e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.080391e-03 │ │ │ Vprtstp: contraction number = 2.667887e-01 │ │ │ Vnewton: Using errtol_s: 4877.386053 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.941106e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.558670e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.625333e+03 │ │ │ Vprtstp: contraction number = 1.625333e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.240293e-04 │ │ │ Vprtstp: contraction number = 2.999187e-01 │ │ │ Vnewton: Using errtol_s: 1462.819304 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.968359e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581134e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.216368e+02 │ │ │ Vprtstp: contraction number = 5.216368e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.039939e-04 │ │ │ Vprtstp: contraction number = 3.209397e-01 │ │ │ Vnewton: Using errtol_s: 469.476847 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.995605e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.602029e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.735595e+02 │ │ │ Vprtstp: contraction number = 1.735595e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.460082e-05 │ │ │ Vprtstp: contraction number = 3.327198e-01 │ │ │ Vnewton: Using errtol_s: 156.204227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.021553e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.622712e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.923935e+01 │ │ │ Vprtstp: contraction number = 5.923935e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.180993e-05 │ │ │ Vprtstp: contraction number = 3.413193e-01 │ │ │ Vnewton: Using errtol_s: 53.315519 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.048736e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.643434e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.118946e+01 │ │ │ Vprtstp: contraction number = 2.118946e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.224316e-06 │ │ │ Vprtstp: contraction number = 3.576919e-01 │ │ │ Vnewton: Using errtol_s: 19.070529 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.076743e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.664558e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.237698e+00 │ │ │ Vprtstp: contraction number = 8.237698e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.642261e-06 │ │ │ Vprtstp: contraction number = 3.887637e-01 │ │ │ Vnewton: Using errtol_s: 7.413930 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.103930e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.685733e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.509994e+00 │ │ │ Vprtstp: contraction number = 3.509994e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.997494e-07 │ │ │ Vprtstp: contraction number = 4.260891e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.150966e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.396932e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.379021e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.392477e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -18258,27 +18258,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.259341430721E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.116108930828E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.059930084642E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.190800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.048000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.158758e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.706068e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:00:24 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 16:03:23 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -18631,129 +18631,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.251267 │ │ │ +Vacc_SASA: Time elapsed: 3.209647 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.880530e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.372717e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.513700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.129400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.617150e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.024557e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.312959e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.824690e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.484769e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.632339e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.897393e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.874982e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.196645e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.641100e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.484860e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.412627e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.785235e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.245534e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.085243e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.015975e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.384646e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.191308e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.678901e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.365755e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.603685e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.853367e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.463806e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.475278e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -18762,15 +18762,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.432004946158E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.213065901878E+03 kT │ │ │ Vpmg_energy: dielEnergy = 6.590634025531E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.540300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.869200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -18818,127 +18818,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00609308 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.242194 │ │ │ +Vacc_SASA: Time elapsed: 3.238945 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.028440e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.589005e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.486000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.619800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.626090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.025758e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.219638e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.580255e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3435589.940646 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.380134e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.604693e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.946642e+05 │ │ │ Vprtstp: contraction number = 2.946642e+05 │ │ │ Vnewton: Attempting damping, relres = 0.078398 │ │ │ Vnewton: Attempting damping, relres = 0.536416 │ │ │ Vnewton: Damping accepted, relres = 0.078398 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.839769e-02 │ │ │ Vprtstp: contraction number = 7.839769e-02 │ │ │ Vnewton: Using errtol_s: 269342.316546 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.765805e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.836940e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.926470e+04 │ │ │ Vprtstp: contraction number = 3.926470e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.037644e-02 │ │ │ Vprtstp: contraction number = 1.323565e-01 │ │ │ Vnewton: Using errtol_s: 35649.206105 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.006619e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.060065e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.330351e+03 │ │ │ Vprtstp: contraction number = 6.330351e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.659520e-03 │ │ │ Vprtstp: contraction number = 1.599315e-01 │ │ │ Vnewton: Using errtol_s: 5701.430665 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035377e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.287898e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.149005e+03 │ │ │ Vprtstp: contraction number = 1.149005e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.009992e-04 │ │ │ Vprtstp: contraction number = 1.813772e-01 │ │ │ Vnewton: Using errtol_s: 1034.109707 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064081e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.509033e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.271091e+02 │ │ │ Vprtstp: contraction number = 2.271091e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.949440e-05 │ │ │ Vprtstp: contraction number = 1.976564e-01 │ │ │ Vnewton: Using errtol_s: 204.398353 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.094638e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.727532e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.795044e+01 │ │ │ Vprtstp: contraction number = 4.795044e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.256128e-05 │ │ │ Vprtstp: contraction number = 2.111338e-01 │ │ │ Vnewton: Using errtol_s: 43.155404 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123488e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.945158e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.083630e+01 │ │ │ Vprtstp: contraction number = 1.083630e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.838717e-06 │ │ │ Vprtstp: contraction number = 2.259895e-01 │ │ │ Vnewton: Using errtol_s: 9.752668 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.153443e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.171236e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677103e+00 │ │ │ Vprtstp: contraction number = 2.677103e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.013038e-07 │ │ │ Vprtstp: contraction number = 2.470496e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.538024e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.785019e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.795227e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.807181e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -18947,17 +18947,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.647117283033E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.061546373318E+04 kT │ │ │ Vpmg_energy: dielEnergy = 5.342705487083E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.198800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.517500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -18978,129 +18978,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.260777 │ │ │ +Vacc_SASA: Time elapsed: 3.023494 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.916417e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.229309e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.562000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.661600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.835680e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.131098e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.496924e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.431262e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.517265e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.458236e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.555138e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.664395e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.582523e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.836538e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.610017e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.012405e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.638658e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.193526e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.666203e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.375138e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.693555e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.547382e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.720821e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.722386e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.452236e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.708755e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.446956e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.459615e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -19109,17 +19109,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.317231145309E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.397951074417E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.196103394551E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.515400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.915400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -19165,149 +19165,149 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0717616 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.262570 │ │ │ +Vacc_SASA: Time elapsed: 3.134299 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.113645e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.509921e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.597700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.919600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.640820e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.195619e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.080142e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.936822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3849668.809256 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.095858e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.963889e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.552766e+05 │ │ │ Vprtstp: contraction number = 3.552766e+05 │ │ │ Vnewton: Attempting damping, relres = 0.084988 │ │ │ Vnewton: Attempting damping, relres = 0.539692 │ │ │ Vnewton: Damping accepted, relres = 0.084988 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.498801e-02 │ │ │ Vprtstp: contraction number = 8.498801e-02 │ │ │ Vnewton: Using errtol_s: 327175.687931 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.131617e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.191338e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.008831e+04 │ │ │ Vprtstp: contraction number = 5.008831e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.180515e-02 │ │ │ Vprtstp: contraction number = 1.389037e-01 │ │ │ Vnewton: Using errtol_s: 45445.906193 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.158497e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.422157e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.515214e+03 │ │ │ Vprtstp: contraction number = 8.515214e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.991773e-03 │ │ │ Vprtstp: contraction number = 1.687207e-01 │ │ │ Vnewton: Using errtol_s: 7667.665331 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.185627e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.662106e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.650417e+03 │ │ │ Vprtstp: contraction number = 1.650417e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.858749e-04 │ │ │ Vprtstp: contraction number = 1.937344e-01 │ │ │ Vnewton: Using errtol_s: 1485.490751 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.211594e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.885143e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.445276e+02 │ │ │ Vprtstp: contraction number = 3.445276e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 8.054589e-05 │ │ │ Vprtstp: contraction number = 2.087357e-01 │ │ │ Vnewton: Using errtol_s: 310.075011 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.238753e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.104102e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.228113e+01 │ │ │ Vprtstp: contraction number = 9.228113e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.157878e-05 │ │ │ Vprtstp: contraction number = 2.679067e-01 │ │ │ Vnewton: Using errtol_s: 83.071163 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.265963e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.317520e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.340270e+01 │ │ │ Vprtstp: contraction number = 3.340270e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.809088e-06 │ │ │ Vprtstp: contraction number = 3.618873e-01 │ │ │ Vnewton: Using errtol_s: 30.062402 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.292015e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.538356e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.311951e+01 │ │ │ Vprtstp: contraction number = 1.311951e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.067793e-06 │ │ │ Vprtstp: contraction number = 3.928491e-01 │ │ │ Vnewton: Using errtol_s: 11.809988 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.319208e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.767902e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.550050e+00 │ │ │ Vprtstp: contraction number = 5.550050e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.297525e-06 │ │ │ Vprtstp: contraction number = 4.229508e-01 │ │ │ Vnewton: Using errtol_s: 4.995043 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.346356e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.983383e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.408064e+00 │ │ │ Vprtstp: contraction number = 2.408064e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 5.629926e-07 │ │ │ Vprtstp: contraction number = 4.338972e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.866809e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.108444e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.245162e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.258273e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -19316,17 +19316,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.480336832725E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.844029166481E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.209478882547E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.158600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.447200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -19347,129 +19347,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.955088 │ │ │ +Vacc_SASA: Time elapsed: 6.541840 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.749773e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.128462e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.566900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.935800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.607910e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.069117e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.968250e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.275387e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.983855e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.301526e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.020969e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.564486e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.049320e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.785873e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.076647e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.011407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.103966e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.231746e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.132470e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.465528e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.159888e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.673675e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.187214e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.877241e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.405918e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.632193e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.797375e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.809224e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -19478,17 +19478,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.111204276616E+00 kT │ │ │ Vpmg_energy: qfEnergy = 3.618165500075E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.858858240156E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.560900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.650100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -19534,138 +19534,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0804427 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.970256 │ │ │ +Vacc_SASA: Time elapsed: 7.139691 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.061019e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.364474e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.600900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.523900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.639040e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.178628e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.842085e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.180654e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7226173.981930 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.858069e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.208552e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.363534e+05 │ │ │ Vprtstp: contraction number = 6.363534e+05 │ │ │ Vnewton: Attempting damping, relres = 0.081351 │ │ │ Vnewton: Attempting damping, relres = 0.537664 │ │ │ Vnewton: Damping accepted, relres = 0.081351 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.135112e-02 │ │ │ Vprtstp: contraction number = 8.135112e-02 │ │ │ Vnewton: Using errtol_s: 587857.310633 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.894344e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.465926e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.753275e+04 │ │ │ Vprtstp: contraction number = 8.753275e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.104343e-02 │ │ │ Vprtstp: contraction number = 1.357502e-01 │ │ │ Vnewton: Using errtol_s: 79801.757672 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.922682e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.687789e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.461031e+04 │ │ │ Vprtstp: contraction number = 1.461031e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.821090e-03 │ │ │ Vprtstp: contraction number = 1.649025e-01 │ │ │ Vnewton: Using errtol_s: 13159.512971 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.950025e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.899549e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.736183e+03 │ │ │ Vprtstp: contraction number = 2.736183e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.408124e-04 │ │ │ Vprtstp: contraction number = 1.871475e-01 │ │ │ Vnewton: Using errtol_s: 2462.769628 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.977294e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.012249e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.483227e+02 │ │ │ Vprtstp: contraction number = 5.483227e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.829255e-05 │ │ │ Vprtstp: contraction number = 2.003817e-01 │ │ │ Vnewton: Using errtol_s: 493.493873 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.004585e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035511e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.327802e+02 │ │ │ Vprtstp: contraction number = 1.327802e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.654140e-05 │ │ │ Vprtstp: contraction number = 2.422139e-01 │ │ │ Vnewton: Using errtol_s: 119.531057 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.031818e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060037e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.724135e+01 │ │ │ Vprtstp: contraction number = 4.724135e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.883780e-06 │ │ │ Vprtstp: contraction number = 3.557002e-01 │ │ │ Vnewton: Using errtol_s: 42.517221 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.059029e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086232e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.799945e+01 │ │ │ Vprtstp: contraction number = 1.799945e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.242401e-06 │ │ │ Vprtstp: contraction number = 3.811157e-01 │ │ │ Vnewton: Using errtol_s: 16.203980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.086285e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112556e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.792899e+00 │ │ │ Vprtstp: contraction number = 7.792899e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 9.705840e-07 │ │ │ Vprtstp: contraction number = 4.328325e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.648846e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.891968e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.158071e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.171221e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -19674,27 +19674,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.121256399906E+00 kT │ │ │ Vpmg_energy: qfEnergy = 2.906327571511E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.455577366311E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.126300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.999500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.139993e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.134483e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:00:54 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 16:27:33 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -20047,129 +20047,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.320911 │ │ │ +Vacc_SASA: Time elapsed: 3.184248 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.979150e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.628464e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.732100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.381520e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.845440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.269027e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.445787e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.368785e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.693783e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.428785e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.099336e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.004897e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.388600e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.837600e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.688608e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.760058e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.977310e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.907322e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.265984e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.094837e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.567602e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.291584e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.868747e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.501009e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.649383e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.925611e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.637778e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.652487e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -20178,17 +20178,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.829504544268E-01 kT │ │ │ Vpmg_energy: qfEnergy = 9.542693128993E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.766198316119E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.569900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.799800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.700000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -20234,127 +20234,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0324776 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.277835 │ │ │ +Vacc_SASA: Time elapsed: 3.598952 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.248450e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.312863e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.589100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.356800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.604610e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.278069e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.619639e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.769823e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6495890.956801 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.806703e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.798987e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.477908e+05 │ │ │ Vprtstp: contraction number = 5.477908e+05 │ │ │ Vnewton: Attempting damping, relres = 0.076573 │ │ │ Vnewton: Attempting damping, relres = 0.536204 │ │ │ Vnewton: Damping accepted, relres = 0.076573 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.657334e-02 │ │ │ Vprtstp: contraction number = 7.657334e-02 │ │ │ Vnewton: Using errtol_s: 497412.042043 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020760e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.076594e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.388713e+04 │ │ │ Vprtstp: contraction number = 7.388713e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.027070e-02 │ │ │ Vprtstp: contraction number = 1.341289e-01 │ │ │ Vnewton: Using errtol_s: 66717.354364 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049596e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.321069e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.213780e+04 │ │ │ Vprtstp: contraction number = 1.213780e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.681990e-03 │ │ │ Vprtstp: contraction number = 1.637659e-01 │ │ │ Vnewton: Using errtol_s: 10926.025346 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079347e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.555013e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.238925e+03 │ │ │ Vprtstp: contraction number = 2.238925e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.102037e-04 │ │ │ Vprtstp: contraction number = 1.844265e-01 │ │ │ Vnewton: Using errtol_s: 2015.049122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109819e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.775604e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.343882e+02 │ │ │ Vprtstp: contraction number = 4.343882e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.018448e-05 │ │ │ Vprtstp: contraction number = 1.940160e-01 │ │ │ Vnewton: Using errtol_s: 390.951807 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140728e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.995212e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.935633e+01 │ │ │ Vprtstp: contraction number = 7.935633e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.099479e-05 │ │ │ Vprtstp: contraction number = 1.826848e-01 │ │ │ Vnewton: Using errtol_s: 71.420957 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.170644e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.221123e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.530287e+01 │ │ │ Vprtstp: contraction number = 1.530287e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.120201e-06 │ │ │ Vprtstp: contraction number = 1.928369e-01 │ │ │ Vnewton: Using errtol_s: 13.772596 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.199314e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.439859e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.453153e+00 │ │ │ Vprtstp: contraction number = 3.453153e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.784317e-07 │ │ │ Vprtstp: contraction number = 2.256539e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.606105e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.854279e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.865463e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.880090e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -20363,17 +20363,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.483471509223E-01 kT │ │ │ Vpmg_energy: qfEnergy = 7.516233054559E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.774236140842E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.017100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.221800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -20394,129 +20394,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.271826 │ │ │ +Vacc_SASA: Time elapsed: 3.200551 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.896587e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.425377e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.486200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.253000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.830700e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.223738e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.541086e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.693463e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.559372e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.720011e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.595579e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.917403e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.624265e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.088244e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.651727e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.262721e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.679141e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.445534e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.708384e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.621118e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.737278e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.803407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.764829e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.992986e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.450428e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.702208e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.474575e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.487966e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -20525,17 +20525,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.849546283812E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 5.146958313419E-02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.520300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.254600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -20581,127 +20581,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00106787 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.298611 │ │ │ +Vacc_SASA: Time elapsed: 3.844250 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.930901e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.263670e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.530000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.178220e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.625050e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.286585e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105647e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.236372e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 652367.043511 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.122341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.263528e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.625442e+04 │ │ │ Vprtstp: contraction number = 6.625442e+04 │ │ │ Vnewton: Attempting damping, relres = 0.091545 │ │ │ Vnewton: Attempting damping, relres = 0.542935 │ │ │ Vnewton: Damping accepted, relres = 0.091545 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.154497e-02 │ │ │ Vprtstp: contraction number = 9.154497e-02 │ │ │ Vnewton: Using errtol_s: 59720.919943 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.159975e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.444052e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.669735e+03 │ │ │ Vprtstp: contraction number = 8.669735e+03 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.196277e-02 │ │ │ Vprtstp: contraction number = 1.306764e-01 │ │ │ Vnewton: Using errtol_s: 7804.116477 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.187467e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.602813e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.277730e+03 │ │ │ Vprtstp: contraction number = 1.277730e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.762772e-03 │ │ │ Vprtstp: contraction number = 1.473548e-01 │ │ │ Vnewton: Using errtol_s: 1149.974141 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.216269e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.762541e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.050893e+02 │ │ │ Vprtstp: contraction number = 2.050893e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.829401e-04 │ │ │ Vprtstp: contraction number = 1.605086e-01 │ │ │ Vnewton: Using errtol_s: 184.580789 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.243815e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.908650e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.556662e+01 │ │ │ Vprtstp: contraction number = 3.556662e+01 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.906742e-05 │ │ │ Vprtstp: contraction number = 1.734198e-01 │ │ │ Vnewton: Using errtol_s: 32.009971 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.271277e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.061811e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.633566e+00 │ │ │ Vprtstp: contraction number = 6.633566e+00 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.151612e-06 │ │ │ Vprtstp: contraction number = 1.865109e-01 │ │ │ Vnewton: Using errtol_s: 5.970210 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.301946e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.226048e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.319897e+00 │ │ │ Vprtstp: contraction number = 1.319897e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.820919e-06 │ │ │ Vprtstp: contraction number = 1.989725e-01 │ │ │ Vnewton: Using errtol_s: 1.187907 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.331989e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.391863e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.771301e-01 │ │ │ Vprtstp: contraction number = 2.771301e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.823263e-07 │ │ │ Vprtstp: contraction number = 2.099634e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.468723e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.708312e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.304796e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.320092e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -20710,17 +20710,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.030362261326E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 4.051459785687E-02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.285400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.189600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -20741,129 +20741,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.079851 │ │ │ +Vacc_SASA: Time elapsed: 8.856833 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.891130e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.049616e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.476200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.938800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.582940e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.212727e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.968017e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.660228e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.983104e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.693671e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.020378e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.944632e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.047763e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.167044e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.074955e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.397420e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.102329e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.631601e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.129724e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.857962e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.157106e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.089938e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.185535e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.318643e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.379449e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.603542e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.873631e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.887232e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -20872,17 +20872,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.211035436477E-01 kT │ │ │ Vpmg_energy: qfEnergy = 9.542244232526E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.766290532541E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.552100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.446300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -20928,127 +20928,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0370217 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.944878 │ │ │ +Vacc_SASA: Time elapsed: 7.957628 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.983267e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.020623e+01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.607300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.148930e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.773440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.274503e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.832674e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.651031e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7064626.020092 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.848283e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.681567e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.009458e+05 │ │ │ Vprtstp: contraction number = 6.009458e+05 │ │ │ Vnewton: Attempting damping, relres = 0.077277 │ │ │ Vnewton: Attempting damping, relres = 0.536445 │ │ │ Vnewton: Damping accepted, relres = 0.077277 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.727667e-02 │ │ │ Vprtstp: contraction number = 7.727667e-02 │ │ │ Vnewton: Using errtol_s: 545930.796082 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.885547e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.954410e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.090350e+04 │ │ │ Vprtstp: contraction number = 8.090350e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.034337e-02 │ │ │ Vprtstp: contraction number = 1.338486e-01 │ │ │ Vnewton: Using errtol_s: 73072.056615 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.912852e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.213047e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.317148e+04 │ │ │ Vprtstp: contraction number = 1.317148e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.678394e-03 │ │ │ Vprtstp: contraction number = 1.622676e-01 │ │ │ Vnewton: Using errtol_s: 11857.226595 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.940056e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.457099e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.401584e+03 │ │ │ Vprtstp: contraction number = 2.401584e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.059541e-04 │ │ │ Vprtstp: contraction number = 1.822898e-01 │ │ │ Vnewton: Using errtol_s: 2161.451428 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.967341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.701179e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.616256e+02 │ │ │ Vprtstp: contraction number = 4.616256e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.880932e-05 │ │ │ Vprtstp: contraction number = 1.922161e-01 │ │ │ Vnewton: Using errtol_s: 415.465831 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.994645e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.936470e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.389879e+01 │ │ │ Vprtstp: contraction number = 8.389879e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.068835e-05 │ │ │ Vprtstp: contraction number = 1.817458e-01 │ │ │ Vnewton: Using errtol_s: 75.509189 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.021880e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.017062e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.600785e+01 │ │ │ Vprtstp: contraction number = 1.600785e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.039328e-06 │ │ │ Vprtstp: contraction number = 1.907991e-01 │ │ │ Vnewton: Using errtol_s: 14.407086 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.049128e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040482e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.576512e+00 │ │ │ Vprtstp: contraction number = 3.576512e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.556310e-07 │ │ │ Vprtstp: contraction number = 2.234222e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.371794e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.626567e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.959024e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.973694e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -21057,27 +21057,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.057106214068E-01 kT │ │ │ Vpmg_energy: qfEnergy = 7.516201956521E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.774250460752E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.043100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.350900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.102316e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.061571e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:01:23 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 16:50:10 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -21430,129 +21430,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.263599 │ │ │ +Vacc_SASA: Time elapsed: 3.290819 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.881599e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.445623e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.486100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.704300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.609350e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.095682e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.302575e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.913399e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.466250e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.677583e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.860082e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.872855e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.170018e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.649118e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.456052e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.360284e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.752792e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.118738e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.038091e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.941900e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.336291e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.170105e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.622632e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.342831e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.550881e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.791822e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.435994e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.448057e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -21561,17 +21561,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.136518672902E-02 kT │ │ │ Vpmg_energy: qfEnergy = 4.355357372613E+01 kT │ │ │ Vpmg_energy: dielEnergy = 4.752320511857E+01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.546800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.304900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -21617,127 +21617,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00231815 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.238658 │ │ │ +Vacc_SASA: Time elapsed: 2.927352 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.963728e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.087656e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.503200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.273500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.609430e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.174572e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.091419e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.549311e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2402140.419777 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.253760e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.574099e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.993407e+05 │ │ │ Vprtstp: contraction number = 1.993407e+05 │ │ │ Vnewton: Attempting damping, relres = 0.074788 │ │ │ Vnewton: Attempting damping, relres = 0.535005 │ │ │ Vnewton: Damping accepted, relres = 0.074788 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.478844e-02 │ │ │ Vprtstp: contraction number = 7.478844e-02 │ │ │ Vnewton: Using errtol_s: 179652.345700 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.639932e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.788132e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.540846e+04 │ │ │ Vprtstp: contraction number = 2.540846e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.520223e-03 │ │ │ Vprtstp: contraction number = 1.272954e-01 │ │ │ Vnewton: Using errtol_s: 22868.913120 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.941239e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.994978e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.863220e+03 │ │ │ Vprtstp: contraction number = 3.863220e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.447432e-03 │ │ │ Vprtstp: contraction number = 1.520376e-01 │ │ │ Vnewton: Using errtol_s: 3476.934666 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023001e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.199485e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.609951e+02 │ │ │ Vprtstp: contraction number = 6.609951e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.476530e-04 │ │ │ Vprtstp: contraction number = 1.710982e-01 │ │ │ Vnewton: Using errtol_s: 594.897360 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.053095e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.415448e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.229316e+02 │ │ │ Vprtstp: contraction number = 1.229316e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.605831e-05 │ │ │ Vprtstp: contraction number = 1.859792e-01 │ │ │ Vnewton: Using errtol_s: 110.638524 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081995e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.623420e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.422381e+01 │ │ │ Vprtstp: contraction number = 2.422381e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.075836e-06 │ │ │ Vprtstp: contraction number = 1.970510e-01 │ │ │ Vnewton: Using errtol_s: 21.801431 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112142e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.834435e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.026312e+00 │ │ │ Vprtstp: contraction number = 5.026312e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.883187e-06 │ │ │ Vprtstp: contraction number = 2.074947e-01 │ │ │ Vnewton: Using errtol_s: 4.523681 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141084e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.041235e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.096485e+00 │ │ │ Vprtstp: contraction number = 1.096485e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.108154e-07 │ │ │ Vprtstp: contraction number = 2.181490e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.549979e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.796126e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.686332e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.699282e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -21746,17 +21746,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.937401577775E-02 kT │ │ │ Vpmg_energy: qfEnergy = 4.174168231022E+02 kT │ │ │ Vpmg_energy: dielEnergy = 2.811735250011E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.277000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.927200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -21777,129 +21777,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.276000 │ │ │ +Vacc_SASA: Time elapsed: 3.027943 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.895753e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.124496e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.544100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.063700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.612810e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.158227e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.481366e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.290433e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.497270e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.318896e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.533217e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.519888e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.561684e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.704990e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.588781e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.879989e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.618300e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.057156e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.645549e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.226584e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.674034e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.397858e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.701257e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.594754e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.417350e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.654380e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.469378e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.482426e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -21908,17 +21908,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.911964187079E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.802931672989E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.840794517786E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.550900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.033700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -21964,127 +21964,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00427913 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.278935 │ │ │ +Vacc_SASA: Time elapsed: 3.702363 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.125340e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.279727e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.630300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.475100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.637780e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.172277e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.062768e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.826407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3438753.706105 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.078756e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.852644e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.983675e+05 │ │ │ Vprtstp: contraction number = 2.983675e+05 │ │ │ Vnewton: Attempting damping, relres = 0.078821 │ │ │ Vnewton: Attempting damping, relres = 0.537150 │ │ │ Vnewton: Damping accepted, relres = 0.078821 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.882110e-02 │ │ │ Vprtstp: contraction number = 7.882110e-02 │ │ │ Vnewton: Using errtol_s: 271046.361497 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.115889e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.084841e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.000218e+04 │ │ │ Vprtstp: contraction number = 4.000218e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.049665e-02 │ │ │ Vprtstp: contraction number = 1.331706e-01 │ │ │ Vnewton: Using errtol_s: 36095.399051 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.143426e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.302968e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.428391e+03 │ │ │ Vprtstp: contraction number = 6.428391e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.682686e-03 │ │ │ Vprtstp: contraction number = 1.603069e-01 │ │ │ Vnewton: Using errtol_s: 5786.342471 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.171990e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.520887e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.149080e+03 │ │ │ Vprtstp: contraction number = 1.149080e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.007422e-04 │ │ │ Vprtstp: contraction number = 1.787275e-01 │ │ │ Vnewton: Using errtol_s: 1034.178484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.201572e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.743583e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.202083e+02 │ │ │ Vprtstp: contraction number = 2.202083e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.763359e-05 │ │ │ Vprtstp: contraction number = 1.916378e-01 │ │ │ Vnewton: Using errtol_s: 198.187725 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.230431e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.985943e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.389925e+01 │ │ │ Vprtstp: contraction number = 4.389925e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.148943e-05 │ │ │ Vprtstp: contraction number = 1.993531e-01 │ │ │ Vnewton: Using errtol_s: 39.509333 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.259049e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.167792e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.964795e+00 │ │ │ Vprtstp: contraction number = 8.964795e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.346291e-06 │ │ │ Vprtstp: contraction number = 2.042129e-01 │ │ │ Vnewton: Using errtol_s: 8.068316 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.286531e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.407154e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.877921e+00 │ │ │ Vprtstp: contraction number = 1.877921e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.914947e-07 │ │ │ Vprtstp: contraction number = 2.094773e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.446114e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.689340e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.823066e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.836385e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -22093,17 +22093,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.727005736130E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.988671053842E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.487788509003E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.136000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.899700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -22124,129 +22124,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.971534 │ │ │ +Vacc_SASA: Time elapsed: 6.797079 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.803122e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.155651e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.877700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.713100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.598860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.162743e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.914339e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.744250e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.929989e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.772140e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.965915e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.021100e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.994490e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.223090e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.021928e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.451685e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.049295e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.672726e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.077918e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.871457e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.105301e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.073677e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.133896e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.275007e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.404254e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.633449e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.717498e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.729976e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -22255,15 +22255,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.095882318015E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.878073055635E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.902406349449E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.784400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.456700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ @@ -22311,127 +22311,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0124605 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.970185 │ │ │ +Vacc_SASA: Time elapsed: 6.109876 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.031765e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.689700e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.631800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.422300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.677390e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.097689e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.786402e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.551386e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 5736524.194850 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.802033e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.576641e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.767730e+05 │ │ │ Vprtstp: contraction number = 4.767730e+05 │ │ │ Vnewton: Attempting damping, relres = 0.075286 │ │ │ Vnewton: Attempting damping, relres = 0.535307 │ │ │ Vnewton: Damping accepted, relres = 0.075286 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.528638e-02 │ │ │ Vprtstp: contraction number = 7.528638e-02 │ │ │ Vnewton: Using errtol_s: 431882.117004 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.839083e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.801697e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.255964e+04 │ │ │ Vprtstp: contraction number = 6.255964e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.827684e-03 │ │ │ Vprtstp: contraction number = 1.305373e-01 │ │ │ Vnewton: Using errtol_s: 56376.745785 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.866482e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.011788e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.936134e+03 │ │ │ Vprtstp: contraction number = 9.936134e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.558974e-03 │ │ │ Vprtstp: contraction number = 1.586309e-01 │ │ │ Vnewton: Using errtol_s: 8943.094496 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.895162e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.223618e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.786775e+03 │ │ │ Vprtstp: contraction number = 1.786775e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.803288e-04 │ │ │ Vprtstp: contraction number = 1.798162e-01 │ │ │ Vnewton: Using errtol_s: 1608.113190 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.925779e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.434573e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.548476e+02 │ │ │ Vprtstp: contraction number = 3.548476e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.567220e-05 │ │ │ Vprtstp: contraction number = 1.985960e-01 │ │ │ Vnewton: Using errtol_s: 319.364924 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.954598e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.648044e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.691838e+01 │ │ │ Vprtstp: contraction number = 7.691838e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.206774e-05 │ │ │ Vprtstp: contraction number = 2.167643e-01 │ │ │ Vnewton: Using errtol_s: 69.226906 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.984592e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.872887e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.836013e+01 │ │ │ Vprtstp: contraction number = 1.836013e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.880520e-06 │ │ │ Vprtstp: contraction number = 2.386958e-01 │ │ │ Vnewton: Using errtol_s: 16.524170 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.013460e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010012e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.825966e+00 │ │ │ Vprtstp: contraction number = 4.825966e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.571442e-07 │ │ │ Vprtstp: contraction number = 2.628499e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.486650e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.734918e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.739846e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.752079e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -22440,27 +22440,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.027416628019E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.032769300439E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.516953015159E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.410600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.601800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.071081e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.029699e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:01:52 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 17:12:27 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -22813,129 +22813,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.296713 │ │ │ +Vacc_SASA: Time elapsed: 3.100885 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.983657e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.226462e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.788700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.280100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.644620e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.036098e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.424429e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.658684e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.591170e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.208265e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.011241e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.821560e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.385285e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.782833e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.713244e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.711929e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.997289e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.443345e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.309737e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023587e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.623321e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.198507e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.948733e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.375033e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.752967e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.008319e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.495848e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.507512e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -22944,17 +22944,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.578940273076E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.464055888829E+04 kT │ │ │ Vpmg_energy: dielEnergy = 7.268608527503E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.711600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.297300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -23000,138 +23000,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.246197 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.314330 │ │ │ +Vacc_SASA: Time elapsed: 3.442069 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.276914e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.317603e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.293300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.099610e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.649790e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.462913e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.746524e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.622888e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 7187187.181934 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.910235e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.657629e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.181171e+05 │ │ │ Vprtstp: contraction number = 6.181171e+05 │ │ │ Vnewton: Attempting damping, relres = 0.078820 │ │ │ Vnewton: Attempting damping, relres = 0.536981 │ │ │ Vnewton: Damping accepted, relres = 0.078820 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.881989e-02 │ │ │ Vprtstp: contraction number = 7.881989e-02 │ │ │ Vnewton: Using errtol_s: 566493.329521 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.030361e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.931838e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.371738e+04 │ │ │ Vprtstp: contraction number = 8.371738e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.055690e-02 │ │ │ Vprtstp: contraction number = 1.339370e-01 │ │ │ Vnewton: Using errtol_s: 75874.442084 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060105e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.153296e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.390337e+04 │ │ │ Vprtstp: contraction number = 1.390337e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.741620e-03 │ │ │ Vprtstp: contraction number = 1.649745e-01 │ │ │ Vnewton: Using errtol_s: 12517.346695 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090425e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.386909e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.648048e+03 │ │ │ Vprtstp: contraction number = 2.648048e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.316551e-04 │ │ │ Vprtstp: contraction number = 1.904291e-01 │ │ │ Vnewton: Using errtol_s: 2383.666964 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120275e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.607719e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.422627e+02 │ │ │ Vprtstp: contraction number = 5.422627e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.790546e-05 │ │ │ Vprtstp: contraction number = 2.047472e-01 │ │ │ Vnewton: Using errtol_s: 488.049223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.150109e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.831087e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.184576e+02 │ │ │ Vprtstp: contraction number = 1.184576e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.483378e-05 │ │ │ Vprtstp: contraction number = 2.184475e-01 │ │ │ Vnewton: Using errtol_s: 106.613126 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.179804e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.047252e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.976808e+01 │ │ │ Vprtstp: contraction number = 2.976808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.727649e-06 │ │ │ Vprtstp: contraction number = 2.512947e-01 │ │ │ Vnewton: Using errtol_s: 26.791312 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.210770e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.257371e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.888808e+00 │ │ │ Vprtstp: contraction number = 8.888808e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.113097e-06 │ │ │ Vprtstp: contraction number = 2.986056e-01 │ │ │ Vnewton: Using errtol_s: 8.000035 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.240453e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.476371e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.963970e+00 │ │ │ Vprtstp: contraction number = 2.963970e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.711568e-07 │ │ │ Vprtstp: contraction number = 3.334452e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.890576e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.155759e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.048971e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.065845e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -23140,17 +23140,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.679263931619E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.125861211589E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.606777456856E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.058900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.324900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -23171,129 +23171,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.332818 │ │ │ +Vacc_SASA: Time elapsed: 2.846747 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.975746e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.961016e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.244900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.012400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.640100e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.052270e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.590021e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.724299e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.604865e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.748480e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.641862e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.948261e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.669024e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.133879e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.697832e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.318769e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.725230e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.512114e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.754353e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.710996e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.783242e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.909992e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.811057e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.104946e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.421329e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.671834e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.570069e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.582105e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -23302,17 +23302,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.880126377174E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 3.532414743910E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.025800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.330600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -23358,127 +23358,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.000694544 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.268366 │ │ │ +Vacc_SASA: Time elapsed: 3.171814 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.977039e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.414787e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.772600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.114900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.900920e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.260370e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.160536e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.353228e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 947577.428093 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.181210e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.387777e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.028571e+05 │ │ │ Vprtstp: contraction number = 1.028571e+05 │ │ │ Vnewton: Attempting damping, relres = 0.100178 │ │ │ Vnewton: Attempting damping, relres = 0.546680 │ │ │ Vnewton: Damping accepted, relres = 0.100178 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.001782e-01 │ │ │ Vprtstp: contraction number = 1.001782e-01 │ │ │ Vnewton: Using errtol_s: 94926.584698 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.217036e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.591594e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.470559e+04 │ │ │ Vprtstp: contraction number = 1.470559e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.405726e-02 │ │ │ Vprtstp: contraction number = 1.403226e-01 │ │ │ Vnewton: Using errtol_s: 13320.343474 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.244309e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.760026e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.349875e+03 │ │ │ Vprtstp: contraction number = 2.349875e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.232971e-03 │ │ │ Vprtstp: contraction number = 1.588482e-01 │ │ │ Vnewton: Using errtol_s: 2115.913123 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273337e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.934501e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.041926e+02 │ │ │ Vprtstp: contraction number = 4.041926e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.839085e-04 │ │ │ Vprtstp: contraction number = 1.719272e-01 │ │ │ Vnewton: Using errtol_s: 363.783073 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.300659e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.096670e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.386262e+01 │ │ │ Vprtstp: contraction number = 7.386262e+01 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.015424e-05 │ │ │ Vprtstp: contraction number = 1.827368e-01 │ │ │ Vnewton: Using errtol_s: 66.476570 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.328099e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.257163e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.423266e+01 │ │ │ Vprtstp: contraction number = 1.423266e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.351805e-05 │ │ │ Vprtstp: contraction number = 1.926905e-01 │ │ │ Vnewton: Using errtol_s: 12.809401 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.355738e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.412345e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.877145e+00 │ │ │ Vprtstp: contraction number = 2.877145e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.732685e-06 │ │ │ Vprtstp: contraction number = 2.021508e-01 │ │ │ Vnewton: Using errtol_s: 2.589431 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.384820e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.565598e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.073349e-01 │ │ │ Vprtstp: contraction number = 6.073349e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.768409e-07 │ │ │ Vprtstp: contraction number = 2.110894e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.441148e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.711237e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.349086e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.363237e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -23487,17 +23487,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.348045314741E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 3.080172074466E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.889000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.493700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -23518,129 +23518,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.077700 │ │ │ +Vacc_SASA: Time elapsed: 6.554037 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.906670e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.128648e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.619200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.604200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.649120e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.192854e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.921880e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.797594e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.937826e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.825144e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.973735e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.054834e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.001902e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.254010e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.029111e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.458839e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.056381e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.666389e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.085816e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.862974e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.113156e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.063986e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.140455e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.295050e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.403342e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.634287e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.710244e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.723534e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -23649,17 +23649,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.727728107537E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.464487511349E+04 kT │ │ │ Vpmg_energy: dielEnergy = 7.268391520583E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.536600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.097400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -23705,138 +23705,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.239586 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.038331 │ │ │ +Vacc_SASA: Time elapsed: 7.380116 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.141423e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.371799e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.591000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.452200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.600300e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.286483e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.803010e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.617124e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8056801.731105 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.819146e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.646923e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.019948e+05 │ │ │ Vprtstp: contraction number = 7.019948e+05 │ │ │ Vnewton: Attempting damping, relres = 0.080001 │ │ │ Vnewton: Attempting damping, relres = 0.537427 │ │ │ Vnewton: Damping accepted, relres = 0.080001 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.000142e-02 │ │ │ Vprtstp: contraction number = 8.000142e-02 │ │ │ Vnewton: Using errtol_s: 644555.552257 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.856233e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.887731e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.545628e+04 │ │ │ Vprtstp: contraction number = 9.545628e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.074028e-02 │ │ │ Vprtstp: contraction number = 1.342512e-01 │ │ │ Vnewton: Using errtol_s: 86532.331514 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.883569e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.146065e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.576216e+04 │ │ │ Vprtstp: contraction number = 1.576216e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.761379e-03 │ │ │ Vprtstp: contraction number = 1.639975e-01 │ │ │ Vnewton: Using errtol_s: 14191.084898 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.909649e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.378562e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.960538e+03 │ │ │ Vprtstp: contraction number = 2.960538e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.307659e-04 │ │ │ Vprtstp: contraction number = 1.877880e-01 │ │ │ Vnewton: Using errtol_s: 2664.915408 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.937047e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.586211e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.967294e+02 │ │ │ Vprtstp: contraction number = 5.967294e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.666049e-05 │ │ │ Vprtstp: contraction number = 2.015337e-01 │ │ │ Vnewton: Using errtol_s: 537.070343 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.964404e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.794092e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.275865e+02 │ │ │ Vprtstp: contraction number = 1.275865e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.425245e-05 │ │ │ Vprtstp: contraction number = 2.138065e-01 │ │ │ Vnewton: Using errtol_s: 114.829153 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.992681e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001448e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.141071e+01 │ │ │ Vprtstp: contraction number = 3.141071e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.508796e-06 │ │ │ Vprtstp: contraction number = 2.461890e-01 │ │ │ Vnewton: Using errtol_s: 28.269675 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.019256e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023101e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.244202e+00 │ │ │ Vprtstp: contraction number = 9.244202e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.032654e-06 │ │ │ Vprtstp: contraction number = 2.943044e-01 │ │ │ Vnewton: Using errtol_s: 8.319891 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.046614e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.044390e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.069585e+00 │ │ │ Vprtstp: contraction number = 3.069585e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.428937e-07 │ │ │ Vprtstp: contraction number = 3.320508e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.647661e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.885577e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.026796e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.041336e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -23845,27 +23845,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.898743294947E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.125893253171E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.606732677067E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.941000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.532000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.102536e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.064890e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:02:21 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 17:35:07 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -24218,129 +24218,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.320359 │ │ │ +Vacc_SASA: Time elapsed: 3.027512 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.979957e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.218307e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.797400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.814100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.646710e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.053041e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.426583e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.649766e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.586979e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.122458e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.980434e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.703688e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.275093e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.403685e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.573545e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.140366e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.866827e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.893860e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.165186e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.654784e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.463247e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.136683e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.762048e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.306838e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.558835e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.817217e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.403758e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.415335e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24349,17 +24349,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.439783180216E-02 kT │ │ │ Vpmg_energy: qfEnergy = 2.890574221449E+02 kT │ │ │ Vpmg_energy: dielEnergy = 1.267284045292E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.563500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.992300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -24405,127 +24405,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00201979 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.252928 │ │ │ +Vacc_SASA: Time elapsed: 3.054361 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.968548e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.214755e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.514900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.547400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.606400e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.118675e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.225908e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.515074e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1602777.342155 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.383651e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.540973e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.455767e+05 │ │ │ Vprtstp: contraction number = 1.455767e+05 │ │ │ Vnewton: Attempting damping, relres = 0.082108 │ │ │ Vnewton: Attempting damping, relres = 0.538752 │ │ │ Vnewton: Damping accepted, relres = 0.082108 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.210786e-02 │ │ │ Vprtstp: contraction number = 8.210786e-02 │ │ │ Vnewton: Using errtol_s: 131600.616465 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.778778e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.773139e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.947215e+04 │ │ │ Vprtstp: contraction number = 1.947215e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.093564e-02 │ │ │ Vprtstp: contraction number = 1.331863e-01 │ │ │ Vnewton: Using errtol_s: 17527.393818 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007773e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.979342e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.986234e+03 │ │ │ Vprtstp: contraction number = 2.986234e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.676878e-03 │ │ │ Vprtstp: contraction number = 1.533407e-01 │ │ │ Vnewton: Using errtol_s: 2687.662365 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.037671e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.181044e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.993905e+02 │ │ │ Vprtstp: contraction number = 4.993905e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.804220e-04 │ │ │ Vprtstp: contraction number = 1.672286e-01 │ │ │ Vnewton: Using errtol_s: 449.454038 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066470e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.387261e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.039598e+01 │ │ │ Vprtstp: contraction number = 9.039598e+01 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.075969e-05 │ │ │ Vprtstp: contraction number = 1.810118e-01 │ │ │ Vnewton: Using errtol_s: 81.356480 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.096515e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.592599e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.755931e+01 │ │ │ Vprtstp: contraction number = 1.755931e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.860000e-06 │ │ │ Vprtstp: contraction number = 1.942486e-01 │ │ │ Vnewton: Using errtol_s: 15.803384 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126396e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.800406e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.630601e+00 │ │ │ Vprtstp: contraction number = 3.630601e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.038674e-06 │ │ │ Vprtstp: contraction number = 2.067621e-01 │ │ │ Vnewton: Using errtol_s: 3.267541 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155187e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.012736e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.904977e-01 │ │ │ Vprtstp: contraction number = 7.904977e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.438845e-07 │ │ │ Vprtstp: contraction number = 2.177319e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.561524e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.808581e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.693681e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.706121e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24534,17 +24534,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.337843047091E-02 kT │ │ │ Vpmg_energy: qfEnergy = 2.452499065480E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.155272443356E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.298300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.344400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -24565,129 +24565,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.259349 │ │ │ +Vacc_SASA: Time elapsed: 3.309875 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.893420e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.396242e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.528200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.516500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.598500e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.177559e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.495636e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.266231e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.511194e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.291801e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.548440e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.488129e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.575787e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.647277e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.603173e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.817237e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.631697e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.988633e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.658923e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.165875e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.685637e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.337564e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.714131e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.512322e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.390244e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.626087e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.395608e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.408449e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24696,17 +24696,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.047547930931E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.326714299389E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.630706107593E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.508800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.706600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -24752,138 +24752,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.208695 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.257774 │ │ │ +Vacc_SASA: Time elapsed: 2.845297 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.224535e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.335166e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.605600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.449500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.603180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.117279e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.083533e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.717903e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6744887.867090 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.098849e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.743100e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.873341e+05 │ │ │ Vprtstp: contraction number = 5.873341e+05 │ │ │ Vnewton: Attempting damping, relres = 0.079798 │ │ │ Vnewton: Attempting damping, relres = 0.537526 │ │ │ Vnewton: Damping accepted, relres = 0.079798 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.979817e-02 │ │ │ Vprtstp: contraction number = 7.979817e-02 │ │ │ Vnewton: Using errtol_s: 538229.715979 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.134791e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.968346e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.003940e+04 │ │ │ Vprtstp: contraction number = 8.003940e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.075173e-02 │ │ │ Vprtstp: contraction number = 1.347366e-01 │ │ │ Vnewton: Using errtol_s: 72519.230886 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.162328e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.177306e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.324771e+04 │ │ │ Vprtstp: contraction number = 1.324771e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.768162e-03 │ │ │ Vprtstp: contraction number = 1.644537e-01 │ │ │ Vnewton: Using errtol_s: 11926.055102 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.191013e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.383629e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.493439e+03 │ │ │ Vprtstp: contraction number = 2.493439e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.328041e-04 │ │ │ Vprtstp: contraction number = 1.882203e-01 │ │ │ Vnewton: Using errtol_s: 2244.726103 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.217202e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.587997e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.093161e+02 │ │ │ Vprtstp: contraction number = 5.093161e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.796477e-05 │ │ │ Vprtstp: contraction number = 2.042186e-01 │ │ │ Vnewton: Using errtol_s: 458.414752 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.245645e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.791158e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115992e+02 │ │ │ Vprtstp: contraction number = 1.115992e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.489139e-05 │ │ │ Vprtstp: contraction number = 2.191046e-01 │ │ │ Vnewton: Using errtol_s: 100.440778 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273094e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.997654e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.141695e+01 │ │ │ Vprtstp: contraction number = 3.141695e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.192112e-06 │ │ │ Vprtstp: contraction number = 2.815124e-01 │ │ │ Vnewton: Using errtol_s: 28.275326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.300749e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.204393e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.143181e+01 │ │ │ Vprtstp: contraction number = 1.143181e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.525422e-06 │ │ │ Vprtstp: contraction number = 3.638791e-01 │ │ │ Vnewton: Using errtol_s: 10.288800 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.327772e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.407278e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.900145e+00 │ │ │ Vprtstp: contraction number = 4.900145e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 6.538480e-07 │ │ │ Vprtstp: contraction number = 4.286342e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.657859e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.898304e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.875384e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.887551e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24892,15 +24892,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.068941239771E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.027128342703E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.130929384938E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.908000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.548200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ @@ -24923,129 +24923,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.977906 │ │ │ +Vacc_SASA: Time elapsed: 6.308878 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.778370e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.595211e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.633700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.486200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.610330e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.090011e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.953904e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.681327e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.969539e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.705488e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.007816e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.927024e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.036348e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.124437e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.063685e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.323225e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.091116e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.519866e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.118531e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.711259e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.147185e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.902516e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.174502e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.097609e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.417070e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.649098e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.596420e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.608260e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -25054,17 +25054,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.318490670487E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.359627523071E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.777157121148E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.535700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.709100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -25110,138 +25110,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.208525 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.971964 │ │ │ +Vacc_SASA: Time elapsed: 6.559492 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.107696e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.217545e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.572100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.517200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.643320e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.048603e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.833808e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.371874e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8257970.099902 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.849269e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.395978e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.174738e+05 │ │ │ Vprtstp: contraction number = 7.174738e+05 │ │ │ Vnewton: Attempting damping, relres = 0.079654 │ │ │ Vnewton: Attempting damping, relres = 0.537366 │ │ │ Vnewton: Damping accepted, relres = 0.079654 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.965353e-02 │ │ │ Vprtstp: contraction number = 7.965353e-02 │ │ │ Vnewton: Using errtol_s: 657776.459467 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.885142e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.611470e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.738355e+04 │ │ │ Vprtstp: contraction number = 9.738355e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.068030e-02 │ │ │ Vprtstp: contraction number = 1.340844e-01 │ │ │ Vnewton: Using errtol_s: 88197.583593 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.912626e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.819904e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.590859e+04 │ │ │ Vprtstp: contraction number = 1.590859e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.734478e-03 │ │ │ Vprtstp: contraction number = 1.623998e-01 │ │ │ Vnewton: Using errtol_s: 14323.269837 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.939871e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.026837e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.927974e+03 │ │ │ Vprtstp: contraction number = 2.927974e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.191803e-04 │ │ │ Vprtstp: contraction number = 1.840209e-01 │ │ │ Vnewton: Using errtol_s: 2635.781086 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.967252e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.238774e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.843569e+02 │ │ │ Vprtstp: contraction number = 5.843569e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.369066e-05 │ │ │ Vprtstp: contraction number = 1.995445e-01 │ │ │ Vnewton: Using errtol_s: 525.955563 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.994675e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.459532e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.235877e+02 │ │ │ Vprtstp: contraction number = 1.235877e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.346947e-05 │ │ │ Vprtstp: contraction number = 2.114827e-01 │ │ │ Vnewton: Using errtol_s: 111.230501 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.020840e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.676877e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.351690e+01 │ │ │ Vprtstp: contraction number = 3.351690e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.652870e-06 │ │ │ Vprtstp: contraction number = 2.711962e-01 │ │ │ Vnewton: Using errtol_s: 30.165292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.049579e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.881815e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.181991e+01 │ │ │ Vprtstp: contraction number = 1.181991e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.288222e-06 │ │ │ Vprtstp: contraction number = 3.526602e-01 │ │ │ Vnewton: Using errtol_s: 10.638098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.077013e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010101e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.017523e+00 │ │ │ Vprtstp: contraction number = 5.017523e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.468381e-07 │ │ │ Vprtstp: contraction number = 4.244906e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.646579e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.893084e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.928468e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.939991e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -25250,27 +25250,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.367295559146E+00 kT │ │ │ Vpmg_energy: qfEnergy = 1.051945297594E+05 kT │ │ │ Vpmg_energy: dielEnergy = 5.247887391423E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.941900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.850600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.132769e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.030486e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:02:50 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 17:57:04 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -25623,129 +25623,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.262750 │ │ │ +Vacc_SASA: Time elapsed: 3.052634 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.911446e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.208375e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.611200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.055000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.583780e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.036157e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.337225e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.647796e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.496257e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.170194e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.895496e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.729801e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.184148e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.480397e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.471998e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.262035e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.759267e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.287467e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.060121e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022210e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.348268e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.213402e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.636866e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.403195e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.527240e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.773144e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.526945e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.539128e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -25754,15 +25754,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.504309500280E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.755208046486E+03 kT │ │ │ Vpmg_energy: dielEnergy = 8.724652508101E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.518500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.248300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -25810,127 +25810,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00330279 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.242137 │ │ │ +Vacc_SASA: Time elapsed: 3.116460 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.036648e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.645855e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.568200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.929200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.612100e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.132326e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.175278e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.643503e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2662068.021804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.337640e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.670447e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.456208e+05 │ │ │ Vprtstp: contraction number = 2.456208e+05 │ │ │ Vnewton: Attempting damping, relres = 0.083386 │ │ │ Vnewton: Attempting damping, relres = 0.539586 │ │ │ Vnewton: Damping accepted, relres = 0.083386 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.338571e-02 │ │ │ Vprtstp: contraction number = 8.338571e-02 │ │ │ Vnewton: Using errtol_s: 221978.424581 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.744865e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.903102e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.405567e+04 │ │ │ Vprtstp: contraction number = 3.405567e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.151500e-02 │ │ │ Vprtstp: contraction number = 1.380932e-01 │ │ │ Vnewton: Using errtol_s: 30653.716000 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004521e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.114629e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.435916e+03 │ │ │ Vprtstp: contraction number = 5.435916e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.837816e-03 │ │ │ Vprtstp: contraction number = 1.596019e-01 │ │ │ Vnewton: Using errtol_s: 4892.390079 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033219e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.320988e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.557902e+02 │ │ │ Vprtstp: contraction number = 9.557902e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.231381e-04 │ │ │ Vprtstp: contraction number = 1.758273e-01 │ │ │ Vnewton: Using errtol_s: 860.215698 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.063152e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.531168e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.830694e+02 │ │ │ Vprtstp: contraction number = 1.830694e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.189280e-05 │ │ │ Vprtstp: contraction number = 1.915367e-01 │ │ │ Vnewton: Using errtol_s: 164.762841 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.091883e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.751970e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.747370e+01 │ │ │ Vprtstp: contraction number = 3.747370e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.266923e-05 │ │ │ Vprtstp: contraction number = 2.046964e-01 │ │ │ Vnewton: Using errtol_s: 33.726360 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121710e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.969593e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.392089e+00 │ │ │ Vprtstp: contraction number = 8.392089e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.837224e-06 │ │ │ Vprtstp: contraction number = 2.239460e-01 │ │ │ Vnewton: Using errtol_s: 7.552883 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.151555e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.203041e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.064121e+00 │ │ │ Vprtstp: contraction number = 2.064121e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.978444e-07 │ │ │ Vprtstp: contraction number = 2.459603e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.563851e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.810746e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.784744e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.797531e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -25939,17 +25939,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.015842175556E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.339968414661E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.688675679646E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.431500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.803900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -25970,129 +25970,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.263658 │ │ │ +Vacc_SASA: Time elapsed: 3.422044 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.913562e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.689300e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.550300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.763600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.140730e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.107078e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.497902e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.488244e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.528538e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.513399e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.572959e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.719477e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.600183e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.893540e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.627522e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.075537e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.654969e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.255470e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682367e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.446870e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.709756e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.666448e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.737021e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.893688e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.606181e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.890697e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.592916e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.605477e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -26101,17 +26101,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.301986990892E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 1.769795919653E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.526000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.293000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -26157,127 +26157,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0030506 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.263118 │ │ │ +Vacc_SASA: Time elapsed: 3.405519 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.909418e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.807985e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.488800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.169800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.604450e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.160192e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.075615e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.142552e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1183078.697095 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.091460e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.166444e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.216317e+05 │ │ │ Vprtstp: contraction number = 1.216317e+05 │ │ │ Vnewton: Attempting damping, relres = 0.092815 │ │ │ Vnewton: Attempting damping, relres = 0.543699 │ │ │ Vnewton: Damping accepted, relres = 0.092815 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.281548e-02 │ │ │ Vprtstp: contraction number = 9.281548e-02 │ │ │ Vnewton: Using errtol_s: 109808.011526 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.127451e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.334125e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.637169e+04 │ │ │ Vprtstp: contraction number = 1.637169e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.245819e-02 │ │ │ Vprtstp: contraction number = 1.342253e-01 │ │ │ Vnewton: Using errtol_s: 14739.016153 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.154760e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.489228e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.481814e+03 │ │ │ Vprtstp: contraction number = 2.481814e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.888035e-03 │ │ │ Vprtstp: contraction number = 1.515497e-01 │ │ │ Vnewton: Using errtol_s: 2233.693882 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.182057e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.682072e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.090266e+02 │ │ │ Vprtstp: contraction number = 4.090266e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.111589e-04 │ │ │ Vprtstp: contraction number = 1.648057e-01 │ │ │ Vnewton: Using errtol_s: 368.125449 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.209310e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.844265e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.284721e+01 │ │ │ Vprtstp: contraction number = 7.284721e+01 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.541690e-05 │ │ │ Vprtstp: contraction number = 1.780984e-01 │ │ │ Vnewton: Using errtol_s: 65.562559 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.236672e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.988544e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.403461e+01 │ │ │ Vprtstp: contraction number = 1.403461e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.067651e-05 │ │ │ Vprtstp: contraction number = 1.926581e-01 │ │ │ Vnewton: Using errtol_s: 12.631156 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.264001e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.127482e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.928656e+00 │ │ │ Vprtstp: contraction number = 2.928656e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.227908e-06 │ │ │ Vprtstp: contraction number = 2.086737e-01 │ │ │ Vnewton: Using errtol_s: 2.635791 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.292302e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.272838e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.633899e-01 │ │ │ Vprtstp: contraction number = 6.633899e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.046587e-07 │ │ │ Vprtstp: contraction number = 2.265168e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.382263e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.617993e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.267241e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.280190e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -26286,17 +26286,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.998704747523E-02 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 1.756383859488E-01 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.311800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.291400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -26317,129 +26317,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.956528 │ │ │ +Vacc_SASA: Time elapsed: 7.192714 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.744091e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.570855e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.491100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.098000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.580960e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.066694e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.914544e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.507932e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.929932e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.535213e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.967193e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.800414e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.994510e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.055100e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.023320e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.271197e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.050650e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.483235e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.077991e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.681530e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.106678e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.893079e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.134066e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.090705e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.404750e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.627542e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.768874e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.780579e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -26448,17 +26448,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.337014891966E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.757508966493E+03 kT │ │ │ Vpmg_energy: dielEnergy = 8.741342460079E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.564200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.332900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -26504,127 +26504,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0127136 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.971732 │ │ │ +Vacc_SASA: Time elapsed: 7.234335 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.922060e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.973704e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.525700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.294000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.626420e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.200141e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.773567e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.380016e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3725039.964738 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.789518e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.406887e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.491722e+05 │ │ │ Vprtstp: contraction number = 3.491722e+05 │ │ │ Vnewton: Attempting damping, relres = 0.084831 │ │ │ Vnewton: Attempting damping, relres = 0.540016 │ │ │ Vnewton: Damping accepted, relres = 0.084831 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.483081e-02 │ │ │ Vprtstp: contraction number = 8.483081e-02 │ │ │ Vnewton: Using errtol_s: 315998.155182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.826577e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.631868e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.811279e+04 │ │ │ Vprtstp: contraction number = 4.811279e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.162816e-02 │ │ │ Vprtstp: contraction number = 1.370747e-01 │ │ │ Vnewton: Using errtol_s: 43315.357930 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.858303e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.849928e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.589005e+03 │ │ │ Vprtstp: contraction number = 7.589005e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.833655e-03 │ │ │ Vprtstp: contraction number = 1.576909e-01 │ │ │ Vnewton: Using errtol_s: 6830.439897 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.885630e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.069645e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.299757e+03 │ │ │ Vprtstp: contraction number = 1.299757e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.140354e-04 │ │ │ Vprtstp: contraction number = 1.712619e-01 │ │ │ Vnewton: Using errtol_s: 1169.794412 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.912889e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.292014e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.408127e+02 │ │ │ Vprtstp: contraction number = 2.408127e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.818247e-05 │ │ │ Vprtstp: contraction number = 1.852736e-01 │ │ │ Vnewton: Using errtol_s: 216.732029 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.941387e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.512746e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.749053e+01 │ │ │ Vprtstp: contraction number = 4.749053e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.147411e-05 │ │ │ Vprtstp: contraction number = 1.972090e-01 │ │ │ Vnewton: Using errtol_s: 42.741516 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.969978e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.740185e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.028045e+01 │ │ │ Vprtstp: contraction number = 1.028045e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.483842e-06 │ │ │ Vprtstp: contraction number = 2.164736e-01 │ │ │ Vnewton: Using errtol_s: 9.252409 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.997275e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.981917e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.462555e+00 │ │ │ Vprtstp: contraction number = 2.462555e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.949733e-07 │ │ │ Vprtstp: contraction number = 2.395375e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.450209e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.689068e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.797297e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.810500e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -26633,27 +26633,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.090781383417E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.340160252589E+04 kT │ │ │ Vpmg_energy: dielEnergy = 6.690276945765E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.245300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.888900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.051637e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.018271e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:03:19 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 18:18:47 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -27006,129 +27006,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.290620 │ │ │ +Vacc_SASA: Time elapsed: 2.859122 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.919345e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.134705e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.637000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.492200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.627370e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.385010e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.353481e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.957299e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.518124e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.543694e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.961428e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.147294e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.246742e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.987985e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.564184e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.791591e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.864872e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.522273e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.168494e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.030092e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.466906e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.198068e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.765911e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.384033e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.638363e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.890567e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.495321e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.510577e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -27137,17 +27137,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.018818357311E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 1.967662971668E+00 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.555400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.342500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -27193,127 +27193,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.000195471 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.245643 │ │ │ +Vacc_SASA: Time elapsed: 3.084145 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.913499e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.289838e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.500300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.952600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.608040e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.231457e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.178010e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612080e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1020818.402503 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.339006e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.637420e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.825199e+04 │ │ │ Vprtstp: contraction number = 9.825199e+04 │ │ │ Vnewton: Attempting damping, relres = 0.087060 │ │ │ Vnewton: Attempting damping, relres = 0.541082 │ │ │ Vnewton: Damping accepted, relres = 0.087060 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.706019e-02 │ │ │ Vprtstp: contraction number = 8.706019e-02 │ │ │ Vnewton: Using errtol_s: 88872.645048 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.733166e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.821042e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.300904e+04 │ │ │ Vprtstp: contraction number = 1.300904e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.147153e-02 │ │ │ Vprtstp: contraction number = 1.317655e-01 │ │ │ Vnewton: Using errtol_s: 11710.349561 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003053e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.990037e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.956340e+03 │ │ │ Vprtstp: contraction number = 1.956340e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.724829e-03 │ │ │ Vprtstp: contraction number = 1.503573e-01 │ │ │ Vnewton: Using errtol_s: 1760.737119 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031621e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.171229e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.204124e+02 │ │ │ Vprtstp: contraction number = 3.204124e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.824911e-04 │ │ │ Vprtstp: contraction number = 1.637792e-01 │ │ │ Vnewton: Using errtol_s: 288.372159 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062451e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.378822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.671470e+01 │ │ │ Vprtstp: contraction number = 5.671470e+01 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.000230e-05 │ │ │ Vprtstp: contraction number = 1.770048e-01 │ │ │ Vnewton: Using errtol_s: 51.043267 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.094011e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.580777e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.076760e+01 │ │ │ Vprtstp: contraction number = 1.076760e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.493208e-06 │ │ │ Vprtstp: contraction number = 1.898554e-01 │ │ │ Vnewton: Using errtol_s: 9.690841 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.124523e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.779242e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.170593e+00 │ │ │ Vprtstp: contraction number = 2.170593e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.913693e-06 │ │ │ Vprtstp: contraction number = 2.015855e-01 │ │ │ Vnewton: Using errtol_s: 1.953533 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155063e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.984168e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.603679e-01 │ │ │ Vprtstp: contraction number = 4.603679e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.058813e-07 │ │ │ Vprtstp: contraction number = 2.120932e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.598081e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.843078e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.555911e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.569813e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -27322,17 +27322,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.464558654899E-03 kT │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ Vpmg_energy: dielEnergy = 1.022303323465E+00 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.741900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.940300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -27353,129 +27353,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.830108 │ │ │ +Vacc_SASA: Time elapsed: 3.055396 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.473352e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.279757e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.100600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.183800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.248430e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.282132e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457767e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.225157e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.475774e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.251127e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.511358e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.458891e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.538636e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.628630e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.566014e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.816832e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.596154e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.006431e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.625232e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.198208e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.652527e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.391301e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.681491e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.575607e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.439263e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.734231e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.510674e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.524423e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -27484,17 +27484,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.242044176092E+00 kT │ │ │ Vpmg_energy: qfEnergy = 9.791375610764E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.948343269624E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.519600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.790100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -27540,127 +27540,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0380116 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.800230 │ │ │ +Vacc_SASA: Time elapsed: 3.038580 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.732698e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.683135e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.931700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.329100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.118620e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.152887e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.005510e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.795923e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6064250.335946 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.023638e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.823128e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.053112e+05 │ │ │ Vprtstp: contraction number = 5.053112e+05 │ │ │ Vnewton: Attempting damping, relres = 0.075900 │ │ │ Vnewton: Attempting damping, relres = 0.535745 │ │ │ Vnewton: Damping accepted, relres = 0.075900 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.590004e-02 │ │ │ Vprtstp: contraction number = 7.590004e-02 │ │ │ Vnewton: Using errtol_s: 460276.842537 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.060076e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.068854e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.689298e+04 │ │ │ Vprtstp: contraction number = 6.689298e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 9.982301e-03 │ │ │ Vprtstp: contraction number = 1.315191e-01 │ │ │ Vnewton: Using errtol_s: 60535.174769 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.086207e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.285864e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.083906e+04 │ │ │ Vprtstp: contraction number = 1.083906e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.608994e-03 │ │ │ Vprtstp: contraction number = 1.611846e-01 │ │ │ Vnewton: Using errtol_s: 9757.339468 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.114760e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.510081e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.965105e+03 │ │ │ Vprtstp: contraction number = 1.965105e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.916449e-04 │ │ │ Vprtstp: contraction number = 1.812592e-01 │ │ │ Vnewton: Using errtol_s: 1768.607683 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.142933e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.754591e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.700829e+02 │ │ │ Vprtstp: contraction number = 3.700829e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.492457e-05 │ │ │ Vprtstp: contraction number = 1.883269e-01 │ │ │ Vnewton: Using errtol_s: 333.076316 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.171290e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.982711e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.574998e+01 │ │ │ Vprtstp: contraction number = 6.574998e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.758048e-06 │ │ │ Vprtstp: contraction number = 1.776627e-01 │ │ │ Vnewton: Using errtol_s: 59.175244 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.198597e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.204961e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.293454e+01 │ │ │ Vprtstp: contraction number = 1.293454e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.919626e-06 │ │ │ Vprtstp: contraction number = 1.967224e-01 │ │ │ Vnewton: Using errtol_s: 11.641095 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.227060e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.411590e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.078562e+00 │ │ │ Vprtstp: contraction number = 3.078562e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.568945e-07 │ │ │ Vprtstp: contraction number = 2.380122e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.422517e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.701572e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.803929e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.816749e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -27669,17 +27669,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.156457994238E+00 kT │ │ │ Vpmg_energy: qfEnergy = 7.809362574174E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.917972751481E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.477400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.982900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -27700,129 +27700,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 4.005886 │ │ │ +Vacc_SASA: Time elapsed: 6.161831 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.836375e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.636900e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.077700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.029700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.946170e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.097342e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.760266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.688668e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.777266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.712705e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.814484e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.929086e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.842275e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.117811e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.872228e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.307940e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.899496e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.497760e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.926828e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.691613e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.955671e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.881532e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.983035e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.073610e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.439332e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.697146e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.561018e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.572912e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -27831,17 +27831,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.221311774650E+00 kT │ │ │ Vpmg_energy: qfEnergy = 9.790964149822E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.950799444075E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.410500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.780500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -27887,127 +27887,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0371815 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 3.936208 │ │ │ +Vacc_SASA: Time elapsed: 6.483383 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.993110e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.193921e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.850800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.314400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.952880e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.096732e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.532399e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.343819e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 6913573.322497 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.552548e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.367778e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.778762e+05 │ │ │ Vprtstp: contraction number = 5.778762e+05 │ │ │ Vnewton: Attempting damping, relres = 0.075994 │ │ │ Vnewton: Attempting damping, relres = 0.535763 │ │ │ Vnewton: Damping accepted, relres = 0.075994 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.599436e-02 │ │ │ Vprtstp: contraction number = 7.599436e-02 │ │ │ Vnewton: Using errtol_s: 525392.598640 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.588825e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.581442e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.670486e+04 │ │ │ Vprtstp: contraction number = 7.670486e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.002063e-02 │ │ │ Vprtstp: contraction number = 1.318602e-01 │ │ │ Vnewton: Using errtol_s: 69278.365005 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.616396e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.781793e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.241801e+04 │ │ │ Vprtstp: contraction number = 1.241801e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.616751e-03 │ │ │ Vprtstp: contraction number = 1.613422e-01 │ │ │ Vnewton: Using errtol_s: 11177.524829 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.643681e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.982822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.271971e+03 │ │ │ Vprtstp: contraction number = 2.271971e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.957685e-04 │ │ │ Vprtstp: contraction number = 1.829401e-01 │ │ │ Vnewton: Using errtol_s: 2044.817292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.673443e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.182846e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.414335e+02 │ │ │ Vprtstp: contraction number = 4.414335e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.746599e-05 │ │ │ Vprtstp: contraction number = 1.942938e-01 │ │ │ Vnewton: Using errtol_s: 397.295336 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.700819e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.385563e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.690501e+01 │ │ │ Vprtstp: contraction number = 8.690501e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.131327e-05 │ │ │ Vprtstp: contraction number = 1.968689e-01 │ │ │ Vnewton: Using errtol_s: 78.215105 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.728385e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.587242e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.879618e+01 │ │ │ Vprtstp: contraction number = 1.879618e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.446866e-06 │ │ │ Vprtstp: contraction number = 2.162828e-01 │ │ │ Vnewton: Using errtol_s: 16.916585 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.755741e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.791467e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.583329e+00 │ │ │ Vprtstp: contraction number = 4.583329e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.966529e-07 │ │ │ Vprtstp: contraction number = 2.438437e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.459543e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.725454e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.632862e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.644758e+02 │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -28016,27 +28016,27 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.139698158758E+00 kT │ │ │ Vpmg_energy: qfEnergy = 7.809316280828E+04 kT │ │ │ Vpmg_energy: dielEnergy = 3.918099666156E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.553300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.162000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.808917e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 9.981470e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:03:46 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 18:40:03 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ @@ -28389,129 +28389,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.822279 │ │ │ +Vacc_SASA: Time elapsed: 3.018606 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.440541e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.110805e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.732600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.561800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.051710e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.026617e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.867509e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.498699e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.072563e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.870522e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.503264e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.636729e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.981154e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.338159e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.289819e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.018996e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.587735e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.705024e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.915372e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.370167e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.221513e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111699e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.605659e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.284624e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.074147e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.353532e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.386706e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.398330e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -28520,15 +28520,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.085287424313E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.020959449622E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.003436009271E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.544500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.783800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -28576,127 +28576,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0111702 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.270539 │ │ │ +Vacc_SASA: Time elapsed: 2.933063 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.126957e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.200993e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.666500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.391600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.612880e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.142959e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.344972e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.496841e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2843800.208997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.506566e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.520991e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.648041e+05 │ │ │ Vprtstp: contraction number = 2.648041e+05 │ │ │ Vnewton: Attempting damping, relres = 0.084229 │ │ │ Vnewton: Attempting damping, relres = 0.539926 │ │ │ Vnewton: Damping accepted, relres = 0.084229 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.422893e-02 │ │ │ Vprtstp: contraction number = 8.422893e-02 │ │ │ Vnewton: Using errtol_s: 239530.237257 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.901344e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.741640e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.601789e+04 │ │ │ Vprtstp: contraction number = 3.601789e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.140061e-02 │ │ │ Vprtstp: contraction number = 1.353527e-01 │ │ │ Vnewton: Using errtol_s: 32421.054732 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019989e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.952747e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.547762e+03 │ │ │ Vprtstp: contraction number = 5.547762e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.755765e-03 │ │ │ Vprtstp: contraction number = 1.540062e-01 │ │ │ Vnewton: Using errtol_s: 4993.043762 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049886e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.157732e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.234937e+02 │ │ │ Vprtstp: contraction number = 9.234937e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.922661e-04 │ │ │ Vprtstp: contraction number = 1.664609e-01 │ │ │ Vnewton: Using errtol_s: 831.146494 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.080238e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.361429e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.647026e+02 │ │ │ Vprtstp: contraction number = 1.647026e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.212477e-05 │ │ │ Vprtstp: contraction number = 1.783469e-01 │ │ │ Vnewton: Using errtol_s: 148.232430 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111101e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.568709e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.095227e+01 │ │ │ Vprtstp: contraction number = 3.095227e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.795714e-06 │ │ │ Vprtstp: contraction number = 1.879282e-01 │ │ │ Vnewton: Using errtol_s: 27.857053 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140872e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.774923e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.500935e+00 │ │ │ Vprtstp: contraction number = 6.500935e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.057403e-06 │ │ │ Vprtstp: contraction number = 2.100309e-01 │ │ │ Vnewton: Using errtol_s: 5.850843 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.170582e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.985959e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.529139e+00 │ │ │ Vprtstp: contraction number = 1.529139e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.839389e-07 │ │ │ Vprtstp: contraction number = 2.352183e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.591721e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.840041e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.681964e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.694657e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -28705,17 +28705,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.004865379330E-01 kT │ │ │ Vpmg_energy: qfEnergy = 1.781523307319E+04 kT │ │ │ Vpmg_energy: dielEnergy = 8.939732950056E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.235700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.146400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -28736,129 +28736,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.289851 │ │ │ +Vacc_SASA: Time elapsed: 2.946830 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.925656e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.063844e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.623200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.610700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.621440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.121514e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.514108e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.232209e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.529441e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.258440e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.567186e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.446880e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.594451e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.615416e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.622914e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.790031e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.653210e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.961574e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682079e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.138952e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.710823e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.319692e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.739238e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.494063e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.472508e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.712428e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.415320e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.427668e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -28867,15 +28867,15 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.162784451104E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.383505562700E+02 kT │ │ │ Vpmg_energy: dielEnergy = 1.754184182339E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.695100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.661200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ @@ -28923,138 +28923,138 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00475113 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 2.157898 │ │ │ +Vacc_SASA: Time elapsed: 3.113744 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.933442e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.296227e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.838300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.942500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.661690e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.124655e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.082433e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.703600e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1712482.416854 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.097954e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.729137e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.778057e+05 │ │ │ Vprtstp: contraction number = 1.778057e+05 │ │ │ Vnewton: Attempting damping, relres = 0.095206 │ │ │ Vnewton: Attempting damping, relres = 0.544528 │ │ │ Vnewton: Damping accepted, relres = 0.095206 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.520604e-02 │ │ │ Vprtstp: contraction number = 9.520604e-02 │ │ │ Vnewton: Using errtol_s: 163038.671160 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.135108e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.906234e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.588526e+04 │ │ │ Vprtstp: contraction number = 2.588526e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.365073e-02 │ │ │ Vprtstp: contraction number = 1.433809e-01 │ │ │ Vnewton: Using errtol_s: 23376.634124 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.165233e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.067137e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.392675e+03 │ │ │ Vprtstp: contraction number = 4.392675e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.309227e-03 │ │ │ Vprtstp: contraction number = 1.691651e-01 │ │ │ Vnewton: Using errtol_s: 3954.509988 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.192541e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.221919e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.232796e+02 │ │ │ Vprtstp: contraction number = 8.232796e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 4.326939e-04 │ │ │ Vprtstp: contraction number = 1.873761e-01 │ │ │ Vnewton: Using errtol_s: 740.980697 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.220839e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.374264e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.669237e+02 │ │ │ Vprtstp: contraction number = 1.669237e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 8.772776e-05 │ │ │ Vprtstp: contraction number = 2.027479e-01 │ │ │ Vnewton: Using errtol_s: 150.232247 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.249199e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.524540e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.642088e+01 │ │ │ Vprtstp: contraction number = 3.642088e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.914112e-05 │ │ │ Vprtstp: contraction number = 2.181877e-01 │ │ │ Vnewton: Using errtol_s: 32.778836 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.276387e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.685355e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.545476e+00 │ │ │ Vprtstp: contraction number = 8.545476e+00 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.491102e-06 │ │ │ Vprtstp: contraction number = 2.346311e-01 │ │ │ Vnewton: Using errtol_s: 7.690933 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.304814e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.838540e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.153814e+00 │ │ │ Vprtstp: contraction number = 2.153814e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.131943e-06 │ │ │ Vprtstp: contraction number = 2.520414e-01 │ │ │ Vnewton: Using errtol_s: 1.938433 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.333557e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.990324e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.814982e-01 │ │ │ Vprtstp: contraction number = 5.814982e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.056081e-07 │ │ │ Vprtstp: contraction number = 2.699853e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.723235e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.973146e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.423683e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.436095e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -29063,17 +29063,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.651168945816E-01 kT │ │ │ Vpmg_energy: qfEnergy = 3.320671858523E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.644537494834E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.381300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.977800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -29094,129 +29094,129 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.123312 │ │ │ +Vacc_SASA: Time elapsed: 6.461889 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.007453e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.937452e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.658700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.318700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.970330e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.121451e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.987439e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.219196e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.007469e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.243792e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.045747e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.466836e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.074408e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.661018e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.102266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.853041e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.129440e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.046823e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.156631e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.236486e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.183692e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.434781e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.210935e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.629496e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.456154e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.734902e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.592002e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.604176e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -29225,17 +29225,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 2.317973104173E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.391935061774E+03 kT │ │ │ Vpmg_energy: dielEnergy = 1.197593144317E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.588700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.964100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ @@ -29281,127 +29281,127 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0257349 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 5.043290 │ │ │ +Vacc_SASA: Time elapsed: 6.542421 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.056546e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.108293e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.827800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.048500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.636990e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.029678e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.866060e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.904035e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 4500132.646352 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.881719e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.928753e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.278020e+05 │ │ │ Vprtstp: contraction number = 4.278020e+05 │ │ │ Vnewton: Attempting damping, relres = 0.086415 │ │ │ Vnewton: Attempting damping, relres = 0.540695 │ │ │ Vnewton: Damping accepted, relres = 0.086415 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.641451e-02 │ │ │ Vprtstp: contraction number = 8.641451e-02 │ │ │ Vnewton: Using errtol_s: 388876.774521 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.918897e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.169323e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.967321e+04 │ │ │ Vprtstp: contraction number = 5.967321e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 1.194851e-02 │ │ │ Vprtstp: contraction number = 1.382697e-01 │ │ │ Vnewton: Using errtol_s: 53769.886692 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.949724e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.415187e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.609884e+03 │ │ │ Vprtstp: contraction number = 9.609884e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.922151e-03 │ │ │ Vprtstp: contraction number = 1.608695e-01 │ │ │ Vnewton: Using errtol_s: 8649.935921 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.977523e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.648838e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.688280e+03 │ │ │ Vprtstp: contraction number = 1.688280e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.376534e-04 │ │ │ Vprtstp: contraction number = 1.756643e-01 │ │ │ Vnewton: Using errtol_s: 1519.485051 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.005647e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.888554e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.185424e+02 │ │ │ Vprtstp: contraction number = 3.185424e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.370679e-05 │ │ │ Vprtstp: contraction number = 1.886751e-01 │ │ │ Vnewton: Using errtol_s: 286.689023 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.033091e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.151661e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.336866e+01 │ │ │ Vprtstp: contraction number = 6.336866e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.267337e-05 │ │ │ Vprtstp: contraction number = 1.989328e-01 │ │ │ Vnewton: Using errtol_s: 57.031849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.060521e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.373949e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.358194e+01 │ │ │ Vprtstp: contraction number = 1.358194e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.716310e-06 │ │ │ Vprtstp: contraction number = 2.143321e-01 │ │ │ Vnewton: Using errtol_s: 12.223755 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.087943e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.596414e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.189745e+00 │ │ │ Vprtstp: contraction number = 3.189745e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.379304e-07 │ │ │ Vprtstp: contraction number = 2.348518e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.425961e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.673324e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.905314e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.916634e+02 │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ @@ -29410,17 +29410,17 @@ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 3.132873625516E-01 kT │ │ │ Vpmg_energy: qfEnergy = 2.116420853422E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.060038494093E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.666300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.160900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.139500e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 9.814371e+02 │ │ ├── ./usr/share/apbs/examples/alkanes/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:04:15 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 19:00:57 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path 2-methylbutane.pdb │ │ │ @@ -302,130 +302,130 @@ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (13.5347, 12.2207, 11.3787) │ │ │ Vclist_setupGrid: Grid lower corner = (-6.76736, -6.11036, -5.68936) │ │ │ Vclist_assignAtoms: Have 6745 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.011709 │ │ │ -initAPOL: Time elapsed: 2.210655 │ │ │ +Vacc_SASA: Time elapsed: 0.015457 │ │ │ +initAPOL: Time elapsed: 2.867467 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 15 x 12 x 11 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (13.0267, 11.7717, 11.1107) │ │ │ Vclist_setupGrid: Grid lower corner = (-2.59636, -5.18336, -14.1304) │ │ │ Vclist_assignAtoms: Have 4888 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.009229 │ │ │ -initAPOL: Time elapsed: 1.800354 │ │ │ +Vacc_SASA: Time elapsed: 0.010670 │ │ │ +initAPOL: Time elapsed: 2.454214 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 14 x 12 x 15 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (12.7417, 11.4947, 13.2787) │ │ │ Vclist_setupGrid: Grid lower corner = (-5.24736, -5.15936, -5.87136) │ │ │ Vclist_assignAtoms: Have 6902 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.012384 │ │ │ -initAPOL: Time elapsed: 2.314457 │ │ │ +Vacc_SASA: Time elapsed: 0.015986 │ │ │ +initAPOL: Time elapsed: 2.982593 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 14 x 12 x 13 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (12.4767, 11.4917, 12.3367) │ │ │ Vclist_setupGrid: Grid lower corner = (-4.91836, -5.22036, -4.87936) │ │ │ Vclist_assignAtoms: Have 4977 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.008779 │ │ │ -initAPOL: Time elapsed: 1.659972 │ │ │ +Vacc_SASA: Time elapsed: 0.009901 │ │ │ +initAPOL: Time elapsed: 2.302850 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 9 x 9 x 10 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (10.0327, 10.2387, 10.6647) │ │ │ Vclist_setupGrid: Grid lower corner = (-4.79536, -5.14036, -4.56736) │ │ │ Vclist_assignAtoms: Have 1946 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.004825 │ │ │ -initAPOL: Time elapsed: 1.019787 │ │ │ +Vacc_SASA: Time elapsed: 0.006297 │ │ │ +initAPOL: Time elapsed: 1.554386 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 19 x 15 x 12 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (15.0957, 13.1957, 11.4487) │ │ │ Vclist_setupGrid: Grid lower corner = (-2.59636, -6.60736, -14.1304) │ │ │ Vclist_assignAtoms: Have 9434 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.013706 │ │ │ -initAPOL: Time elapsed: 2.609709 │ │ │ +Vacc_SASA: Time elapsed: 0.018488 │ │ │ +initAPOL: Time elapsed: 3.584152 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 13 x 12 x 14 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (12.0577, 11.5517, 12.5037) │ │ │ Vclist_setupGrid: Grid lower corner = (12.5656, 12.8626, 12.9606) │ │ │ Vclist_assignAtoms: Have 5377 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.009032 │ │ │ -initAPOL: Time elapsed: 1.856072 │ │ │ +Vacc_SASA: Time elapsed: 0.010544 │ │ │ +initAPOL: Time elapsed: 2.772463 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 9 x 9 x 8 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (10.1767, 10.1117, 9.66772) │ │ │ Vclist_setupGrid: Grid lower corner = (12.9396, 12.7376, 12.9816) │ │ │ Vclist_assignAtoms: Have 1014 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.002766 │ │ │ -initAPOL: Time elapsed: 0.654583 │ │ │ +Vacc_SASA: Time elapsed: 0.004430 │ │ │ +initAPOL: Time elapsed: 1.005910 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 13 x 13 x 14 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (12.2347, 12.1667, 12.6837) │ │ │ Vclist_setupGrid: Grid lower corner = (12.5496, 12.8526, 12.8586) │ │ │ Vclist_assignAtoms: Have 6725 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.011587 │ │ │ -initAPOL: Time elapsed: 2.262500 │ │ │ +Vacc_SASA: Time elapsed: 0.012643 │ │ │ +initAPOL: Time elapsed: 3.148180 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 17 x 14 x 11 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (14.1127, 12.8537, 11.1297) │ │ │ Vclist_setupGrid: Grid lower corner = (-2.59636, -6.26536, -14.1304) │ │ │ Vclist_assignAtoms: Have 6650 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.010926 │ │ │ -initAPOL: Time elapsed: 2.194743 │ │ │ +Vacc_SASA: Time elapsed: 0.012096 │ │ │ +initAPOL: Time elapsed: 2.876861 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 10 x 14 x 12 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ Vclist_setupGrid: Grid lengths = (10.9097, 12.4407, 11.4747) │ │ │ Vclist_setupGrid: Grid lower corner = (12.9086, 12.7426, 12.8736) │ │ │ Vclist_assignAtoms: Have 3766 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ -Vacc_SASA: Time elapsed: 0.006757 │ │ │ -initAPOL: Time elapsed: 1.455977 │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.004886e+01 │ │ │ +Vacc_SASA: Time elapsed: 0.009112 │ │ │ +initAPOL: Time elapsed: 2.037948 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.760705e+01 │ │ ├── ./usr/share/apbs/examples/born/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:44 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 07:54:43 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -194,32 +194,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000165 │ │ │ +Vacc_SASA: Time elapsed: 0.000310 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.930900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.822420e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.735000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.618600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.010200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.257156e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.124980e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.737127e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -242,33 +242,33 @@ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.564100e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.262470e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.363497e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.587340e+01 │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.750853990251E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.490000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.364000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -315,30 +315,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.111569 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000133 │ │ │ +Vacc_SASA: Time elapsed: 0.000443 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.995100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.241550e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.659000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.268900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.073700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.136391e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.923860e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.884639e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.284366e-01 │ │ │ Vprtstp: contraction number = 1.284366e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -370,33 +370,33 @@ │ │ │ Vprtstp: contraction number = 3.689006e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.340984e-06 │ │ │ Vprtstp: contraction number = 3.689051e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.946966e-07 │ │ │ Vprtstp: contraction number = 3.689058e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.840600e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.547370e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.539973e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.750855e+01 │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.775144565213E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.780000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.516000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -443,30 +443,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.339539 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000130 │ │ │ +Vacc_SASA: Time elapsed: 0.000367 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.163390e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.761350e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.696200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.919600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.043600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.170643e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.277244e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.698515e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.377836e-01 │ │ │ Vprtstp: contraction number = 1.377836e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -501,33 +501,33 @@ │ │ │ Vprtstp: contraction number = 3.896678e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.022958e-06 │ │ │ Vprtstp: contraction number = 3.896627e-01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 3.986147e-07 │ │ │ Vprtstp: contraction number = 3.896686e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.973900e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.833180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.887345e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.104733e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 3.817909770059E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.800000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.657000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ WARNING │ │ │ Vgrid_readGZ: gzip read/write support is disabled in this build │ │ │ Vgrid_readGZ: configure and compile without the --disable-zlib flag. │ │ │ WARNING │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ @@ -552,28 +552,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.604100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.125290e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.697300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.132000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.239000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.195104e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.875758e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.382006e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -590,33 +590,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.693960e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.394970e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.545795e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.761931e+01 │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 9.607786035504E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.560000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.029000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -661,28 +661,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 8.7631 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.797200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.101500e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.675600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.988900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.140500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.170006e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.245440e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.658985e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114981e-01 │ │ │ Vprtstp: contraction number = 1.114981e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -699,33 +699,33 @@ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473476e-06 │ │ │ Vprtstp: contraction number = 1.075295e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.593050e-07 │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.696020e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.386060e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.560399e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.774108e+01 │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.961195484638E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.370000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.011200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -770,28 +770,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 26.656 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.119900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.924200e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.340100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.642600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 3.995500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.223699e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.606502e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.936874e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114975e-01 │ │ │ Vprtstp: contraction number = 1.114975e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -808,39 +808,39 @@ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473471e-06 │ │ │ Vprtstp: contraction number = 1.075296e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.593045e-07 │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.736050e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.296740e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.637898e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.847963e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 4.003287887017E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.780000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.458000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.884673e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.200919e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:45 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 07:59:24 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -1028,32 +1028,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000161 │ │ │ +Vacc_SASA: Time elapsed: 0.000344 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.050440e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.264710e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.269000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.687500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.577800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.220567e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.996820e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.824014e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1073,33 +1073,33 @@ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.603970e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.469930e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.069946e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.288414e+01 │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.691034776619E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.080000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.967000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1146,30 +1146,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.111618 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000132 │ │ │ +Vacc_SASA: Time elapsed: 0.000366 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.223520e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.482680e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.686800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.000300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.556500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.266532e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.624960e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.622832e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.204709e-01 │ │ │ Vprtstp: contraction number = 1.204709e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1186,33 +1186,33 @@ │ │ │ Vprtstp: contraction number = 1.476379e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 5.011380e-06 │ │ │ Vprtstp: contraction number = 1.603001e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.492596e-07 │ │ │ Vprtstp: contraction number = 1.694662e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.350740e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.027390e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.654848e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.880045e+01 │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.775933047078E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.250000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.338000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1259,30 +1259,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.339781 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.002686 │ │ │ +Vacc_SASA: Time elapsed: 0.000372 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.964580e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.280100e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.754200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.633800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.994100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.175789e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.476026e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.542222e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.298995e-01 │ │ │ Vprtstp: contraction number = 1.298995e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1302,33 +1302,33 @@ │ │ │ Vprtstp: contraction number = 1.916174e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.164097e-06 │ │ │ Vprtstp: contraction number = 1.993376e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.370219e-07 │ │ │ Vprtstp: contraction number = 2.019420e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.810390e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.538170e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.964941e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.171841e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 3.818523837085E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.050000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.800000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1349,28 +1349,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.346100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.746490e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.775800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.893000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.073200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.173039e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.965250e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.753617e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1387,33 +1387,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.115460e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.937620e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.762466e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.982715e+01 │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 9.607786035504E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.880000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.557000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1458,28 +1458,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 8.7631 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.073900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.434600e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.731700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.075200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.137700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.316049e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.479222e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.274081e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114981e-01 │ │ │ Vprtstp: contraction number = 1.114981e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1496,31 +1496,31 @@ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473476e-06 │ │ │ Vprtstp: contraction number = 1.075295e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.593050e-07 │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.081680e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.828910e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.967377e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.186610e+01 │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.961195484638E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.720000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.142000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ @@ -1567,28 +1567,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 26.656 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.315800e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.945100e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.372300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.777700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.179500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.293146e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.391983e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.594463e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114975e-01 │ │ │ Vprtstp: contraction number = 1.114975e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1605,39 +1605,39 @@ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473471e-06 │ │ │ Vprtstp: contraction number = 1.075296e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.593045e-07 │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.374050e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.056960e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.844078e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.066609e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 4.003287887017E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.580000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.092000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.735284e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.879477e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:46 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:03:24 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -1885,32 +1885,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000168 │ │ │ +Vacc_SASA: Time elapsed: 0.000309 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.048400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.595140e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.865400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.319900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.181100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.191664e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.304250e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.724966e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1933,31 +1933,31 @@ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.932600e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.850640e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.461110e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.683989e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.937713497535E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.190000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.934000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ @@ -2006,30 +2006,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0318856 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000226 │ │ │ +Vacc_SASA: Time elapsed: 0.008321 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.245200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.533050e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.802200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.395600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.173700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.201939e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.743680e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.999376e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.311479e-01 │ │ │ Vprtstp: contraction number = 1.311479e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2061,33 +2061,33 @@ │ │ │ Vprtstp: contraction number = 3.924056e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.308381e-06 │ │ │ Vprtstp: contraction number = 3.934819e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 9.098344e-07 │ │ │ Vprtstp: contraction number = 3.941440e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.612420e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.444320e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.605717e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.829167e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.569607552225E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.220000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.305500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2134,30 +2134,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0917244 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000135 │ │ │ +Vacc_SASA: Time elapsed: 0.023205 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.239120e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.783320e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.709200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.781600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.918000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.223540e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.747952e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.869397e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.316256e-01 │ │ │ Vprtstp: contraction number = 1.316256e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2195,33 +2195,33 @@ │ │ │ Vprtstp: contraction number = 4.543160e-01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.790206e-06 │ │ │ Vprtstp: contraction number = 4.616591e-01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.377288e-07 │ │ │ Vprtstp: contraction number = 4.679511e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.068918e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.149482e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.419375e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.630713e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198283392867E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.830000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.411000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.700000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2242,28 +2242,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.179000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.466530e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.720500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.122200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.053000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.301308e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.919884e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.453817e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2280,33 +2280,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.937970e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.749520e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.925532e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.152495e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.640000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.124000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2351,28 +2351,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.50448 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.982600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.110900e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.677800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.992200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.003300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.441192e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.329135e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.771704e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2392,33 +2392,33 @@ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.350460e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.126580e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.196118e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.445885e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.470000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.563000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2463,28 +2463,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.21011 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.286600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.019100e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.403400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.620400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.429900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.414453e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.864303e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.116495e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2516,39 +2516,39 @@ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.481060e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.095650e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.597154e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.832605e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.250000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.665400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.718858e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.576528e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:48 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:08:53 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -2796,32 +2796,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000168 │ │ │ +Vacc_SASA: Time elapsed: 0.007422 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.875500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.129160e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.706700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.579500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.152100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.209856e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183060e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.624408e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2844,33 +2844,33 @@ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.987070e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.798770e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.433276e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.642886e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.937713497535E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.890000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.183000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2917,30 +2917,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.031798 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000134 │ │ │ +Vacc_SASA: Time elapsed: 0.000601 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.586300e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.351250e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.713500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.079700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.728600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.247782e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.563170e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.948633e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.311630e-01 │ │ │ Vprtstp: contraction number = 1.311630e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2972,33 +2972,33 @@ │ │ │ Vprtstp: contraction number = 3.943689e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.411496e-06 │ │ │ Vprtstp: contraction number = 3.954554e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 9.552609e-07 │ │ │ Vprtstp: contraction number = 3.961279e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.161080e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.886130e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.603278e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.820353e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.569480660622E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.070000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.165700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3045,30 +3045,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0914959 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000151 │ │ │ +Vacc_SASA: Time elapsed: 0.000239 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.288990e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.512780e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.696300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.503800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.611800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.208099e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.784132e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.823557e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.316347e-01 │ │ │ Vprtstp: contraction number = 1.316347e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3106,33 +3106,33 @@ │ │ │ Vprtstp: contraction number = 4.560576e-01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.840082e-06 │ │ │ Vprtstp: contraction number = 4.634922e-01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.644979e-07 │ │ │ Vprtstp: contraction number = 4.698149e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.523140e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.248210e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.212466e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.434405e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198276421620E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.350000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.882000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3153,28 +3153,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.329900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.743400e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.688800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.188100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.031800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.190716e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.642124e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.426156e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3191,33 +3191,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.059970e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.865990e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.600740e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.809428e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.460000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.984000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3262,28 +3262,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.137400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.963300e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.730900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.708300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.754100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.227093e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.054797e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.707641e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3303,33 +3303,33 @@ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.001680e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.726550e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.028771e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.236241e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.550000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.023000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3374,28 +3374,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.368100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.074600e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.365000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.034700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.536900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.259990e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.554912e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.032795e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3427,39 +3427,39 @@ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.106040e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.724760e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.555619e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.772891e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.910000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.000000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.076185e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.488627e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:50 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:14:11 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -3707,32 +3707,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000188 │ │ │ +Vacc_SASA: Time elapsed: 0.000412 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.860400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.968470e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.705500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.286600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.639600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.274571e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.144540e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.798143e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3755,33 +3755,33 @@ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.149000e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.926370e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.409609e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.634593e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.937713497591E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.060000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.793000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3828,30 +3828,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.031798 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000150 │ │ │ +Vacc_SASA: Time elapsed: 0.000489 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.005500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.720410e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.706800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.538700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.362200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.272870e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.694250e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.943443e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.311246e-01 │ │ │ Vprtstp: contraction number = 1.311246e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3883,33 +3883,33 @@ │ │ │ Vprtstp: contraction number = 3.922726e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.295236e-06 │ │ │ Vprtstp: contraction number = 3.933610e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 9.043960e-07 │ │ │ Vprtstp: contraction number = 3.940319e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.072590e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.821280e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.627782e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.840812e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.569607562894E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.870000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.932000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3956,30 +3956,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0914865 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000139 │ │ │ +Vacc_SASA: Time elapsed: 0.000262 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.229130e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.329220e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.703600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.752900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.099700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.204567e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.491191e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.835325e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.312535e-01 │ │ │ Vprtstp: contraction number = 1.312535e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4017,33 +4017,33 @@ │ │ │ Vprtstp: contraction number = 4.543257e-01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.762407e-06 │ │ │ Vprtstp: contraction number = 4.617179e-01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.248702e-07 │ │ │ Vprtstp: contraction number = 4.680361e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.918610e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.737640e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.254029e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.469708e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198283391562E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.630000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.533000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -4064,28 +4064,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.482400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.030280e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.699200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.585000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.617300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.208701e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.382710e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.431431e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4102,33 +4102,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.906820e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.656790e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.608400e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.822585e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.620000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.288000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -4173,28 +4173,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.835500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.243400e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.787400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.547000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.098200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.244758e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.779168e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.714177e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4214,31 +4214,31 @@ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.305350e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.066930e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.974513e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.186347e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.480000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.230000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ @@ -4285,28 +4285,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.292100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.725700e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.367900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.436900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.290000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.209831e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.207847e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.032620e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4338,39 +4338,39 @@ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.859700e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.454910e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.597109e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.800010e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.620000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.586000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.600000e-05 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.700424e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.492894e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:51 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:19:30 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -4618,32 +4618,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000162 │ │ │ +Vacc_SASA: Time elapsed: 0.000300 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.022700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.042780e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.712200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.097900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.439400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.310458e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141390e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.810360e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4666,33 +4666,33 @@ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.765980e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.519490e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.375377e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.604613e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.937713497591E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.780000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.094000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -4739,30 +4739,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0317109 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000136 │ │ │ +Vacc_SASA: Time elapsed: 0.000761 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.022200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.451570e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.712500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.851700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.223500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.155856e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.221770e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.903850e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.311373e-01 │ │ │ Vprtstp: contraction number = 1.311373e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4794,33 +4794,33 @@ │ │ │ Vprtstp: contraction number = 3.942499e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.398436e-06 │ │ │ Vprtstp: contraction number = 3.953474e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 9.498453e-07 │ │ │ Vprtstp: contraction number = 3.960269e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.701300e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.431000e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.608514e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.816627e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.569480671365E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.080000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.432000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -4867,30 +4867,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0912591 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000142 │ │ │ +Vacc_SASA: Time elapsed: 0.012024 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.219130e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.784900e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.851200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.941400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.430600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.262182e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.298492e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.788273e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.312625e-01 │ │ │ Vprtstp: contraction number = 1.312625e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -4928,33 +4928,33 @@ │ │ │ Vprtstp: contraction number = 4.561186e-01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 1.813861e-06 │ │ │ Vprtstp: contraction number = 4.635791e-01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 8.523872e-07 │ │ │ Vprtstp: contraction number = 4.699296e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.613770e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.342210e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.354017e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.586503e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198276420222E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.510000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.871000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -4975,28 +4975,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.294500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.591880e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.701700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.341500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.419600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.310849e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.952617e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.438856e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5013,33 +5013,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.806560e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.539190e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.826944e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.054462e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.040000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.211000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -5084,28 +5084,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.49076 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.942700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.690600e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.751200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.000800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.254400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.239305e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.335638e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.745149e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5125,33 +5125,33 @@ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.130890e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.854430e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.069813e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.300078e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.790000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.738000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -5196,28 +5196,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.17281 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.338200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.047300e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.367700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.824500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.049300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.197594e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.740962e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.075092e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5249,39 +5249,39 @@ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.741330e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.310630e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.428201e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.641117e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.650000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.785000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.224204e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.518077e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:53 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:24:51 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -5529,32 +5529,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000167 │ │ │ +Vacc_SASA: Time elapsed: 0.000293 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.041330e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.199350e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.650100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.019700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.128700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.184174e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.828250e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.852235e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5574,31 +5574,31 @@ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.122720e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.821780e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.966675e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.188268e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.922758694117E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.780000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.280000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ @@ -5647,30 +5647,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0319041 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000134 │ │ │ +Vacc_SASA: Time elapsed: 0.000683 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.278300e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.410710e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.732000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.009800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.032500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.253825e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.031090e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.508332e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.251607e-01 │ │ │ Vprtstp: contraction number = 1.251607e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5693,33 +5693,33 @@ │ │ │ Vprtstp: contraction number = 2.197650e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.342799e-06 │ │ │ Vprtstp: contraction number = 2.223851e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.012580e-07 │ │ │ Vprtstp: contraction number = 2.243508e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.554890e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.219490e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.352052e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.563095e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.571571268982E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.130000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.089000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.100000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -5766,30 +5766,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0918985 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000133 │ │ │ +Vacc_SASA: Time elapsed: 0.004940 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.966550e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.429180e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.680100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.755200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.069300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.192019e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.328690e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.131155e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.287586e-01 │ │ │ Vprtstp: contraction number = 1.287586e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5821,33 +5821,33 @@ │ │ │ Vprtstp: contraction number = 3.624968e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.194036e-06 │ │ │ Vprtstp: contraction number = 3.635428e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.993852e-07 │ │ │ Vprtstp: contraction number = 3.643446e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.759160e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.385020e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.446602e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.656424e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198500974871E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.890000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.870000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -5868,28 +5868,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.482700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.255210e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.673700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.213300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.105800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.197773e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.898413e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180490e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -5906,33 +5906,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.721250e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.411020e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.669343e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.880601e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.730000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.720000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -5977,28 +5977,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.50448 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.898400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.874900e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.672400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.081200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.103900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.175546e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.268847e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.469531e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6018,33 +6018,33 @@ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.131480e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.767140e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.945506e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.161640e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.320000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.098600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -6089,28 +6089,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.21011 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.174500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.060400e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.340100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.361800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 3.921400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.206545e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.674499e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.786176e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6142,39 +6142,39 @@ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.675580e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.228750e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.399457e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.608466e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.760000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.831600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.152968e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.226400e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:54 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:29:34 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -6422,32 +6422,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000155 │ │ │ +Vacc_SASA: Time elapsed: 0.000328 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.034030e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.818370e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.717000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.940900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.166300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.147719e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.825570e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.738166e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6467,33 +6467,33 @@ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.219380e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.923250e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.924670e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.138754e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.922758694117E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.900000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.925000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -6540,30 +6540,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0318166 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000141 │ │ │ +Vacc_SASA: Time elapsed: 0.000422 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.360740e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.472780e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.739800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.008400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.024000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.169415e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.207870e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.458386e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.251837e-01 │ │ │ Vprtstp: contraction number = 1.251837e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6586,33 +6586,33 @@ │ │ │ Vprtstp: contraction number = 2.194352e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.332747e-06 │ │ │ Vprtstp: contraction number = 2.220306e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.985011e-07 │ │ │ Vprtstp: contraction number = 2.239743e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.535060e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.196470e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.309463e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.520056e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.571611855754E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.550000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.870000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -6659,30 +6659,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0916405 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000133 │ │ │ +Vacc_SASA: Time elapsed: 0.000287 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.989590e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.193330e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.670800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.689500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.373000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.199798e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.350550e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.027344e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.287503e-01 │ │ │ Vprtstp: contraction number = 1.287503e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6714,33 +6714,33 @@ │ │ │ Vprtstp: contraction number = 3.625355e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.195364e-06 │ │ │ Vprtstp: contraction number = 3.635887e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.999739e-07 │ │ │ Vprtstp: contraction number = 3.643923e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.283280e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.977360e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.429870e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.636373e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198504468748E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.480000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.731000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -6761,28 +6761,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.537100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.516650e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.635900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.112300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.077700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.178825e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.970182e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.168961e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6799,33 +6799,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.761710e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.426110e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.597492e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.809948e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.380000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.765000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -6870,28 +6870,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.941000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.527600e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.729100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.741000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.385100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.181455e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.349763e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.451255e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -6911,33 +6911,33 @@ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.138610e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.820790e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.956055e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.173791e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.460000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.498000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -6982,28 +6982,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.335200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.887600e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.335100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.506300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.177900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.204571e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.758997e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.768379e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7035,39 +7035,39 @@ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.768990e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.347860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.533675e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.741467e+01 │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.350000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.195000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.243558e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.222403e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:55 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:34:18 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -7315,32 +7315,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000156 │ │ │ +Vacc_SASA: Time elapsed: 0.000305 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.030490e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.980220e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.775800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.053000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 3.996800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.188434e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.796190e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.758300e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7360,33 +7360,33 @@ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.407110e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.091660e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.018233e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.233425e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.922758694192E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.490000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.597000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.100000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -7433,30 +7433,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0318166 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000148 │ │ │ +Vacc_SASA: Time elapsed: 0.000251 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.284040e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.250250e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.687300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.108600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.069200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.221931e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.203930e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.553270e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.252629e-01 │ │ │ Vprtstp: contraction number = 1.252629e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7479,33 +7479,33 @@ │ │ │ Vprtstp: contraction number = 2.198448e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.343869e-06 │ │ │ Vprtstp: contraction number = 2.224198e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.015100e-07 │ │ │ Vprtstp: contraction number = 2.243596e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.628310e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.255830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.354471e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.570073e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.571571270505E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.870000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.670000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -7552,30 +7552,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0916602 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000130 │ │ │ +Vacc_SASA: Time elapsed: 0.000613 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.980380e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.494720e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.708100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.126900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.043300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.218046e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.352948e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.187679e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.283061e-01 │ │ │ Vprtstp: contraction number = 1.283061e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7607,33 +7607,33 @@ │ │ │ Vprtstp: contraction number = 3.626484e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.188308e-06 │ │ │ Vprtstp: contraction number = 3.636628e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.975574e-07 │ │ │ Vprtstp: contraction number = 3.644631e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.803500e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.432320e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.464268e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.685509e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198500974608E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.740000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.574000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -7654,28 +7654,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.323700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.932700e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.753800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.046700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.390900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.217665e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.936119e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188885e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7692,33 +7692,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.785860e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.536140e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.585257e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.812626e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.080000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.005000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -7763,28 +7763,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.852000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.675500e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.652800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.335000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.335800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.169643e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.320492e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.468905e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7804,33 +7804,33 @@ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.116370e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.829270e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.945585e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.154280e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.480000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.375000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -7875,28 +7875,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.192000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.907100e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.336100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.509900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 3.894800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.167158e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.720828e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.784816e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -7928,39 +7928,39 @@ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.598470e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.148980e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.423889e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.627829e+01 │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.660000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.216600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.192361e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.227075e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 10:53:57 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 08:39:02 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ @@ -8208,32 +8208,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000160 │ │ │ +Vacc_SASA: Time elapsed: 0.030532 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.023570e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.147520e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.716100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.511000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.220700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.203987e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.815840e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.754617e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -8253,33 +8253,33 @@ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.151640e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.859110e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.032712e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.245297e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.922758694192E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.850000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.508000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -8326,30 +8326,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0317294 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000208 │ │ │ +Vacc_SASA: Time elapsed: 0.000523 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.339480e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.511820e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.704000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.842000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.016900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.171775e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.082940e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.571962e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.252944e-01 │ │ │ Vprtstp: contraction number = 1.252944e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -8372,33 +8372,33 @@ │ │ │ Vprtstp: contraction number = 2.195054e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.334000e-06 │ │ │ Vprtstp: contraction number = 2.220609e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.987906e-07 │ │ │ Vprtstp: contraction number = 2.239810e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.571780e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.189840e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.364901e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.580120e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.571611857350E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.830000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.840000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -8445,30 +8445,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0914032 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000132 │ │ │ +Vacc_SASA: Time elapsed: 0.000467 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.981980e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.208730e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.752100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.671600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 3.949200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.255519e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.341433e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.215523e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.282975e-01 │ │ │ Vprtstp: contraction number = 1.282975e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -8500,33 +8500,33 @@ │ │ │ Vprtstp: contraction number = 3.626822e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.189511e-06 │ │ │ Vprtstp: contraction number = 3.637026e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.980984e-07 │ │ │ Vprtstp: contraction number = 3.645099e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.715260e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.338210e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.482399e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.701599e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.198504468496E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.710000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.866000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -8547,28 +8547,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.345900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.812650e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.749700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.223800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 3.934900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.301253e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.908752e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.195102e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -8585,33 +8585,33 @@ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.715190e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.403390e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.689117e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.914788e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.640000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.048900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -8656,28 +8656,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2.49076 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.855000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.606900e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.688800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.433900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.204700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.187832e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.280529e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.486689e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -8697,33 +8697,33 @@ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.194290e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.855280e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.027231e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.247007e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.520000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.043000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -8768,28 +8768,28 @@ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 7.17281 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.312900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.803100e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.334500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.474700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.042300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.308933e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.694477e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.812346e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -8821,29 +8821,29 @@ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.617660e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.182730e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.642993e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.861535e+01 │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.650000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.593000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.167287e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.277155e+02 │ │ ├── ./usr/share/apbs/examples/hca-bind/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:05:22 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 19:45:35 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path acet.pqr │ │ │ @@ -289,32 +289,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.010134 │ │ │ +Vacc_SASA: Time elapsed: 0.034021 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.304000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.537700e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.738500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.905200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.953100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.291361e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568540e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.556877e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.087255e-01 │ │ │ Vprtstp: contraction number = 1.087255e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -331,32 +331,32 @@ │ │ │ Vprtstp: contraction number = 1.074047e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.481057e-06 │ │ │ Vprtstp: contraction number = 1.080656e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.608051e-07 │ │ │ Vprtstp: contraction number = 1.085746e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.009600e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.860530e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.456169e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.679474e+01 │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.785902379684E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.590300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -402,30 +402,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.104294 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.009733 │ │ │ +Vacc_SASA: Time elapsed: 0.047411 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.132000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.868160e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.681400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.455400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.761900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.685863e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.812630e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.031650e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.287269e-01 │ │ │ Vprtstp: contraction number = 1.287269e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -451,32 +451,32 @@ │ │ │ Vprtstp: contraction number = 3.073619e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.517211e-06 │ │ │ Vprtstp: contraction number = 3.092055e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 4.703221e-07 │ │ │ Vprtstp: contraction number = 3.099912e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.992560e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.765770e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.726767e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.024446e+01 │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.473001739532E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.510000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -522,30 +522,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.504504 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.010315 │ │ │ +Vacc_SASA: Time elapsed: 0.037825 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.164000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.223310e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.674700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.117700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.724200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.679102e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103167e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.065933e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.402627e-01 │ │ │ Vprtstp: contraction number = 1.402627e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -574,32 +574,32 @@ │ │ │ Vprtstp: contraction number = 3.281873e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.285796e-06 │ │ │ Vprtstp: contraction number = 3.294777e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.250794e-07 │ │ │ Vprtstp: contraction number = 3.305964e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.677610e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.491320e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.027417e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.303867e+01 │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.210605041355E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.600000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.180000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -620,32 +620,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.237279 │ │ │ +Vacc_SASA: Time elapsed: 1.979325 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.391207e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.424117e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.371100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.344700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.777900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.398671e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.047905e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.461874e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.838248e-02 │ │ │ Vprtstp: contraction number = 7.838248e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -707,32 +707,32 @@ │ │ │ Vprtstp: contraction number = 6.567898e-01 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 1.365716e-06 │ │ │ Vprtstp: contraction number = 6.589433e-01 │ │ │ Vprtstp: iteration = 22 │ │ │ Vprtstp: relative residual = 9.028429e-07 │ │ │ Vprtstp: contraction number = 6.610767e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.268360e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.001612e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.083121e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.111065e+02 │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.689092374656E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.250000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.490000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -778,30 +778,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 4518.73 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2191.64 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.190319 │ │ │ +Vacc_SASA: Time elapsed: 1.636442 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.372982e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.999067e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.831200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.906900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.529200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.411375e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.431647e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.590570e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.397950e-01 │ │ │ Vprtstp: contraction number = 1.397950e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -842,32 +842,32 @@ │ │ │ Vprtstp: contraction number = 5.527064e-01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 1.277233e-06 │ │ │ Vprtstp: contraction number = 5.598610e-01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 7.227170e-07 │ │ │ Vprtstp: contraction number = 5.658458e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.083930e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.839850e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.973073e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.222941e+01 │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.222630775541E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.180000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.600000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -913,30 +913,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 110988 kT │ │ │ VPMG::extEnergy: extDiEnergy = 56275.9 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.200608 │ │ │ +Vacc_SASA: Time elapsed: 2.610765 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.353704e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.960267e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.378100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.692800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.109500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.652084e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.481883e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.345836e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115653e-01 │ │ │ Vprtstp: contraction number = 1.115653e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -962,32 +962,32 @@ │ │ │ Vprtstp: contraction number = 3.498142e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.355176e-06 │ │ │ Vprtstp: contraction number = 3.685616e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.245419e-07 │ │ │ Vprtstp: contraction number = 3.925575e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.600620e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.392660e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.880030e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.156740e+01 │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.441218006192E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.290000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.480000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1008,32 +1008,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.209202 │ │ │ +Vacc_SASA: Time elapsed: 2.212254 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.356461e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.598785e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.339800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.212700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.092300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.424780e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.381080e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.887042e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.658858e-02 │ │ │ Vprtstp: contraction number = 7.658858e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1095,32 +1095,32 @@ │ │ │ Vprtstp: contraction number = 6.561084e-01 │ │ │ Vprtstp: iteration = 21 │ │ │ Vprtstp: relative residual = 1.508067e-06 │ │ │ Vprtstp: contraction number = 6.580134e-01 │ │ │ Vprtstp: iteration = 22 │ │ │ Vprtstp: relative residual = 9.954065e-07 │ │ │ Vprtstp: contraction number = 6.600544e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.082620e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.762890e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.060922e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.088539e+02 │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.698545237167E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.120000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.990000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1166,30 +1166,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 4519.43 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2191.49 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.222069 │ │ │ +Vacc_SASA: Time elapsed: 1.798830 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.377124e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.238437e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.720200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.127500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.636200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.525410e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.175039e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.999049e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.396668e-01 │ │ │ Vprtstp: contraction number = 1.396668e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1230,32 +1230,32 @@ │ │ │ Vprtstp: contraction number = 5.525486e-01 │ │ │ Vprtstp: iteration = 14 │ │ │ Vprtstp: relative residual = 1.290655e-06 │ │ │ Vprtstp: contraction number = 5.600207e-01 │ │ │ Vprtstp: iteration = 15 │ │ │ Vprtstp: relative residual = 7.308313e-07 │ │ │ Vprtstp: contraction number = 5.662486e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.127120e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.891430e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.130225e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.407318e+01 │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.237049215096E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.390000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.140000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1301,30 +1301,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 110994 kT │ │ │ VPMG::extEnergy: extDiEnergy = 56275.1 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.211710 │ │ │ +Vacc_SASA: Time elapsed: 1.837863 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.366819e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.269836e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.350900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.439400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.038900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.489071e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.381250e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.762734e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.163858e-01 │ │ │ Vprtstp: contraction number = 1.163858e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1353,38 +1353,38 @@ │ │ │ Vprtstp: contraction number = 3.950088e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.396547e-06 │ │ │ Vprtstp: contraction number = 4.328810e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.612158e-07 │ │ │ Vprtstp: contraction number = 4.734646e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.461540e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.194140e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.999394e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.271248e+01 │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.492900778210E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.100000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.760000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.428305e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.263810e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:05:32 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 19:58:58 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path acet.pqr │ │ │ @@ -1669,32 +1669,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.010913 │ │ │ +Vacc_SASA: Time elapsed: 0.061567 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.018540e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.721470e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.702800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.098500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.687300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.444281e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.306750e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.208765e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.084928e-01 │ │ │ Vprtstp: contraction number = 1.084928e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1711,32 +1711,32 @@ │ │ │ Vprtstp: contraction number = 1.067805e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.430429e-06 │ │ │ Vprtstp: contraction number = 1.075005e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.545898e-07 │ │ │ Vprtstp: contraction number = 1.080723e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.927630e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.722100e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.081872e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.348820e+01 │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.520701614302E+02 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.310000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1782,30 +1782,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.105108 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.009681 │ │ │ +Vacc_SASA: Time elapsed: 0.074771 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.064020e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.198080e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.730900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.751600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.694800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.278309e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.246790e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.662864e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.225646e-01 │ │ │ Vprtstp: contraction number = 1.225646e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1822,32 +1822,32 @@ │ │ │ Vprtstp: contraction number = 1.454441e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 5.669194e-06 │ │ │ Vprtstp: contraction number = 1.566066e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 9.449546e-07 │ │ │ Vprtstp: contraction number = 1.666823e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.932340e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.729400e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.497217e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.723660e+01 │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.468387819400E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.230000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1893,30 +1893,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.520445 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.010527 │ │ │ +Vacc_SASA: Time elapsed: 0.032739 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.056020e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.751400e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.716500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.038200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.777400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.459282e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222373e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.472141e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.305252e-01 │ │ │ Vprtstp: contraction number = 1.305252e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1936,32 +1936,32 @@ │ │ │ Vprtstp: contraction number = 1.733670e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.357163e-06 │ │ │ Vprtstp: contraction number = 1.824572e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.550194e-07 │ │ │ Vprtstp: contraction number = 1.879063e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.406720e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.246180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.967671e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.238000e+01 │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.211840549614E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.800000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.620000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1982,32 +1982,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.226422 │ │ │ +Vacc_SASA: Time elapsed: 2.010265 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.456426e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.475856e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.341700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.305000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.588300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.653227e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.103944e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.197560e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.136636e-02 │ │ │ Vprtstp: contraction number = 5.136636e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2027,32 +2027,32 @@ │ │ │ Vprtstp: contraction number = 2.406804e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.980432e-06 │ │ │ Vprtstp: contraction number = 2.704556e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.800745e-07 │ │ │ Vprtstp: contraction number = 2.929030e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.329050e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.054540e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.231741e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.517550e+01 │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.766185147917E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.260000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.260000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2098,30 +2098,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 4619.67 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2259.75 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.216482 │ │ │ +Vacc_SASA: Time elapsed: 2.219191 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.462407e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.659542e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.849900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.074400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.082500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.791391e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.986607e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.677138e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.613067e-02 │ │ │ Vprtstp: contraction number = 9.613067e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2141,32 +2141,32 @@ │ │ │ Vprtstp: contraction number = 1.833548e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.811522e-06 │ │ │ Vprtstp: contraction number = 1.939744e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.707504e-07 │ │ │ Vprtstp: contraction number = 2.046624e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.349550e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.119010e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.094779e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.389869e+01 │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.226315327863E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.790000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.267000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2212,30 +2212,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 111278 kT │ │ │ VPMG::extEnergy: extDiEnergy = 55995.6 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.215873 │ │ │ +Vacc_SASA: Time elapsed: 2.011706 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.430407e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.668348e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.408900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.438300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.663700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.601200e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.843718e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.140860e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.009208e-01 │ │ │ Vprtstp: contraction number = 1.009208e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2252,32 +2252,32 @@ │ │ │ Vprtstp: contraction number = 1.451140e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 3.266673e-06 │ │ │ Vprtstp: contraction number = 1.668260e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.985159e-07 │ │ │ Vprtstp: contraction number = 1.832188e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.914640e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.713170e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.507247e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.775615e+01 │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.444499098932E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.100000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.138100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2298,32 +2298,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.198265 │ │ │ +Vacc_SASA: Time elapsed: 2.256021 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.417330e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.743136e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.345500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.724900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.260900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.679771e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.645211e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.550157e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.894768e-02 │ │ │ Vprtstp: contraction number = 4.894768e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2343,32 +2343,32 @@ │ │ │ Vprtstp: contraction number = 2.414708e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.098574e-06 │ │ │ Vprtstp: contraction number = 2.683582e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.050680e-07 │ │ │ Vprtstp: contraction number = 2.883234e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.206400e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.003490e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.087060e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.392930e+01 │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.771575298437E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.160000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.007000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2414,30 +2414,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 4620.09 kT │ │ │ VPMG::extEnergy: extDiEnergy = 2259.49 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.202643 │ │ │ +Vacc_SASA: Time elapsed: 2.085047 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.425639e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.560559e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.701600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.299800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.920100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.372004e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057856e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.010174e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.547807e-02 │ │ │ Vprtstp: contraction number = 9.547807e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2457,32 +2457,32 @@ │ │ │ Vprtstp: contraction number = 1.878215e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.896640e-06 │ │ │ Vprtstp: contraction number = 1.994763e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.991489e-07 │ │ │ Vprtstp: contraction number = 2.104505e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.267420e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.987780e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.866680e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.121460e+01 │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.240652812594E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.480000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.087000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2528,30 +2528,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 111288 kT │ │ │ VPMG::extEnergy: extDiEnergy = 55994.2 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.210019 │ │ │ +Vacc_SASA: Time elapsed: 2.175782 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.429327e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.783512e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.392600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.812000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.660000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.481473e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.242303e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.451976e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.031999e-01 │ │ │ Vprtstp: contraction number = 1.031999e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2568,28 +2568,28 @@ │ │ │ Vprtstp: contraction number = 1.434980e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 3.331639e-06 │ │ │ Vprtstp: contraction number = 1.622112e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.872183e-07 │ │ │ Vprtstp: contraction number = 1.762551e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.900040e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.639860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.489644e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.751826e+01 │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.496181357535E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.090000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.380000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.273904e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.801642e+02 │ │ ├── ./usr/share/apbs/examples/ion-pmf/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:05:47 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:26:07 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path ion-pmf.pdb │ │ │ @@ -161,28 +161,28 @@ │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefSpline... │ │ │ Vpmg_fillco: filling coefficient arrays │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.499600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.815610e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.704400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.942000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.231800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.214368e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074210e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.607186e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.194542e-01 │ │ │ Vprtstp: contraction number = 1.194542e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -202,33 +202,33 @@ │ │ │ Vprtstp: contraction number = 1.749569e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.117484e-06 │ │ │ Vprtstp: contraction number = 1.874072e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.180018e-07 │ │ │ Vprtstp: contraction number = 1.950826e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.362110e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.205440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.178772e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.414252e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.324828953427E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.130000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.348000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.021000e-03 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.408000e-03 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 4 │ │ │ Vpbe_ctor2: solute dimensions = 8 x 4 x 4 │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -249,28 +249,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.465400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.260300e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.774000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.128400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.975100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.277640e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.589130e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.682952e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.110640e-01 │ │ │ Vprtstp: contraction number = 1.110640e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -287,50 +287,50 @@ │ │ │ Vprtstp: contraction number = 1.067494e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.466502e-06 │ │ │ Vprtstp: contraction number = 1.074548e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.584103e-07 │ │ │ Vprtstp: contraction number = 1.080191e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.918470e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.745770e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.788802e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.016960e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 7.232617942545E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.400000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.589000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vpmg_dbForce: No force for uniform dielectric! │ │ │ Vpmg_dbForce: No force for uniform dielectric! │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.300000e-05 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.300000e-04 │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ Vclist_ctor2: Using 16 x 8 x 8 hash table │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ Vclist_ctor2: Using 1.8 max radius │ │ │ Vclist_setupGrid: Grid lengths = (14.792, 10.792, 10.792) │ │ │ Vclist_setupGrid: Grid lower corner = (-8.396, -5.396, -5.396) │ │ │ Vclist_assignAtoms: Have 720 atom entries │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ Vacc_storeParms: Max area = 181.458 │ │ │ Vacc_storeParms: Using 18030-point reference sphere │ │ │ forceAPOL: Trying atom surf... │ │ │ -forceAPOL: atom surf: Time elapsed: 0.001825 │ │ │ -forceAPOL: Time elapsed: 4.131305 │ │ │ -Vacc_SASA: Time elapsed: 0.000002 │ │ │ -initAPOL: Time elapsed: 11.180857 │ │ │ +forceAPOL: atom surf: Time elapsed: 0.002871 │ │ │ +forceAPOL: Time elapsed: 5.367020 │ │ │ +Vacc_SASA: Time elapsed: 0.000003 │ │ │ +initAPOL: Time elapsed: 14.695108 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ @@ -339,8 +339,8 @@ │ │ │ printForce: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.204178e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.941601e+01 │ │ ├── ./usr/share/apbs/examples/ionize/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:05:42 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:07:07 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path acetic-acid.xml │ │ │ @@ -481,32 +481,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001610 │ │ │ +Vacc_SASA: Time elapsed: 0.005572 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.334600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.718420e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.728200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.847700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 7.057900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.504810e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.589550e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.155348e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.188999e-01 │ │ │ Vprtstp: contraction number = 3.188999e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -535,32 +535,32 @@ │ │ │ Vprtstp: contraction number = 2.912126e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.816386e-06 │ │ │ Vprtstp: contraction number = 2.924708e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.271441e-07 │ │ │ Vprtstp: contraction number = 2.936899e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.414280e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.466440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.267981e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.542627e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 4.781227236323E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.018100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -606,30 +606,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0505207 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001142 │ │ │ +Vacc_SASA: Time elapsed: 0.011835 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.658600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.640460e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.743700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.451900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.229200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.435776e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.248380e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.893393e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.598074e-01 │ │ │ Vprtstp: contraction number = 2.598074e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -661,32 +661,32 @@ │ │ │ Vprtstp: contraction number = 3.326351e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 2.087103e-06 │ │ │ Vprtstp: contraction number = 3.343120e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 7.014192e-07 │ │ │ Vprtstp: contraction number = 3.360731e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.367090e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.149260e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.078495e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.358631e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.039953678525E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.900000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -707,28 +707,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.111100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.093220e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.723600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.511900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.026800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.707629e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.486932e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.228597e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.679930e-01 │ │ │ Vprtstp: contraction number = 1.679930e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -745,32 +745,32 @@ │ │ │ Vprtstp: contraction number = 1.043091e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.862252e-06 │ │ │ Vprtstp: contraction number = 1.059323e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.994142e-07 │ │ │ Vprtstp: contraction number = 1.070823e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.931510e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.839790e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.203045e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.495019e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 4.800125490193E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.600000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.300000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -814,28 +814,28 @@ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 1.14339 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.139900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.734200e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.840900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.058200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.800100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.276271e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.899244e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.573130e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.651787e-01 │ │ │ Vprtstp: contraction number = 1.651787e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -852,32 +852,32 @@ │ │ │ Vprtstp: contraction number = 1.055047e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.934803e-06 │ │ │ Vprtstp: contraction number = 1.064764e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.073576e-07 │ │ │ Vprtstp: contraction number = 1.071724e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.941450e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.788180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.693394e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.924959e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.058572238076E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.794000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -898,32 +898,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.004576 │ │ │ +Vacc_SASA: Time elapsed: 0.006475 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.990100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.949940e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.721400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.639000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.864900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.180491e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.336184e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.867305e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.669750e-01 │ │ │ Vprtstp: contraction number = 1.669750e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -952,32 +952,32 @@ │ │ │ Vprtstp: contraction number = 3.348642e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.783762e-06 │ │ │ Vprtstp: contraction number = 3.348981e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 9.322590e-07 │ │ │ Vprtstp: contraction number = 3.348918e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.552570e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.626260e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.135202e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.350542e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 6.748221698410E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.120000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -1023,30 +1023,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.600233 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.006058 │ │ │ +Vacc_SASA: Time elapsed: 0.001605 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.898100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.062160e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.835900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.964100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.775400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.207561e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.929735e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.304901e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.532338e-01 │ │ │ Vprtstp: contraction number = 1.532338e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1078,32 +1078,32 @@ │ │ │ Vprtstp: contraction number = 3.529902e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.276975e-06 │ │ │ Vprtstp: contraction number = 3.528897e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.504551e-07 │ │ │ Vprtstp: contraction number = 3.527516e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.093590e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.937670e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.587770e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.801634e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.143395002184E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.230000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1124,28 +1124,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.973200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.489200e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.479600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 8.361400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.924800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.176611e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.556188e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.787443e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.140338e-01 │ │ │ Vprtstp: contraction number = 1.140338e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1162,32 +1162,32 @@ │ │ │ Vprtstp: contraction number = 1.066400e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.493481e-06 │ │ │ Vprtstp: contraction number = 1.074330e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.613267e-07 │ │ │ Vprtstp: contraction number = 1.080206e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.949700e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.820700e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.590662e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.812568e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 6.912847895210E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1231,28 +1231,28 @@ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 22.4432 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.977000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.029500e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.833200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.460000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.387000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.211959e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.969950e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.068049e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.151233e-01 │ │ │ Vprtstp: contraction number = 1.151233e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1269,32 +1269,32 @@ │ │ │ Vprtstp: contraction number = 1.065071e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.498104e-06 │ │ │ Vprtstp: contraction number = 1.072349e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.614370e-07 │ │ │ Vprtstp: contraction number = 1.077609e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.085570e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.991460e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.729458e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.934788e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.159793508256E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.499000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -1315,32 +1315,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000086 │ │ │ +Vacc_SASA: Time elapsed: 0.001754 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.942000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.277070e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.358900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.132000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.528700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.299501e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.392615e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.369026e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.470644e-01 │ │ │ Vprtstp: contraction number = 1.470644e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1366,32 +1366,32 @@ │ │ │ Vprtstp: contraction number = 2.846821e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.962532e-06 │ │ │ Vprtstp: contraction number = 2.852652e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 5.602483e-07 │ │ │ Vprtstp: contraction number = 2.854722e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.127580e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.018530e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.902837e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.143130e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.170869129315E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.080000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -1437,30 +1437,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.650584 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000069 │ │ │ +Vacc_SASA: Time elapsed: 0.000130 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.082100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.633730e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.830700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.903300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.750500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.311636e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.939201e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.784767e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.382011e-01 │ │ │ Vprtstp: contraction number = 1.382011e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1489,32 +1489,32 @@ │ │ │ Vprtstp: contraction number = 3.143969e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.077403e-06 │ │ │ Vprtstp: contraction number = 3.146378e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.391862e-07 │ │ │ Vprtstp: contraction number = 3.148184e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.475740e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.420380e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.370547e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.602014e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.162367825044E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.550000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1535,28 +1535,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.678600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.587880e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.689600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.525800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.604800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.274119e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.519515e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.247722e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.118955e-01 │ │ │ Vprtstp: contraction number = 1.118955e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1573,32 +1573,32 @@ │ │ │ Vprtstp: contraction number = 1.069169e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.490424e-06 │ │ │ Vprtstp: contraction number = 1.076150e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.611536e-07 │ │ │ Vprtstp: contraction number = 1.081260e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.392340e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.407210e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.771227e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.007004e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.417301695136E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.800000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.600000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1642,28 +1642,28 @@ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 27.9953 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.984600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.720200e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.823300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.674500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.216800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.505622e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.968924e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.551006e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.111894e-01 │ │ │ Vprtstp: contraction number = 1.111894e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1680,44 +1680,44 @@ │ │ │ Vprtstp: contraction number = 1.067651e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.469870e-06 │ │ │ Vprtstp: contraction number = 1.074950e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.588283e-07 │ │ │ Vprtstp: contraction number = 1.080560e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.094910e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.877570e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.894203e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.151477e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.406572492944E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.550000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.287908e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.840597e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:05:45 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:17:30 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path acetic-acid.xml │ │ │ @@ -2194,32 +2194,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001294 │ │ │ +Vacc_SASA: Time elapsed: 0.005699 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.043800e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.274720e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.765500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.299600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.516200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.330664e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.230470e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.905123e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.596091e-01 │ │ │ Vprtstp: contraction number = 2.596091e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2239,32 +2239,32 @@ │ │ │ Vprtstp: contraction number = 1.697798e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.455171e-06 │ │ │ Vprtstp: contraction number = 1.730577e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.805682e-07 │ │ │ Vprtstp: contraction number = 1.752050e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.392570e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.417270e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.472117e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.704801e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 4.781452735910E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.053700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -2310,30 +2310,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0553032 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001161 │ │ │ +Vacc_SASA: Time elapsed: 0.034926 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.050170e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.295460e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.820300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.327200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.689700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.323819e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.595190e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.025385e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.192618e-01 │ │ │ Vprtstp: contraction number = 2.192618e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2353,32 +2353,32 @@ │ │ │ Vprtstp: contraction number = 1.807641e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.267839e-06 │ │ │ Vprtstp: contraction number = 1.838237e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.807397e-07 │ │ │ Vprtstp: contraction number = 1.861749e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.373990e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.186170e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.298457e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.526654e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.040239618722E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.060000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2399,28 +2399,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.278700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.424120e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.842600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.962900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.751100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.389387e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222916e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.588080e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.679930e-01 │ │ │ Vprtstp: contraction number = 1.679930e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2437,32 +2437,32 @@ │ │ │ Vprtstp: contraction number = 1.043091e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.862252e-06 │ │ │ Vprtstp: contraction number = 1.059323e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.994142e-07 │ │ │ Vprtstp: contraction number = 1.070823e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.964420e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.899200e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.161606e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.392590e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 4.800125490193E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.000000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2506,28 +2506,28 @@ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 1.14339 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.031800e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.877100e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.744900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.637600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.933200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.419557e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.632308e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101321e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.651787e-01 │ │ │ Vprtstp: contraction number = 1.651787e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2544,30 +2544,30 @@ │ │ │ Vprtstp: contraction number = 1.055047e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.934803e-06 │ │ │ Vprtstp: contraction number = 1.064764e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.073576e-07 │ │ │ Vprtstp: contraction number = 1.071724e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.052800e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.903300e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.848244e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.107658e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.058572238076E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.800000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ @@ -2590,32 +2590,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001163 │ │ │ +Vacc_SASA: Time elapsed: 0.003429 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.262120e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.061460e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.852700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.315600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.979300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.327789e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.163235e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.412981e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.505354e-01 │ │ │ Vprtstp: contraction number = 1.505354e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2635,32 +2635,32 @@ │ │ │ Vprtstp: contraction number = 1.898671e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.115563e-06 │ │ │ Vprtstp: contraction number = 1.948490e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.143002e-07 │ │ │ Vprtstp: contraction number = 1.971715e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.320960e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.251530e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.115542e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.341673e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 6.749438220873E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.000000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.600000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -2706,30 +2706,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.607375 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.001172 │ │ │ +Vacc_SASA: Time elapsed: 0.003065 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.073670e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.817330e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.779500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.494500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.450200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.553894e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.689947e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.751613e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.420228e-01 │ │ │ Vprtstp: contraction number = 1.420228e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2749,32 +2749,32 @@ │ │ │ Vprtstp: contraction number = 1.900725e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.720330e-06 │ │ │ Vprtstp: contraction number = 1.966740e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.430374e-07 │ │ │ Vprtstp: contraction number = 1.996219e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.207660e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.986000e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.260870e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.507447e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.143498275233E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.600000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.800000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2795,28 +2795,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.852900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.052160e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.362900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.117960e-01 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.004000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.471626e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.214886e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105086e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.140338e-01 │ │ │ Vprtstp: contraction number = 1.140338e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2833,32 +2833,32 @@ │ │ │ Vprtstp: contraction number = 1.066400e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.493481e-06 │ │ │ Vprtstp: contraction number = 1.074330e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.613267e-07 │ │ │ Vprtstp: contraction number = 1.080206e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.854810e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.588620e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.804692e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.064834e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 6.912847895210E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.500000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2902,28 +2902,28 @@ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 22.4432 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.802100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.739100e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.708000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.138500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.612800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.214955e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.619749e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.407695e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.151233e-01 │ │ │ Vprtstp: contraction number = 1.151233e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2940,32 +2940,32 @@ │ │ │ Vprtstp: contraction number = 1.065071e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.498104e-06 │ │ │ Vprtstp: contraction number = 1.072349e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.614370e-07 │ │ │ Vprtstp: contraction number = 1.077609e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.817020e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.685230e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.688041e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.902341e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.159793508256E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.681400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -2986,32 +2986,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000069 │ │ │ +Vacc_SASA: Time elapsed: 0.000451 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.168200e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.861380e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.368300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.847800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.090700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.244277e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.081835e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.703781e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.382442e-01 │ │ │ Vprtstp: contraction number = 1.382442e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3031,32 +3031,32 @@ │ │ │ Vprtstp: contraction number = 1.741425e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.778515e-06 │ │ │ Vprtstp: contraction number = 1.810766e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.297938e-07 │ │ │ Vprtstp: contraction number = 1.854322e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.196850e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.938290e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.121026e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.346532e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.171449807940E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.300000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ @@ -3102,30 +3102,30 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.654498 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000068 │ │ │ +Vacc_SASA: Time elapsed: 0.002802 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.870600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.832910e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.661100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.429300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.887600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.223278e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.582107e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.042221e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.297624e-01 │ │ │ Vprtstp: contraction number = 1.297624e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3145,32 +3145,32 @@ │ │ │ Vprtstp: contraction number = 1.701143e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.306208e-06 │ │ │ Vprtstp: contraction number = 1.773242e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.371381e-07 │ │ │ Vprtstp: contraction number = 1.815470e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.115580e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.816720e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.279411e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.507090e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.163593499843E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.720000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3191,28 +3191,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.649400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.295420e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.757700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.417000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.067100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.446268e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.010709e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.399480e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.118955e-01 │ │ │ Vprtstp: contraction number = 1.118955e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3229,32 +3229,32 @@ │ │ │ Vprtstp: contraction number = 1.069169e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.490424e-06 │ │ │ Vprtstp: contraction number = 1.076150e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.611536e-07 │ │ │ Vprtstp: contraction number = 1.081260e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.694810e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.557850e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.145883e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.419191e+01 │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 3.417301695136E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.370000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3298,28 +3298,28 @@ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 27.9953 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.894300e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.476500e-02 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.667800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.143800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.109900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.411394e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.387949e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.739199e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.111894e-01 │ │ │ Vprtstp: contraction number = 1.111894e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3336,34 +3336,34 @@ │ │ │ Vprtstp: contraction number = 1.067651e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.469870e-06 │ │ │ Vprtstp: contraction number = 1.074950e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.588283e-07 │ │ │ Vprtstp: contraction number = 1.080560e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.811910e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.555260e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.971634e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.214497e+01 │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 5.406572492944E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.900000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.190000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.681733e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.036915e+02 │ │ ├── ./usr/share/apbs/examples/pka-lig/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:05:59 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:27:49 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ @@ -340,31 +340,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.018342 │ │ │ +Vacc_SASA: Time elapsed: 0.104866 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.456400e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.195910e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.695200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 9.821800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.751680e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.207934e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.693040e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.556529e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.561608e-01 │ │ │ Vprtstp: contraction number = 1.561608e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -390,32 +390,32 @@ │ │ │ Vprtstp: contraction number = 2.750705e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.932473e-06 │ │ │ Vprtstp: contraction number = 2.767817e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 5.373027e-07 │ │ │ Vprtstp: contraction number = 2.780389e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.426942e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.702123e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.608734e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.825677e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.795090079491E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.900000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.630000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -461,29 +461,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.123733 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.018827 │ │ │ +Vacc_SASA: Time elapsed: 0.030840 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.200700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.265670e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.564000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 6.475900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.727040e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.298308e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.122635e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.119589e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.152775e-01 │ │ │ Vprtstp: contraction number = 2.152775e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -515,32 +515,32 @@ │ │ │ Vprtstp: contraction number = 3.353090e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.328976e-06 │ │ │ Vprtstp: contraction number = 3.371305e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.496116e-07 │ │ │ Vprtstp: contraction number = 3.383143e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.841729e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.085752e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.446634e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.664070e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.468794426258E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.460000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -561,31 +561,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.608412 │ │ │ +Vacc_SASA: Time elapsed: 2.295099 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.782052e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.603087e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.540700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 9.091800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.969090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.182127e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.032325e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.042594e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.188493e-01 │ │ │ Vprtstp: contraction number = 1.188493e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -638,32 +638,32 @@ │ │ │ Vprtstp: contraction number = 6.152114e-01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.141886e-06 │ │ │ Vprtstp: contraction number = 6.186689e-01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 7.101689e-07 │ │ │ Vprtstp: contraction number = 6.219261e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.716699e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.991868e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.367896e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.573756e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.467100888191E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.990000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.095000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -709,29 +709,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 119417 kT │ │ │ VPMG::extEnergy: extDiEnergy = 58605.1 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.576958 │ │ │ +Vacc_SASA: Time elapsed: 2.503878 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.838476e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.034502e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.587000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 8.944100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.744790e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.271866e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.083742e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.694353e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.393577e-01 │ │ │ Vprtstp: contraction number = 1.393577e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -766,32 +766,32 @@ │ │ │ Vprtstp: contraction number = 4.796270e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.074713e-06 │ │ │ Vprtstp: contraction number = 4.999984e-01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 5.553244e-07 │ │ │ Vprtstp: contraction number = 5.167187e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.694169e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.931823e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.284349e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.511539e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.427017897319E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.760000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.660000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -812,31 +812,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.606240 │ │ │ +Vacc_SASA: Time elapsed: 2.505455 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.800385e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.974563e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.544100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.053580e-01 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.051170e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.295795e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.461040e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.274690e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189544e-01 │ │ │ Vprtstp: contraction number = 1.189544e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -889,32 +889,32 @@ │ │ │ Vprtstp: contraction number = 6.138674e-01 │ │ │ Vprtstp: iteration = 18 │ │ │ Vprtstp: relative residual = 1.173454e-06 │ │ │ Vprtstp: contraction number = 6.173088e-01 │ │ │ Vprtstp: iteration = 19 │ │ │ Vprtstp: relative residual = 7.281097e-07 │ │ │ Vprtstp: contraction number = 6.204841e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.610509e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.883413e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.693483e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.915819e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.485227452845E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.260000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.330000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -960,29 +960,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 119415 kT │ │ │ VPMG::extEnergy: extDiEnergy = 58604.6 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.624555 │ │ │ +Vacc_SASA: Time elapsed: 2.035356 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.851966e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.564212e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.644500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.550300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.750570e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.245421e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.932646e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.091961e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.423446e-01 │ │ │ Vprtstp: contraction number = 1.423446e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1017,38 +1017,38 @@ │ │ │ Vprtstp: contraction number = 4.820331e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 1.206020e-06 │ │ │ Vprtstp: contraction number = 5.012326e-01 │ │ │ Vprtstp: iteration = 13 │ │ │ Vprtstp: relative residual = 6.232432e-07 │ │ │ Vprtstp: contraction number = 5.167767e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.715543e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.960870e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.585303e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.794091e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.511771058265E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.980000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.120000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.106886e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.551673e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:12 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:35:25 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ @@ -1384,31 +1384,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.018433 │ │ │ +Vacc_SASA: Time elapsed: 0.080997 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.124670e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.761690e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.584200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 9.728000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.720750e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.133457e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.304900e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.663077e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.452428e-01 │ │ │ Vprtstp: contraction number = 1.452428e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1428,32 +1428,32 @@ │ │ │ Vprtstp: contraction number = 1.683190e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.126022e-06 │ │ │ Vprtstp: contraction number = 1.729184e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.755158e-07 │ │ │ Vprtstp: contraction number = 1.766283e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.161678e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.417728e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.742380e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.938955e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.796545857614E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.900000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.420000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1499,29 +1499,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.131443 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.018691 │ │ │ +Vacc_SASA: Time elapsed: 0.021436 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.401740e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.610530e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.546200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 6.391200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.711320e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.232383e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.376809e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.275430e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.793309e-01 │ │ │ Vprtstp: contraction number = 1.793309e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1541,32 +1541,32 @@ │ │ │ Vprtstp: contraction number = 1.800338e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.360443e-06 │ │ │ Vprtstp: contraction number = 1.860813e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.400789e-07 │ │ │ Vprtstp: contraction number = 1.904746e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.159189e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.398071e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.892583e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.104317e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.475324562943E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.100000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.330000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1587,31 +1587,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.598052 │ │ │ +Vacc_SASA: Time elapsed: 2.195762 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.000700e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.008509e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.593600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.312130e-01 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.739530e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.362820e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.793865e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.701556e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.027357e-02 │ │ │ Vprtstp: contraction number = 9.027357e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1631,32 +1631,32 @@ │ │ │ Vprtstp: contraction number = 1.817922e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.545186e-06 │ │ │ Vprtstp: contraction number = 1.999061e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.371519e-07 │ │ │ Vprtstp: contraction number = 2.181950e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.078606e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.322297e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.398046e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.624187e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.474786197493E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.260000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.751000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1702,29 +1702,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 120029 kT │ │ │ VPMG::extEnergy: extDiEnergy = 58911.7 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.268857 │ │ │ +Vacc_SASA: Time elapsed: 2.415407 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.715646e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.271001e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.450500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.980100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.251390e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.236141e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.891243e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065427e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.164650e-01 │ │ │ Vprtstp: contraction number = 1.164650e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1744,32 +1744,32 @@ │ │ │ Vprtstp: contraction number = 1.751675e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.167167e-06 │ │ │ Vprtstp: contraction number = 1.847486e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.216013e-07 │ │ │ Vprtstp: contraction number = 1.898626e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.003173e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.289681e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.876364e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.098406e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.434258164340E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.860000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.760000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1790,31 +1790,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.609450 │ │ │ +Vacc_SASA: Time elapsed: 2.291792 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.045351e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.111489e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.545500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 8.998200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.870560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.225468e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.221217e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.406199e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.976616e-02 │ │ │ Vprtstp: contraction number = 8.976616e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1834,30 +1834,30 @@ │ │ │ Vprtstp: contraction number = 1.851080e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.610068e-06 │ │ │ Vprtstp: contraction number = 2.038795e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.565510e-07 │ │ │ Vprtstp: contraction number = 2.214509e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.039097e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.294804e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.756441e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.972113e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.493215172512E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.240000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.890000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ @@ -1905,29 +1905,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 120027 kT │ │ │ VPMG::extEnergy: extDiEnergy = 58911 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.604351 │ │ │ +Vacc_SASA: Time elapsed: 2.363057 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.005694e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.021634e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.442700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 6.400200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.701240e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.147264e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.549459e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.731422e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.180177e-01 │ │ │ Vprtstp: contraction number = 1.180177e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1947,38 +1947,38 @@ │ │ │ Vprtstp: contraction number = 1.739107e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.163103e-06 │ │ │ Vprtstp: contraction number = 1.834388e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.205019e-07 │ │ │ Vprtstp: contraction number = 1.895807e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.739140e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.198017e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.680869e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.871928e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.519180536568E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.830000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.700000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.649742e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.000559e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:23 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:39:49 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ @@ -2314,31 +2314,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.018588 │ │ │ +Vacc_SASA: Time elapsed: 0.078853 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.589000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.626080e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.750800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 8.163800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.862260e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.155221e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.259860e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.540619e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.599213e-01 │ │ │ Vprtstp: contraction number = 1.599213e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2367,32 +2367,32 @@ │ │ │ Vprtstp: contraction number = 2.963523e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.017970e-06 │ │ │ Vprtstp: contraction number = 2.969958e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.027030e-07 │ │ │ Vprtstp: contraction number = 2.973596e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.673089e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.961958e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.720781e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.921219e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.810710599589E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.140000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2438,29 +2438,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.127039 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.020626 │ │ │ +Vacc_SASA: Time elapsed: 0.071018 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.282470e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.933820e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.598200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.375300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.719620e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.401283e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.687130e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.285033e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.128592e-01 │ │ │ Vprtstp: contraction number = 2.128592e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2492,32 +2492,32 @@ │ │ │ Vprtstp: contraction number = 3.367480e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 1.365284e-06 │ │ │ Vprtstp: contraction number = 3.379196e-01 │ │ │ Vprtstp: iteration = 12 │ │ │ Vprtstp: relative residual = 4.626034e-07 │ │ │ Vprtstp: contraction number = 3.388332e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.705974e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.948015e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.179158e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.403319e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.488596110069E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.100000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.190000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2538,31 +2538,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.135223 │ │ │ +Vacc_SASA: Time elapsed: 1.371887 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.694879e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.489176e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.651200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 9.882800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.825790e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.327644e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.357632e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.939767e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.008467e-01 │ │ │ Vprtstp: contraction number = 1.008467e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2591,32 +2591,32 @@ │ │ │ Vprtstp: contraction number = 4.011046e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.434965e-06 │ │ │ Vprtstp: contraction number = 4.261259e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.351498e-07 │ │ │ Vprtstp: contraction number = 4.426237e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.421662e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.687004e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.945912e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.163792e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.502732517701E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.280000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.310000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2662,29 +2662,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 122258 kT │ │ │ VPMG::extEnergy: extDiEnergy = 60015.6 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.117791 │ │ │ +Vacc_SASA: Time elapsed: 1.806894 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.839928e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.422638e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.533300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.666000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.709090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.172618e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.862083e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.344393e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.444678e-01 │ │ │ Vprtstp: contraction number = 1.444678e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2713,32 +2713,32 @@ │ │ │ Vprtstp: contraction number = 3.502797e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.520619e-06 │ │ │ Vprtstp: contraction number = 3.554465e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.554489e-07 │ │ │ Vprtstp: contraction number = 3.652782e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.363961e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.598745e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.006328e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.225167e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.462158714651E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.950000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.890000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -2759,31 +2759,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.130253 │ │ │ +Vacc_SASA: Time elapsed: 1.661566 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.721165e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.908674e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.754400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 8.594000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.865940e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.236523e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321347e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.795838e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.951095e-02 │ │ │ Vprtstp: contraction number = 9.951095e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2812,30 +2812,30 @@ │ │ │ Vprtstp: contraction number = 3.973081e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.298337e-06 │ │ │ Vprtstp: contraction number = 4.223462e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.734047e-07 │ │ │ Vprtstp: contraction number = 4.416455e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.461166e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.711692e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.890290e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.098998e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.522103263384E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.290000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.730000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ @@ -2883,29 +2883,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 122254 kT │ │ │ VPMG::extEnergy: extDiEnergy = 60014.8 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.141399 │ │ │ +Vacc_SASA: Time elapsed: 1.457974 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.792267e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.592472e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.651400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.902200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.947280e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.120705e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.673641e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.230138e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.413483e-01 │ │ │ Vprtstp: contraction number = 1.413483e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -2934,38 +2934,38 @@ │ │ │ Vprtstp: contraction number = 3.543205e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.106047e-06 │ │ │ Vprtstp: contraction number = 3.675340e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.216013e-07 │ │ │ Vprtstp: contraction number = 3.811783e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.522695e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.782253e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.766034e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.954728e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.548006855100E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.990000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.370000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.200000e-05 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.829056e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.607700e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:34 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:45:29 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ @@ -3301,31 +3301,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.017606 │ │ │ +Vacc_SASA: Time elapsed: 0.097878 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.621190e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.701760e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 6.070400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 7.888200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.416830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.115523e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.547110e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.871323e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.452175e-01 │ │ │ Vprtstp: contraction number = 1.452175e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3345,32 +3345,32 @@ │ │ │ Vprtstp: contraction number = 1.752116e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.443360e-06 │ │ │ Vprtstp: contraction number = 1.802654e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 4.491907e-07 │ │ │ Vprtstp: contraction number = 1.838414e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.274093e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.612570e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.812573e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.012630e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.816452194100E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.500000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.300000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3416,29 +3416,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.133537 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.022710 │ │ │ +Vacc_SASA: Time elapsed: 0.068427 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.182810e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.124887e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.006100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.004600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.312080e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.116031e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.961028e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.411118e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.775500e-01 │ │ │ Vprtstp: contraction number = 1.775500e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3458,32 +3458,32 @@ │ │ │ Vprtstp: contraction number = 1.827663e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.496113e-06 │ │ │ Vprtstp: contraction number = 1.891043e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.759954e-07 │ │ │ Vprtstp: contraction number = 1.933563e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.199417e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.500618e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.031120e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.227189e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.493961459749E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.100000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3504,31 +3504,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.878974 │ │ │ +Vacc_SASA: Time elapsed: 1.737906 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.652456e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.345935e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.869800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 7.815300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.696860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.215260e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.067657e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.994166e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.789951e-02 │ │ │ Vprtstp: contraction number = 8.789951e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3545,32 +3545,32 @@ │ │ │ Vprtstp: contraction number = 1.398889e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 4.364929e-06 │ │ │ Vprtstp: contraction number = 1.509054e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.472971e-07 │ │ │ Vprtstp: contraction number = 1.941148e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.744240e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.125038e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.488870e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.699386e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.503907197961E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.880000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.500000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3616,29 +3616,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 122356 kT │ │ │ VPMG::extEnergy: extDiEnergy = 60065 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.104799 │ │ │ +Vacc_SASA: Time elapsed: 1.534426 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.955333e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.051397e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.552500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.962400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.716060e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.139364e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.133197e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.977830e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.361361e-01 │ │ │ Vprtstp: contraction number = 1.361361e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3658,32 +3658,32 @@ │ │ │ Vprtstp: contraction number = 1.780896e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.357861e-06 │ │ │ Vprtstp: contraction number = 1.814853e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.460991e-07 │ │ │ Vprtstp: contraction number = 1.812402e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.030477e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.252587e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.680844e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.868596e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.463376211100E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.740000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.470000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.600000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3704,31 +3704,31 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.127191 │ │ │ +Vacc_SASA: Time elapsed: 1.489567 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.917578e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.873273e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.056800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 7.084700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.825440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.145013e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233592e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.314104e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.694592e-02 │ │ │ Vprtstp: contraction number = 8.694592e-02 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3745,32 +3745,32 @@ │ │ │ Vprtstp: contraction number = 1.389852e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 4.160523e-06 │ │ │ Vprtstp: contraction number = 1.496124e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.105844e-07 │ │ │ Vprtstp: contraction number = 1.948275e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.742740e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.225550e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.273084e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.462709e+01 │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.523234125638E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.110000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.370000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -3816,29 +3816,29 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 122353 kT │ │ │ VPMG::extEnergy: extDiEnergy = 60064.1 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 1.119172 │ │ │ +Vacc_SASA: Time elapsed: 1.476136 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.891165e+00 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.801121e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.500000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.930400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.767940e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.062979e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.544296e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.588556e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.348493e-01 │ │ │ Vprtstp: contraction number = 1.348493e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -3858,28 +3858,28 @@ │ │ │ Vprtstp: contraction number = 1.735657e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.117086e-06 │ │ │ Vprtstp: contraction number = 1.891826e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.184693e-07 │ │ │ Vprtstp: contraction number = 1.955708e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.071959e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.300449e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.591775e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.777655e+01 │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.549194232887E+05 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.960000e-04 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.570000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.654489e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.848199e+02 │ │ ├── ./usr/share/apbs/examples/point-pmf/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:45 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:49:26 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ @@ -184,28 +184,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.649100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.572710e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.736300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.769100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.004700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.168477e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103750e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.316494e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -222,33 +222,33 @@ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.909860e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.744100e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.567188e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.778049e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.623000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.161400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -269,28 +269,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.422500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.437000e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.721900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.996700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.363200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.192183e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.135390e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.028965e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.116487e-01 │ │ │ Vprtstp: contraction number = 1.116487e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -307,33 +307,33 @@ │ │ │ Vprtstp: contraction number = 1.068390e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.476968e-06 │ │ │ Vprtstp: contraction number = 1.075610e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.596976e-07 │ │ │ Vprtstp: contraction number = 1.081253e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.930480e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.771610e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.600192e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.809489e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.241648379021E+01 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.600000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.270400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 0.5 │ │ │ Vpbe_ctor2: solute dimensions = 1 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -354,28 +354,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.567900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.719300e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.373400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.998100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.910900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.165027e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.042590e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.861736e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.110273e-01 │ │ │ Vprtstp: contraction number = 1.110273e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -392,39 +392,39 @@ │ │ │ Vprtstp: contraction number = 1.067630e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.464818e-06 │ │ │ Vprtstp: contraction number = 1.074713e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.582462e-07 │ │ │ Vprtstp: contraction number = 1.080314e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.887870e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.597110e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.623876e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.831206e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.660589930493E+02 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.565000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.952000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.204965e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.488379e+01 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:45 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:51:15 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ @@ -604,28 +604,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.231300e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.867660e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.630000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.591800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.622500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.195794e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016450e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.418004e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -642,33 +642,33 @@ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.862030e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.673560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.662782e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.883862e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.623000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.698000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -689,28 +689,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.453700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.479340e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.129300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.467800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.076600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.228969e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.051160e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.141095e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115116e-01 │ │ │ Vprtstp: contraction number = 1.115116e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -727,33 +727,33 @@ │ │ │ Vprtstp: contraction number = 1.068563e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.477070e-06 │ │ │ Vprtstp: contraction number = 1.075813e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.597562e-07 │ │ │ Vprtstp: contraction number = 1.081575e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.811690e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.653440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.664414e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.884555e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.209948502984E+01 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.763000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.664900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1 │ │ │ Vpbe_ctor2: solute dimensions = 2 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -774,28 +774,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.442000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.635770e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.356200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.031300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.889300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.222628e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.907600e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.036829e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.112280e-01 │ │ │ Vprtstp: contraction number = 1.112280e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -812,39 +812,39 @@ │ │ │ Vprtstp: contraction number = 1.067265e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.466596e-06 │ │ │ Vprtstp: contraction number = 1.074314e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.583845e-07 │ │ │ Vprtstp: contraction number = 1.079946e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.825560e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.542090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.773903e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.984884e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.681569832028E+02 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.586000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.831000e-03 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.187480e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.811369e+01 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:46 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:53:08 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ @@ -1024,28 +1024,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.612700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.577280e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.724100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.599500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.809900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.239789e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.176060e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.464617e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1062,33 +1062,33 @@ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.951360e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.868660e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.743395e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.968062e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.632000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.605300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1109,28 +1109,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.436600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.304130e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.683800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.273300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.166100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.321583e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.256880e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.241626e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.122494e-01 │ │ │ Vprtstp: contraction number = 1.122494e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1147,33 +1147,33 @@ │ │ │ Vprtstp: contraction number = 1.068256e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.484900e-06 │ │ │ Vprtstp: contraction number = 1.075504e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.605755e-07 │ │ │ Vprtstp: contraction number = 1.081389e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.810320e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.673350e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.790947e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.024271e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.079207063662E+02 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.570000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.291200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 1.5 │ │ │ Vpbe_ctor2: solute dimensions = 3 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1194,28 +1194,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.513600e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.617820e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.386300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.502400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.783100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.201303e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.131970e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.278544e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.117126e-01 │ │ │ Vprtstp: contraction number = 1.117126e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1232,39 +1232,39 @@ │ │ │ Vprtstp: contraction number = 1.067223e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.472511e-06 │ │ │ Vprtstp: contraction number = 1.074345e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.590395e-07 │ │ │ Vprtstp: contraction number = 1.080057e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.874250e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.583420e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.737346e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.962533e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.915601904303E+02 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.561000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.746100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.300000e-05 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.211220e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 9.023296e+01 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:46 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:55:04 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ @@ -1444,28 +1444,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.207500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.927490e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.731400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.627500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.566200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.254955e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112000e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.494626e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1482,33 +1482,33 @@ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.947730e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.863650e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.696239e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.925371e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.607000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.365200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1529,28 +1529,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.401900e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.376210e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.743400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.333000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.979500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.226888e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.111110e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.179302e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.115116e-01 │ │ │ Vprtstp: contraction number = 1.115116e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1567,33 +1567,33 @@ │ │ │ Vprtstp: contraction number = 1.068563e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.477070e-06 │ │ │ Vprtstp: contraction number = 1.075813e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.597562e-07 │ │ │ Vprtstp: contraction number = 1.081575e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.818390e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.623430e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.817578e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.036041e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 8.209948502984E+01 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.598000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.131500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 2 │ │ │ Vpbe_ctor2: solute dimensions = 4 x 0 x 0 │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1614,28 +1614,28 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.434700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.574390e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.401100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.503600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.847000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.256479e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.932990e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.240278e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.113661e-01 │ │ │ Vprtstp: contraction number = 1.113661e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1652,29 +1652,29 @@ │ │ │ Vprtstp: contraction number = 1.067553e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.470482e-06 │ │ │ Vprtstp: contraction number = 1.074604e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.588507e-07 │ │ │ Vprtstp: contraction number = 1.080263e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.813180e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.533560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.753162e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.973759e+01 │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.645453654146E+02 kT │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.595000e-03 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.286200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.183128e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 9.001080e+01 │ │ ├── ./usr/share/apbs/examples/protein-rna/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:48 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 21:02:59 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -274,151 +274,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.303925 │ │ │ +Vacc_SASA: Time elapsed: 0.432097 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.993320e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.204872e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.142600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.673800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.465160e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.051921e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.473450e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.467632e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3489953.107213 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.930480e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.887603e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.541420e+05 │ │ │ Vprtstp: contraction number = 4.541420e+05 │ │ │ Vnewton: Attempting damping, relres = 0.152961 │ │ │ Vnewton: Attempting damping, relres = 0.557868 │ │ │ Vnewton: Damping accepted, relres = 0.152961 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.529613e-01 │ │ │ Vprtstp: contraction number = 1.529613e-01 │ │ │ Vnewton: Using errtol_s: 533827.862441 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.315721e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.434239e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.616204e+04 │ │ │ Vprtstp: contraction number = 7.616204e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.889845e-02 │ │ │ Vprtstp: contraction number = 1.889265e-01 │ │ │ Vnewton: Using errtol_s: 100854.249053 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.566258e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.580951e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.621156e+04 │ │ │ Vprtstp: contraction number = 1.621156e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.485254e-03 │ │ │ Vprtstp: contraction number = 2.244153e-01 │ │ │ Vnewton: Using errtol_s: 22633.233232 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.816993e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.751648e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.163481e+03 │ │ │ Vprtstp: contraction number = 4.163481e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.448984e-03 │ │ │ Vprtstp: contraction number = 2.234275e-01 │ │ │ Vnewton: Using errtol_s: 5056.886378 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.067564e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.903953e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.135331e+03 │ │ │ Vprtstp: contraction number = 1.135331e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.105204e-04 │ │ │ Vprtstp: contraction number = 2.143021e-01 │ │ │ Vnewton: Using errtol_s: 1083.701574 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.330058e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074565e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.001303e+02 │ │ │ Vprtstp: contraction number = 3.001303e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 7.746175e-05 │ │ │ Vprtstp: contraction number = 2.494579e-01 │ │ │ Vnewton: Using errtol_s: 270.337872 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.578583e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.265371e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.503484e+01 │ │ │ Vprtstp: contraction number = 8.503484e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.192913e-05 │ │ │ Vprtstp: contraction number = 2.830962e-01 │ │ │ Vnewton: Using errtol_s: 76.531632 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.830477e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.460581e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.526272e+01 │ │ │ Vprtstp: contraction number = 2.526272e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.514831e-06 │ │ │ Vprtstp: contraction number = 2.970857e-01 │ │ │ Vnewton: Using errtol_s: 22.736454 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.079659e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.667293e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.640103e+00 │ │ │ Vprtstp: contraction number = 7.640103e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.970254e-06 │ │ │ Vprtstp: contraction number = 3.024259e-01 │ │ │ Vnewton: Using errtol_s: 6.876093 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.342669e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.876480e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.337433e+00 │ │ │ Vprtstp: contraction number = 2.337433e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.027844e-07 │ │ │ Vprtstp: contraction number = 3.059426e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.681791e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.902330e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.038796e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.050974e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -428,17 +428,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.965827433401E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.569434563500E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.283478359962E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.104300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.759800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.025 │ │ │ Vpbe_ctor2: xkappa = 0.0514861 │ │ │ @@ -485,160 +485,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.194992 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.295690 │ │ │ +Vacc_SASA: Time elapsed: 0.491658 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.611690e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.287522e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.971500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.350800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.470340e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.185332e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.462312e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.090649e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3601925.484823 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.599362e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.117880e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.484865e+05 │ │ │ Vprtstp: contraction number = 5.484865e+05 │ │ │ Vnewton: Attempting damping, relres = 0.170948 │ │ │ Vnewton: Attempting damping, relres = 0.567920 │ │ │ Vnewton: Damping accepted, relres = 0.170948 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.709480e-01 │ │ │ Vprtstp: contraction number = 1.709480e-01 │ │ │ Vnewton: Using errtol_s: 615741.974888 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.932916e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.347674e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.034638e+05 │ │ │ Vprtstp: contraction number = 1.034638e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.462084e-02 │ │ │ Vprtstp: contraction number = 2.025226e-01 │ │ │ Vnewton: Using errtol_s: 124701.671212 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.193877e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.564389e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.424561e+04 │ │ │ Vprtstp: contraction number = 2.424561e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.233375e-03 │ │ │ Vprtstp: contraction number = 2.378156e-01 │ │ │ Vnewton: Using errtol_s: 29656.002425 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.443809e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.777789e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.562093e+03 │ │ │ Vprtstp: contraction number = 6.562093e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.983416e-03 │ │ │ Vprtstp: contraction number = 2.408995e-01 │ │ │ Vnewton: Using errtol_s: 7144.117639 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.693265e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.987424e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.862413e+03 │ │ │ Vprtstp: contraction number = 1.862413e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.794286e-04 │ │ │ Vprtstp: contraction number = 2.417186e-01 │ │ │ Vnewton: Using errtol_s: 1726.865972 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.930925e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.188287e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.263950e+02 │ │ │ Vprtstp: contraction number = 5.263950e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.315588e-04 │ │ │ Vprtstp: contraction number = 2.744075e-01 │ │ │ Vnewton: Using errtol_s: 473.865007 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.176836e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.391353e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.568838e+02 │ │ │ Vprtstp: contraction number = 1.568838e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.920007e-05 │ │ │ Vprtstp: contraction number = 2.979661e-01 │ │ │ Vnewton: Using errtol_s: 141.195715 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.410137e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.604623e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.889017e+01 │ │ │ Vprtstp: contraction number = 4.889017e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.221601e-05 │ │ │ Vprtstp: contraction number = 3.116325e-01 │ │ │ Vnewton: Using errtol_s: 44.001172 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.644806e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.816694e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.562922e+01 │ │ │ Vprtstp: contraction number = 1.562922e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.905217e-06 │ │ │ Vprtstp: contraction number = 3.196802e-01 │ │ │ Vnewton: Using errtol_s: 14.066301 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.890931e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.025084e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.094993e+00 │ │ │ Vprtstp: contraction number = 5.094993e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.273067e-06 │ │ │ Vprtstp: contraction number = 3.259914e-01 │ │ │ Vnewton: Using errtol_s: 4.585493 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.124570e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.233295e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.686155e+00 │ │ │ Vprtstp: contraction number = 1.686155e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.213135e-07 │ │ │ Vprtstp: contraction number = 3.309436e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.843300e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.064764e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.334434e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.347370e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -648,17 +648,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.946137752289E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.954048421546E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475783126623E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.015200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.829600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -685,151 +685,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.107186 │ │ │ +Vacc_SASA: Time elapsed: 0.206578 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.554430e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.079120e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.935600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.075050e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.460250e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.130708e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.823172e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.460103e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 990625.209730 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.964731e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.483755e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.350454e+05 │ │ │ Vprtstp: contraction number = 1.350454e+05 │ │ │ Vnewton: Attempting damping, relres = 0.127353 │ │ │ Vnewton: Attempting damping, relres = 0.559577 │ │ │ Vnewton: Damping accepted, relres = 0.127353 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.273531e-01 │ │ │ Vprtstp: contraction number = 1.273531e-01 │ │ │ Vnewton: Using errtol_s: 126159.215622 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.285298e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.650802e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.277893e+04 │ │ │ Vprtstp: contraction number = 2.277893e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.085042e-02 │ │ │ Vprtstp: contraction number = 1.637213e-01 │ │ │ Vnewton: Using errtol_s: 20654.953727 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.518732e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.807168e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.649050e+03 │ │ │ Vprtstp: contraction number = 4.649050e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.224159e-03 │ │ │ Vprtstp: contraction number = 2.025935e-01 │ │ │ Vnewton: Using errtol_s: 4184.558722 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.754569e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.961944e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.091881e+03 │ │ │ Vprtstp: contraction number = 1.091881e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 9.919956e-04 │ │ │ Vprtstp: contraction number = 2.348386e-01 │ │ │ Vnewton: Using errtol_s: 982.695801 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000191e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.107736e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.793836e+02 │ │ │ Vprtstp: contraction number = 2.793836e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 2.538250e-04 │ │ │ Vprtstp: contraction number = 2.558731e-01 │ │ │ Vnewton: Using errtol_s: 251.445454 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023718e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.261463e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.524959e+01 │ │ │ Vprtstp: contraction number = 7.524959e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 6.836556e-05 │ │ │ Vprtstp: contraction number = 2.693413e-01 │ │ │ Vnewton: Using errtol_s: 67.724647 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048448e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.413830e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.096668e+01 │ │ │ Vprtstp: contraction number = 2.096668e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.904859e-05 │ │ │ Vprtstp: contraction number = 2.786284e-01 │ │ │ Vnewton: Using errtol_s: 18.870009 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073317e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.567228e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.985543e+00 │ │ │ Vprtstp: contraction number = 5.985543e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 5.437969e-06 │ │ │ Vprtstp: contraction number = 2.854789e-01 │ │ │ Vnewton: Using errtol_s: 5.386989 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.098250e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.725505e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.740420e+00 │ │ │ Vprtstp: contraction number = 1.740420e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.581202e-06 │ │ │ Vprtstp: contraction number = 2.907706e-01 │ │ │ Vnewton: Using errtol_s: 1.566378 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121937e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.885601e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.132173e-01 │ │ │ Vprtstp: contraction number = 5.132173e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 4.662667e-07 │ │ │ Vprtstp: contraction number = 2.948812e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.588311e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.806297e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.565366e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.578284e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -839,17 +839,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.196703875366E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.838438031793E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.417360829181E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.171700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.044700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.025 │ │ │ Vpbe_ctor2: xkappa = 0.0514861 │ │ │ @@ -896,149 +896,149 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.017697 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108014 │ │ │ +Vacc_SASA: Time elapsed: 0.206359 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.902340e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.276140e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.947300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.238800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.444830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.254487e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.196077e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.047565e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1033125.204115 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.210408e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.076427e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.675387e+05 │ │ │ Vprtstp: contraction number = 1.675387e+05 │ │ │ Vnewton: Attempting damping, relres = 0.150147 │ │ │ Vnewton: Attempting damping, relres = 0.571307 │ │ │ Vnewton: Damping accepted, relres = 0.150147 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.501469e-01 │ │ │ Vprtstp: contraction number = 1.501469e-01 │ │ │ Vnewton: Using errtol_s: 155120.525305 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.242691e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.257619e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.209762e+04 │ │ │ Vprtstp: contraction number = 3.209762e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.810624e-02 │ │ │ Vprtstp: contraction number = 1.871917e-01 │ │ │ Vnewton: Using errtol_s: 29037.270087 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.267602e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.416027e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.331420e+03 │ │ │ Vprtstp: contraction number = 7.331420e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.387218e-03 │ │ │ Vprtstp: contraction number = 2.272526e-01 │ │ │ Vnewton: Using errtol_s: 6598.796330 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.291289e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.576128e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.824095e+03 │ │ │ Vprtstp: contraction number = 1.824095e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.589055e-03 │ │ │ Vprtstp: contraction number = 2.487867e-01 │ │ │ Vnewton: Using errtol_s: 1641.692880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.316838e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.735193e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.792383e+02 │ │ │ Vprtstp: contraction number = 4.792383e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.174858e-04 │ │ │ Vprtstp: contraction number = 2.627258e-01 │ │ │ Vnewton: Using errtol_s: 431.315051 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.341617e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.895205e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.310006e+02 │ │ │ Vprtstp: contraction number = 1.310006e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.141203e-04 │ │ │ Vprtstp: contraction number = 2.733515e-01 │ │ │ Vnewton: Using errtol_s: 117.900599 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.366449e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.065809e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.696481e+01 │ │ │ Vprtstp: contraction number = 3.696481e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.220165e-05 │ │ │ Vprtstp: contraction number = 2.821727e-01 │ │ │ Vnewton: Using errtol_s: 33.268335 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.390114e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.226022e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.072629e+01 │ │ │ Vprtstp: contraction number = 1.072629e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.344133e-06 │ │ │ Vprtstp: contraction number = 2.901756e-01 │ │ │ Vnewton: Using errtol_s: 9.653659 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.415049e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.385890e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.196371e+00 │ │ │ Vprtstp: contraction number = 3.196371e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.784497e-06 │ │ │ Vprtstp: contraction number = 2.979941e-01 │ │ │ Vnewton: Using errtol_s: 2.876734 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.439930e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.550338e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.745912e-01 │ │ │ Vprtstp: contraction number = 9.745912e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.490085e-07 │ │ │ Vprtstp: contraction number = 3.049056e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.629590e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.839926e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.649947e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.663808e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -1048,17 +1048,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.190473517167E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.070936043953E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.033615774534E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.175200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.870600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -1085,151 +1085,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.175070 │ │ │ +Vacc_SASA: Time elapsed: 0.262526 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.940600e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.970470e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.987900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.154400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.493440e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.030692e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.624092e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.736209e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3098216.768197 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.639378e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.761336e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.288533e+05 │ │ │ Vprtstp: contraction number = 4.288533e+05 │ │ │ Vnewton: Attempting damping, relres = 0.287242 │ │ │ Vnewton: Attempting damping, relres = 0.564665 │ │ │ Vnewton: Damping accepted, relres = 0.287242 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.872423e-01 │ │ │ Vprtstp: contraction number = 2.872423e-01 │ │ │ Vnewton: Using errtol_s: 889939.028652 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.671473e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.944478e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.459682e+04 │ │ │ Vprtstp: contraction number = 8.459682e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 7.479655e-02 │ │ │ Vprtstp: contraction number = 2.603953e-01 │ │ │ Vnewton: Using errtol_s: 231735.935287 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.697697e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.156382e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.140926e+04 │ │ │ Vprtstp: contraction number = 2.140926e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.197950e-02 │ │ │ Vprtstp: contraction number = 2.938571e-01 │ │ │ Vnewton: Using errtol_s: 68097.244831 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.722695e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.368341e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.306461e+03 │ │ │ Vprtstp: contraction number = 6.306461e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 6.113198e-03 │ │ │ Vprtstp: contraction number = 2.781319e-01 │ │ │ Vnewton: Using errtol_s: 18940.013709 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.747565e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.565502e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.039254e+03 │ │ │ Vprtstp: contraction number = 2.039254e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.310252e-03 │ │ │ Vprtstp: contraction number = 2.143317e-01 │ │ │ Vnewton: Using errtol_s: 4059.444466 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.772530e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.728012e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.729156e+02 │ │ │ Vprtstp: contraction number = 5.729156e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.010708e-04 │ │ │ Vprtstp: contraction number = 1.534596e-01 │ │ │ Vnewton: Using errtol_s: 622.960837 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.797487e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.874717e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.140542e+02 │ │ │ Vprtstp: contraction number = 1.140542e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.330907e-05 │ │ │ Vprtstp: contraction number = 1.656585e-01 │ │ │ Vnewton: Using errtol_s: 103.198728 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.822429e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.027705e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.743226e+01 │ │ │ Vprtstp: contraction number = 2.743226e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.968958e-06 │ │ │ Vprtstp: contraction number = 2.392429e-01 │ │ │ Vnewton: Using errtol_s: 24.689560 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.847379e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.176944e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.960222e+00 │ │ │ Vprtstp: contraction number = 7.960222e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.312364e-06 │ │ │ Vprtstp: contraction number = 2.901714e-01 │ │ │ Vnewton: Using errtol_s: 7.164205 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.872322e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.326404e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.414518e+00 │ │ │ Vprtstp: contraction number = 2.414518e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.013925e-07 │ │ │ Vprtstp: contraction number = 3.033227e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.674255e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.891112e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.727862e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.739437e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -1239,17 +1239,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.097220464694E+01 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.877310278267E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.366275092847E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.188800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.435600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.025 │ │ │ Vpbe_ctor2: xkappa = 0.0514861 │ │ │ @@ -1296,160 +1296,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.182726 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.177039 │ │ │ +Vacc_SASA: Time elapsed: 0.281901 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.525050e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.591770e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.987600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.267500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.736190e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.148004e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.966676e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.486358e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3179322.196917 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.981599e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.511758e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.157153e+05 │ │ │ Vprtstp: contraction number = 5.157153e+05 │ │ │ Vnewton: Attempting damping, relres = 0.300823 │ │ │ Vnewton: Attempting damping, relres = 0.575285 │ │ │ Vnewton: Damping accepted, relres = 0.300823 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.008234e-01 │ │ │ Vprtstp: contraction number = 3.008234e-01 │ │ │ Vnewton: Using errtol_s: 956414.609494 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.013658e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.679823e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.112831e+05 │ │ │ Vprtstp: contraction number = 1.112831e+05 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 7.919694e-02 │ │ │ Vprtstp: contraction number = 2.632672e-01 │ │ │ Vnewton: Using errtol_s: 251792.580740 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.038547e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.887638e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.912764e+04 │ │ │ Vprtstp: contraction number = 2.912764e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.322957e-02 │ │ │ Vprtstp: contraction number = 2.933140e-01 │ │ │ Vnewton: Using errtol_s: 73854.286564 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.064668e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010635e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.683374e+03 │ │ │ Vprtstp: contraction number = 8.683374e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 6.478032e-03 │ │ │ Vprtstp: contraction number = 2.788701e-01 │ │ │ Vnewton: Using errtol_s: 20595.750772 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.092778e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.030914e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.778111e+03 │ │ │ Vprtstp: contraction number = 2.778111e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.439717e-03 │ │ │ Vprtstp: contraction number = 2.222460e-01 │ │ │ Vnewton: Using errtol_s: 4577.322906 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.116176e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048890e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.948966e+02 │ │ │ Vprtstp: contraction number = 7.948966e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.541519e-04 │ │ │ Vprtstp: contraction number = 1.765291e-01 │ │ │ Vnewton: Using errtol_s: 808.030623 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.141075e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065414e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.884080e+02 │ │ │ Vprtstp: contraction number = 1.884080e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.345432e-05 │ │ │ Vprtstp: contraction number = 2.103243e-01 │ │ │ Vnewton: Using errtol_s: 169.948515 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.166009e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081351e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.248467e+01 │ │ │ Vprtstp: contraction number = 5.248467e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.485742e-05 │ │ │ Vprtstp: contraction number = 2.779462e-01 │ │ │ Vnewton: Using errtol_s: 47.236538 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.192546e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.097689e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.636645e+01 │ │ │ Vprtstp: contraction number = 1.636645e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.633006e-06 │ │ │ Vprtstp: contraction number = 3.118310e-01 │ │ │ Vnewton: Using errtol_s: 14.729818 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.216248e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.113938e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.289991e+00 │ │ │ Vprtstp: contraction number = 5.289991e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.497487e-06 │ │ │ Vprtstp: contraction number = 3.232214e-01 │ │ │ Vnewton: Using errtol_s: 4.760992 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.241062e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.130439e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.736329e+00 │ │ │ Vprtstp: contraction number = 1.736329e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.915187e-07 │ │ │ Vprtstp: contraction number = 3.282291e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.928927e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.176418e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.978385e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.991115e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -1459,29 +1459,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.094905051954E+01 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.139048085008E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.067494556843E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.336900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.013970e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.362852e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.148410e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:07:00 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 21:27:29 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -1751,151 +1751,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.304113 │ │ │ +Vacc_SASA: Time elapsed: 0.481547 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.984100e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.279708e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.904500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.024950e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.412270e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.182150e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.392560e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.680374e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2974958.994733 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.837420e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.414415e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.870275e+05 │ │ │ Vprtstp: contraction number = 3.870275e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153059 │ │ │ Vnewton: Attempting damping, relres = 0.557808 │ │ │ Vnewton: Damping accepted, relres = 0.153059 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.530588e-01 │ │ │ Vprtstp: contraction number = 1.530588e-01 │ │ │ Vnewton: Using errtol_s: 455343.743026 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.317271e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.536192e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.695400e+04 │ │ │ Vprtstp: contraction number = 6.695400e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.920739e-02 │ │ │ Vprtstp: contraction number = 1.908246e-01 │ │ │ Vnewton: Using errtol_s: 86890.793846 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.566487e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.714722e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.482146e+04 │ │ │ Vprtstp: contraction number = 1.482146e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.545819e-03 │ │ │ Vprtstp: contraction number = 2.241151e-01 │ │ │ Vnewton: Using errtol_s: 19473.541826 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.816410e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.754191e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.884267e+03 │ │ │ Vprtstp: contraction number = 3.884267e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.453691e-03 │ │ │ Vprtstp: contraction number = 2.220793e-01 │ │ │ Vnewton: Using errtol_s: 4324.671146 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.065891e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.652847e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.057768e+03 │ │ │ Vprtstp: contraction number = 1.057768e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.284783e-04 │ │ │ Vprtstp: contraction number = 2.259615e-01 │ │ │ Vnewton: Using errtol_s: 977.209364 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.315681e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060267e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.866048e+02 │ │ │ Vprtstp: contraction number = 2.866048e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 8.672414e-05 │ │ │ Vprtstp: contraction number = 2.640179e-01 │ │ │ Vnewton: Using errtol_s: 258.000773 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.553469e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.261214e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.283684e+01 │ │ │ Vprtstp: contraction number = 8.283684e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.506027e-05 │ │ │ Vprtstp: contraction number = 2.889653e-01 │ │ │ Vnewton: Using errtol_s: 74.553271 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.803423e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.454588e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.472736e+01 │ │ │ Vprtstp: contraction number = 2.472736e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.480652e-06 │ │ │ Vprtstp: contraction number = 2.985065e-01 │ │ │ Vnewton: Using errtol_s: 22.254632 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.053534e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.650104e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.490971e+00 │ │ │ Vprtstp: contraction number = 7.490971e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.266207e-06 │ │ │ Vprtstp: contraction number = 3.029425e-01 │ │ │ Vnewton: Using errtol_s: 6.741874 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.303018e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.846747e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.293363e+00 │ │ │ Vprtstp: contraction number = 2.293363e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.938001e-07 │ │ │ Vprtstp: contraction number = 3.061503e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.654208e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.867958e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.002723e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.016086e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -1905,17 +1905,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.155593608885E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.568720386421E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.283293314758E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.048200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.038740e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0728124 │ │ │ @@ -1962,160 +1962,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.103051 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.300582 │ │ │ +Vacc_SASA: Time elapsed: 0.424870 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.510220e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.192958e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.940700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.234500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.573850e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.224295e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.416862e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.056310e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 3077114.923847 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.592257e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.083692e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.742704e+05 │ │ │ Vprtstp: contraction number = 4.742704e+05 │ │ │ Vnewton: Attempting damping, relres = 0.172865 │ │ │ Vnewton: Attempting damping, relres = 0.568730 │ │ │ Vnewton: Damping accepted, relres = 0.172865 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.728651e-01 │ │ │ Vprtstp: contraction number = 1.728651e-01 │ │ │ Vnewton: Using errtol_s: 531925.831070 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.961148e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.314489e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.143761e+04 │ │ │ Vprtstp: contraction number = 9.143761e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.526713e-02 │ │ │ Vprtstp: contraction number = 2.040153e-01 │ │ │ Vnewton: Using errtol_s: 108521.009470 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.210270e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.530521e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.196947e+04 │ │ │ Vprtstp: contraction number = 2.196947e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.376912e-03 │ │ │ Vprtstp: contraction number = 2.375275e-01 │ │ │ Vnewton: Using errtol_s: 25776.719868 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.460371e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.749835e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.034692e+03 │ │ │ Vprtstp: contraction number = 6.034692e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.018356e-03 │ │ │ Vprtstp: contraction number = 2.409428e-01 │ │ │ Vnewton: Using errtol_s: 6210.714220 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.720449e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.976502e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.718760e+03 │ │ │ Vprtstp: contraction number = 1.718760e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.089360e-04 │ │ │ Vprtstp: contraction number = 2.521537e-01 │ │ │ Vnewton: Using errtol_s: 1566.054712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.970338e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.188952e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.951703e+02 │ │ │ Vprtstp: contraction number = 4.951703e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.448376e-04 │ │ │ Vprtstp: contraction number = 2.845889e-01 │ │ │ Vnewton: Using errtol_s: 445.681818 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.220254e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.401520e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.503700e+02 │ │ │ Vprtstp: contraction number = 1.503700e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.398054e-05 │ │ │ Vprtstp: contraction number = 3.036542e-01 │ │ │ Vnewton: Using errtol_s: 135.333176 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.469771e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.628906e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.725124e+01 │ │ │ Vprtstp: contraction number = 4.725124e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.382013e-05 │ │ │ Vprtstp: contraction number = 3.142328e-01 │ │ │ Vnewton: Using errtol_s: 42.526127 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.720472e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.850857e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.517823e+01 │ │ │ Vprtstp: contraction number = 1.517823e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.439356e-06 │ │ │ Vprtstp: contraction number = 3.212239e-01 │ │ │ Vnewton: Using errtol_s: 13.660408 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.970392e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.066970e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.961627e+00 │ │ │ Vprtstp: contraction number = 4.961627e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.451185e-06 │ │ │ Vprtstp: contraction number = 3.268910e-01 │ │ │ Vnewton: Using errtol_s: 4.465464 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.220143e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.295688e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.644451e+00 │ │ │ Vprtstp: contraction number = 1.644451e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.809720e-07 │ │ │ Vprtstp: contraction number = 3.314339e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.000871e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.225654e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.444322e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.457998e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2125,17 +2125,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.136719459534E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.953334472721E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475599755841E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.961500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.122400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -2162,151 +2162,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108896 │ │ │ +Vacc_SASA: Time elapsed: 0.232577 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.551080e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.241930e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.896800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.320200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.420610e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.133935e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.925350e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.537086e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 847635.298627 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.063797e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.564380e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.156652e+05 │ │ │ Vprtstp: contraction number = 1.156652e+05 │ │ │ Vnewton: Attempting damping, relres = 0.129563 │ │ │ Vnewton: Attempting damping, relres = 0.559453 │ │ │ Vnewton: Damping accepted, relres = 0.129563 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.295633e-01 │ │ │ Vprtstp: contraction number = 1.295633e-01 │ │ │ Vnewton: Using errtol_s: 109822.397033 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.398018e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.752823e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.025826e+04 │ │ │ Vprtstp: contraction number = 2.025826e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.180592e-02 │ │ │ Vprtstp: contraction number = 1.683033e-01 │ │ │ Vnewton: Using errtol_s: 18483.468929 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.643506e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.904699e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.307643e+03 │ │ │ Vprtstp: contraction number = 4.307643e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.574915e-03 │ │ │ Vprtstp: contraction number = 2.098015e-01 │ │ │ Vnewton: Using errtol_s: 3877.859579 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.892300e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.065228e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.042197e+03 │ │ │ Vprtstp: contraction number = 1.042197e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.106587e-03 │ │ │ Vprtstp: contraction number = 2.418813e-01 │ │ │ Vnewton: Using errtol_s: 937.981802 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014183e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.217133e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.719312e+02 │ │ │ Vprtstp: contraction number = 2.719312e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 2.887307e-04 │ │ │ Vprtstp: contraction number = 2.609201e-01 │ │ │ Vnewton: Using errtol_s: 244.738306 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039144e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.369532e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.411670e+01 │ │ │ Vprtstp: contraction number = 7.411670e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 7.869545e-05 │ │ │ Vprtstp: contraction number = 2.725566e-01 │ │ │ Vnewton: Using errtol_s: 66.705044 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064163e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.522148e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.079247e+01 │ │ │ Vprtstp: contraction number = 2.079247e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.207697e-05 │ │ │ Vprtstp: contraction number = 2.805368e-01 │ │ │ Vnewton: Using errtol_s: 18.713222 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089020e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.675292e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.958188e+00 │ │ │ Vprtstp: contraction number = 5.958188e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.326270e-06 │ │ │ Vprtstp: contraction number = 2.865551e-01 │ │ │ Vnewton: Using errtol_s: 5.362370 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112690e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.829917e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.735927e+00 │ │ │ Vprtstp: contraction number = 1.735927e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.843168e-06 │ │ │ Vprtstp: contraction number = 2.913515e-01 │ │ │ Vnewton: Using errtol_s: 1.562335 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137621e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.975987e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.124069e-01 │ │ │ Vprtstp: contraction number = 5.124069e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 5.440621e-07 │ │ │ Vprtstp: contraction number = 2.951777e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.639920e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.847158e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.566522e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.579354e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2316,17 +2316,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.454852948136E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.836680918650E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.416367945808E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.177200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.923100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0728124 │ │ │ @@ -2373,149 +2373,149 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0108218 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.109346 │ │ │ +Vacc_SASA: Time elapsed: 0.238723 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.908890e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.099720e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.976600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.118100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.475360e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.057787e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.212740e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.123690e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 886073.910303 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.226646e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.149055e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.444647e+05 │ │ │ Vprtstp: contraction number = 1.444647e+05 │ │ │ Vnewton: Attempting damping, relres = 0.152834 │ │ │ Vnewton: Attempting damping, relres = 0.571521 │ │ │ Vnewton: Damping accepted, relres = 0.152834 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.528340e-01 │ │ │ Vprtstp: contraction number = 1.528340e-01 │ │ │ Vnewton: Using errtol_s: 135422.205259 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.260185e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.317269e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.834174e+04 │ │ │ Vprtstp: contraction number = 2.834174e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.906007e-02 │ │ │ Vprtstp: contraction number = 1.901414e-01 │ │ │ Vnewton: Using errtol_s: 25749.370228 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.284988e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.477795e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.624232e+03 │ │ │ Vprtstp: contraction number = 6.624232e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.729649e-03 │ │ │ Vprtstp: contraction number = 2.315772e-01 │ │ │ Vnewton: Using errtol_s: 5962.966787 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.310021e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.643683e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.678296e+03 │ │ │ Vprtstp: contraction number = 1.678296e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.704684e-03 │ │ │ Vprtstp: contraction number = 2.533095e-01 │ │ │ Vnewton: Using errtol_s: 1510.476086 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.334991e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.797742e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.484576e+02 │ │ │ Vprtstp: contraction number = 4.484576e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.555067e-04 │ │ │ Vprtstp: contraction number = 2.672089e-01 │ │ │ Vnewton: Using errtol_s: 403.612606 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.358708e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.970187e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.244400e+02 │ │ │ Vprtstp: contraction number = 1.244400e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.263959e-04 │ │ │ Vprtstp: contraction number = 2.774841e-01 │ │ │ Vnewton: Using errtol_s: 111.996087 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.383618e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.139031e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.556127e+01 │ │ │ Vprtstp: contraction number = 3.556127e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.612018e-05 │ │ │ Vprtstp: contraction number = 2.857702e-01 │ │ │ Vnewton: Using errtol_s: 32.005148 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.407394e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.301064e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.042544e+01 │ │ │ Vprtstp: contraction number = 1.042544e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.058929e-05 │ │ │ Vprtstp: contraction number = 2.931684e-01 │ │ │ Vnewton: Using errtol_s: 9.382897 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.432384e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.460071e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.131407e+00 │ │ │ Vprtstp: contraction number = 3.131407e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.180622e-06 │ │ │ Vprtstp: contraction number = 3.003620e-01 │ │ │ Vnewton: Using errtol_s: 2.818266 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.456095e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.619808e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.605131e-01 │ │ │ Vprtstp: contraction number = 9.605131e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.756091e-07 │ │ │ Vprtstp: contraction number = 3.067353e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.624192e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.846568e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.635698e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.647725e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2525,17 +2525,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.447897988359E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.069186882543E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.032629667471E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.166200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.618400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -2562,151 +2562,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.168704 │ │ │ +Vacc_SASA: Time elapsed: 0.284973 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.889280e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.558030e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.922100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.050880e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.424610e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.138950e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.640209e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.796403e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2425643.021917 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.654236e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.822510e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.395849e+05 │ │ │ Vprtstp: contraction number = 3.395849e+05 │ │ │ Vnewton: Attempting damping, relres = 0.271218 │ │ │ Vnewton: Attempting damping, relres = 0.565917 │ │ │ Vnewton: Damping accepted, relres = 0.271218 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.712177e-01 │ │ │ Vprtstp: contraction number = 2.712177e-01 │ │ │ Vnewton: Using errtol_s: 657877.293778 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.686384e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.993495e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.802706e+04 │ │ │ Vprtstp: contraction number = 6.802706e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 6.815619e-02 │ │ │ Vprtstp: contraction number = 2.512970e-01 │ │ │ Vnewton: Using errtol_s: 165322.578504 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.711382e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.216367e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.706699e+04 │ │ │ Vprtstp: contraction number = 1.706699e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.896759e-02 │ │ │ Vprtstp: contraction number = 2.782960e-01 │ │ │ Vnewton: Using errtol_s: 46008.609864 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.736397e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.437385e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.017255e+03 │ │ │ Vprtstp: contraction number = 5.017255e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 4.765082e-03 │ │ │ Vprtstp: contraction number = 2.512223e-01 │ │ │ Vnewton: Using errtol_s: 11558.387363 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.762448e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.613376e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.518068e+03 │ │ │ Vprtstp: contraction number = 1.518068e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 8.818480e-04 │ │ │ Vprtstp: contraction number = 1.850646e-01 │ │ │ Vnewton: Using errtol_s: 2139.048483 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.786086e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.772214e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.762132e+02 │ │ │ Vprtstp: contraction number = 3.762132e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.458866e-04 │ │ │ Vprtstp: contraction number = 1.654328e-01 │ │ │ Vnewton: Using errtol_s: 353.868838 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.810761e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.929697e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.902937e+01 │ │ │ Vprtstp: contraction number = 8.902937e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.304341e-05 │ │ │ Vprtstp: contraction number = 2.265007e-01 │ │ │ Vnewton: Using errtol_s: 80.151522 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.834065e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.080339e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.527505e+01 │ │ │ Vprtstp: contraction number = 2.527505e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.377960e-06 │ │ │ Vprtstp: contraction number = 2.838073e-01 │ │ │ Vnewton: Using errtol_s: 22.747583 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.857347e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.233256e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.628220e+00 │ │ │ Vprtstp: contraction number = 7.628220e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.830342e-06 │ │ │ Vprtstp: contraction number = 3.018078e-01 │ │ │ Vnewton: Using errtol_s: 6.865399 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.881959e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.389636e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.330827e+00 │ │ │ Vprtstp: contraction number = 2.330827e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.648198e-07 │ │ │ Vprtstp: contraction number = 3.055531e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.587997e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.802650e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.733962e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.746813e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2716,17 +2716,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.060833611390E+01 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.876241790075E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.364173698262E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.114300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.973300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ Vpbe_ctor2: xkappa = 0.0728124 │ │ │ @@ -2773,160 +2773,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0855205 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.183118 │ │ │ +Vacc_SASA: Time elapsed: 0.249087 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.659510e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.962000e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.377500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.825700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.574640e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.270335e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.974655e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.555438e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2500270.754638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.991445e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.583711e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.160810e+05 │ │ │ Vprtstp: contraction number = 4.160810e+05 │ │ │ Vnewton: Attempting damping, relres = 0.288431 │ │ │ Vnewton: Attempting damping, relres = 0.577725 │ │ │ Vnewton: Damping accepted, relres = 0.288431 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.884309e-01 │ │ │ Vprtstp: contraction number = 2.884309e-01 │ │ │ Vnewton: Using errtol_s: 721155.339967 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.023341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.782771e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.034405e+04 │ │ │ Vprtstp: contraction number = 9.034405e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 7.349134e-02 │ │ │ Vprtstp: contraction number = 2.547970e-01 │ │ │ Vnewton: Using errtol_s: 183748.247493 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048203e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000463e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.360950e+04 │ │ │ Vprtstp: contraction number = 2.360950e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 2.053916e-02 │ │ │ Vprtstp: contraction number = 2.794773e-01 │ │ │ Vnewton: Using errtol_s: 51353.458771 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.071813e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023860e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.072490e+03 │ │ │ Vprtstp: contraction number = 7.072490e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 5.268603e-03 │ │ │ Vprtstp: contraction number = 2.565150e-01 │ │ │ Vnewton: Using errtol_s: 13172.933437 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.096674e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.043390e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.172100e+03 │ │ │ Vprtstp: contraction number = 2.172100e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 1.067554e-03 │ │ │ Vprtstp: contraction number = 2.026257e-01 │ │ │ Vnewton: Using errtol_s: 2669.175106 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.120170e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062431e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.851792e+02 │ │ │ Vprtstp: contraction number = 5.851792e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.156116e-04 │ │ │ Vprtstp: contraction number = 2.019677e-01 │ │ │ Vnewton: Using errtol_s: 539.087280 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.143984e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.080916e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.590368e+02 │ │ │ Vprtstp: contraction number = 1.590368e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.725368e-05 │ │ │ Vprtstp: contraction number = 2.655409e-01 │ │ │ Vnewton: Using errtol_s: 143.149712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.168731e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.098557e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.862838e+01 │ │ │ Vprtstp: contraction number = 4.862838e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.750434e-05 │ │ │ Vprtstp: contraction number = 3.057329e-01 │ │ │ Vnewton: Using errtol_s: 43.765584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.192273e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.118227e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.560157e+01 │ │ │ Vprtstp: contraction number = 1.560157e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.615959e-06 │ │ │ Vprtstp: contraction number = 3.208324e-01 │ │ │ Vnewton: Using errtol_s: 14.041419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.217101e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.136056e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.091636e+00 │ │ │ Vprtstp: contraction number = 5.091636e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.832791e-06 │ │ │ Vprtstp: contraction number = 3.263540e-01 │ │ │ Vnewton: Using errtol_s: 4.582473 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.240531e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.152840e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.679382e+00 │ │ │ Vprtstp: contraction number = 1.679382e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.045119e-07 │ │ │ Vprtstp: contraction number = 3.298314e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.840067e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.079767e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.121289e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.135404e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -2936,29 +2936,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.058843361489E+01 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.137979732190E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.067286106944E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.109800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.812000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.362690e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.169284e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:07:11 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 21:52:25 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -3228,151 +3228,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.303222 │ │ │ +Vacc_SASA: Time elapsed: 0.432229 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.930640e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.170140e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.111700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.094290e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.541540e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.093753e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.458340e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.505079e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2729151.378915 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.968510e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.258314e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.548080e+05 │ │ │ Vprtstp: contraction number = 3.548080e+05 │ │ │ Vnewton: Attempting damping, relres = 0.149964 │ │ │ Vnewton: Attempting damping, relres = 0.557619 │ │ │ Vnewton: Damping accepted, relres = 0.149964 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.499638e-01 │ │ │ Vprtstp: contraction number = 1.499638e-01 │ │ │ Vnewton: Using errtol_s: 409273.850655 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.334024e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.719701e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.220624e+04 │ │ │ Vprtstp: contraction number = 6.220624e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.835999e-02 │ │ │ Vprtstp: contraction number = 1.891123e-01 │ │ │ Vnewton: Using errtol_s: 77398.710345 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581710e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.965048e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.402989e+04 │ │ │ Vprtstp: contraction number = 1.402989e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.278471e-03 │ │ │ Vprtstp: contraction number = 2.213848e-01 │ │ │ Vnewton: Using errtol_s: 17134.898633 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.833980e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.146191e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.695573e+03 │ │ │ Vprtstp: contraction number = 3.695573e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.396538e-03 │ │ │ Vprtstp: contraction number = 2.224328e-01 │ │ │ Vnewton: Using errtol_s: 3811.362986 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.081777e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.290594e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.003191e+03 │ │ │ Vprtstp: contraction number = 1.003191e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.340894e-04 │ │ │ Vprtstp: contraction number = 2.392269e-01 │ │ │ Vnewton: Using errtol_s: 911.780505 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.331668e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.134219e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.777519e+02 │ │ │ Vprtstp: contraction number = 2.777519e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.159963e-05 │ │ │ Vprtstp: contraction number = 2.741770e-01 │ │ │ Vnewton: Using errtol_s: 249.989261 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.581735e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.342987e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.121282e+01 │ │ │ Vprtstp: contraction number = 8.121282e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.678181e-05 │ │ │ Vprtstp: contraction number = 2.923790e-01 │ │ │ Vnewton: Using errtol_s: 73.091601 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.830844e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.559390e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.430204e+01 │ │ │ Vprtstp: contraction number = 2.430204e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.014155e-06 │ │ │ Vprtstp: contraction number = 2.992388e-01 │ │ │ Vnewton: Using errtol_s: 21.871842 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.147907e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.775953e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.369042e+00 │ │ │ Vprtstp: contraction number = 7.369042e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.430110e-06 │ │ │ Vprtstp: contraction number = 3.032272e-01 │ │ │ Vnewton: Using errtol_s: 6.632138 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.397027e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.991241e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.256893e+00 │ │ │ Vprtstp: contraction number = 2.256893e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.442621e-07 │ │ │ Vprtstp: contraction number = 3.062668e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.741597e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.971469e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.146223e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.159236e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -3382,17 +3382,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.061471335399E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.568309380303E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.283186160859E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.407000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.030980e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.075 │ │ │ Vpbe_ctor2: xkappa = 0.0891766 │ │ │ @@ -3439,160 +3439,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0651756 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.303803 │ │ │ +Vacc_SASA: Time elapsed: 0.425818 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.634500e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.422146e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.813700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.417250e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.524650e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.123328e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.548143e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.200275e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2820294.276955 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.691400e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.226319e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.376310e+05 │ │ │ Vprtstp: contraction number = 4.376310e+05 │ │ │ Vnewton: Attempting damping, relres = 0.171074 │ │ │ Vnewton: Attempting damping, relres = 0.569073 │ │ │ Vnewton: Damping accepted, relres = 0.171074 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.710740e-01 │ │ │ Vprtstp: contraction number = 1.710740e-01 │ │ │ Vnewton: Using errtol_s: 482478.932943 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.021012e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.461671e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.516733e+04 │ │ │ Vprtstp: contraction number = 8.516733e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.468956e-02 │ │ │ Vprtstp: contraction number = 2.027752e-01 │ │ │ Vnewton: Using errtol_s: 97834.754534 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.267799e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.693722e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.072493e+04 │ │ │ Vprtstp: contraction number = 2.072493e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.178682e-03 │ │ │ Vprtstp: contraction number = 2.357678e-01 │ │ │ Vnewton: Using errtol_s: 23066.288642 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.512458e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.933743e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.715545e+03 │ │ │ Vprtstp: contraction number = 5.715545e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.982874e-03 │ │ │ Vprtstp: contraction number = 2.424442e-01 │ │ │ Vnewton: Using errtol_s: 5592.288694 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.769418e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.166796e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.627358e+03 │ │ │ Vprtstp: contraction number = 1.627358e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.213861e-04 │ │ │ Vprtstp: contraction number = 2.629446e-01 │ │ │ Vnewton: Using errtol_s: 1470.462342 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.032251e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.382134e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.759299e+02 │ │ │ Vprtstp: contraction number = 4.759299e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.518795e-04 │ │ │ Vprtstp: contraction number = 2.912995e-01 │ │ │ Vnewton: Using errtol_s: 428.344902 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.274028e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.602554e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.460718e+02 │ │ │ Vprtstp: contraction number = 1.460718e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.661385e-05 │ │ │ Vprtstp: contraction number = 3.069133e-01 │ │ │ Vnewton: Using errtol_s: 131.464764 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.519563e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.816322e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.608450e+01 │ │ │ Vprtstp: contraction number = 4.608450e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.470629e-05 │ │ │ Vprtstp: contraction number = 3.154918e-01 │ │ │ Vnewton: Using errtol_s: 41.476059 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.753911e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.032367e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.483594e+01 │ │ │ Vprtstp: contraction number = 1.483594e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.734380e-06 │ │ │ Vprtstp: contraction number = 3.219290e-01 │ │ │ Vnewton: Using errtol_s: 13.352345 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.998885e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.249100e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.855098e+00 │ │ │ Vprtstp: contraction number = 4.855098e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.549338e-06 │ │ │ Vprtstp: contraction number = 3.272525e-01 │ │ │ Vnewton: Using errtol_s: 4.369588 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.243925e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.485852e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.609852e+00 │ │ │ Vprtstp: contraction number = 1.609852e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.137291e-07 │ │ │ Vprtstp: contraction number = 3.315798e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.892826e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.136342e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.488821e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.502311e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -3602,17 +3602,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.043656925356E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.952923600964E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475493408028E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.185700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.371700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -3639,151 +3639,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.110602 │ │ │ +Vacc_SASA: Time elapsed: 0.176456 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.692020e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.908210e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.883500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.213500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.441800e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.172338e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.994689e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.726403e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 782805.209515 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.172997e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.751367e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.066964e+05 │ │ │ Vprtstp: contraction number = 1.066964e+05 │ │ │ Vnewton: Attempting damping, relres = 0.130466 │ │ │ Vnewton: Attempting damping, relres = 0.559276 │ │ │ Vnewton: Damping accepted, relres = 0.130466 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.304657e-01 │ │ │ Vprtstp: contraction number = 1.304657e-01 │ │ │ Vnewton: Using errtol_s: 102129.196068 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.490827e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.925465e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.906966e+04 │ │ │ Vprtstp: contraction number = 1.906966e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.228836e-02 │ │ │ Vprtstp: contraction number = 1.708370e-01 │ │ │ Vnewton: Using errtol_s: 17447.447142 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.777431e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.094675e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.144180e+03 │ │ │ Vprtstp: contraction number = 4.144180e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.766221e-03 │ │ │ Vprtstp: contraction number = 2.138435e-01 │ │ │ Vnewton: Using errtol_s: 3731.022666 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002279e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.259721e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.018149e+03 │ │ │ Vprtstp: contraction number = 1.018149e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.170583e-03 │ │ │ Vprtstp: contraction number = 2.455999e-01 │ │ │ Vnewton: Using errtol_s: 916.338711 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.027097e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.423365e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.682787e+02 │ │ │ Vprtstp: contraction number = 2.682787e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.084434e-04 │ │ │ Vprtstp: contraction number = 2.634955e-01 │ │ │ Vnewton: Using errtol_s: 241.451081 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051566e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.583395e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.355327e+01 │ │ │ Vprtstp: contraction number = 7.355327e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 8.456504e-05 │ │ │ Vprtstp: contraction number = 2.741672e-01 │ │ │ Vnewton: Using errtol_s: 66.197957 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074876e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.742694e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.070399e+01 │ │ │ Vprtstp: contraction number = 2.070399e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.380361e-05 │ │ │ Vprtstp: contraction number = 2.814829e-01 │ │ │ Vnewton: Using errtol_s: 18.633591 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099287e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.902407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.943814e+00 │ │ │ Vprtstp: contraction number = 5.943814e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 6.833671e-06 │ │ │ Vprtstp: contraction number = 2.870855e-01 │ │ │ Vnewton: Using errtol_s: 5.349433 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123695e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.050960e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.733432e+00 │ │ │ Vprtstp: contraction number = 1.733432e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.992946e-06 │ │ │ Vprtstp: contraction number = 2.916363e-01 │ │ │ Vnewton: Using errtol_s: 1.560089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.148206e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.195850e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.119221e-01 │ │ │ Vprtstp: contraction number = 5.119221e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 5.885626e-07 │ │ │ Vprtstp: contraction number = 2.953228e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.683924e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.896410e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.601478e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.614388e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -3793,17 +3793,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.580382874271E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.835549724492E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.415749841387E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.316800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.718800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.075 │ │ │ Vpbe_ctor2: xkappa = 0.0891766 │ │ │ @@ -3850,160 +3850,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00827481 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.111092 │ │ │ +Vacc_SASA: Time elapsed: 0.195874 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.833710e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.110920e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.164900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.071000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.455670e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.061772e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222992e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.347883e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 817942.139336 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237695e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.373653e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.333917e+05 │ │ │ Vprtstp: contraction number = 1.333917e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153834 │ │ │ Vnewton: Attempting damping, relres = 0.571434 │ │ │ Vnewton: Damping accepted, relres = 0.153834 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.538338e-01 │ │ │ Vprtstp: contraction number = 1.538338e-01 │ │ │ Vnewton: Using errtol_s: 125827.150717 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.273827e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.559730e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.649228e+04 │ │ │ Vprtstp: contraction number = 2.649228e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.948474e-02 │ │ │ Vprtstp: contraction number = 1.916662e-01 │ │ │ Vnewton: Using errtol_s: 24116.815003 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.304122e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.718460e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.270875e+03 │ │ │ Vprtstp: contraction number = 6.270875e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.901762e-03 │ │ │ Vprtstp: contraction number = 2.340791e-01 │ │ │ Vnewton: Using errtol_s: 5645.242129 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.333351e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.879765e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.605106e+03 │ │ │ Vprtstp: contraction number = 1.605106e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.766147e-03 │ │ │ Vprtstp: contraction number = 2.558981e-01 │ │ │ Vnewton: Using errtol_s: 1444.606457 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.360864e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.044549e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.329441e+02 │ │ │ Vprtstp: contraction number = 4.329441e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.763791e-04 │ │ │ Vprtstp: contraction number = 2.697278e-01 │ │ │ Vnewton: Using errtol_s: 389.650539 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.385360e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.210866e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.211228e+02 │ │ │ Vprtstp: contraction number = 1.211228e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.332742e-04 │ │ │ Vprtstp: contraction number = 2.797649e-01 │ │ │ Vnewton: Using errtol_s: 109.010550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.410725e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.367129e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.484891e+01 │ │ │ Vprtstp: contraction number = 3.484891e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.834504e-05 │ │ │ Vprtstp: contraction number = 2.877155e-01 │ │ │ Vnewton: Using errtol_s: 31.364026 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.434082e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.525862e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.027201e+01 │ │ │ Vprtstp: contraction number = 1.027201e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.130252e-05 │ │ │ Vprtstp: contraction number = 2.947583e-01 │ │ │ Vnewton: Using errtol_s: 9.244807 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.458633e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.698240e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.098070e+00 │ │ │ Vprtstp: contraction number = 3.098070e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.408876e-06 │ │ │ Vprtstp: contraction number = 3.016032e-01 │ │ │ Vnewton: Using errtol_s: 2.788263 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.483202e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.877726e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.532281e-01 │ │ │ Vprtstp: contraction number = 9.532281e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.048858e-06 │ │ │ Vprtstp: contraction number = 3.076845e-01 │ │ │ Vnewton: Using errtol_s: 0.857905 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.507430e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.048021e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.981595e-01 │ │ │ Vprtstp: contraction number = 2.981595e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.280716e-07 │ │ │ Vprtstp: contraction number = 3.127892e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.017504e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.234698e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.850554e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.862570e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -4013,17 +4013,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.573110826930E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.068060919052E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.032015460715E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.266200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.124200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -4050,151 +4050,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.180744 │ │ │ +Vacc_SASA: Time elapsed: 0.188695 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.122450e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.242710e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.054800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.177400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.619770e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.087129e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.694763e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.235330e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2117741.361264 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.711266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.261887e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.981667e+05 │ │ │ Vprtstp: contraction number = 2.981667e+05 │ │ │ Vnewton: Attempting damping, relres = 0.251946 │ │ │ Vnewton: Attempting damping, relres = 0.566227 │ │ │ Vnewton: Damping accepted, relres = 0.251946 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.519462e-01 │ │ │ Vprtstp: contraction number = 2.519462e-01 │ │ │ Vnewton: Using errtol_s: 533556.965989 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.746653e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.425397e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.927315e+04 │ │ │ Vprtstp: contraction number = 5.927315e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 6.069562e-02 │ │ │ Vprtstp: contraction number = 2.409070e-01 │ │ │ Vnewton: Using errtol_s: 128537.620946 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.771741e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.636949e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.480174e+04 │ │ │ Vprtstp: contraction number = 1.480174e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.600227e-02 │ │ │ Vprtstp: contraction number = 2.636478e-01 │ │ │ Vnewton: Using errtol_s: 33888.662126 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.796625e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.823665e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.318636e+03 │ │ │ Vprtstp: contraction number = 4.318636e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.683613e-03 │ │ │ Vprtstp: contraction number = 2.301932e-01 │ │ │ Vnewton: Using errtol_s: 7800.938716 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.821637e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.006730e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.240563e+03 │ │ │ Vprtstp: contraction number = 1.240563e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 6.541706e-04 │ │ │ Vprtstp: contraction number = 1.775894e-01 │ │ │ Vnewton: Using errtol_s: 1385.364119 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.846613e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.175671e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.070828e+02 │ │ │ Vprtstp: contraction number = 3.070828e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.315622e-04 │ │ │ Vprtstp: contraction number = 2.011130e-01 │ │ │ Vnewton: Using errtol_s: 278.614703 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.871682e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.336931e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.245841e+01 │ │ │ Vprtstp: contraction number = 8.245841e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.504428e-05 │ │ │ Vprtstp: contraction number = 2.663704e-01 │ │ │ Vnewton: Using errtol_s: 74.214712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.896669e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.501474e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.449789e+01 │ │ │ Vprtstp: contraction number = 2.449789e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.041114e-05 │ │ │ Vprtstp: contraction number = 2.970854e-01 │ │ │ Vnewton: Using errtol_s: 22.048109 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.921972e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.672415e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.450269e+00 │ │ │ Vprtstp: contraction number = 7.450269e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.166223e-06 │ │ │ Vprtstp: contraction number = 3.041187e-01 │ │ │ Vnewton: Using errtol_s: 6.705242 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.946936e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.846600e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.280137e+00 │ │ │ Vprtstp: contraction number = 2.280137e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.690153e-07 │ │ │ Vprtstp: contraction number = 3.060477e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.710384e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.953068e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.756668e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.768830e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -4204,17 +4204,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.019051099333E+01 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.875636108518E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.362891956470E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.187800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.477900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.075 │ │ │ Vpbe_ctor2: xkappa = 0.0891766 │ │ │ @@ -4261,160 +4261,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0483679 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.184695 │ │ │ +Vacc_SASA: Time elapsed: 0.277230 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.702280e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.003128e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.579500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.225050e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.061310e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.427047e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048092e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001953e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2182522.884057 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.064644e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004474e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.686053e+05 │ │ │ Vprtstp: contraction number = 3.686053e+05 │ │ │ Vnewton: Attempting damping, relres = 0.272056 │ │ │ Vnewton: Attempting damping, relres = 0.578831 │ │ │ Vnewton: Damping accepted, relres = 0.272056 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.720560e-01 │ │ │ Vprtstp: contraction number = 2.720560e-01 │ │ │ Vnewton: Using errtol_s: 593768.373592 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.098275e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022636e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.934239e+04 │ │ │ Vprtstp: contraction number = 7.934239e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 6.680635e-02 │ │ │ Vprtstp: contraction number = 2.455611e-01 │ │ │ Vnewton: Using errtol_s: 145806.393631 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.121893e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.044889e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.075932e+04 │ │ │ Vprtstp: contraction number = 2.075932e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.784022e-02 │ │ │ Vprtstp: contraction number = 2.670438e-01 │ │ │ Vnewton: Using errtol_s: 38936.692163 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.149285e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068348e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.202423e+03 │ │ │ Vprtstp: contraction number = 6.202423e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 4.287010e-03 │ │ │ Vprtstp: contraction number = 2.403003e-01 │ │ │ Vnewton: Using errtol_s: 9356.498262 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.182309e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086553e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.844032e+03 │ │ │ Vprtstp: contraction number = 1.844032e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 8.713644e-04 │ │ │ Vprtstp: contraction number = 2.032569e-01 │ │ │ Vnewton: Using errtol_s: 1901.772758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.214050e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102491e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.035865e+02 │ │ │ Vprtstp: contraction number = 5.035865e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.084187e-04 │ │ │ Vprtstp: contraction number = 2.391867e-01 │ │ │ Vnewton: Using errtol_s: 454.878668 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.245979e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120157e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.482404e+02 │ │ │ Vprtstp: contraction number = 1.482404e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 6.113004e-05 │ │ │ Vprtstp: contraction number = 2.933039e-01 │ │ │ Vnewton: Using errtol_s: 133.417702 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273645e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137592e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.685160e+01 │ │ │ Vprtstp: contraction number = 4.685160e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.932006e-05 │ │ │ Vprtstp: contraction number = 3.160485e-01 │ │ │ Vnewton: Using errtol_s: 42.166463 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.301510e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155229e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.516259e+01 │ │ │ Vprtstp: contraction number = 1.516259e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 6.252549e-06 │ │ │ Vprtstp: contraction number = 3.236300e-01 │ │ │ Vnewton: Using errtol_s: 13.646331 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.329259e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.173626e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.968000e+00 │ │ │ Vprtstp: contraction number = 4.968000e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.048639e-06 │ │ │ Vprtstp: contraction number = 3.276485e-01 │ │ │ Vnewton: Using errtol_s: 4.471200 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.357045e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193062e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.642278e+00 │ │ │ Vprtstp: contraction number = 1.642278e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.772208e-07 │ │ │ Vprtstp: contraction number = 3.305711e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.290226e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.591473e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.075424e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.092141e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -4424,29 +4424,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.017305990862E+01 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.137374131733E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.067158704261E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.715100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.704200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.471579e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.211361e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:07:23 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 22:18:47 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -4716,151 +4716,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.313007 │ │ │ +Vacc_SASA: Time elapsed: 0.450500 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.079930e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.214504e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.012200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.029450e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.439570e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.243962e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.517370e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.636939e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2581577.235420 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004564e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.571982e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.353899e+05 │ │ │ Vprtstp: contraction number = 3.353899e+05 │ │ │ Vnewton: Attempting damping, relres = 0.146634 │ │ │ Vnewton: Attempting damping, relres = 0.557407 │ │ │ Vnewton: Damping accepted, relres = 0.146634 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.466339e-01 │ │ │ Vprtstp: contraction number = 1.466339e-01 │ │ │ Vnewton: Using errtol_s: 378546.858038 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322859e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.841454e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.923639e+04 │ │ │ Vprtstp: contraction number = 5.923639e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.740677e-02 │ │ │ Vprtstp: contraction number = 1.869061e-01 │ │ │ Vnewton: Using errtol_s: 70752.704235 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.605971e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.239111e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.351296e+04 │ │ │ Vprtstp: contraction number = 1.351296e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.004523e-03 │ │ │ Vprtstp: contraction number = 2.190890e-01 │ │ │ Vnewton: Using errtol_s: 15501.138648 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.884668e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.420032e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.562530e+03 │ │ │ Vprtstp: contraction number = 3.562530e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.351206e-03 │ │ │ Vprtstp: contraction number = 2.250314e-01 │ │ │ Vnewton: Using errtol_s: 3488.243698 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.156784e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.410016e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.669348e+02 │ │ │ Vprtstp: contraction number = 9.669348e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.383252e-04 │ │ │ Vprtstp: contraction number = 2.503875e-01 │ │ │ Vnewton: Using errtol_s: 873.412615 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.420746e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.139007e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.719290e+02 │ │ │ Vprtstp: contraction number = 2.719290e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.480245e-05 │ │ │ Vprtstp: contraction number = 2.802110e-01 │ │ │ Vnewton: Using errtol_s: 244.739841 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.669581e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.331330e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.995844e+01 │ │ │ Vprtstp: contraction number = 7.995844e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.787545e-05 │ │ │ Vprtstp: contraction number = 2.940373e-01 │ │ │ Vnewton: Using errtol_s: 71.962638 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.919654e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.525113e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.395977e+01 │ │ │ Vprtstp: contraction number = 2.395977e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.352954e-06 │ │ │ Vprtstp: contraction number = 2.996527e-01 │ │ │ Vnewton: Using errtol_s: 21.563797 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.169414e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.731780e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.269734e+00 │ │ │ Vprtstp: contraction number = 7.269734e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.534405e-06 │ │ │ Vprtstp: contraction number = 3.034141e-01 │ │ │ Vnewton: Using errtol_s: 6.542761 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.419496e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.925215e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.227052e+00 │ │ │ Vprtstp: contraction number = 2.227052e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.764038e-07 │ │ │ Vprtstp: contraction number = 3.063457e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.754721e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.972830e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.086621e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.100425e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -4870,15 +4870,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.906130010441E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.568022982352E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.283111172254E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.130600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.357500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ @@ -4927,160 +4927,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.046103 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.312150 │ │ │ +Vacc_SASA: Time elapsed: 0.490990 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.898490e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.324621e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.873600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.951600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.555320e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.153699e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.568022e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.139510e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2663765.095172 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.771334e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.165738e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.151111e+05 │ │ │ Vprtstp: contraction number = 4.151111e+05 │ │ │ Vnewton: Attempting damping, relres = 0.168665 │ │ │ Vnewton: Attempting damping, relres = 0.569219 │ │ │ Vnewton: Damping accepted, relres = 0.168665 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.686646e-01 │ │ │ Vprtstp: contraction number = 1.686646e-01 │ │ │ Vnewton: Using errtol_s: 449282.900987 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.101447e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.395974e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.120110e+04 │ │ │ Vprtstp: contraction number = 8.120110e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.393027e-02 │ │ │ Vprtstp: contraction number = 2.011700e-01 │ │ │ Vnewton: Using errtol_s: 90382.255629 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.361972e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.609665e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.991839e+04 │ │ │ Vprtstp: contraction number = 1.991839e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.954387e-03 │ │ │ Vprtstp: contraction number = 2.344334e-01 │ │ │ Vnewton: Using errtol_s: 21188.618171 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.595701e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.826589e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.497898e+03 │ │ │ Vprtstp: contraction number = 5.497898e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.952447e-03 │ │ │ Vprtstp: contraction number = 2.454554e-01 │ │ │ Vnewton: Using errtol_s: 5200.860154 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.842534e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.036740e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.566684e+03 │ │ │ Vprtstp: contraction number = 1.566684e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.300165e-04 │ │ │ Vprtstp: contraction number = 2.714627e-01 │ │ │ Vnewton: Using errtol_s: 1411.839327 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.076881e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.241392e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.634720e+02 │ │ │ Vprtstp: contraction number = 4.634720e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.565934e-04 │ │ │ Vprtstp: contraction number = 2.954500e-01 │ │ │ Vnewton: Using errtol_s: 417.127917 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.310459e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.469141e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.430369e+02 │ │ │ Vprtstp: contraction number = 1.430369e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.832756e-05 │ │ │ Vprtstp: contraction number = 3.086182e-01 │ │ │ Vnewton: Using errtol_s: 128.733272 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.557070e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.709848e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.523062e+01 │ │ │ Vprtstp: contraction number = 4.523062e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.528197e-05 │ │ │ Vprtstp: contraction number = 3.162164e-01 │ │ │ Vnewton: Using errtol_s: 40.707568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.791678e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.952905e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.458043e+01 │ │ │ Vprtstp: contraction number = 1.458043e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.926255e-06 │ │ │ Vprtstp: contraction number = 3.223574e-01 │ │ │ Vnewton: Using errtol_s: 13.122387 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.037904e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.175876e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.774711e+00 │ │ │ Vprtstp: contraction number = 4.774711e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.613220e-06 │ │ │ Vprtstp: contraction number = 3.274740e-01 │ │ │ Vnewton: Using errtol_s: 4.297240 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.283989e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.376856e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.583552e+00 │ │ │ Vprtstp: contraction number = 1.583552e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.350309e-07 │ │ │ Vprtstp: contraction number = 3.316539e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.896334e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.119790e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.421681e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.434315e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -5090,17 +5090,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.889253587078E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.952637303887E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475418891145E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.994600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.916000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -5127,151 +5127,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108189 │ │ │ +Vacc_SASA: Time elapsed: 0.150598 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.519790e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.658610e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.994700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.278700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.445680e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.062958e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.977179e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.597052e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 745120.170523 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.115499e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.624470e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.014015e+05 │ │ │ Vprtstp: contraction number = 1.014015e+05 │ │ │ Vnewton: Attempting damping, relres = 0.130811 │ │ │ Vnewton: Attempting damping, relres = 0.559104 │ │ │ Vnewton: Damping accepted, relres = 0.130811 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.308109e-01 │ │ │ Vprtstp: contraction number = 1.308109e-01 │ │ │ Vnewton: Using errtol_s: 97469.809951 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.433160e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.808282e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.835986e+04 │ │ │ Vprtstp: contraction number = 1.835986e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.256558e-02 │ │ │ Vprtstp: contraction number = 1.725054e-01 │ │ │ Vnewton: Using errtol_s: 16814.071331 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.679735e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.965933e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.045264e+03 │ │ │ Vprtstp: contraction number = 4.045264e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.887910e-03 │ │ │ Vprtstp: contraction number = 2.166091e-01 │ │ │ Vnewton: Using errtol_s: 3642.080543 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.913756e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.108074e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.003527e+03 │ │ │ Vprtstp: contraction number = 1.003527e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.212126e-03 │ │ │ Vprtstp: contraction number = 2.479845e-01 │ │ │ Vnewton: Using errtol_s: 903.179662 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014698e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.254389e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660395e+02 │ │ │ Vprtstp: contraction number = 2.660395e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.213385e-04 │ │ │ Vprtstp: contraction number = 2.651031e-01 │ │ │ Vnewton: Using errtol_s: 239.435768 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039362e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.400358e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.320387e+01 │ │ │ Vprtstp: contraction number = 7.320387e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 8.841996e-05 │ │ │ Vprtstp: contraction number = 2.751615e-01 │ │ │ Vnewton: Using errtol_s: 65.883497 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062817e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.543584e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.064818e+01 │ │ │ Vprtstp: contraction number = 2.064818e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.494009e-05 │ │ │ Vprtstp: contraction number = 2.820641e-01 │ │ │ Vnewton: Using errtol_s: 18.583367 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087285e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.688226e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.934502e+00 │ │ │ Vprtstp: contraction number = 5.934502e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.168040e-06 │ │ │ Vprtstp: contraction number = 2.874103e-01 │ │ │ Vnewton: Using errtol_s: 5.341051 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111879e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.829993e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.731750e+00 │ │ │ Vprtstp: contraction number = 1.731750e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.091710e-06 │ │ │ Vprtstp: contraction number = 2.918105e-01 │ │ │ Vnewton: Using errtol_s: 1.558575 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.135173e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.974032e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.115793e-01 │ │ │ Vprtstp: contraction number = 5.115793e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.179156e-07 │ │ │ Vprtstp: contraction number = 2.954117e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.564011e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.781852e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.505320e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.517592e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -5281,17 +5281,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.655453691226E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.834706672328E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.415300525959E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.239700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.133200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.1 │ │ │ Vpbe_ctor2: xkappa = 0.102972 │ │ │ @@ -5338,160 +5338,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00688905 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108374 │ │ │ +Vacc_SASA: Time elapsed: 0.202430 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.869720e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.985880e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.890900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.921400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.458040e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.135792e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.210004e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.122730e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 777935.905465 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.224342e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.148959e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.267239e+05 │ │ │ Vprtstp: contraction number = 1.267239e+05 │ │ │ Vnewton: Attempting damping, relres = 0.154165 │ │ │ Vnewton: Attempting damping, relres = 0.571273 │ │ │ Vnewton: Damping accepted, relres = 0.154165 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.541646e-01 │ │ │ Vprtstp: contraction number = 1.541646e-01 │ │ │ Vnewton: Using errtol_s: 119930.213668 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.258752e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.315097e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.535999e+04 │ │ │ Vprtstp: contraction number = 2.535999e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.969700e-02 │ │ │ Vprtstp: contraction number = 1.926317e-01 │ │ │ Vnewton: Using errtol_s: 23102.366146 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.284955e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.475160e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.051917e+03 │ │ │ Vprtstp: contraction number = 6.051917e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.003479e-03 │ │ │ Vprtstp: contraction number = 2.358312e-01 │ │ │ Vnewton: Using errtol_s: 5448.257890 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.310854e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.626138e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.559687e+03 │ │ │ Vprtstp: contraction number = 1.559687e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.804429e-03 │ │ │ Vprtstp: contraction number = 2.576475e-01 │ │ │ Vnewton: Using errtol_s: 1403.729913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.335533e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.776376e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.232949e+02 │ │ │ Vprtstp: contraction number = 4.232949e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.897143e-04 │ │ │ Vprtstp: contraction number = 2.713957e-01 │ │ │ Vnewton: Using errtol_s: 380.966319 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.366618e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.925307e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.190545e+02 │ │ │ Vprtstp: contraction number = 1.190545e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.377351e-04 │ │ │ Vprtstp: contraction number = 2.812561e-01 │ │ │ Vnewton: Using errtol_s: 107.149093 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.397424e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.080285e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.440341e+01 │ │ │ Vprtstp: contraction number = 3.440341e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.980158e-05 │ │ │ Vprtstp: contraction number = 2.889719e-01 │ │ │ Vnewton: Using errtol_s: 30.963075 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.422344e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.230541e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.017569e+01 │ │ │ Vprtstp: contraction number = 1.017569e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.177234e-05 │ │ │ Vprtstp: contraction number = 2.957757e-01 │ │ │ Vnewton: Using errtol_s: 9.158125 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.447273e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.383299e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.077041e+00 │ │ │ Vprtstp: contraction number = 3.077041e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.559852e-06 │ │ │ Vprtstp: contraction number = 3.023913e-01 │ │ │ Vnewton: Using errtol_s: 2.769337 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472269e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.535628e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.486014e-01 │ │ │ Vprtstp: contraction number = 9.486014e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.097444e-06 │ │ │ Vprtstp: contraction number = 3.082837e-01 │ │ │ Vnewton: Using errtol_s: 0.853741 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.497274e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.687775e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.971293e-01 │ │ │ Vprtstp: contraction number = 2.971293e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.437512e-07 │ │ │ Vprtstp: contraction number = 3.132288e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.101062e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.323304e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.703848e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.716179e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -5501,17 +5501,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.647978359783E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.067221403363E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.031568484712E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.270200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.163600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -5538,162 +5538,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.165050 │ │ │ +Vacc_SASA: Time elapsed: 0.230180 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.026040e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.589770e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.947100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.161800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.429800e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.866160e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.684875e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.860432e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1939359.308692 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.699266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.886373e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.739516e+05 │ │ │ Vprtstp: contraction number = 2.739516e+05 │ │ │ Vnewton: Attempting damping, relres = 0.235690 │ │ │ Vnewton: Attempting damping, relres = 0.566181 │ │ │ Vnewton: Damping accepted, relres = 0.235690 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.356901e-01 │ │ │ Vprtstp: contraction number = 2.356901e-01 │ │ │ Vnewton: Using errtol_s: 457087.767732 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.730822e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.049218e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.385706e+04 │ │ │ Vprtstp: contraction number = 5.385706e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.455782e-02 │ │ │ Vprtstp: contraction number = 2.314812e-01 │ │ │ Vnewton: Using errtol_s: 105807.213748 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.754264e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.264316e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.345524e+04 │ │ │ Vprtstp: contraction number = 1.345524e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.370821e-02 │ │ │ Vprtstp: contraction number = 2.512602e-01 │ │ │ Vnewton: Using errtol_s: 26585.137711 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.777698e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.440901e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.888746e+03 │ │ │ Vprtstp: contraction number = 3.888746e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.963355e-03 │ │ │ Vprtstp: contraction number = 2.161738e-01 │ │ │ Vnewton: Using errtol_s: 5747.009743 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.801021e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.593170e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.082322e+03 │ │ │ Vprtstp: contraction number = 1.082322e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.510650e-04 │ │ │ Vprtstp: contraction number = 1.859598e-01 │ │ │ Vnewton: Using errtol_s: 1068.713018 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.824409e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.742795e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.783449e+02 │ │ │ Vprtstp: contraction number = 2.783449e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.293604e-04 │ │ │ Vprtstp: contraction number = 2.347461e-01 │ │ │ Vnewton: Using errtol_s: 250.876218 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.848940e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.892961e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.935007e+01 │ │ │ Vprtstp: contraction number = 7.935007e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.682419e-05 │ │ │ Vprtstp: contraction number = 2.846636e-01 │ │ │ Vnewton: Using errtol_s: 71.415338 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.872312e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.042500e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.391930e+01 │ │ │ Vprtstp: contraction number = 2.391930e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.110025e-05 │ │ │ Vprtstp: contraction number = 3.014391e-01 │ │ │ Vnewton: Using errtol_s: 21.527377 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.895579e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.191007e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.292472e+00 │ │ │ Vprtstp: contraction number = 7.292472e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.384223e-06 │ │ │ Vprtstp: contraction number = 3.048781e-01 │ │ │ Vnewton: Using errtol_s: 6.563225 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.920519e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.341431e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.233482e+00 │ │ │ Vprtstp: contraction number = 2.233482e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.036494e-06 │ │ │ Vprtstp: contraction number = 3.062723e-01 │ │ │ Vnewton: Using errtol_s: 2.010134 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.943831e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.495412e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.858053e-01 │ │ │ Vprtstp: contraction number = 6.858053e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.182622e-07 │ │ │ Vprtstp: contraction number = 3.070566e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.766098e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.976570e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.777618e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.788746e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -5703,17 +5703,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.820035378222E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.875217906563E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.361966912953E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.117000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.027800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.1 │ │ │ Vpbe_ctor2: xkappa = 0.102972 │ │ │ @@ -5760,160 +5760,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0305183 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.172572 │ │ │ +Vacc_SASA: Time elapsed: 0.230752 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.459250e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.633180e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.928400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.552000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.434380e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.188977e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.032665e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.661481e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1996023.779999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.047651e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.690181e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.403294e+05 │ │ │ Vprtstp: contraction number = 3.403294e+05 │ │ │ Vnewton: Attempting damping, relres = 0.257870 │ │ │ Vnewton: Attempting damping, relres = 0.579346 │ │ │ Vnewton: Damping accepted, relres = 0.257870 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.578703e-01 │ │ │ Vprtstp: contraction number = 2.578703e-01 │ │ │ Vnewton: Using errtol_s: 514715.207917 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.078232e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.881929e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.253173e+04 │ │ │ Vprtstp: contraction number = 7.253173e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 6.121431e-02 │ │ │ Vprtstp: contraction number = 2.373841e-01 │ │ │ Vnewton: Using errtol_s: 122185.216313 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.101593e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.009529e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.904030e+04 │ │ │ Vprtstp: contraction number = 1.904030e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.572892e-02 │ │ │ Vprtstp: contraction number = 2.569484e-01 │ │ │ Vnewton: Using errtol_s: 31395.299569 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.126251e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.029812e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.659593e+03 │ │ │ Vprtstp: contraction number = 5.659593e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.629998e-03 │ │ │ Vprtstp: contraction number = 2.307850e-01 │ │ │ Vnewton: Using errtol_s: 7245.562904 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.149642e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047680e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.651310e+03 │ │ │ Vprtstp: contraction number = 1.651310e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.856291e-04 │ │ │ Vprtstp: contraction number = 2.164268e-01 │ │ │ Vnewton: Using errtol_s: 1568.134340 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.172974e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066636e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.661219e+02 │ │ │ Vprtstp: contraction number = 4.661219e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.102913e-04 │ │ │ Vprtstp: contraction number = 2.676725e-01 │ │ │ Vnewton: Using errtol_s: 419.746448 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.197628e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.083770e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.425822e+02 │ │ │ Vprtstp: contraction number = 1.425822e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 6.428993e-05 │ │ │ Vprtstp: contraction number = 3.057184e-01 │ │ │ Vnewton: Using errtol_s: 128.324228 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.220986e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.100341e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.557507e+01 │ │ │ Vprtstp: contraction number = 4.557507e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.054964e-05 │ │ │ Vprtstp: contraction number = 3.196401e-01 │ │ │ Vnewton: Using errtol_s: 41.017570 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.244309e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.116157e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.480670e+01 │ │ │ Vprtstp: contraction number = 1.480670e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 6.676290e-06 │ │ │ Vprtstp: contraction number = 3.248860e-01 │ │ │ Vnewton: Using errtol_s: 13.326033 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.267706e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.132609e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.862220e+00 │ │ │ Vprtstp: contraction number = 4.862220e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.192358e-06 │ │ │ Vprtstp: contraction number = 3.283797e-01 │ │ │ Vnewton: Using errtol_s: 4.375998 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.291103e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.149087e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.609470e+00 │ │ │ Vprtstp: contraction number = 1.609470e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.257041e-07 │ │ │ Vprtstp: contraction number = 3.310154e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.764232e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.977587e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.987586e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.000396e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -5923,29 +5923,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.804365657787E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.136955879048E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.067066513912E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.032900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.902700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.411073e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.166318e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:07:35 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 22:43:38 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -6215,151 +6215,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.300983 │ │ │ +Vacc_SASA: Time elapsed: 0.477047 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.957720e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.241127e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.013800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.613900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.453950e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.103526e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.405190e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.578391e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2482316.849131 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.885720e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.984607e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.222887e+05 │ │ │ Vprtstp: contraction number = 3.222887e+05 │ │ │ Vnewton: Attempting damping, relres = 0.143642 │ │ │ Vnewton: Attempting damping, relres = 0.557204 │ │ │ Vnewton: Damping accepted, relres = 0.143642 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.436423e-01 │ │ │ Vprtstp: contraction number = 1.436423e-01 │ │ │ Vnewton: Using errtol_s: 356565.753990 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.335663e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.619588e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.719340e+04 │ │ │ Vprtstp: contraction number = 5.719340e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.655317e-02 │ │ │ Vprtstp: contraction number = 1.848561e-01 │ │ │ Vnewton: Using errtol_s: 65913.370564 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.586300e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.715682e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.314754e+04 │ │ │ Vprtstp: contraction number = 1.314754e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.777425e-03 │ │ │ Vprtstp: contraction number = 2.175795e-01 │ │ │ Vnewton: Using errtol_s: 14341.400512 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.837118e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.795158e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.464763e+03 │ │ │ Vprtstp: contraction number = 3.464763e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.322569e-03 │ │ │ Vprtstp: contraction number = 2.289202e-01 │ │ │ Vnewton: Using errtol_s: 3283.035896 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.087381e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.794201e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.430238e+02 │ │ │ Vprtstp: contraction number = 9.430238e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.423711e-04 │ │ │ Vprtstp: contraction number = 2.588682e-01 │ │ │ Vnewton: Using errtol_s: 849.873571 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.349197e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079747e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.680844e+02 │ │ │ Vprtstp: contraction number = 2.680844e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.719850e-05 │ │ │ Vprtstp: contraction number = 2.838981e-01 │ │ │ Vnewton: Using errtol_s: 241.277472 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.598346e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.276826e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.904724e+01 │ │ │ Vprtstp: contraction number = 7.904724e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.865974e-05 │ │ │ Vprtstp: contraction number = 2.948578e-01 │ │ │ Vnewton: Using errtol_s: 71.142545 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.859658e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472510e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.370878e+01 │ │ │ Vprtstp: contraction number = 2.370878e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.595964e-06 │ │ │ Vprtstp: contraction number = 2.999317e-01 │ │ │ Vnewton: Using errtol_s: 21.337905 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.119485e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.673654e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.196546e+00 │ │ │ Vprtstp: contraction number = 7.196546e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.609212e-06 │ │ │ Vprtstp: contraction number = 3.035392e-01 │ │ │ Vnewton: Using errtol_s: 6.476891 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.368819e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.886526e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.205063e+00 │ │ │ Vprtstp: contraction number = 2.205063e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.994776e-07 │ │ │ Vprtstp: contraction number = 3.064057e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.722498e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.937920e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.051845e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.064917e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -6369,17 +6369,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.741026947407E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.567804611788E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.283053686435E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.072300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.816500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.200000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.125 │ │ │ Vpbe_ctor2: xkappa = 0.115127 │ │ │ @@ -6426,160 +6426,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0353875 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.296691 │ │ │ +Vacc_SASA: Time elapsed: 0.517907 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.515050e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.381435e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.992200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.496400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.464290e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.173192e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.475412e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105285e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2557475.753383 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.618196e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.131275e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.996924e+05 │ │ │ Vprtstp: contraction number = 3.996924e+05 │ │ │ Vnewton: Attempting damping, relres = 0.166335 │ │ │ Vnewton: Attempting damping, relres = 0.569269 │ │ │ Vnewton: Damping accepted, relres = 0.166335 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.663353e-01 │ │ │ Vprtstp: contraction number = 1.663353e-01 │ │ │ Vnewton: Using errtol_s: 425398.550037 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.953464e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.357152e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.844641e+04 │ │ │ Vprtstp: contraction number = 7.844641e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.321581e-02 │ │ │ Vprtstp: contraction number = 1.996918e-01 │ │ │ Vnewton: Using errtol_s: 84948.619306 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.203322e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.576790e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.934802e+04 │ │ │ Vprtstp: contraction number = 1.934802e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.763061e-03 │ │ │ Vprtstp: contraction number = 2.337159e-01 │ │ │ Vnewton: Using errtol_s: 19853.840744 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.454160e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.806933e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.339655e+03 │ │ │ Vprtstp: contraction number = 5.339655e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.934926e-03 │ │ │ Vprtstp: contraction number = 2.492478e-01 │ │ │ Vnewton: Using errtol_s: 4948.526141 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.704889e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.042330e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.525404e+03 │ │ │ Vprtstp: contraction number = 1.525404e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.370526e-04 │ │ │ Vprtstp: contraction number = 2.775572e-01 │ │ │ Vnewton: Using errtol_s: 1373.498967 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.955511e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.259438e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.551328e+02 │ │ │ Vprtstp: contraction number = 4.551328e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.601661e-04 │ │ │ Vprtstp: contraction number = 2.982316e-01 │ │ │ Vnewton: Using errtol_s: 409.620859 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.206125e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.475429e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.409185e+02 │ │ │ Vprtstp: contraction number = 1.409185e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.959057e-05 │ │ │ Vprtstp: contraction number = 3.096197e-01 │ │ │ Vnewton: Using errtol_s: 126.826691 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.457362e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.693259e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.462999e+01 │ │ │ Vprtstp: contraction number = 4.462999e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.570572e-05 │ │ │ Vprtstp: contraction number = 3.167077e-01 │ │ │ Vnewton: Using errtol_s: 40.166995 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.708511e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.913856e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.440051e+01 │ │ │ Vprtstp: contraction number = 1.440051e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.067675e-06 │ │ │ Vprtstp: contraction number = 3.226643e-01 │ │ │ Vnewton: Using errtol_s: 12.960456 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.960089e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.134344e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.718013e+00 │ │ │ Vprtstp: contraction number = 4.718013e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.660314e-06 │ │ │ Vprtstp: contraction number = 3.276283e-01 │ │ │ Vnewton: Using errtol_s: 4.246212 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.209561e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.366879e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.564985e+00 │ │ │ Vprtstp: contraction number = 1.564985e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.507330e-07 │ │ │ Vprtstp: contraction number = 3.317042e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.926130e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.141162e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.479420e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.492458e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -6589,17 +6589,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.724934425703E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.952419017164E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475361712291E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.999500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.513200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -6626,151 +6626,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.111540 │ │ │ +Vacc_SASA: Time elapsed: 0.155751 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.566010e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.464860e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.939300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.360400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.459040e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.301522e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.917024e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.625724e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 720364.541598 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.057082e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.654130e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.787737e+04 │ │ │ Vprtstp: contraction number = 9.787737e+04 │ │ │ Vnewton: Attempting damping, relres = 0.130881 │ │ │ Vnewton: Attempting damping, relres = 0.558946 │ │ │ Vnewton: Damping accepted, relres = 0.130881 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.308815e-01 │ │ │ Vprtstp: contraction number = 1.308815e-01 │ │ │ Vnewton: Using errtol_s: 94282.387082 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.392005e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.828825e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.788353e+04 │ │ │ Vprtstp: contraction number = 1.788353e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.273611e-02 │ │ │ Vprtstp: contraction number = 1.737152e-01 │ │ │ Vnewton: Using errtol_s: 16378.286782 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.641332e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.992599e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.978150e+03 │ │ │ Vprtstp: contraction number = 3.978150e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 4.972005e-03 │ │ │ Vprtstp: contraction number = 2.186832e-01 │ │ │ Vnewton: Using errtol_s: 3581.655852 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.890860e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.157048e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.935846e+02 │ │ │ Vprtstp: contraction number = 9.935846e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.241360e-03 │ │ │ Vprtstp: contraction number = 2.496698e-01 │ │ │ Vnewton: Using errtol_s: 894.231472 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014014e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.320603e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.645071e+02 │ │ │ Vprtstp: contraction number = 2.645071e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.304670e-04 │ │ │ Vprtstp: contraction number = 2.662137e-01 │ │ │ Vnewton: Using errtol_s: 238.056677 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038949e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.511321e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.296267e+01 │ │ │ Vprtstp: contraction number = 7.296267e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.115721e-05 │ │ │ Vprtstp: contraction number = 2.758437e-01 │ │ │ Vnewton: Using errtol_s: 65.666425 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067054e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.693782e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.060915e+01 │ │ │ Vprtstp: contraction number = 2.060915e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.574840e-05 │ │ │ Vprtstp: contraction number = 2.824615e-01 │ │ │ Vnewton: Using errtol_s: 18.548236 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.093106e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.842219e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.927860e+00 │ │ │ Vprtstp: contraction number = 5.927860e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.406076e-06 │ │ │ Vprtstp: contraction number = 2.876324e-01 │ │ │ Vnewton: Using errtol_s: 5.335074 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119204e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.990636e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.730517e+00 │ │ │ Vprtstp: contraction number = 1.730517e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.162052e-06 │ │ │ Vprtstp: contraction number = 2.919295e-01 │ │ │ Vnewton: Using errtol_s: 1.557466 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.143845e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.139630e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.113205e-01 │ │ │ Vprtstp: contraction number = 5.113205e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.388271e-07 │ │ │ Vprtstp: contraction number = 2.954726e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.711902e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.930377e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.650935e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.664984e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -6780,17 +6780,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.705203011942E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.834032014754E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.414947804784E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.238300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.871800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.125 │ │ │ Vpbe_ctor2: xkappa = 0.115127 │ │ │ @@ -6837,160 +6837,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0059523 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.106140 │ │ │ +Vacc_SASA: Time elapsed: 0.222329 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.874880e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.194300e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.941400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.056700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.428040e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.151300e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.218090e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.297369e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 751497.765770 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.231958e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.323691e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.222283e+05 │ │ │ Vprtstp: contraction number = 1.222283e+05 │ │ │ Vnewton: Attempting damping, relres = 0.154183 │ │ │ Vnewton: Attempting damping, relres = 0.571098 │ │ │ Vnewton: Damping accepted, relres = 0.154183 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.541833e-01 │ │ │ Vprtstp: contraction number = 1.541833e-01 │ │ │ Vnewton: Using errtol_s: 115868.383651 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.264267e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.509414e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.458734e+04 │ │ │ Vprtstp: contraction number = 2.458734e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.980652e-02 │ │ │ Vprtstp: contraction number = 1.933188e-01 │ │ │ Vnewton: Using errtol_s: 22399.536309 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289303e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.670687e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.900997e+03 │ │ │ Vprtstp: contraction number = 5.900997e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.069086e-03 │ │ │ Vprtstp: contraction number = 2.371657e-01 │ │ │ Vnewton: Using errtol_s: 5312.402554 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.314318e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.839134e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.528364e+03 │ │ │ Vprtstp: contraction number = 1.528364e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.830398e-03 │ │ │ Vprtstp: contraction number = 2.589300e-01 │ │ │ Vnewton: Using errtol_s: 1375.540379 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.339386e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.007804e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.166306e+02 │ │ │ Vprtstp: contraction number = 4.166306e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.989616e-04 │ │ │ Vprtstp: contraction number = 2.725973e-01 │ │ │ Vnewton: Using errtol_s: 374.968546 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.362147e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.184320e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.176231e+02 │ │ │ Vprtstp: contraction number = 1.176231e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.408665e-04 │ │ │ Vprtstp: contraction number = 2.823194e-01 │ │ │ Vnewton: Using errtol_s: 105.860894 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.385929e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.368421e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.409436e+01 │ │ │ Vprtstp: contraction number = 3.409436e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.083170e-05 │ │ │ Vprtstp: contraction number = 2.898609e-01 │ │ │ Vnewton: Using errtol_s: 30.684933 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.409767e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.564918e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.010867e+01 │ │ │ Vprtstp: contraction number = 1.010867e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.210623e-05 │ │ │ Vprtstp: contraction number = 2.964909e-01 │ │ │ Vnewton: Using errtol_s: 9.097804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.433646e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.729634e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.062356e+00 │ │ │ Vprtstp: contraction number = 3.062356e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.667504e-06 │ │ │ Vprtstp: contraction number = 3.029435e-01 │ │ │ Vnewton: Using errtol_s: 2.756121 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457569e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.899090e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.453520e-01 │ │ │ Vprtstp: contraction number = 9.453520e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.132162e-06 │ │ │ Vprtstp: contraction number = 3.087009e-01 │ │ │ Vnewton: Using errtol_s: 0.850817 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.480264e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.083036e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.964013e-01 │ │ │ Vprtstp: contraction number = 2.964013e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.549727e-07 │ │ │ Vprtstp: contraction number = 3.135354e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.805114e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.020083e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.940835e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.953527e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -7000,17 +7000,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.697571697895E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.066549555181E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.031217527268E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.421700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.921700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -7037,162 +7037,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.170767 │ │ │ +Vacc_SASA: Time elapsed: 0.242415 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.926010e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.053591e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.913400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.064030e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.451290e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.490675e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.651275e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.283329e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1823063.193603 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.665808e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.314026e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.580519e+05 │ │ │ Vprtstp: contraction number = 2.580519e+05 │ │ │ Vnewton: Attempting damping, relres = 0.222567 │ │ │ Vnewton: Attempting damping, relres = 0.565989 │ │ │ Vnewton: Damping accepted, relres = 0.222567 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.225671e-01 │ │ │ Vprtstp: contraction number = 2.225671e-01 │ │ │ Vnewton: Using errtol_s: 405753.919509 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.701713e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.505070e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.022631e+04 │ │ │ Vprtstp: contraction number = 5.022631e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.970113e-02 │ │ │ Vprtstp: contraction number = 2.233085e-01 │ │ │ Vnewton: Using errtol_s: 90608.292404 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.726743e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.752465e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.257885e+04 │ │ │ Vprtstp: contraction number = 1.257885e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.198700e-02 │ │ │ Vprtstp: contraction number = 2.411816e-01 │ │ │ Vnewton: Using errtol_s: 21853.051255 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.751766e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.949297e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.600602e+03 │ │ │ Vprtstp: contraction number = 3.600602e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.500944e-03 │ │ │ Vprtstp: contraction number = 2.086381e-01 │ │ │ Vnewton: Using errtol_s: 4559.378536 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.776478e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.120891e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.867332e+02 │ │ │ Vprtstp: contraction number = 9.867332e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.056164e-04 │ │ │ Vprtstp: contraction number = 2.021702e-01 │ │ │ Vnewton: Using errtol_s: 921.770690 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.801507e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.275543e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.646218e+02 │ │ │ Vprtstp: contraction number = 2.646218e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.306754e-04 │ │ │ Vprtstp: contraction number = 2.584478e-01 │ │ │ Vnewton: Using errtol_s: 238.229561 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.826519e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.435343e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.765679e+01 │ │ │ Vprtstp: contraction number = 7.765679e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.833723e-05 │ │ │ Vprtstp: contraction number = 2.933775e-01 │ │ │ Vnewton: Using errtol_s: 69.891187 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.851538e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.615271e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.351839e+01 │ │ │ Vprtstp: contraction number = 2.351839e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.161043e-05 │ │ │ Vprtstp: contraction number = 3.028501e-01 │ │ │ Vnewton: Using errtol_s: 21.166555 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.875239e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.788307e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.178418e+00 │ │ │ Vprtstp: contraction number = 7.178418e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.543803e-06 │ │ │ Vprtstp: contraction number = 3.052257e-01 │ │ │ Vnewton: Using errtol_s: 6.460576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.901403e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.955919e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.199458e+00 │ │ │ Vprtstp: contraction number = 2.199458e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.085817e-06 │ │ │ Vprtstp: contraction number = 3.063988e-01 │ │ │ Vnewton: Using errtol_s: 1.979513 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.925204e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.011550e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.755609e-01 │ │ │ Vprtstp: contraction number = 6.755609e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.335073e-07 │ │ │ Vprtstp: contraction number = 3.071488e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.935135e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.148828e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.978263e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.994772e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -7202,17 +7202,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.498944659129E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.874900883074E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.361242882871E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.118900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.541900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.125 │ │ │ Vpbe_ctor2: xkappa = 0.115127 │ │ │ @@ -7259,160 +7259,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0207746 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173427 │ │ │ +Vacc_SASA: Time elapsed: 0.243099 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.463180e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.285630e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.953900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.703400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.446830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.092048e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.016253e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028376e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1873431.596335 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.030098e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031441e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.215071e+05 │ │ │ Vprtstp: contraction number = 3.215071e+05 │ │ │ Vnewton: Attempting damping, relres = 0.246235 │ │ │ Vnewton: Attempting damping, relres = 0.579562 │ │ │ Vnewton: Damping accepted, relres = 0.246235 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.462348e-01 │ │ │ Vprtstp: contraction number = 2.462348e-01 │ │ │ Vnewton: Using errtol_s: 461304.132219 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.063553e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.053447e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.793925e+04 │ │ │ Vprtstp: contraction number = 6.793925e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.674078e-02 │ │ │ Vprtstp: contraction number = 2.304336e-01 │ │ │ Vnewton: Using errtol_s: 106299.974305 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.088586e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.076223e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.790128e+04 │ │ │ Vprtstp: contraction number = 1.790128e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.413343e-02 │ │ │ Vprtstp: contraction number = 2.490877e-01 │ │ │ Vnewton: Using errtol_s: 26478.015957 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.113604e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.096008e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.289572e+03 │ │ │ Vprtstp: contraction number = 5.289572e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 3.207748e-03 │ │ │ Vprtstp: contraction number = 2.269618e-01 │ │ │ Vnewton: Using errtol_s: 6009.496862 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.138630e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.113169e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.531645e+03 │ │ │ Vprtstp: contraction number = 1.531645e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.505521e-04 │ │ │ Vprtstp: contraction number = 2.339810e-01 │ │ │ Vnewton: Using errtol_s: 1406.107935 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.162341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.131314e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.459814e+02 │ │ │ Vprtstp: contraction number = 4.459814e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.142740e-04 │ │ │ Vprtstp: contraction number = 2.854885e-01 │ │ │ Vnewton: Using errtol_s: 401.427706 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.187286e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.148852e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.392761e+02 │ │ │ Vprtstp: contraction number = 1.392761e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 6.690856e-05 │ │ │ Vprtstp: contraction number = 3.122570e-01 │ │ │ Vnewton: Using errtol_s: 125.348607 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.212493e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.166083e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.474617e+01 │ │ │ Vprtstp: contraction number = 4.474617e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.149615e-05 │ │ │ Vprtstp: contraction number = 3.212765e-01 │ │ │ Vnewton: Using errtol_s: 40.271562 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.237489e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183644e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.457086e+01 │ │ │ Vprtstp: contraction number = 1.457086e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 6.999869e-06 │ │ │ Vprtstp: contraction number = 3.256337e-01 │ │ │ Vnewton: Using errtol_s: 13.113776 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.262441e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.201591e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.791596e+00 │ │ │ Vprtstp: contraction number = 4.791596e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.301892e-06 │ │ │ Vprtstp: contraction number = 3.288478e-01 │ │ │ Vnewton: Using errtol_s: 4.312437 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.287314e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.219517e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.587543e+00 │ │ │ Vprtstp: contraction number = 1.587543e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.626585e-07 │ │ │ Vprtstp: contraction number = 3.313182e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.901014e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.118578e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.089057e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.100982e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -7422,29 +7422,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.484583962909E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.136638905481E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066994369938E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.119500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.021000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.412276e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.239102e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:07:46 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 23:10:01 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -7714,151 +7714,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.306382 │ │ │ +Vacc_SASA: Time elapsed: 0.714166 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.996410e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.559890e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.976500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.647900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.463360e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.460942e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.396010e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.167540e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2410732.356899 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.842040e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.103975e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.128143e+05 │ │ │ Vprtstp: contraction number = 3.128143e+05 │ │ │ Vnewton: Attempting damping, relres = 0.141068 │ │ │ Vnewton: Attempting damping, relres = 0.557017 │ │ │ Vnewton: Damping accepted, relres = 0.141068 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.410683e-01 │ │ │ Vprtstp: contraction number = 1.410683e-01 │ │ │ Vnewton: Using errtol_s: 340078.014247 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.318962e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.978216e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.570013e+04 │ │ │ Vprtstp: contraction number = 5.570013e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.582927e-02 │ │ │ Vprtstp: contraction number = 1.830975e-01 │ │ │ Vnewton: Using errtol_s: 62267.446259 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568864e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.600683e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.287475e+04 │ │ │ Vprtstp: contraction number = 1.287475e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.599207e-03 │ │ │ Vprtstp: contraction number = 2.167776e-01 │ │ │ Vnewton: Using errtol_s: 13498.190114 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.817002e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.026600e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.390785e+03 │ │ │ Vprtstp: contraction number = 3.390785e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.306467e-03 │ │ │ Vprtstp: contraction number = 2.333308e-01 │ │ │ Vnewton: Using errtol_s: 3149.543372 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.077754e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.045264e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.269338e+02 │ │ │ Vprtstp: contraction number = 9.269338e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.462424e-04 │ │ │ Vprtstp: contraction number = 2.650218e-01 │ │ │ Vnewton: Using errtol_s: 834.697770 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.348991e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.282669e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.654672e+02 │ │ │ Vprtstp: contraction number = 2.654672e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.910734e-05 │ │ │ Vprtstp: contraction number = 2.862369e-01 │ │ │ Vnewton: Using errtol_s: 238.921266 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.609419e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.509698e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.840492e+01 │ │ │ Vprtstp: contraction number = 7.840492e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.927096e-05 │ │ │ Vprtstp: contraction number = 2.953460e-01 │ │ │ Vnewton: Using errtol_s: 70.564451 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.892012e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.740476e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.353183e+01 │ │ │ Vprtstp: contraction number = 2.353183e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.785152e-06 │ │ │ Vprtstp: contraction number = 3.001320e-01 │ │ │ Vnewton: Using errtol_s: 21.178651 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.163688e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.965892e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.144902e+00 │ │ │ Vprtstp: contraction number = 7.144902e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.667410e-06 │ │ │ Vprtstp: contraction number = 3.036271e-01 │ │ │ Vnewton: Using errtol_s: 6.430412 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.426656e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.207056e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.189586e+00 │ │ │ Vprtstp: contraction number = 2.189586e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.174393e-07 │ │ │ Vprtstp: contraction number = 3.064543e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.780070e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.996017e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.405626e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.421399e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -7868,17 +7868,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.581693957245E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.567629004923E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.283007133277E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.102100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.036300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.126115 │ │ │ @@ -7925,160 +7925,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0289035 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.299746 │ │ │ +Vacc_SASA: Time elapsed: 0.459005 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.448760e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.495587e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.862000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.277060e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.431630e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.479526e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.529314e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.470034e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2480363.897694 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.674456e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.502243e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.884147e+05 │ │ │ Vprtstp: contraction number = 3.884147e+05 │ │ │ Vnewton: Attempting damping, relres = 0.164249 │ │ │ Vnewton: Attempting damping, relres = 0.569268 │ │ │ Vnewton: Damping accepted, relres = 0.164249 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.642495e-01 │ │ │ Vprtstp: contraction number = 1.642495e-01 │ │ │ Vnewton: Using errtol_s: 407398.416424 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.996875e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.773878e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.641742e+04 │ │ │ Vprtstp: contraction number = 7.641742e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.259356e-02 │ │ │ Vprtstp: contraction number = 1.984394e-01 │ │ │ Vnewton: Using errtol_s: 80843.885291 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.246657e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.061151e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.892121e+04 │ │ │ Vprtstp: contraction number = 1.892121e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.611596e-03 │ │ │ Vprtstp: contraction number = 2.335307e-01 │ │ │ Vnewton: Using errtol_s: 18879.528241 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.496376e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.324067e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.219825e+03 │ │ │ Vprtstp: contraction number = 5.219825e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.927310e-03 │ │ │ Vprtstp: contraction number = 2.532071e-01 │ │ │ Vnewton: Using errtol_s: 4780.429766 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.746108e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.590294e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.496544e+03 │ │ │ Vprtstp: contraction number = 1.496544e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.431250e-04 │ │ │ Vprtstp: contraction number = 2.818047e-01 │ │ │ Vnewton: Using errtol_s: 1347.147545 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.995916e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.839483e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.492633e+02 │ │ │ Vprtstp: contraction number = 4.492633e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.630155e-04 │ │ │ Vprtstp: contraction number = 3.001437e-01 │ │ │ Vnewton: Using errtol_s: 404.337796 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.245153e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.094124e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.394005e+02 │ │ │ Vprtstp: contraction number = 1.394005e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.058149e-05 │ │ │ Vprtstp: contraction number = 3.102863e-01 │ │ │ Vnewton: Using errtol_s: 125.460496 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.495166e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.359910e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.420063e+01 │ │ │ Vprtstp: contraction number = 4.420063e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.603820e-05 │ │ │ Vprtstp: contraction number = 3.170765e-01 │ │ │ Vnewton: Using errtol_s: 39.780577 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.732816e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.592846e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.427219e+01 │ │ │ Vprtstp: contraction number = 1.427219e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.178663e-06 │ │ │ Vprtstp: contraction number = 3.228955e-01 │ │ │ Vnewton: Using errtol_s: 12.844969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.995505e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.827144e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.677701e+00 │ │ │ Vprtstp: contraction number = 4.677701e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.697304e-06 │ │ │ Vprtstp: contraction number = 3.277495e-01 │ │ │ Vnewton: Using errtol_s: 4.209931 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.244348e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.065359e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.551790e+00 │ │ │ Vprtstp: contraction number = 1.551790e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.630670e-07 │ │ │ Vprtstp: contraction number = 3.317420e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.902125e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.118440e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.801001e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.817859e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8088,15 +8088,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.566249593084E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.952243483734E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475315373786E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.973800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.176000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ @@ -8125,151 +8125,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.107593 │ │ │ +Vacc_SASA: Time elapsed: 0.294622 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.526910e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.559470e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.878800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.046140e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.442050e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.237410e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.945956e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.312491e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 702833.844391 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.091798e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.340730e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.535199e+04 │ │ │ Vprtstp: contraction number = 9.535199e+04 │ │ │ Vnewton: Attempting damping, relres = 0.130807 │ │ │ Vnewton: Attempting damping, relres = 0.558803 │ │ │ Vnewton: Damping accepted, relres = 0.130807 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.308068e-01 │ │ │ Vprtstp: contraction number = 1.308068e-01 │ │ │ Vnewton: Using errtol_s: 91935.456218 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.414350e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.524589e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.754021e+04 │ │ │ Vprtstp: contraction number = 1.754021e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.284568e-02 │ │ │ Vprtstp: contraction number = 1.746521e-01 │ │ │ Vnewton: Using errtol_s: 16056.717423 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.682745e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.696168e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.929316e+03 │ │ │ Vprtstp: contraction number = 3.929316e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.033389e-03 │ │ │ Vprtstp: contraction number = 2.203212e-01 │ │ │ Vnewton: Using errtol_s: 3537.635824 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.932207e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.850510e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.863417e+02 │ │ │ Vprtstp: contraction number = 9.863417e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.263048e-03 │ │ │ Vprtstp: contraction number = 2.509340e-01 │ │ │ Vnewton: Using errtol_s: 887.712932 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016973e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.022956e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.633855e+02 │ │ │ Vprtstp: contraction number = 2.633855e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.372735e-04 │ │ │ Vprtstp: contraction number = 2.670314e-01 │ │ │ Vnewton: Using errtol_s: 237.047224 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.041920e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.183769e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.278494e+01 │ │ │ Vprtstp: contraction number = 7.278494e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.320334e-05 │ │ │ Vprtstp: contraction number = 2.763435e-01 │ │ │ Vnewton: Using errtol_s: 65.506461 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066968e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.356620e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.058009e+01 │ │ │ Vprtstp: contraction number = 2.058009e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.635343e-05 │ │ │ Vprtstp: contraction number = 2.827520e-01 │ │ │ Vnewton: Using errtol_s: 18.522083 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.093418e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.526357e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.922842e+00 │ │ │ Vprtstp: contraction number = 5.922842e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.584378e-06 │ │ │ Vprtstp: contraction number = 2.877947e-01 │ │ │ Vnewton: Using errtol_s: 5.330558 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.118317e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.691623e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.729569e+00 │ │ │ Vprtstp: contraction number = 1.729569e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.214765e-06 │ │ │ Vprtstp: contraction number = 2.920167e-01 │ │ │ Vnewton: Using errtol_s: 1.556612 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.142165e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.859944e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.111172e-01 │ │ │ Vprtstp: contraction number = 5.111172e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.545011e-07 │ │ │ Vprtstp: contraction number = 2.955171e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.676915e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.892474e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.699515e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.713308e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8279,17 +8279,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.740193498696E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.833468589698E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.414657798024E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.191100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.843000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.126115 │ │ │ @@ -8336,160 +8336,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00524143 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.109363 │ │ │ +Vacc_SASA: Time elapsed: 0.192683 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.887400e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.061300e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.971000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.667100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.537900e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.156369e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.219130e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.032897e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 732702.640135 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.234688e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.058146e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.189776e+05 │ │ │ Vprtstp: contraction number = 1.189776e+05 │ │ │ Vnewton: Attempting damping, relres = 0.154045 │ │ │ Vnewton: Attempting damping, relres = 0.570927 │ │ │ Vnewton: Damping accepted, relres = 0.154045 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.540451e-01 │ │ │ Vprtstp: contraction number = 1.540451e-01 │ │ │ Vnewton: Using errtol_s: 112869.287383 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.266973e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.240763e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.402351e+04 │ │ │ Vprtstp: contraction number = 2.402351e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.986126e-02 │ │ │ Vprtstp: contraction number = 1.938474e-01 │ │ │ Vnewton: Using errtol_s: 21879.422460 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.290771e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.406028e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.789967e+03 │ │ │ Vprtstp: contraction number = 5.789967e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.113936e-03 │ │ │ Vprtstp: contraction number = 2.382330e-01 │ │ │ Vnewton: Using errtol_s: 5212.399665 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.315740e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.571609e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.505316e+03 │ │ │ Vprtstp: contraction number = 1.505316e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.849041e-03 │ │ │ Vprtstp: contraction number = 2.599182e-01 │ │ │ Vnewton: Using errtol_s: 1354.797457 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.340700e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.737784e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.117226e+02 │ │ │ Vprtstp: contraction number = 4.117226e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.057322e-04 │ │ │ Vprtstp: contraction number = 2.735105e-01 │ │ │ Vnewton: Using errtol_s: 370.551343 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.365685e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.900394e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.165670e+02 │ │ │ Vprtstp: contraction number = 1.165670e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.431828e-04 │ │ │ Vprtstp: contraction number = 2.831198e-01 │ │ │ Vnewton: Using errtol_s: 104.910419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.389518e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.063590e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.386584e+01 │ │ │ Vprtstp: contraction number = 3.386584e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.159841e-05 │ │ │ Vprtstp: contraction number = 2.905266e-01 │ │ │ Vnewton: Using errtol_s: 30.479265 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.414478e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.219614e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.005899e+01 │ │ │ Vprtstp: contraction number = 1.005899e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.235575e-05 │ │ │ Vprtstp: contraction number = 2.970246e-01 │ │ │ Vnewton: Using errtol_s: 9.053091 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.439527e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.380563e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.051439e+00 │ │ │ Vprtstp: contraction number = 3.051439e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.748171e-06 │ │ │ Vprtstp: contraction number = 3.033544e-01 │ │ │ Vnewton: Using errtol_s: 2.746295 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.464526e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.540593e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.429257e-01 │ │ │ Vprtstp: contraction number = 9.429257e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.158223e-06 │ │ │ Vprtstp: contraction number = 3.090102e-01 │ │ │ Vnewton: Using errtol_s: 0.848633 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.489587e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.709459e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.958550e-01 │ │ │ Vprtstp: contraction number = 2.958550e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.634073e-07 │ │ │ Vprtstp: contraction number = 3.137628e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.893457e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.124117e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.828031e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.841113e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8499,15 +8499,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.732432041867E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.065988471810E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.030928944477E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.337000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.256100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ @@ -8536,162 +8536,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.182954 │ │ │ +Vacc_SASA: Time elapsed: 0.323861 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.964160e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.329220e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.909800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.163580e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.469020e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.272303e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.671873e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.901041e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1741500.081736 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.686058e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.930850e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.468341e+05 │ │ │ Vprtstp: contraction number = 2.468341e+05 │ │ │ Vnewton: Attempting damping, relres = 0.211968 │ │ │ Vnewton: Attempting damping, relres = 0.565739 │ │ │ Vnewton: Damping accepted, relres = 0.211968 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.119682e-01 │ │ │ Vprtstp: contraction number = 2.119682e-01 │ │ │ Vnewton: Using errtol_s: 369142.647388 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.718306e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.109123e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.765545e+04 │ │ │ Vprtstp: contraction number = 4.765545e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.585316e-02 │ │ │ Vprtstp: contraction number = 2.163209e-01 │ │ │ Vnewton: Using errtol_s: 79853.288161 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.743301e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.367276e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.196657e+04 │ │ │ Vprtstp: contraction number = 1.196657e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.069307e-02 │ │ │ Vprtstp: contraction number = 2.332024e-01 │ │ │ Vnewton: Using errtol_s: 18621.978068 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.768152e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.571077e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.396204e+03 │ │ │ Vprtstp: contraction number = 3.396204e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.206422e-03 │ │ │ Vprtstp: contraction number = 2.063414e-01 │ │ │ Vnewton: Using errtol_s: 3842.484890 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.793139e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.742911e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.262198e+02 │ │ │ Vprtstp: contraction number = 9.262198e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.857523e-04 │ │ │ Vprtstp: contraction number = 2.201538e-01 │ │ │ Vnewton: Using errtol_s: 845.937714 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.816793e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.901899e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.568315e+02 │ │ │ Vprtstp: contraction number = 2.568315e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.327389e-04 │ │ │ Vprtstp: contraction number = 2.732646e-01 │ │ │ Vnewton: Using errtol_s: 231.164809 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.841673e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005678e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.648381e+01 │ │ │ Vprtstp: contraction number = 7.648381e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.952654e-05 │ │ │ Vprtstp: contraction number = 2.977766e-01 │ │ │ Vnewton: Using errtol_s: 68.835472 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.866658e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021627e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.321302e+01 │ │ │ Vprtstp: contraction number = 2.321302e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.199639e-05 │ │ │ Vprtstp: contraction number = 3.035022e-01 │ │ │ Vnewton: Using errtol_s: 20.891720 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.890425e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038193e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.089761e+00 │ │ │ Vprtstp: contraction number = 7.089761e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.663959e-06 │ │ │ Vprtstp: contraction number = 3.054217e-01 │ │ │ Vnewton: Using errtol_s: 6.380785 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.915395e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.054234e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.172932e+00 │ │ │ Vprtstp: contraction number = 2.172932e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.122962e-06 │ │ │ Vprtstp: contraction number = 3.064887e-01 │ │ │ Vnewton: Using errtol_s: 1.955639 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.940333e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.070326e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.675659e-01 │ │ │ Vprtstp: contraction number = 6.675659e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.449953e-07 │ │ │ Vprtstp: contraction number = 3.072190e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.867620e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.080485e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.948354e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.963000e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8701,17 +8701,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.219214525491E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.874647090507E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.360649736533E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.127700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.335300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.100000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ Vpbe_ctor2: xkappa = 0.126115 │ │ │ @@ -8758,160 +8758,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0149776 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173307 │ │ │ +Vacc_SASA: Time elapsed: 0.394852 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.476960e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.108274e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.868500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.050450e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.464680e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.301843e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.029853e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087536e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1787000.080841 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.044919e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090264e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.080871e+05 │ │ │ Vprtstp: contraction number = 3.080871e+05 │ │ │ Vnewton: Attempting damping, relres = 0.236727 │ │ │ Vnewton: Attempting damping, relres = 0.579616 │ │ │ Vnewton: Damping accepted, relres = 0.236727 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.367272e-01 │ │ │ Vprtstp: contraction number = 2.367272e-01 │ │ │ Vnewton: Using errtol_s: 423031.456074 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.077157e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109362e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.466075e+04 │ │ │ Vprtstp: contraction number = 6.466075e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.316615e-02 │ │ │ Vprtstp: contraction number = 2.245883e-01 │ │ │ Vnewton: Using errtol_s: 95007.918174 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.100976e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.131439e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.709590e+04 │ │ │ Vprtstp: contraction number = 1.709590e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.292750e-02 │ │ │ Vprtstp: contraction number = 2.431528e-01 │ │ │ Vnewton: Using errtol_s: 23101.438026 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.126074e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.152762e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.023315e+03 │ │ │ Vprtstp: contraction number = 5.023315e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.939979e-03 │ │ │ Vprtstp: contraction number = 2.274206e-01 │ │ │ Vnewton: Using errtol_s: 5253.742566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.155936e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.172623e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.453031e+03 │ │ │ Vprtstp: contraction number = 1.453031e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.371716e-04 │ │ │ Vprtstp: contraction number = 2.507404e-01 │ │ │ Vnewton: Using errtol_s: 1317.325709 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.179615e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.191668e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.332970e+02 │ │ │ Vprtstp: contraction number = 4.332970e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.182303e-04 │ │ │ Vprtstp: contraction number = 2.960373e-01 │ │ │ Vnewton: Using errtol_s: 389.977573 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.204559e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.210038e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.367395e+02 │ │ │ Vprtstp: contraction number = 1.367395e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 6.886719e-05 │ │ │ Vprtstp: contraction number = 3.155711e-01 │ │ │ Vnewton: Using errtol_s: 123.065671 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.229539e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.227659e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.406045e+01 │ │ │ Vprtstp: contraction number = 4.406045e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.219049e-05 │ │ │ Vprtstp: contraction number = 3.222216e-01 │ │ │ Vnewton: Using errtol_s: 39.654416 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.254499e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.246248e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.437042e+01 │ │ │ Vprtstp: contraction number = 1.437042e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.237482e-06 │ │ │ Vprtstp: contraction number = 3.261524e-01 │ │ │ Vnewton: Using errtol_s: 12.933382 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.277143e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.263280e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.730536e+00 │ │ │ Vprtstp: contraction number = 4.730536e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.382475e-06 │ │ │ Vprtstp: contraction number = 3.291856e-01 │ │ │ Vnewton: Using errtol_s: 4.257482 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.301045e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.280007e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.568402e+00 │ │ │ Vprtstp: contraction number = 1.568402e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 7.899057e-07 │ │ │ Vprtstp: contraction number = 3.315484e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.889916e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.101694e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.087346e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.101727e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -8921,29 +8921,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 9.205829898099E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.136385155975E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066935223116E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.407100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.325800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.406488e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.298226e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:07:58 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 23:37:42 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -9213,151 +9213,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.256594 │ │ │ +Vacc_SASA: Time elapsed: 0.493482 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.628290e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.370257e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.367000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.301800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.944160e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.240132e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.439750e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.801682e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2356583.284651 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000837e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.448179e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.056288e+05 │ │ │ Vprtstp: contraction number = 3.056288e+05 │ │ │ Vnewton: Attempting damping, relres = 0.138875 │ │ │ Vnewton: Attempting damping, relres = 0.556850 │ │ │ Vnewton: Damping accepted, relres = 0.138875 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.388745e-01 │ │ │ Vprtstp: contraction number = 1.388745e-01 │ │ │ Vnewton: Using errtol_s: 327269.333015 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321621e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.818973e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.456208e+04 │ │ │ Vprtstp: contraction number = 5.456208e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.522390e-02 │ │ │ Vprtstp: contraction number = 1.816309e-01 │ │ │ Vnewton: Using errtol_s: 59442.210907 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.560221e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.294071e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.266310e+04 │ │ │ Vprtstp: contraction number = 1.266310e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.461794e-03 │ │ │ Vprtstp: contraction number = 2.165325e-01 │ │ │ Vnewton: Using errtol_s: 12871.173067 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.826864e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.916478e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.333848e+03 │ │ │ Vprtstp: contraction number = 3.333848e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.298357e-03 │ │ │ Vprtstp: contraction number = 2.377162e-01 │ │ │ Vnewton: Using errtol_s: 3059.685767 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.067415e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008027e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.158069e+02 │ │ │ Vprtstp: contraction number = 9.158069e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.498387e-04 │ │ │ Vprtstp: contraction number = 2.694473e-01 │ │ │ Vnewton: Using errtol_s: 824.424114 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.314849e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206798e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.635874e+02 │ │ │ Vprtstp: contraction number = 2.635874e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.006665e-04 │ │ │ Vprtstp: contraction number = 2.877513e-01 │ │ │ Vnewton: Using errtol_s: 237.229108 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.550014e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.421766e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.793651e+01 │ │ │ Vprtstp: contraction number = 7.793651e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.976465e-05 │ │ │ Vprtstp: contraction number = 2.956757e-01 │ │ │ Vnewton: Using errtol_s: 70.142875 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.797323e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.636887e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.340231e+01 │ │ │ Vprtstp: contraction number = 2.340231e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.937548e-06 │ │ │ Vprtstp: contraction number = 3.002739e-01 │ │ │ Vnewton: Using errtol_s: 21.062077 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.043091e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.853658e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.107171e+00 │ │ │ Vprtstp: contraction number = 7.107171e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.714292e-06 │ │ │ Vprtstp: contraction number = 3.036953e-01 │ │ │ Vnewton: Using errtol_s: 6.396454 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.278112e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.116662e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.178301e+00 │ │ │ Vprtstp: contraction number = 2.178301e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.319126e-07 │ │ │ Vprtstp: contraction number = 3.064934e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.620077e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.878708e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.325281e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.339305e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -9367,17 +9367,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.432923079367E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.567482695315E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282968021669E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.318300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.983500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.175 │ │ │ Vpbe_ctor2: xkappa = 0.13622 │ │ │ @@ -9424,160 +9424,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.024752 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.296165 │ │ │ +Vacc_SASA: Time elapsed: 0.474603 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.643730e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.305360e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.055600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.057600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.486250e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.194491e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.405623e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.380658e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2421825.168549 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.561649e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.409314e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.797843e+05 │ │ │ Vprtstp: contraction number = 3.797843e+05 │ │ │ Vnewton: Attempting damping, relres = 0.162423 │ │ │ Vnewton: Attempting damping, relres = 0.569239 │ │ │ Vnewton: Damping accepted, relres = 0.162423 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.624227e-01 │ │ │ Vprtstp: contraction number = 1.624227e-01 │ │ │ Vnewton: Using errtol_s: 393359.388162 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.878823e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.645815e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.485976e+04 │ │ │ Vprtstp: contraction number = 7.485976e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.206345e-02 │ │ │ Vprtstp: contraction number = 1.974075e-01 │ │ │ Vnewton: Using errtol_s: 77652.078067 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.127475e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.865515e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.858810e+04 │ │ │ Vprtstp: contraction number = 1.858810e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.494162e-03 │ │ │ Vprtstp: contraction number = 2.337291e-01 │ │ │ Vnewton: Using errtol_s: 18149.549466 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.363754e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.097227e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.126907e+03 │ │ │ Vprtstp: contraction number = 5.126907e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.925418e-03 │ │ │ Vprtstp: contraction number = 2.569223e-01 │ │ │ Vnewton: Using errtol_s: 4663.024844 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.637931e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.321475e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.475836e+03 │ │ │ Vprtstp: contraction number = 1.475836e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.485012e-04 │ │ │ Vprtstp: contraction number = 2.848739e-01 │ │ │ Vnewton: Using errtol_s: 1328.373956 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.886848e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.541745e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.449115e+02 │ │ │ Vprtstp: contraction number = 4.449115e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.653385e-04 │ │ │ Vprtstp: contraction number = 3.014369e-01 │ │ │ Vnewton: Using errtol_s: 400.420960 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.147218e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.767046e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.382677e+02 │ │ │ Vprtstp: contraction number = 1.382677e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.138313e-05 │ │ │ Vprtstp: contraction number = 3.107753e-01 │ │ │ Vnewton: Using errtol_s: 124.440953 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.396077e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.996393e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.388153e+01 │ │ │ Vprtstp: contraction number = 4.388153e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.630728e-05 │ │ │ Vprtstp: contraction number = 3.173665e-01 │ │ │ Vnewton: Using errtol_s: 39.493386 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.744296e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.224833e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.417721e+01 │ │ │ Vprtstp: contraction number = 1.417721e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.268543e-06 │ │ │ Vprtstp: contraction number = 3.230792e-01 │ │ │ Vnewton: Using errtol_s: 12.759491 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.025744e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.465335e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.647969e+00 │ │ │ Vprtstp: contraction number = 4.647969e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.727281e-06 │ │ │ Vprtstp: contraction number = 3.278479e-01 │ │ │ Vnewton: Using errtol_s: 4.183172 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.287926e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.695667e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.542077e+00 │ │ │ Vprtstp: contraction number = 1.542077e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.730676e-07 │ │ │ Vprtstp: contraction number = 3.317744e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.072440e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.299203e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.531222e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.544586e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -9587,17 +9587,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.418015826462E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.952097240352E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475276420502E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.041300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.208900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.300000e-05 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -9624,151 +9624,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.110945 │ │ │ +Vacc_SASA: Time elapsed: 0.138445 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.665450e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.792180e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.077900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.482800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.570190e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.138258e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002810e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.951966e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 689766.139707 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022037e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.982618e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.344903e+04 │ │ │ Vprtstp: contraction number = 9.344903e+04 │ │ │ Vnewton: Attempting damping, relres = 0.130653 │ │ │ Vnewton: Attempting damping, relres = 0.558674 │ │ │ Vnewton: Damping accepted, relres = 0.130653 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.306530e-01 │ │ │ Vprtstp: contraction number = 1.306530e-01 │ │ │ Vnewton: Using errtol_s: 90120.018484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056978e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.160571e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.728022e+04 │ │ │ Vprtstp: contraction number = 1.728022e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.291797e-02 │ │ │ Vprtstp: contraction number = 1.754110e-01 │ │ │ Vnewton: Using errtol_s: 15808.042794 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.080565e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.328049e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.892059e+03 │ │ │ Vprtstp: contraction number = 3.892059e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.080008e-03 │ │ │ Vprtstp: contraction number = 2.216604e-01 │ │ │ Vnewton: Using errtol_s: 3504.017199 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.106639e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.498163e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.808109e+02 │ │ │ Vprtstp: contraction number = 9.808109e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.279760e-03 │ │ │ Vprtstp: contraction number = 2.519209e-01 │ │ │ Vnewton: Using errtol_s: 882.735296 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.131483e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.655676e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.625258e+02 │ │ │ Vprtstp: contraction number = 2.625258e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.425414e-04 │ │ │ Vprtstp: contraction number = 2.676606e-01 │ │ │ Vnewton: Using errtol_s: 236.273473 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156236e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.813079e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.264793e+01 │ │ │ Vprtstp: contraction number = 7.264793e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.479032e-05 │ │ │ Vprtstp: contraction number = 2.767266e-01 │ │ │ Vnewton: Using errtol_s: 65.383155 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.181172e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.970366e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.055752e+01 │ │ │ Vprtstp: contraction number = 2.055752e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.682325e-05 │ │ │ Vprtstp: contraction number = 2.829746e-01 │ │ │ Vnewton: Using errtol_s: 18.501770 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.204783e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.123281e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.918897e+00 │ │ │ Vprtstp: contraction number = 5.918897e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.722918e-06 │ │ │ Vprtstp: contraction number = 2.879188e-01 │ │ │ Vnewton: Using errtol_s: 5.327008 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229550e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.276956e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.728813e+00 │ │ │ Vprtstp: contraction number = 1.728813e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.255738e-06 │ │ │ Vprtstp: contraction number = 2.920837e-01 │ │ │ Vnewton: Using errtol_s: 1.555932 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.253022e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.426450e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.109531e-01 │ │ │ Vprtstp: contraction number = 5.109531e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.666866e-07 │ │ │ Vprtstp: contraction number = 2.955514e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.687344e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.915991e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.606620e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.619230e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -9778,17 +9778,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.765725415923E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.832984433292E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.414411854652E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.407100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.996100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.175 │ │ │ Vpbe_ctor2: xkappa = 0.13622 │ │ │ @@ -9835,160 +9835,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00466833 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.113458 │ │ │ +Vacc_SASA: Time elapsed: 0.168184 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.036640e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.136230e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.140700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.760200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.557460e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.155487e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330323e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.579793e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 718654.980128 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.345589e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.607387e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.165117e+05 │ │ │ Vprtstp: contraction number = 1.165117e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153827 │ │ │ Vnewton: Attempting damping, relres = 0.570766 │ │ │ Vnewton: Damping accepted, relres = 0.153827 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.538266e-01 │ │ │ Vprtstp: contraction number = 1.538266e-01 │ │ │ Vnewton: Using errtol_s: 110548.228061 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.378175e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.777331e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.359273e+04 │ │ │ Vprtstp: contraction number = 2.359273e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.988514e-02 │ │ │ Vprtstp: contraction number = 1.942782e-01 │ │ │ Vnewton: Using errtol_s: 21477.106835 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.405215e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.940299e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.704562e+03 │ │ │ Vprtstp: contraction number = 5.704562e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.145907e-03 │ │ │ Vprtstp: contraction number = 2.391124e-01 │ │ │ Vnewton: Using errtol_s: 5135.441496 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.431255e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.107902e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.487585e+03 │ │ │ Vprtstp: contraction number = 1.487585e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.862980e-03 │ │ │ Vprtstp: contraction number = 2.607059e-01 │ │ │ Vnewton: Using errtol_s: 1338.839679 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.455903e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.289047e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.079440e+02 │ │ │ Vprtstp: contraction number = 4.079440e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.108858e-04 │ │ │ Vprtstp: contraction number = 2.742305e-01 │ │ │ Vnewton: Using errtol_s: 367.150629 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.480526e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.461696e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.157528e+02 │ │ │ Vprtstp: contraction number = 1.157528e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.449619e-04 │ │ │ Vprtstp: contraction number = 2.837461e-01 │ │ │ Vnewton: Using errtol_s: 104.177567 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.505543e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.638530e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.368933e+01 │ │ │ Vprtstp: contraction number = 3.368933e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.219048e-05 │ │ │ Vprtstp: contraction number = 2.910454e-01 │ │ │ Vnewton: Using errtol_s: 30.320401 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.529282e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.810775e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.002053e+01 │ │ │ Vprtstp: contraction number = 1.002053e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.254910e-05 │ │ │ Vprtstp: contraction number = 2.974392e-01 │ │ │ Vnewton: Using errtol_s: 9.018476 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.553215e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.990398e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.042966e+00 │ │ │ Vprtstp: contraction number = 3.042966e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.810826e-06 │ │ │ Vprtstp: contraction number = 3.036732e-01 │ │ │ Vnewton: Using errtol_s: 2.738669 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.577981e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.173154e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.410367e-01 │ │ │ Vprtstp: contraction number = 9.410367e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.178497e-06 │ │ │ Vprtstp: contraction number = 3.092499e-01 │ │ │ Vnewton: Using errtol_s: 0.846933 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.601967e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.357176e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.954277e-01 │ │ │ Vprtstp: contraction number = 2.954277e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.699758e-07 │ │ │ Vprtstp: contraction number = 3.139386e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.900347e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.132974e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.937982e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.951293e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -9998,17 +9998,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.757851015992E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.065506328732E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.030684199537E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.444900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.127300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -10035,162 +10035,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.149225 │ │ │ +Vacc_SASA: Time elapsed: 0.228204 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.943080e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.392270e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.882800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.867200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.809640e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.033318e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.772325e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.558173e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1681345.800904 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.787870e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.586006e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.385175e+05 │ │ │ Vprtstp: contraction number = 2.385175e+05 │ │ │ Vnewton: Attempting damping, relres = 0.203314 │ │ │ Vnewton: Attempting damping, relres = 0.565471 │ │ │ Vnewton: Damping accepted, relres = 0.203314 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.033139e-01 │ │ │ Vprtstp: contraction number = 2.033139e-01 │ │ │ Vnewton: Using errtol_s: 341841.011255 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.818815e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.772168e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.575913e+04 │ │ │ Vprtstp: contraction number = 4.575913e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.277261e-02 │ │ │ Vprtstp: contraction number = 2.103772e-01 │ │ │ Vnewton: Using errtol_s: 71915.546235 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.844984e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.978314e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.151626e+04 │ │ │ Vprtstp: contraction number = 1.151626e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.711565e-03 │ │ │ Vprtstp: contraction number = 2.270510e-01 │ │ │ Vnewton: Using errtol_s: 16328.498943 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.868858e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.163412e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.244716e+03 │ │ │ Vprtstp: contraction number = 3.244716e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.018619e-03 │ │ │ Vprtstp: contraction number = 2.078572e-01 │ │ │ Vnewton: Using errtol_s: 3393.995992 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.891574e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.347299e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.861858e+02 │ │ │ Vprtstp: contraction number = 8.861858e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.771677e-04 │ │ │ Vprtstp: contraction number = 2.363833e-01 │ │ │ Vnewton: Using errtol_s: 802.283944 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.915546e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.513983e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.516488e+02 │ │ │ Vprtstp: contraction number = 2.516488e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.347069e-04 │ │ │ Vprtstp: contraction number = 2.823051e-01 │ │ │ Vnewton: Using errtol_s: 226.488825 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.939307e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.686565e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.546930e+01 │ │ │ Vprtstp: contraction number = 7.546930e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.039764e-05 │ │ │ Vprtstp: contraction number = 2.998929e-01 │ │ │ Vnewton: Using errtol_s: 67.922396 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.963181e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.862923e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.293241e+01 │ │ │ Vprtstp: contraction number = 2.293241e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.227539e-05 │ │ │ Vprtstp: contraction number = 3.038640e-01 │ │ │ Vnewton: Using errtol_s: 20.639168 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.987050e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004645e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.006994e+00 │ │ │ Vprtstp: contraction number = 7.006994e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.750742e-06 │ │ │ Vprtstp: contraction number = 3.055499e-01 │ │ │ Vnewton: Using errtol_s: 6.306295 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.010813e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022105e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.148054e+00 │ │ │ Vprtstp: contraction number = 2.148054e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.149822e-06 │ │ │ Vprtstp: contraction number = 3.065586e-01 │ │ │ Vnewton: Using errtol_s: 1.933249 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.034616e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039854e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.600422e-01 │ │ │ Vprtstp: contraction number = 6.600422e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.533110e-07 │ │ │ Vprtstp: contraction number = 3.072745e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.808558e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.073614e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.002401e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.014178e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -10200,17 +10200,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.973061479643E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.874436395142E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.360148310218E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.490100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.634500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.175 │ │ │ Vpbe_ctor2: xkappa = 0.13622 │ │ │ @@ -10257,160 +10257,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.011302 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.147680 │ │ │ +Vacc_SASA: Time elapsed: 0.244904 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.495570e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.078767e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.477400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.679400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.885910e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.254586e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.129128e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.058685e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1723046.376364 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.143684e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.061622e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.980547e+05 │ │ │ Vprtstp: contraction number = 2.980547e+05 │ │ │ Vnewton: Attempting damping, relres = 0.228891 │ │ │ Vnewton: Attempting damping, relres = 0.579579 │ │ │ Vnewton: Damping accepted, relres = 0.228891 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.288909e-01 │ │ │ Vprtstp: contraction number = 2.288909e-01 │ │ │ Vnewton: Using errtol_s: 394389.718028 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.175877e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082895e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.222537e+04 │ │ │ Vprtstp: contraction number = 6.222537e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 5.028364e-02 │ │ │ Vprtstp: contraction number = 2.196838e-01 │ │ │ Vnewton: Using errtol_s: 86641.047132 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.201056e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107396e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.649630e+04 │ │ │ Vprtstp: contraction number = 1.649630e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.200939e-02 │ │ │ Vprtstp: contraction number = 2.388330e-01 │ │ │ Vnewton: Using errtol_s: 20692.741964 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.224899e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.128091e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.824465e+03 │ │ │ Vprtstp: contraction number = 4.824465e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.771121e-03 │ │ │ Vprtstp: contraction number = 2.307461e-01 │ │ │ Vnewton: Using errtol_s: 4774.769213 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.248498e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.147197e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.399802e+03 │ │ │ Vprtstp: contraction number = 1.399802e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.332377e-04 │ │ │ Vprtstp: contraction number = 2.645997e-01 │ │ │ Vnewton: Using errtol_s: 1263.402543 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.272286e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.165768e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.245121e+02 │ │ │ Vprtstp: contraction number = 4.245121e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.217376e-04 │ │ │ Vprtstp: contraction number = 3.024089e-01 │ │ │ Vnewton: Using errtol_s: 382.064121 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.295014e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183570e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.346888e+02 │ │ │ Vprtstp: contraction number = 1.346888e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.035216e-05 │ │ │ Vprtstp: contraction number = 3.172767e-01 │ │ │ Vnewton: Using errtol_s: 121.220033 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.319510e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.201375e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.348380e+01 │ │ │ Vprtstp: contraction number = 4.348380e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.271293e-05 │ │ │ Vprtstp: contraction number = 3.228462e-01 │ │ │ Vnewton: Using errtol_s: 39.135424 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.343260e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.218838e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.419901e+01 │ │ │ Vprtstp: contraction number = 1.419901e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.416577e-06 │ │ │ Vprtstp: contraction number = 3.265355e-01 │ │ │ Vnewton: Using errtol_s: 12.779106 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.367072e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.236317e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.677787e+00 │ │ │ Vprtstp: contraction number = 4.677787e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.443352e-06 │ │ │ Vprtstp: contraction number = 3.294447e-01 │ │ │ Vnewton: Using errtol_s: 4.210009 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.390911e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.253258e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.551755e+00 │ │ │ Vprtstp: contraction number = 1.551755e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.105291e-07 │ │ │ Vprtstp: contraction number = 3.317283e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.800304e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.067151e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.098398e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.112979e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -10420,29 +10420,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.960413626041E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.136174499148E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066885194167E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.594800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.584800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.498433e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.270310e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:08:09 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 00:04:49 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -10712,151 +10712,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.303954 │ │ │ +Vacc_SASA: Time elapsed: 0.472021 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.160720e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.235612e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.015700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.787600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.571810e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.139654e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.666780e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.629700e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2314164.846818 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.036233e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.240767e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.999858e+05 │ │ │ Vprtstp: contraction number = 2.999858e+05 │ │ │ Vnewton: Attempting damping, relres = 0.137001 │ │ │ Vnewton: Attempting damping, relres = 0.556699 │ │ │ Vnewton: Damping accepted, relres = 0.137001 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.370010e-01 │ │ │ Vprtstp: contraction number = 1.370010e-01 │ │ │ Vnewton: Using errtol_s: 317042.938668 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.356415e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.871424e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.366653e+04 │ │ │ Vprtstp: contraction number = 5.366653e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.471777e-02 │ │ │ Vprtstp: contraction number = 1.804203e-01 │ │ │ Vnewton: Using errtol_s: 57200.987288 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.606789e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.208004e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.249422e+04 │ │ │ Vprtstp: contraction number = 1.249422e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.356401e-03 │ │ │ Vprtstp: contraction number = 2.167025e-01 │ │ │ Vnewton: Using errtol_s: 12395.595920 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.856743e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.547540e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.289496e+03 │ │ │ Vprtstp: contraction number = 3.289496e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.295127e-03 │ │ │ Vprtstp: contraction number = 2.417905e-01 │ │ │ Vnewton: Using errtol_s: 2997.137107 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105848e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.840667e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.079428e+02 │ │ │ Vprtstp: contraction number = 9.079428e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.531481e-04 │ │ │ Vprtstp: contraction number = 2.726745e-01 │ │ │ Vnewton: Using errtol_s: 817.243005 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.377282e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.226121e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.621817e+02 │ │ │ Vprtstp: contraction number = 2.621817e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.019650e-04 │ │ │ Vprtstp: contraction number = 2.887315e-01 │ │ │ Vnewton: Using errtol_s: 235.963838 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.641684e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.460165e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.758363e+01 │ │ │ Vprtstp: contraction number = 7.758363e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.017299e-05 │ │ │ Vprtstp: contraction number = 2.959152e-01 │ │ │ Vnewton: Using errtol_s: 69.825280 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.891546e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.687990e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.330457e+01 │ │ │ Vprtstp: contraction number = 2.330457e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.063361e-06 │ │ │ Vprtstp: contraction number = 3.003799e-01 │ │ │ Vnewton: Using errtol_s: 20.974111 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.141568e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.910431e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.078759e+00 │ │ │ Vprtstp: contraction number = 7.078759e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.752995e-06 │ │ │ Vprtstp: contraction number = 3.037499e-01 │ │ │ Vnewton: Using errtol_s: 6.370884 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.392359e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.131941e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.169820e+00 │ │ │ Vprtstp: contraction number = 2.169820e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.438628e-07 │ │ │ Vprtstp: contraction number = 3.065254e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.736253e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.962387e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.313684e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.327019e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -10866,17 +10866,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.295748470746E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.567357663948E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282934286498E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.192900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.708400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.2 │ │ │ Vpbe_ctor2: xkappa = 0.145625 │ │ │ @@ -10923,160 +10923,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0219675 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.301619 │ │ │ +Vacc_SASA: Time elapsed: 0.467073 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.482050e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.360300e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.001900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.648900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.441590e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.131234e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.617429e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.367085e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2375881.010490 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.762780e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.394034e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.729565e+05 │ │ │ Vprtstp: contraction number = 3.729565e+05 │ │ │ Vnewton: Attempting damping, relres = 0.160831 │ │ │ Vnewton: Attempting damping, relres = 0.569195 │ │ │ Vnewton: Damping accepted, relres = 0.160831 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.608306e-01 │ │ │ Vprtstp: contraction number = 1.608306e-01 │ │ │ Vnewton: Using errtol_s: 382114.425441 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.082654e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.661024e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.362534e+04 │ │ │ Vprtstp: contraction number = 7.362534e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.161380e-02 │ │ │ Vprtstp: contraction number = 1.965658e-01 │ │ │ Vnewton: Using errtol_s: 75110.631839 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.318713e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.912220e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.832017e+04 │ │ │ Vprtstp: contraction number = 1.832017e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.403849e-03 │ │ │ Vprtstp: contraction number = 2.341967e-01 │ │ │ Vnewton: Using errtol_s: 17590.663892 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.555794e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.150650e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.053669e+03 │ │ │ Vprtstp: contraction number = 5.053669e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.926673e-03 │ │ │ Vprtstp: contraction number = 2.602258e-01 │ │ │ Vnewton: Using errtol_s: 4577.545268 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.789726e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.390972e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.460468e+03 │ │ │ Vprtstp: contraction number = 1.460468e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.532624e-04 │ │ │ Vprtstp: contraction number = 2.871595e-01 │ │ │ Vnewton: Using errtol_s: 1314.485731 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.041707e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.618855e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.415879e+02 │ │ │ Vprtstp: contraction number = 4.415879e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.672767e-04 │ │ │ Vprtstp: contraction number = 3.023461e-01 │ │ │ Vnewton: Using errtol_s: 397.429641 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.316143e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.843324e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.374012e+02 │ │ │ Vprtstp: contraction number = 1.374012e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.204853e-05 │ │ │ Vprtstp: contraction number = 3.111522e-01 │ │ │ Vnewton: Using errtol_s: 123.661104 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.552793e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.081997e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.363894e+01 │ │ │ Vprtstp: contraction number = 4.363894e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.653073e-05 │ │ │ Vprtstp: contraction number = 3.176023e-01 │ │ │ Vnewton: Using errtol_s: 39.275049 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.802569e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.310672e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.410540e+01 │ │ │ Vprtstp: contraction number = 1.410540e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.343223e-06 │ │ │ Vprtstp: contraction number = 3.232297e-01 │ │ │ Vnewton: Using errtol_s: 12.694863 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.052199e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.527097e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.625592e+00 │ │ │ Vprtstp: contraction number = 4.625592e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.752206e-06 │ │ │ Vprtstp: contraction number = 3.279305e-01 │ │ │ Vnewton: Using errtol_s: 4.163033 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.286856e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.750149e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.534788e+00 │ │ │ Vprtstp: contraction number = 1.534788e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.813881e-07 │ │ │ Vprtstp: contraction number = 3.318035e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.852464e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.070269e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.580068e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.592687e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11086,15 +11086,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.281289332707E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951972269789E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475242807069E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.004700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.985600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ @@ -11123,151 +11123,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108327 │ │ │ +Vacc_SASA: Time elapsed: 0.217495 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.512920e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.007250e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.919500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.205700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.434170e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.147637e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.977261e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.984890e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 679651.374556 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.120254e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.009931e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.196081e+04 │ │ │ Vprtstp: contraction number = 9.196081e+04 │ │ │ Vnewton: Attempting damping, relres = 0.130456 │ │ │ Vnewton: Attempting damping, relres = 0.558557 │ │ │ Vnewton: Damping accepted, relres = 0.130456 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.304558e-01 │ │ │ Vprtstp: contraction number = 1.304558e-01 │ │ │ Vnewton: Using errtol_s: 88664.431621 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.449418e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.168995e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.707604e+04 │ │ │ Vprtstp: contraction number = 1.707604e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.296641e-02 │ │ │ Vprtstp: contraction number = 1.760475e-01 │ │ │ Vnewton: Using errtol_s: 15609.155466 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.684250e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.316868e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.862634e+03 │ │ │ Vprtstp: contraction number = 3.862634e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.116511e-03 │ │ │ Vprtstp: contraction number = 2.227823e-01 │ │ │ Vnewton: Using errtol_s: 3477.443419 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.978239e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.465717e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.764405e+02 │ │ │ Vprtstp: contraction number = 9.764405e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.293019e-03 │ │ │ Vprtstp: contraction number = 2.527150e-01 │ │ │ Vnewton: Using errtol_s: 878.801976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021297e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.610745e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.618442e+02 │ │ │ Vprtstp: contraction number = 2.618442e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.467366e-04 │ │ │ Vprtstp: contraction number = 2.681606e-01 │ │ │ Vnewton: Using errtol_s: 235.660041 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.044723e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.754377e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.253883e+01 │ │ │ Vprtstp: contraction number = 7.253883e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.605654e-05 │ │ │ Vprtstp: contraction number = 2.770303e-01 │ │ │ Vnewton: Using errtol_s: 65.284962 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.069293e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.901429e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.053942e+01 │ │ │ Vprtstp: contraction number = 2.053942e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.719848e-05 │ │ │ Vprtstp: contraction number = 2.831507e-01 │ │ │ Vnewton: Using errtol_s: 18.485484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.092631e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.052014e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.915703e+00 │ │ │ Vprtstp: contraction number = 5.915703e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.833623e-06 │ │ │ Vprtstp: contraction number = 2.880170e-01 │ │ │ Vnewton: Using errtol_s: 5.324133 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.116058e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.233508e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.728194e+00 │ │ │ Vprtstp: contraction number = 1.728194e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.288489e-06 │ │ │ Vprtstp: contraction number = 2.921367e-01 │ │ │ Vnewton: Using errtol_s: 1.555375 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.139407e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.401855e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.108177e-01 │ │ │ Vprtstp: contraction number = 5.108177e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.764290e-07 │ │ │ Vprtstp: contraction number = 2.955789e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.600576e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.809512e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.571798e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.585060e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11277,17 +11277,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.784786682149E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.832559781230E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.414198595280E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.546300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.438040e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.2 │ │ │ Vpbe_ctor2: xkappa = 0.145625 │ │ │ @@ -11334,160 +11334,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00419075 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.105492 │ │ │ +Vacc_SASA: Time elapsed: 0.275601 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.858840e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.586140e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.924600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.236700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.421470e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.243442e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.212916e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.580633e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 707760.874892 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.227286e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.608337e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.145732e+05 │ │ │ Vprtstp: contraction number = 1.145732e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153567 │ │ │ Vnewton: Attempting damping, relres = 0.570617 │ │ │ Vnewton: Damping accepted, relres = 0.153567 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.535669e-01 │ │ │ Vprtstp: contraction number = 1.535669e-01 │ │ │ Vnewton: Using errtol_s: 108688.631756 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.258063e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.790930e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.325223e+04 │ │ │ Vprtstp: contraction number = 2.325223e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.989096e-02 │ │ │ Vprtstp: contraction number = 1.946446e-01 │ │ │ Vnewton: Using errtol_s: 21155.653880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.281936e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.959940e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.636674e+03 │ │ │ Vprtstp: contraction number = 5.636674e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.169438e-03 │ │ │ Vprtstp: contraction number = 2.398530e-01 │ │ │ Vnewton: Using errtol_s: 5074.248008 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.306916e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.111892e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.473491e+03 │ │ │ Vprtstp: contraction number = 1.473491e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.873734e-03 │ │ │ Vprtstp: contraction number = 2.613502e-01 │ │ │ Vnewton: Using errtol_s: 1326.155494 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.331913e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.260533e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.049387e+02 │ │ │ Vprtstp: contraction number = 4.049387e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.149280e-04 │ │ │ Vprtstp: contraction number = 2.748139e-01 │ │ │ Vnewton: Using errtol_s: 364.445920 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355760e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.409290e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.151043e+02 │ │ │ Vprtstp: contraction number = 1.151043e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.463685e-04 │ │ │ Vprtstp: contraction number = 2.842504e-01 │ │ │ Vnewton: Using errtol_s: 103.593915 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.382078e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.562424e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.354853e+01 │ │ │ Vprtstp: contraction number = 3.354853e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.266085e-05 │ │ │ Vprtstp: contraction number = 2.914619e-01 │ │ │ Vnewton: Using errtol_s: 30.193683 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.407060e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.719718e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.989786e+00 │ │ │ Vprtstp: contraction number = 9.989786e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.270317e-05 │ │ │ Vprtstp: contraction number = 2.977712e-01 │ │ │ Vnewton: Using errtol_s: 8.990808 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.432017e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.879909e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.036177e+00 │ │ │ Vprtstp: contraction number = 3.036177e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.860851e-06 │ │ │ Vprtstp: contraction number = 3.039281e-01 │ │ │ Vnewton: Using errtol_s: 2.732559 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.455778e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.036666e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.395196e-01 │ │ │ Vprtstp: contraction number = 9.395196e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.194708e-06 │ │ │ Vprtstp: contraction number = 3.094416e-01 │ │ │ Vnewton: Using errtol_s: 0.845568 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.480707e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.193968e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.950830e-01 │ │ │ Vprtstp: contraction number = 2.950830e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.752323e-07 │ │ │ Vprtstp: contraction number = 3.140786e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.866754e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.079555e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.756466e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.770156e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11497,17 +11497,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.776812399064E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.065083445518E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.030471976313E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.192300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.946400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -11534,162 +11534,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.175858 │ │ │ +Vacc_SASA: Time elapsed: 0.276257 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.075830e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.864910e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.068900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.750000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.478150e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.047717e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.665139e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.375977e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1635307.042590 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.678863e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.401279e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.321219e+05 │ │ │ Vprtstp: contraction number = 2.321219e+05 │ │ │ Vnewton: Attempting damping, relres = 0.196154 │ │ │ Vnewton: Attempting damping, relres = 0.565205 │ │ │ Vnewton: Damping accepted, relres = 0.196154 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.961538e-01 │ │ │ Vprtstp: contraction number = 1.961538e-01 │ │ │ Vnewton: Using errtol_s: 320771.668801 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.712158e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.562688e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.431372e+04 │ │ │ Vprtstp: contraction number = 4.431372e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.027511e-02 │ │ │ Vprtstp: contraction number = 2.053242e-01 │ │ │ Vnewton: Using errtol_s: 65862.177446 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.738299e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.756045e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.117167e+04 │ │ │ Vprtstp: contraction number = 1.117167e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.959711e-03 │ │ │ Vprtstp: contraction number = 2.224627e-01 │ │ │ Vnewton: Using errtol_s: 14651.878140 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.762006e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.923174e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.129072e+03 │ │ │ Vprtstp: contraction number = 3.129072e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.898262e-03 │ │ │ Vprtstp: contraction number = 2.118664e-01 │ │ │ Vnewton: Using errtol_s: 3104.240662 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.790898e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.079197e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.589092e+02 │ │ │ Vprtstp: contraction number = 8.589092e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.739068e-04 │ │ │ Vprtstp: contraction number = 2.496530e-01 │ │ │ Vnewton: Using errtol_s: 774.983094 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.818513e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.239560e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.479971e+02 │ │ │ Vprtstp: contraction number = 2.479971e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.364875e-04 │ │ │ Vprtstp: contraction number = 2.880050e-01 │ │ │ Vnewton: Using errtol_s: 223.198993 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.844185e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.404974e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.463517e+01 │ │ │ Vprtstp: contraction number = 7.463517e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.107588e-05 │ │ │ Vprtstp: contraction number = 3.009497e-01 │ │ │ Vnewton: Using errtol_s: 67.171671 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.870107e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.561029e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.269594e+01 │ │ │ Vprtstp: contraction number = 2.269594e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.249083e-05 │ │ │ Vprtstp: contraction number = 3.040916e-01 │ │ │ Vnewton: Using errtol_s: 20.426343 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.893856e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.712067e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.936769e+00 │ │ │ Vprtstp: contraction number = 6.936769e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.817688e-06 │ │ │ Vprtstp: contraction number = 3.056392e-01 │ │ │ Vnewton: Using errtol_s: 6.243092 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.918716e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.864472e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.126909e+00 │ │ │ Vprtstp: contraction number = 2.126909e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.170556e-06 │ │ │ Vprtstp: contraction number = 3.066138e-01 │ │ │ Vnewton: Using errtol_s: 1.914218 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.942440e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001610e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.536389e-01 │ │ │ Vprtstp: contraction number = 6.536389e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.597337e-07 │ │ │ Vprtstp: contraction number = 3.073187e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.974714e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.196853e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.776667e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.788769e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11699,17 +11699,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.754232717219E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.874256879798E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.359714713535E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.180800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.292900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.2 │ │ │ Vpbe_ctor2: xkappa = 0.145625 │ │ │ @@ -11756,160 +11756,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00885234 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.169976 │ │ │ +Vacc_SASA: Time elapsed: 0.260574 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.450970e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.890500e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.885300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.547900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.424730e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.133798e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.033510e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.017590e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1674007.100681 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.047795e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020087e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.902880e+05 │ │ │ Vprtstp: contraction number = 2.902880e+05 │ │ │ Vnewton: Attempting damping, relres = 0.222356 │ │ │ Vnewton: Attempting damping, relres = 0.579491 │ │ │ Vnewton: Damping accepted, relres = 0.222356 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.223561e-01 │ │ │ Vprtstp: contraction number = 2.223561e-01 │ │ │ Vnewton: Using errtol_s: 372225.695633 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.081901e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038250e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.035839e+04 │ │ │ Vprtstp: contraction number = 6.035839e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.793121e-02 │ │ │ Vprtstp: contraction number = 2.155606e-01 │ │ │ Vnewton: Using errtol_s: 80237.189117 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105701e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062786e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.603151e+04 │ │ │ Vprtstp: contraction number = 1.603151e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.130393e-02 │ │ │ Vprtstp: contraction number = 2.358364e-01 │ │ │ Vnewton: Using errtol_s: 18922.853010 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.130600e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085970e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.671524e+03 │ │ │ Vprtstp: contraction number = 4.671524e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.665747e-03 │ │ │ Vprtstp: contraction number = 2.358248e-01 │ │ │ Vnewton: Using errtol_s: 4462.478601 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.155553e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.105690e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.362565e+03 │ │ │ Vprtstp: contraction number = 1.362565e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.334180e-04 │ │ │ Vprtstp: contraction number = 2.751267e-01 │ │ │ Vnewton: Using errtol_s: 1227.746995 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.179341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.124180e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.182590e+02 │ │ │ Vprtstp: contraction number = 4.182590e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.248702e-04 │ │ │ Vprtstp: contraction number = 3.066058e-01 │ │ │ Vnewton: Using errtol_s: 376.434346 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.204342e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.143368e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.331321e+02 │ │ │ Vprtstp: contraction number = 1.331321e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.157615e-05 │ │ │ Vprtstp: contraction number = 3.182998e-01 │ │ │ Vnewton: Using errtol_s: 119.818985 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.229300e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.162391e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.304104e+01 │ │ │ Vprtstp: contraction number = 4.304104e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.314025e-05 │ │ │ Vprtstp: contraction number = 3.232955e-01 │ │ │ Vnewton: Using errtol_s: 38.736937 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.253092e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.182178e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.406731e+01 │ │ │ Vprtstp: contraction number = 1.406731e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.563038e-06 │ │ │ Vprtstp: contraction number = 3.268348e-01 │ │ │ Vnewton: Using errtol_s: 12.660580 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.278111e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.201657e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.637253e+00 │ │ │ Vprtstp: contraction number = 4.637253e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.493136e-06 │ │ │ Vprtstp: contraction number = 3.296474e-01 │ │ │ Vnewton: Using errtol_s: 4.173527 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.303264e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.219712e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.538961e+00 │ │ │ Vprtstp: contraction number = 1.538961e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.273947e-07 │ │ │ Vprtstp: contraction number = 3.318691e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.890959e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.105457e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.170135e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.182686e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -11919,29 +11919,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.742146487539E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.135995019180E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066841914089E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.044300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.004000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.424401e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.236211e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:08:21 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 00:31:07 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -12211,151 +12211,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.300174 │ │ │ +Vacc_SASA: Time elapsed: 0.432582 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.956200e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.193103e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.978800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.317700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.433810e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.001334e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.337920e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.342350e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2280031.151733 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.790520e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.909285e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.954329e+05 │ │ │ Vprtstp: contraction number = 2.954329e+05 │ │ │ Vnewton: Attempting damping, relres = 0.135391 │ │ │ Vnewton: Attempting damping, relres = 0.556564 │ │ │ Vnewton: Damping accepted, relres = 0.135391 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.353914e-01 │ │ │ Vprtstp: contraction number = 1.353914e-01 │ │ │ Vnewton: Using errtol_s: 308696.705205 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.300824e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.565329e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.294410e+04 │ │ │ Vprtstp: contraction number = 5.294410e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.429290e-02 │ │ │ Vprtstp: contraction number = 1.794272e-01 │ │ │ Vnewton: Using errtol_s: 55388.580044 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.550103e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.953218e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.235644e+04 │ │ │ Vprtstp: contraction number = 1.235644e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.275732e-03 │ │ │ Vprtstp: contraction number = 2.171717e-01 │ │ │ Vnewton: Using errtol_s: 12028.832542 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.799963e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.045007e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.254639e+03 │ │ │ Vprtstp: contraction number = 3.254639e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.294905e-03 │ │ │ Vprtstp: contraction number = 2.454457e-01 │ │ │ Vnewton: Using errtol_s: 2952.424699 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.038252e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.011394e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.022338e+02 │ │ │ Vprtstp: contraction number = 9.022338e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.561621e-04 │ │ │ Vprtstp: contraction number = 2.750487e-01 │ │ │ Vnewton: Using errtol_s: 812.060580 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.288307e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088522e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.611146e+02 │ │ │ Vprtstp: contraction number = 2.611146e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.030702e-04 │ │ │ Vprtstp: contraction number = 2.893914e-01 │ │ │ Vnewton: Using errtol_s: 235.003369 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.538153e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.276998e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.731468e+01 │ │ │ Vprtstp: contraction number = 7.731468e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.051854e-05 │ │ │ Vprtstp: contraction number = 2.960946e-01 │ │ │ Vnewton: Using errtol_s: 69.583224 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.787450e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.470262e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.323028e+01 │ │ │ Vprtstp: contraction number = 2.323028e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.169724e-06 │ │ │ Vprtstp: contraction number = 3.004640e-01 │ │ │ Vnewton: Using errtol_s: 20.907256 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.038210e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.669875e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.057246e+00 │ │ │ Vprtstp: contraction number = 7.057246e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.785717e-06 │ │ │ Vprtstp: contraction number = 3.037951e-01 │ │ │ Vnewton: Using errtol_s: 6.351522 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.275741e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.860210e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.163411e+00 │ │ │ Vprtstp: contraction number = 2.163411e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.539662e-07 │ │ │ Vprtstp: contraction number = 3.065517e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.638172e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.852061e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.030299e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.041304e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -12365,17 +12365,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.169811385763E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.567248755988E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282904610946E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.037100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.291200e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.225 │ │ │ Vpbe_ctor2: xkappa = 0.154458 │ │ │ @@ -12422,160 +12422,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0200222 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.296039 │ │ │ +Vacc_SASA: Time elapsed: 0.506755 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.407200e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.482165e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.878700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.759400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.629600e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.201127e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.389910e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.083499e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2338884.582029 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.587383e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.109275e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.674153e+05 │ │ │ Vprtstp: contraction number = 3.674153e+05 │ │ │ Vnewton: Attempting damping, relres = 0.159441 │ │ │ Vnewton: Attempting damping, relres = 0.569142 │ │ │ Vnewton: Damping accepted, relres = 0.159441 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.594406e-01 │ │ │ Vprtstp: contraction number = 1.594406e-01 │ │ │ Vnewton: Using errtol_s: 372913.066228 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.908584e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.345114e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.262273e+04 │ │ │ Vprtstp: contraction number = 7.262273e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.123186e-02 │ │ │ Vprtstp: contraction number = 1.958841e-01 │ │ │ Vnewton: Using errtol_s: 73047.725996 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.158021e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.574820e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.810013e+04 │ │ │ Vprtstp: contraction number = 1.810013e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.334559e-03 │ │ │ Vprtstp: contraction number = 2.348422e-01 │ │ │ Vnewton: Using errtol_s: 17154.687500 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.395456e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.794841e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.995290e+03 │ │ │ Vprtstp: contraction number = 4.995290e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.929832e-03 │ │ │ Vprtstp: contraction number = 2.631149e-01 │ │ │ Vnewton: Using errtol_s: 4513.654553 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.644980e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.025590e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.448761e+03 │ │ │ Vprtstp: contraction number = 1.448761e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.574979e-04 │ │ │ Vprtstp: contraction number = 2.888841e-01 │ │ │ Vnewton: Using errtol_s: 1303.923175 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.882545e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.248970e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.389996e+02 │ │ │ Vprtstp: contraction number = 4.389996e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.689267e-04 │ │ │ Vprtstp: contraction number = 3.030087e-01 │ │ │ Vnewton: Using errtol_s: 395.100089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.131100e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.462732e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.367279e+02 │ │ │ Vprtstp: contraction number = 1.367279e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.261275e-05 │ │ │ Vprtstp: contraction number = 3.114531e-01 │ │ │ Vnewton: Using errtol_s: 123.055159 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.380343e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.687339e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.345198e+01 │ │ │ Vprtstp: contraction number = 4.345198e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.672027e-05 │ │ │ Vprtstp: contraction number = 3.177988e-01 │ │ │ Vnewton: Using errtol_s: 39.106785 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.618321e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.919105e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.405050e+01 │ │ │ Vprtstp: contraction number = 1.405050e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.406615e-06 │ │ │ Vprtstp: contraction number = 3.233569e-01 │ │ │ Vnewton: Using errtol_s: 12.645449 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.867603e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.136067e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.608577e+00 │ │ │ Vprtstp: contraction number = 4.608577e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.773375e-06 │ │ │ Vprtstp: contraction number = 3.280010e-01 │ │ │ Vnewton: Using errtol_s: 4.147720 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.117299e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.345913e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.529264e+00 │ │ │ Vprtstp: contraction number = 1.529264e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.884589e-07 │ │ │ Vprtstp: contraction number = 3.318299e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.915221e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.146795e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.450913e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.464263e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -12585,17 +12585,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.155729316700E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951863418321E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475213228301E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.011200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.693300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -12622,151 +12622,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.110614 │ │ │ +Vacc_SASA: Time elapsed: 0.133278 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.566680e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.326470e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.034700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.309900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.462060e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.069570e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.830756e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.567719e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 671593.797102 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.976016e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.592796e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.076362e+04 │ │ │ Vprtstp: contraction number = 9.076362e+04 │ │ │ Vnewton: Attempting damping, relres = 0.130235 │ │ │ Vnewton: Attempting damping, relres = 0.558450 │ │ │ Vnewton: Damping accepted, relres = 0.130235 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.302353e-01 │ │ │ Vprtstp: contraction number = 1.302353e-01 │ │ │ Vnewton: Using errtol_s: 87465.248573 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.308509e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.748960e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.691112e+04 │ │ │ Vprtstp: contraction number = 1.691112e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.299894e-02 │ │ │ Vprtstp: contraction number = 1.765952e-01 │ │ │ Vnewton: Using errtol_s: 15445.947049 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.557883e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.889850e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.838772e+03 │ │ │ Vprtstp: contraction number = 3.838772e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.145781e-03 │ │ │ Vprtstp: contraction number = 2.237399e-01 │ │ │ Vnewton: Using errtol_s: 3455.874833 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.806938e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.031272e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.728949e+02 │ │ │ Vprtstp: contraction number = 9.728949e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.303780e-03 │ │ │ Vprtstp: contraction number = 2.533688e-01 │ │ │ Vnewton: Using errtol_s: 875.610893 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005550e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.172802e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.612895e+02 │ │ │ Vprtstp: contraction number = 2.612895e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.501534e-04 │ │ │ Vprtstp: contraction number = 2.685677e-01 │ │ │ Vnewton: Using errtol_s: 235.160844 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.030499e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.319519e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.244969e+01 │ │ │ Vprtstp: contraction number = 7.244969e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.708955e-05 │ │ │ Vprtstp: contraction number = 2.772772e-01 │ │ │ Vnewton: Using errtol_s: 65.204742 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.055402e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.458506e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.052456e+01 │ │ │ Vprtstp: contraction number = 2.052456e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.750488e-05 │ │ │ Vprtstp: contraction number = 2.832939e-01 │ │ │ Vnewton: Using errtol_s: 18.472107 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081909e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.599650e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.913055e+00 │ │ │ Vprtstp: contraction number = 5.913055e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.924060e-06 │ │ │ Vprtstp: contraction number = 2.880965e-01 │ │ │ Vnewton: Using errtol_s: 5.321750 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.106776e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.738621e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.727677e+00 │ │ │ Vprtstp: contraction number = 1.727677e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.315252e-06 │ │ │ Vprtstp: contraction number = 2.921800e-01 │ │ │ Vnewton: Using errtol_s: 1.554909 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.131694e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.882565e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.107037e-01 │ │ │ Vprtstp: contraction number = 5.107037e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.843918e-07 │ │ │ Vprtstp: contraction number = 2.956014e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.676797e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.892995e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.437898e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.450099e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -12776,17 +12776,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.799206762061E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.832181524092E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.414010557344E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.261600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.066010e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.225 │ │ │ Vpbe_ctor2: xkappa = 0.154458 │ │ │ @@ -12833,160 +12833,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00378487 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.111211 │ │ │ +Vacc_SASA: Time elapsed: 0.185193 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.928050e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.574240e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.038100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.781800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.442780e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.076619e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.207052e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.027022e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 699069.872719 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.221348e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.051617e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.130075e+05 │ │ │ Vprtstp: contraction number = 1.130075e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153289 │ │ │ Vnewton: Attempting damping, relres = 0.570479 │ │ │ Vnewton: Damping accepted, relres = 0.153289 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.532887e-01 │ │ │ Vprtstp: contraction number = 1.532887e-01 │ │ │ Vnewton: Using errtol_s: 107159.480370 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.254837e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.229248e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.297596e+04 │ │ │ Vprtstp: contraction number = 2.297596e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.988594e-02 │ │ │ Vprtstp: contraction number = 1.949651e-01 │ │ │ Vnewton: Using errtol_s: 20892.361484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.279613e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.401314e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.581341e+03 │ │ │ Vprtstp: contraction number = 5.581341e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.187204e-03 │ │ │ Vprtstp: contraction number = 2.404878e-01 │ │ │ Vnewton: Using errtol_s: 5024.357995 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.304545e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.566525e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.462004e+03 │ │ │ Vprtstp: contraction number = 1.462004e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.882240e-03 │ │ │ Vprtstp: contraction number = 2.618876e-01 │ │ │ Vnewton: Using errtol_s: 1315.817196 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329476e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.730175e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.024878e+02 │ │ │ Vprtstp: contraction number = 4.024878e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.181744e-04 │ │ │ Vprtstp: contraction number = 2.752967e-01 │ │ │ Vnewton: Using errtol_s: 362.240101 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.354377e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.887695e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.145747e+02 │ │ │ Vprtstp: contraction number = 1.145747e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.475065e-04 │ │ │ Vprtstp: contraction number = 2.846658e-01 │ │ │ Vnewton: Using errtol_s: 103.117357 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.378041e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.048079e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.343339e+01 │ │ │ Vprtstp: contraction number = 3.343339e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.304299e-05 │ │ │ Vprtstp: contraction number = 2.918040e-01 │ │ │ Vnewton: Using errtol_s: 30.090059 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.402875e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.211103e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.964601e+00 │ │ │ Vprtstp: contraction number = 9.964601e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.282868e-05 │ │ │ Vprtstp: contraction number = 2.980433e-01 │ │ │ Vnewton: Using errtol_s: 8.968142 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427828e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.369164e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.030606e+00 │ │ │ Vprtstp: contraction number = 3.030606e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.901677e-06 │ │ │ Vprtstp: contraction number = 3.041372e-01 │ │ │ Vnewton: Using errtol_s: 2.727545 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452763e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.523722e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.382714e-01 │ │ │ Vprtstp: contraction number = 9.382714e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.207954e-06 │ │ │ Vprtstp: contraction number = 3.095986e-01 │ │ │ Vnewton: Using errtol_s: 0.844444 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.476494e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.676071e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.947982e-01 │ │ │ Vprtstp: contraction number = 2.947982e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.795306e-07 │ │ │ Vprtstp: contraction number = 3.141929e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.885982e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.105906e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.783776e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.795741e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -12996,17 +12996,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.791143336195E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.064706767372E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.030284850929E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.251000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.313500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -13033,162 +13033,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.175537 │ │ │ +Vacc_SASA: Time elapsed: 0.268570 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.937060e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.894810e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.046400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.988800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.453990e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.073194e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.662065e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.845605e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1599051.147684 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.676715e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.870248e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.270628e+05 │ │ │ Vprtstp: contraction number = 2.270628e+05 │ │ │ Vnewton: Attempting damping, relres = 0.190153 │ │ │ Vnewton: Attempting damping, relres = 0.564950 │ │ │ Vnewton: Damping accepted, relres = 0.190153 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.901527e-01 │ │ │ Vprtstp: contraction number = 1.901527e-01 │ │ │ Vnewton: Using errtol_s: 304063.886192 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.709940e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.030990e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.318204e+04 │ │ │ Vprtstp: contraction number = 4.318204e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.822370e-02 │ │ │ Vprtstp: contraction number = 2.010158e-01 │ │ │ Vnewton: Using errtol_s: 61121.655411 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.734996e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.212613e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.090069e+04 │ │ │ Vprtstp: contraction number = 1.090069e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.378283e-03 │ │ │ Vprtstp: contraction number = 2.191908e-01 │ │ │ Vnewton: Using errtol_s: 13397.302580 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.759911e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.370444e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.039014e+03 │ │ │ Vprtstp: contraction number = 3.039014e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.821126e-03 │ │ │ Vprtstp: contraction number = 2.173626e-01 │ │ │ Vnewton: Using errtol_s: 2912.073157 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.784806e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.525478e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.399695e+02 │ │ │ Vprtstp: contraction number = 8.399695e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.733052e-04 │ │ │ Vprtstp: contraction number = 2.598970e-01 │ │ │ Vnewton: Using errtol_s: 756.839199 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.809614e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.675954e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.453869e+02 │ │ │ Vprtstp: contraction number = 2.453869e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.381125e-04 │ │ │ Vprtstp: contraction number = 2.918043e-01 │ │ │ Vnewton: Using errtol_s: 220.848913 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.836789e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.829369e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.399321e+01 │ │ │ Vprtstp: contraction number = 7.399321e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.164589e-05 │ │ │ Vprtstp: contraction number = 3.015360e-01 │ │ │ Vnewton: Using errtol_s: 66.593908 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.861631e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.986820e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.251212e+01 │ │ │ Vprtstp: contraction number = 2.251212e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.267058e-05 │ │ │ Vprtstp: contraction number = 3.042457e-01 │ │ │ Vnewton: Using errtol_s: 20.260912 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.886490e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.139816e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.882100e+00 │ │ │ Vprtstp: contraction number = 6.882100e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.873479e-06 │ │ │ Vprtstp: contraction number = 3.057064e-01 │ │ │ Vnewton: Using errtol_s: 6.193891 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.910217e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.299023e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.110443e+00 │ │ │ Vprtstp: contraction number = 2.110443e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.187828e-06 │ │ │ Vprtstp: contraction number = 3.066568e-01 │ │ │ Vnewton: Using errtol_s: 1.899398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.934986e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.459155e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.486511e-01 │ │ │ Vprtstp: contraction number = 6.486511e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.650828e-07 │ │ │ Vprtstp: contraction number = 3.073531e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.923949e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.142992e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.755138e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.766890e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -13198,17 +13198,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.557875288957E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.874100920803E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.359333289528E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.192700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.239700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.225 │ │ │ Vpbe_ctor2: xkappa = 0.154458 │ │ │ @@ -13255,160 +13255,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00715191 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.174601 │ │ │ +Vacc_SASA: Time elapsed: 0.286019 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.479950e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.672230e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.940400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.762900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.459870e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.197346e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.026066e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.624444e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1635353.597903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.039498e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.652280e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.841111e+05 │ │ │ Vprtstp: contraction number = 2.841111e+05 │ │ │ Vnewton: Attempting damping, relres = 0.216841 │ │ │ Vnewton: Attempting damping, relres = 0.579374 │ │ │ Vnewton: Damping accepted, relres = 0.216841 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.168415e-01 │ │ │ Vprtstp: contraction number = 2.168415e-01 │ │ │ Vnewton: Using errtol_s: 354612.472828 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.072737e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.843880e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.888895e+04 │ │ │ Vprtstp: contraction number = 5.888895e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.598888e-02 │ │ │ Vprtstp: contraction number = 2.120853e-01 │ │ │ Vnewton: Using errtol_s: 75208.075023 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.097719e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.006612e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.566082e+04 │ │ │ Vprtstp: contraction number = 1.566082e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.075687e-02 │ │ │ Vprtstp: contraction number = 2.339015e-01 │ │ │ Vnewton: Using errtol_s: 17591.280350 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.122651e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.025231e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.551176e+03 │ │ │ Vprtstp: contraction number = 4.551176e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.599859e-03 │ │ │ Vprtstp: contraction number = 2.416930e-01 │ │ │ Vnewton: Using errtol_s: 4251.688603 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.147445e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042998e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.335913e+03 │ │ │ Vprtstp: contraction number = 1.335913e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.355871e-04 │ │ │ Vprtstp: contraction number = 2.829335e-01 │ │ │ Vnewton: Using errtol_s: 1202.945014 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.172313e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.059695e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.136155e+02 │ │ │ Vprtstp: contraction number = 4.136155e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.276295e-04 │ │ │ Vprtstp: contraction number = 3.094528e-01 │ │ │ Vnewton: Using errtol_s: 372.254692 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.197178e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.076665e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.319427e+02 │ │ │ Vprtstp: contraction number = 1.319427e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.261334e-05 │ │ │ Vprtstp: contraction number = 3.189980e-01 │ │ │ Vnewton: Using errtol_s: 118.748486 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.224539e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.093988e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.270247e+01 │ │ │ Vprtstp: contraction number = 4.270247e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.350087e-05 │ │ │ Vprtstp: contraction number = 3.236440e-01 │ │ │ Vnewton: Using errtol_s: 38.432230 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.249440e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.110498e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.396688e+01 │ │ │ Vprtstp: contraction number = 1.396688e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.686528e-06 │ │ │ Vprtstp: contraction number = 3.270742e-01 │ │ │ Vnewton: Using errtol_s: 12.570191 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.274462e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.127510e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.606421e+00 │ │ │ Vprtstp: contraction number = 4.606421e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.535096e-06 │ │ │ Vprtstp: contraction number = 3.298104e-01 │ │ │ Vnewton: Using errtol_s: 4.145779 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.299314e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.144185e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.529247e+00 │ │ │ Vprtstp: contraction number = 1.529247e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.416053e-07 │ │ │ Vprtstp: contraction number = 3.319816e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.933170e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.151519e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.978359e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.991392e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -13418,29 +13418,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.546220466896E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.135839093340E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066803828890E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.083800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.558100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.422206e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.162134e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:08:33 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 00:55:49 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -13710,151 +13710,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.304285 │ │ │ +Vacc_SASA: Time elapsed: 0.405421 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.302030e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.264102e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.915800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.218300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.464500e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.113401e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.740860e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.502211e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2251971.697064 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021173e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.051952e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.916802e+05 │ │ │ Vprtstp: contraction number = 2.916802e+05 │ │ │ Vnewton: Attempting damping, relres = 0.133998 │ │ │ Vnewton: Attempting damping, relres = 0.556443 │ │ │ Vnewton: Damping accepted, relres = 0.133998 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.339981e-01 │ │ │ Vprtstp: contraction number = 1.339981e-01 │ │ │ Vnewton: Using errtol_s: 301759.930673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.343623e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.699982e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.235007e+04 │ │ │ Vprtstp: contraction number = 5.235007e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.393476e-02 │ │ │ Vprtstp: contraction number = 1.786201e-01 │ │ │ Vnewton: Using errtol_s: 53900.402880 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.593541e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.140059e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.224190e+04 │ │ │ Vprtstp: contraction number = 1.224190e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.213784e-03 │ │ │ Vprtstp: contraction number = 2.178331e-01 │ │ │ Vnewton: Using errtol_s: 11741.294295 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.842213e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.256579e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.226956e+03 │ │ │ Vprtstp: contraction number = 3.226956e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.296373e-03 │ │ │ Vprtstp: contraction number = 2.486433e-01 │ │ │ Vnewton: Using errtol_s: 2919.394410 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.092128e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.231121e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.979745e+02 │ │ │ Vprtstp: contraction number = 8.979745e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.588880e-04 │ │ │ Vprtstp: contraction number = 2.768402e-01 │ │ │ Vnewton: Using errtol_s: 808.205614 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.353955e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120423e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.602996e+02 │ │ │ Vprtstp: contraction number = 2.602996e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.040288e-04 │ │ │ Vprtstp: contraction number = 2.898642e-01 │ │ │ Vnewton: Using errtol_s: 234.269873 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.603681e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321822e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.710898e+01 │ │ │ Vprtstp: contraction number = 7.710898e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.081659e-05 │ │ │ Vprtstp: contraction number = 2.962314e-01 │ │ │ Vnewton: Using errtol_s: 69.398097 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.853266e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.525613e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.317379e+01 │ │ │ Vprtstp: contraction number = 2.317379e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.261402e-06 │ │ │ Vprtstp: contraction number = 3.005329e-01 │ │ │ Vnewton: Using errtol_s: 20.856415 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.102481e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.738153e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.040959e+00 │ │ │ Vprtstp: contraction number = 7.040959e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.813918e-06 │ │ │ Vprtstp: contraction number = 3.038328e-01 │ │ │ Vnewton: Using errtol_s: 6.336864 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.352553e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.955978e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.158573e+00 │ │ │ Vprtstp: contraction number = 2.158573e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.626731e-07 │ │ │ Vprtstp: contraction number = 3.065736e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.675162e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.894977e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.159715e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.171843e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -13864,17 +13864,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.054258370854E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.567152466024E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282878106932E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.085300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.269200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-05 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.25 │ │ │ Vpbe_ctor2: xkappa = 0.162813 │ │ │ @@ -13921,160 +13921,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0186115 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.298711 │ │ │ +Vacc_SASA: Time elapsed: 0.644585 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.547240e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.766123e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.938700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.769500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.466950e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.486997e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.475794e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219707e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2308477.613734 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.619509e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.256306e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.628256e+05 │ │ │ Vprtstp: contraction number = 3.628256e+05 │ │ │ Vnewton: Attempting damping, relres = 0.158221 │ │ │ Vnewton: Attempting damping, relres = 0.569085 │ │ │ Vnewton: Damping accepted, relres = 0.158221 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.582211e-01 │ │ │ Vprtstp: contraction number = 1.582211e-01 │ │ │ Vnewton: Using errtol_s: 365249.935342 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.950940e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.576858e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.179371e+04 │ │ │ Vprtstp: contraction number = 7.179371e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.090684e-02 │ │ │ Vprtstp: contraction number = 1.953395e-01 │ │ │ Vnewton: Using errtol_s: 71347.745828 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.200528e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.836243e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.791601e+04 │ │ │ Vprtstp: contraction number = 1.791601e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.281434e-03 │ │ │ Vprtstp: contraction number = 2.355930e-01 │ │ │ Vnewton: Using errtol_s: 16809.026903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.438312e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.099404e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.947991e+03 │ │ │ Vprtstp: contraction number = 4.947991e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.933961e-03 │ │ │ Vprtstp: contraction number = 2.656017e-01 │ │ │ Vnewton: Using errtol_s: 4464.506758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.688194e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.319673e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.439628e+03 │ │ │ Vprtstp: contraction number = 1.439628e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.612744e-04 │ │ │ Vprtstp: contraction number = 2.902201e-01 │ │ │ Vnewton: Using errtol_s: 1295.689464 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.937725e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.533888e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.369472e+02 │ │ │ Vprtstp: contraction number = 4.369472e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.703516e-04 │ │ │ Vprtstp: contraction number = 3.035087e-01 │ │ │ Vnewton: Using errtol_s: 393.252962 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.193947e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.771495e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.361967e+02 │ │ │ Vprtstp: contraction number = 1.361967e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.309866e-05 │ │ │ Vprtstp: contraction number = 3.117003e-01 │ │ │ Vnewton: Using errtol_s: 122.577063 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.431039e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.046632e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.330599e+01 │ │ │ Vprtstp: contraction number = 4.330599e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.688359e-05 │ │ │ Vprtstp: contraction number = 3.179665e-01 │ │ │ Vnewton: Using errtol_s: 38.975398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.680288e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.317975e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.400799e+01 │ │ │ Vprtstp: contraction number = 1.400799e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.461259e-06 │ │ │ Vprtstp: contraction number = 3.234655e-01 │ │ │ Vnewton: Using errtol_s: 12.607195 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.929620e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.570407e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.595493e+00 │ │ │ Vprtstp: contraction number = 4.595493e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.791632e-06 │ │ │ Vprtstp: contraction number = 3.280621e-01 │ │ │ Vnewton: Using errtol_s: 4.135943 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.179037e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.799276e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.525032e+00 │ │ │ Vprtstp: contraction number = 1.525032e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.945603e-07 │ │ │ Vprtstp: contraction number = 3.318539e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.887172e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.108455e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.792922e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.809200e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -14084,17 +14084,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.040496519362E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951767181280E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475186803356E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.973500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.575900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -14121,151 +14121,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.111294 │ │ │ +Vacc_SASA: Time elapsed: 0.233569 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.743150e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.042580e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.955900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.705600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.688070e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.080217e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.906285e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.047659e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 665026.668065 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.115596e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.074091e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.977874e+04 │ │ │ Vprtstp: contraction number = 8.977874e+04 │ │ │ Vnewton: Attempting damping, relres = 0.130004 │ │ │ Vnewton: Attempting damping, relres = 0.558352 │ │ │ Vnewton: Damping accepted, relres = 0.130004 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.300040e-01 │ │ │ Vprtstp: contraction number = 1.300040e-01 │ │ │ Vnewton: Using errtol_s: 86456.120106 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.437932e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.231136e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.677494e+04 │ │ │ Vprtstp: contraction number = 1.677494e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.302058e-02 │ │ │ Vprtstp: contraction number = 1.770760e-01 │ │ │ Vnewton: Using errtol_s: 15309.299757 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.698367e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.369147e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.819009e+03 │ │ │ Vprtstp: contraction number = 3.819009e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.169720e-03 │ │ │ Vprtstp: contraction number = 2.245695e-01 │ │ │ Vnewton: Using errtol_s: 3438.001701 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.947815e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.506735e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.699577e+02 │ │ │ Vprtstp: contraction number = 9.699577e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.312680e-03 │ │ │ Vprtstp: contraction number = 2.539171e-01 │ │ │ Vnewton: Using errtol_s: 872.967407 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018543e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.644620e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.608286e+02 │ │ │ Vprtstp: contraction number = 2.608286e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.529874e-04 │ │ │ Vprtstp: contraction number = 2.689059e-01 │ │ │ Vnewton: Using errtol_s: 234.746058 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.043464e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.782892e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.237536e+01 │ │ │ Vprtstp: contraction number = 7.237536e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.794772e-05 │ │ │ Vprtstp: contraction number = 2.774822e-01 │ │ │ Vnewton: Using errtol_s: 65.137847 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068304e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.927119e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.051211e+01 │ │ │ Vprtstp: contraction number = 2.051211e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.775964e-05 │ │ │ Vprtstp: contraction number = 2.834128e-01 │ │ │ Vnewton: Using errtol_s: 18.460901 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.093280e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.091593e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.910817e+00 │ │ │ Vprtstp: contraction number = 5.910817e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 7.999282e-06 │ │ │ Vprtstp: contraction number = 2.881623e-01 │ │ │ Vnewton: Using errtol_s: 5.319736 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.118211e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.267094e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.727236e+00 │ │ │ Vprtstp: contraction number = 1.727236e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.337519e-06 │ │ │ Vprtstp: contraction number = 2.922161e-01 │ │ │ Vnewton: Using errtol_s: 1.554512 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.143191e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.441647e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.106059e-01 │ │ │ Vprtstp: contraction number = 5.106059e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.910179e-07 │ │ │ Vprtstp: contraction number = 2.956203e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.714619e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.948769e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.533415e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.545509e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -14275,17 +14275,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.810176987891E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.831840502654E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.413842577574E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.458200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.838000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.25 │ │ │ Vpbe_ctor2: xkappa = 0.162813 │ │ │ @@ -14332,160 +14332,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00343543 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.109736 │ │ │ +Vacc_SASA: Time elapsed: 0.204866 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.900110e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.702190e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.951100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.818600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.474000e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.248444e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.218507e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.603200e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 691979.805773 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232920e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.635725e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.117154e+05 │ │ │ Vprtstp: contraction number = 1.117154e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153004 │ │ │ Vnewton: Attempting damping, relres = 0.570353 │ │ │ Vnewton: Damping accepted, relres = 0.153004 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.530041e-01 │ │ │ Vprtstp: contraction number = 1.530041e-01 │ │ │ Vnewton: Using errtol_s: 105875.763511 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.265266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.826392e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.274708e+04 │ │ │ Vprtstp: contraction number = 2.274708e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.987439e-02 │ │ │ Vprtstp: contraction number = 1.952522e-01 │ │ │ Vnewton: Using errtol_s: 20672.472417 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.290239e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.996120e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.535330e+03 │ │ │ Vprtstp: contraction number = 5.535330e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.200880e-03 │ │ │ Vprtstp: contraction number = 2.410386e-01 │ │ │ Vnewton: Using errtol_s: 4982.863785 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.315226e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.150966e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.452451e+03 │ │ │ Vprtstp: contraction number = 1.452451e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.889102e-03 │ │ │ Vprtstp: contraction number = 2.623432e-01 │ │ │ Vnewton: Using errtol_s: 1307.220185 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.340254e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.307242e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.004485e+02 │ │ │ Vprtstp: contraction number = 4.004485e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.208313e-04 │ │ │ Vprtstp: contraction number = 2.757032e-01 │ │ │ Vnewton: Using errtol_s: 360.404730 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.365257e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.456165e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.141337e+02 │ │ │ Vprtstp: contraction number = 1.141337e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.484443e-04 │ │ │ Vprtstp: contraction number = 2.850142e-01 │ │ │ Vnewton: Using errtol_s: 102.720463 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.390198e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.603952e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.333734e+01 │ │ │ Vprtstp: contraction number = 3.333734e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.335909e-05 │ │ │ Vprtstp: contraction number = 2.920899e-01 │ │ │ Vnewton: Using errtol_s: 30.003614 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.415109e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.750296e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.943557e+00 │ │ │ Vprtstp: contraction number = 9.943557e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.293275e-05 │ │ │ Vprtstp: contraction number = 2.982708e-01 │ │ │ Vnewton: Using errtol_s: 8.949202 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.438870e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.901500e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.025944e+00 │ │ │ Vprtstp: contraction number = 3.025944e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.935591e-06 │ │ │ Vprtstp: contraction number = 3.043120e-01 │ │ │ Vnewton: Using errtol_s: 2.723350 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.464784e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.051944e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.372238e-01 │ │ │ Vprtstp: contraction number = 9.372238e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.218968e-06 │ │ │ Vprtstp: contraction number = 3.097294e-01 │ │ │ Vnewton: Using errtol_s: 0.843501 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.489808e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.208247e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.945582e-01 │ │ │ Vprtstp: contraction number = 2.945582e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.831071e-07 │ │ │ Vprtstp: contraction number = 3.142880e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.898574e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.120694e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.738063e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.751782e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -14495,17 +14495,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.802033666464E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.064367172760E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.030117685645E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.180600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.254500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -14532,162 +14532,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173181 │ │ │ +Vacc_SASA: Time elapsed: 0.228854 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.907700e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.987170e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.922900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.745100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.431840e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.020556e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.672265e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.378172e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1569842.241791 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.686373e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.402057e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.229696e+05 │ │ │ Vprtstp: contraction number = 2.229696e+05 │ │ │ Vnewton: Attempting damping, relres = 0.185061 │ │ │ Vnewton: Attempting damping, relres = 0.564709 │ │ │ Vnewton: Damping accepted, relres = 0.185061 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.850613e-01 │ │ │ Vprtstp: contraction number = 1.850613e-01 │ │ │ Vnewton: Using errtol_s: 290517.094461 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.718638e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.560974e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.227646e+04 │ │ │ Vprtstp: contraction number = 4.227646e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.651895e-02 │ │ │ Vprtstp: contraction number = 1.973343e-01 │ │ │ Vnewton: Using errtol_s: 57328.986523 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.743540e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.740781e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.068153e+04 │ │ │ Vprtstp: contraction number = 1.068153e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.924548e-03 │ │ │ Vprtstp: contraction number = 2.169982e-01 │ │ │ Vnewton: Using errtol_s: 12440.289572 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.771120e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.894055e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.967582e+03 │ │ │ Vprtstp: contraction number = 2.967582e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.771235e-03 │ │ │ Vprtstp: contraction number = 2.235125e-01 │ │ │ Vnewton: Using errtol_s: 2780.560196 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.804405e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.040377e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.265098e+02 │ │ │ Vprtstp: contraction number = 8.265098e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.740960e-04 │ │ │ Vprtstp: contraction number = 2.676640e-01 │ │ │ Vnewton: Using errtol_s: 744.255948 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.829428e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.189489e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.434115e+02 │ │ │ Vprtstp: contraction number = 2.434115e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.395496e-04 │ │ │ Vprtstp: contraction number = 2.943487e-01 │ │ │ Vnewton: Using errtol_s: 219.070780 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.853208e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.350639e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.348771e+01 │ │ │ Vprtstp: contraction number = 7.348771e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.213095e-05 │ │ │ Vprtstp: contraction number = 3.019068e-01 │ │ │ Vnewton: Using errtol_s: 66.138952 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.878708e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.501370e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.236672e+01 │ │ │ Vprtstp: contraction number = 2.236672e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.282298e-05 │ │ │ Vprtstp: contraction number = 3.043600e-01 │ │ │ Vnewton: Using errtol_s: 20.130053 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.903713e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.653354e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.838847e+00 │ │ │ Vprtstp: contraction number = 6.838847e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.920752e-06 │ │ │ Vprtstp: contraction number = 3.057599e-01 │ │ │ Vnewton: Using errtol_s: 6.154962 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.928630e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.815979e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.097413e+00 │ │ │ Vprtstp: contraction number = 2.097413e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.202459e-06 │ │ │ Vprtstp: contraction number = 3.066910e-01 │ │ │ Vnewton: Using errtol_s: 1.887672 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.952428e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.982146e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.447028e-01 │ │ │ Vprtstp: contraction number = 6.447028e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.696120e-07 │ │ │ Vprtstp: contraction number = 3.073800e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.995961e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.211153e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.747259e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.759071e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -14697,17 +14697,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.380223605804E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.873963354108E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.358993220617E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.128400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.151400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.25 │ │ │ Vpbe_ctor2: xkappa = 0.162813 │ │ │ @@ -14754,160 +14754,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00593059 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.168716 │ │ │ +Vacc_SASA: Time elapsed: 0.318438 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.425190e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.044485e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.883300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.789200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.445370e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.123896e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.041980e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014930e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1604207.937715 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.056462e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.017779e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.790911e+05 │ │ │ Vprtstp: contraction number = 2.790911e+05 │ │ │ Vnewton: Attempting damping, relres = 0.212135 │ │ │ Vnewton: Attempting damping, relres = 0.579242 │ │ │ Vnewton: Damping accepted, relres = 0.212135 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.121354e-01 │ │ │ Vprtstp: contraction number = 2.121354e-01 │ │ │ Vnewton: Using errtol_s: 340309.311873 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.088646e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038502e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.770596e+04 │ │ │ Vprtstp: contraction number = 5.770596e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.436697e-02 │ │ │ Vprtstp: contraction number = 2.091445e-01 │ │ │ Vnewton: Using errtol_s: 71173.837804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.113698e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062857e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.535772e+04 │ │ │ Vprtstp: contraction number = 1.535772e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 1.032915e-02 │ │ │ Vprtstp: contraction number = 2.328117e-01 │ │ │ Vnewton: Using errtol_s: 16570.101449 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.138691e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081249e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.454547e+03 │ │ │ Vprtstp: contraction number = 4.454547e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.558458e-03 │ │ │ Vprtstp: contraction number = 2.476930e-01 │ │ │ Vnewton: Using errtol_s: 4104.298326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.163682e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.098947e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.316329e+03 │ │ │ Vprtstp: contraction number = 1.316329e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.386763e-04 │ │ │ Vprtstp: contraction number = 2.887193e-01 │ │ │ Vnewton: Using errtol_s: 1184.990339 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.187431e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.116880e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.099732e+02 │ │ │ Vprtstp: contraction number = 4.099732e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.300054e-04 │ │ │ Vprtstp: contraction number = 3.113751e-01 │ │ │ Vnewton: Using errtol_s: 368.976439 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.212438e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.136199e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.309902e+02 │ │ │ Vprtstp: contraction number = 1.309902e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.348872e-05 │ │ │ Vprtstp: contraction number = 3.195087e-01 │ │ │ Vnewton: Using errtol_s: 117.891195 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.236121e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.154758e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.243118e+01 │ │ │ Vprtstp: contraction number = 4.243118e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.380494e-05 │ │ │ Vprtstp: contraction number = 3.239264e-01 │ │ │ Vnewton: Using errtol_s: 38.188070 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.261085e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.171506e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.388647e+01 │ │ │ Vprtstp: contraction number = 1.388647e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.790652e-06 │ │ │ Vprtstp: contraction number = 3.272704e-01 │ │ │ Vnewton: Using errtol_s: 12.497826 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.286085e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188510e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.581763e+00 │ │ │ Vprtstp: contraction number = 4.581763e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.570482e-06 │ │ │ Vprtstp: contraction number = 3.299443e-01 │ │ │ Vnewton: Using errtol_s: 4.123587 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.310882e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.205339e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.521483e+00 │ │ │ Vprtstp: contraction number = 1.521483e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.535894e-07 │ │ │ Vprtstp: contraction number = 3.320737e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.885226e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.095369e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.049540e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.062166e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -14917,29 +14917,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.368902130517E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.135701558187E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066769863960E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.070300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.399100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.200000e-05 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.433402e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.221906e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:08:44 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 01:22:12 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -15209,151 +15209,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.307331 │ │ │ +Vacc_SASA: Time elapsed: 0.555422 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.939380e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.252079e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.916600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.389000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.440800e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.023262e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.288750e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.440149e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2228500.711111 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004719e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.928972e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.885324e+05 │ │ │ Vprtstp: contraction number = 2.885324e+05 │ │ │ Vnewton: Attempting damping, relres = 0.132783 │ │ │ Vnewton: Attempting damping, relres = 0.556333 │ │ │ Vnewton: Damping accepted, relres = 0.132783 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.327828e-01 │ │ │ Vprtstp: contraction number = 1.327828e-01 │ │ │ Vnewton: Using errtol_s: 295906.495800 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.406373e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.496654e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.185298e+04 │ │ │ Vprtstp: contraction number = 5.185298e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.363031e-02 │ │ │ Vprtstp: contraction number = 1.779622e-01 │ │ │ Vnewton: Using errtol_s: 52660.160944 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682256e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.558713e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.214543e+04 │ │ │ Vprtstp: contraction number = 1.214543e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.166063e-03 │ │ │ Vprtstp: contraction number = 2.186202e-01 │ │ │ Vnewton: Using errtol_s: 11512.574293 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.945659e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.610103e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.204841e+03 │ │ │ Vprtstp: contraction number = 3.204841e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.298834e-03 │ │ │ Vprtstp: contraction number = 2.514166e-01 │ │ │ Vnewton: Using errtol_s: 2894.452376 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.196834e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.597764e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.947420e+02 │ │ │ Vprtstp: contraction number = 8.947420e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.613575e-04 │ │ │ Vprtstp: contraction number = 2.782168e-01 │ │ │ Vnewton: Using errtol_s: 805.285400 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.486466e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.050237e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.596666e+02 │ │ │ Vprtstp: contraction number = 2.596666e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.048688e-04 │ │ │ Vprtstp: contraction number = 2.902078e-01 │ │ │ Vnewton: Using errtol_s: 233.700117 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.750142e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.240197e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.695052e+01 │ │ │ Vprtstp: contraction number = 7.695052e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.107716e-05 │ │ │ Vprtstp: contraction number = 2.963434e-01 │ │ │ Vnewton: Using errtol_s: 69.255484 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.095787e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.432150e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.313064e+01 │ │ │ Vprtstp: contraction number = 2.313064e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.341518e-06 │ │ │ Vprtstp: contraction number = 3.005911e-01 │ │ │ Vnewton: Using errtol_s: 20.817580 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.402598e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.624845e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.028571e+00 │ │ │ Vprtstp: contraction number = 7.028571e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.838551e-06 │ │ │ Vprtstp: contraction number = 3.038640e-01 │ │ │ Vnewton: Using errtol_s: 6.325714 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.657874e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.822776e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.154905e+00 │ │ │ Vprtstp: contraction number = 2.154905e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.702776e-07 │ │ │ Vprtstp: contraction number = 3.065922e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.023883e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.235541e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.987537e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.998964e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15363,17 +15363,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.948103828558E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.567066305004E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282854148760E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.162200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.430500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.275 │ │ │ Vpbe_ctor2: xkappa = 0.17076 │ │ │ @@ -15420,160 +15420,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0175518 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.307917 │ │ │ +Vacc_SASA: Time elapsed: 0.421500 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.781940e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.320028e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.051100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.808400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.638630e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.023462e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.817588e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.037329e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2283064.573073 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.972844e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.062573e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.589605e+05 │ │ │ Vprtstp: contraction number = 3.589605e+05 │ │ │ Vnewton: Attempting damping, relres = 0.157146 │ │ │ Vnewton: Attempting damping, relres = 0.569027 │ │ │ Vnewton: Damping accepted, relres = 0.157146 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.571455e-01 │ │ │ Vprtstp: contraction number = 1.571455e-01 │ │ │ Vnewton: Using errtol_s: 358773.390898 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.476321e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.304247e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.109555e+04 │ │ │ Vprtstp: contraction number = 7.109555e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.062803e-02 │ │ │ Vprtstp: contraction number = 1.949023e-01 │ │ │ Vnewton: Using errtol_s: 69925.774403 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.839017e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.518650e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.775956e+04 │ │ │ Vprtstp: contraction number = 1.775956e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.240527e-03 │ │ │ Vprtstp: contraction number = 2.364020e-01 │ │ │ Vnewton: Using errtol_s: 16530.590965 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.123054e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.724779e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.909187e+03 │ │ │ Vprtstp: contraction number = 4.909187e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.938451e-03 │ │ │ Vprtstp: contraction number = 2.677224e-01 │ │ │ Vnewton: Using errtol_s: 4425.608962 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.513680e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.923000e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.432328e+03 │ │ │ Vprtstp: contraction number = 1.432328e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.646405e-04 │ │ │ Vprtstp: contraction number = 2.912844e-01 │ │ │ Vnewton: Using errtol_s: 1289.110788 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.895738e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.129425e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.352860e+02 │ │ │ Vprtstp: contraction number = 4.352860e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.715930e-04 │ │ │ Vprtstp: contraction number = 3.038977e-01 │ │ │ Vnewton: Using errtol_s: 391.757810 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.237044e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.341614e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.357704e+02 │ │ │ Vprtstp: contraction number = 1.357704e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.352166e-05 │ │ │ Vprtstp: contraction number = 3.119106e-01 │ │ │ Vnewton: Using errtol_s: 122.193412 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.584936e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.552797e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.319013e+01 │ │ │ Vprtstp: contraction number = 4.319013e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.702585e-05 │ │ │ Vprtstp: contraction number = 3.181115e-01 │ │ │ Vnewton: Using errtol_s: 38.871124 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.892011e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.764517e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.397456e+01 │ │ │ Vprtstp: contraction number = 1.397456e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.508868e-06 │ │ │ Vprtstp: contraction number = 3.235590e-01 │ │ │ Vnewton: Using errtol_s: 12.577101 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.211802e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.992937e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.585274e+00 │ │ │ Vprtstp: contraction number = 4.585274e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.807547e-06 │ │ │ Vprtstp: contraction number = 3.281159e-01 │ │ │ Vnewton: Using errtol_s: 4.126746 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.475984e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.231425e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.521742e+00 │ │ │ Vprtstp: contraction number = 1.521742e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 5.998813e-07 │ │ │ Vprtstp: contraction number = 3.318759e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.875624e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.109592e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.402612e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.413925e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15583,17 +15583,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.934616474565E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951681070136E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475162911234E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.046000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.624400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -15620,151 +15620,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.109025 │ │ │ +Vacc_SASA: Time elapsed: 0.180399 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.723040e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.771140e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.087800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.403900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.462900e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.135769e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038913e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.476020e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 659573.848020 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056607e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.502298e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.895379e+04 │ │ │ Vprtstp: contraction number = 8.895379e+04 │ │ │ Vnewton: Attempting damping, relres = 0.129769 │ │ │ Vnewton: Attempting damping, relres = 0.558262 │ │ │ Vnewton: Damping accepted, relres = 0.129769 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.297694e-01 │ │ │ Vprtstp: contraction number = 1.297694e-01 │ │ │ Vnewton: Using errtol_s: 85592.483355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.098841e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.666745e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.666045e+04 │ │ │ Vprtstp: contraction number = 1.666045e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.303462e-02 │ │ │ Vprtstp: contraction number = 1.775043e-01 │ │ │ Vnewton: Using errtol_s: 15193.035895 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.124685e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.830003e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.802357e+03 │ │ │ Vprtstp: contraction number = 3.802357e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.189623e-03 │ │ │ Vprtstp: contraction number = 2.252966e-01 │ │ │ Vnewton: Using errtol_s: 3422.939434 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.150726e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.000260e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.674822e+02 │ │ │ Vprtstp: contraction number = 9.674822e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.320155e-03 │ │ │ Vprtstp: contraction number = 2.543835e-01 │ │ │ Vnewton: Using errtol_s: 870.739405 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.178379e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.170058e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.604392e+02 │ │ │ Vprtstp: contraction number = 2.604392e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.553742e-04 │ │ │ Vprtstp: contraction number = 2.691914e-01 │ │ │ Vnewton: Using errtol_s: 234.395549 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.207980e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.328782e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.231232e+01 │ │ │ Vprtstp: contraction number = 7.231232e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.867144e-05 │ │ │ Vprtstp: contraction number = 2.776550e-01 │ │ │ Vnewton: Using errtol_s: 65.081104 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.242075e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.474350e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.050149e+01 │ │ │ Vprtstp: contraction number = 2.050149e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.797465e-05 │ │ │ Vprtstp: contraction number = 2.835131e-01 │ │ │ Vnewton: Using errtol_s: 18.451347 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.275001e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.625343e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.908895e+00 │ │ │ Vprtstp: contraction number = 5.908895e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.062791e-06 │ │ │ Vprtstp: contraction number = 2.882178e-01 │ │ │ Vnewton: Using errtol_s: 5.318006 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.303572e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.778472e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.726854e+00 │ │ │ Vprtstp: contraction number = 1.726854e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.356322e-06 │ │ │ Vprtstp: contraction number = 2.922465e-01 │ │ │ Vnewton: Using errtol_s: 1.554169 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329774e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.938832e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.105208e-01 │ │ │ Vprtstp: contraction number = 5.105208e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.966145e-07 │ │ │ Vprtstp: contraction number = 2.956364e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.125982e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.350912e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.609834e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.621984e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15774,17 +15774,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.818510917310E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.831530055588E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.413690932719E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.556000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.313430e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.275 │ │ │ Vpbe_ctor2: xkappa = 0.17076 │ │ │ @@ -15831,160 +15831,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00313173 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.110277 │ │ │ +Vacc_SASA: Time elapsed: 0.179197 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.988840e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.555820e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.914700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.265800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.445080e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.129806e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.408158e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.107764e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 686089.077180 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.422821e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.137014e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.106303e+05 │ │ │ Vprtstp: contraction number = 1.106303e+05 │ │ │ Vnewton: Attempting damping, relres = 0.152721 │ │ │ Vnewton: Attempting damping, relres = 0.570236 │ │ │ Vnewton: Damping accepted, relres = 0.152721 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.527207e-01 │ │ │ Vprtstp: contraction number = 1.527207e-01 │ │ │ Vnewton: Using errtol_s: 104780.035977 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.456452e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.315927e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.255423e+04 │ │ │ Vprtstp: contraction number = 2.255423e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.985893e-02 │ │ │ Vprtstp: contraction number = 1.955132e-01 │ │ │ Vnewton: Using errtol_s: 20485.884926 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.481960e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.479230e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.496448e+03 │ │ │ Vprtstp: contraction number = 5.496448e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.211588e-03 │ │ │ Vprtstp: contraction number = 2.415220e-01 │ │ │ Vnewton: Using errtol_s: 4947.791442 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.507008e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.629394e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.444377e+03 │ │ │ Vprtstp: contraction number = 1.444377e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.894730e-03 │ │ │ Vprtstp: contraction number = 2.627341e-01 │ │ │ Vnewton: Using errtol_s: 1299.953373 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.531887e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.776719e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.987236e+02 │ │ │ Vprtstp: contraction number = 3.987236e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.230404e-04 │ │ │ Vprtstp: contraction number = 2.760502e-01 │ │ │ Vnewton: Using errtol_s: 358.852327 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.556827e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.932609e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.137605e+02 │ │ │ Vprtstp: contraction number = 1.137605e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.492292e-04 │ │ │ Vprtstp: contraction number = 2.853110e-01 │ │ │ Vnewton: Using errtol_s: 102.384499 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581835e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.091446e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.325592e+01 │ │ │ Vprtstp: contraction number = 3.325592e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.362456e-05 │ │ │ Vprtstp: contraction number = 2.923327e-01 │ │ │ Vnewton: Using errtol_s: 29.930336 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.608801e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.263479e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.925690e+00 │ │ │ Vprtstp: contraction number = 9.925690e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.302035e-05 │ │ │ Vprtstp: contraction number = 2.984638e-01 │ │ │ Vnewton: Using errtol_s: 8.933121 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.633805e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.422164e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.021979e+00 │ │ │ Vprtstp: contraction number = 3.021979e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.964181e-06 │ │ │ Vprtstp: contraction number = 3.044603e-01 │ │ │ Vnewton: Using errtol_s: 2.719781 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.664403e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.590023e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.363300e-01 │ │ │ Vprtstp: contraction number = 9.363300e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.228262e-06 │ │ │ Vprtstp: contraction number = 3.098400e-01 │ │ │ Vnewton: Using errtol_s: 0.842697 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.690891e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.740917e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.943527e-01 │ │ │ Vprtstp: contraction number = 2.943527e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.861268e-07 │ │ │ Vprtstp: contraction number = 3.143685e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.013840e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.227802e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.767806e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.780291e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -15994,17 +15994,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.810295872225E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.064058027536E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.029966775084E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.155200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.240200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -16031,162 +16031,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173421 │ │ │ +Vacc_SASA: Time elapsed: 0.222552 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.947830e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.545450e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.014300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.854900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.641090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.096090e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.875289e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.909463e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1545868.713233 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.897696e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.935072e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.195959e+05 │ │ │ Vprtstp: contraction number = 2.195959e+05 │ │ │ Vnewton: Attempting damping, relres = 0.180695 │ │ │ Vnewton: Attempting damping, relres = 0.564482 │ │ │ Vnewton: Damping accepted, relres = 0.180695 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.806948e-01 │ │ │ Vprtstp: contraction number = 1.806948e-01 │ │ │ Vnewton: Using errtol_s: 279330.491277 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.931212e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.111074e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.153850e+04 │ │ │ Vprtstp: contraction number = 4.153850e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.508737e-02 │ │ │ Vprtstp: contraction number = 1.941803e-01 │ │ │ Vnewton: Using errtol_s: 54240.471315 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.956189e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.307653e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.050009e+04 │ │ │ Vprtstp: contraction number = 1.050009e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.567269e-03 │ │ │ Vprtstp: contraction number = 2.156693e-01 │ │ │ Vnewton: Using errtol_s: 11698.005091 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.981141e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.482948e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.909851e+03 │ │ │ Vprtstp: contraction number = 2.909851e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.738825e-03 │ │ │ Vprtstp: contraction number = 2.297824e-01 │ │ │ Vnewton: Using errtol_s: 2687.995161 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.006024e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.637901e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.166574e+02 │ │ │ Vprtstp: contraction number = 8.166574e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.755829e-04 │ │ │ Vprtstp: contraction number = 2.735082e-01 │ │ │ Vnewton: Using errtol_s: 735.188760 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.030864e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.796565e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.418263e+02 │ │ │ Vprtstp: contraction number = 2.418263e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.407907e-04 │ │ │ Vprtstp: contraction number = 2.960382e-01 │ │ │ Vnewton: Using errtol_s: 217.643927 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.055726e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.954331e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.307074e+01 │ │ │ Vprtstp: contraction number = 7.307074e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.254157e-05 │ │ │ Vprtstp: contraction number = 3.021618e-01 │ │ │ Vnewton: Using errtol_s: 65.763679 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.082162e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.104079e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.224627e+01 │ │ │ Vprtstp: contraction number = 2.224627e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.295171e-05 │ │ │ Vprtstp: contraction number = 3.044484e-01 │ │ │ Vnewton: Using errtol_s: 20.021644 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.107081e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.263563e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.802985e+00 │ │ │ Vprtstp: contraction number = 6.802985e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.960677e-06 │ │ │ Vprtstp: contraction number = 3.058034e-01 │ │ │ Vnewton: Using errtol_s: 6.122687 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.131965e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.414988e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.086607e+00 │ │ │ Vprtstp: contraction number = 2.086607e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.214816e-06 │ │ │ Vprtstp: contraction number = 3.067192e-01 │ │ │ Vnewton: Using errtol_s: 1.877946 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.156905e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.559788e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.414261e-01 │ │ │ Vprtstp: contraction number = 6.414261e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.734363e-07 │ │ │ Vprtstp: contraction number = 3.074016e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.007527e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.239608e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.782282e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.794528e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -16196,17 +16196,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.218327471785E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.873840524527E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.358686721845E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.218800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.419000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.275 │ │ │ Vpbe_ctor2: xkappa = 0.17076 │ │ │ @@ -16253,160 +16253,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00502725 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.171178 │ │ │ +Vacc_SASA: Time elapsed: 0.214125 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.482190e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.947400e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.922600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.903800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.443370e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.069845e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.247686e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.713394e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1578654.561343 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.262150e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.737354e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.749391e+05 │ │ │ Vprtstp: contraction number = 2.749391e+05 │ │ │ Vnewton: Attempting damping, relres = 0.208079 │ │ │ Vnewton: Attempting damping, relres = 0.579104 │ │ │ Vnewton: Damping accepted, relres = 0.208079 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.080792e-01 │ │ │ Vprtstp: contraction number = 2.080792e-01 │ │ │ Vnewton: Using errtol_s: 328485.121608 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.295523e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.906543e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.673641e+04 │ │ │ Vprtstp: contraction number = 5.673641e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.299902e-02 │ │ │ Vprtstp: contraction number = 2.066474e-01 │ │ │ Vnewton: Using errtol_s: 67880.597256 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.328680e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.009586e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.510541e+04 │ │ │ Vprtstp: contraction number = 1.510541e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.991987e-03 │ │ │ Vprtstp: contraction number = 2.323771e-01 │ │ │ Vnewton: Using errtol_s: 15773.896333 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.353720e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026536e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.375823e+03 │ │ │ Vprtstp: contraction number = 4.375823e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.532644e-03 │ │ │ Vprtstp: contraction number = 2.534675e-01 │ │ │ Vnewton: Using errtol_s: 3998.170369 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.379949e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042791e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.301537e+03 │ │ │ Vprtstp: contraction number = 1.301537e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.421078e-04 │ │ │ Vprtstp: contraction number = 2.930170e-01 │ │ │ Vnewton: Using errtol_s: 1171.531808 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.403777e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.058973e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.070189e+02 │ │ │ Vprtstp: contraction number = 4.070189e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.320441e-04 │ │ │ Vprtstp: contraction number = 3.126824e-01 │ │ │ Vnewton: Using errtol_s: 366.317427 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.428818e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.075061e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.302066e+02 │ │ │ Vprtstp: contraction number = 1.302066e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.423158e-05 │ │ │ Vprtstp: contraction number = 3.199029e-01 │ │ │ Vnewton: Using errtol_s: 117.186019 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.453841e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.092158e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.220788e+01 │ │ │ Vprtstp: contraction number = 4.220788e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.406296e-05 │ │ │ Vprtstp: contraction number = 3.241606e-01 │ │ │ Vnewton: Using errtol_s: 37.987094 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.478840e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.108684e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.382030e+01 │ │ │ Vprtstp: contraction number = 1.382030e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.879032e-06 │ │ │ Vprtstp: contraction number = 3.274341e-01 │ │ │ Vnewton: Using errtol_s: 12.438270 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.503852e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.125494e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.561479e+00 │ │ │ Vprtstp: contraction number = 4.561479e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.600526e-06 │ │ │ Vprtstp: contraction number = 3.300565e-01 │ │ │ Vnewton: Using errtol_s: 4.105331 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.528867e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.143215e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.515099e+00 │ │ │ Vprtstp: contraction number = 1.515099e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.637667e-07 │ │ │ Vprtstp: contraction number = 3.321508e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.999040e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.217160e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.877953e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.889887e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -16416,29 +16416,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.207264728497E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.135578758917E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066739245337E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.124800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.119700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.650689e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.161039e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:08:57 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 01:46:56 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -16708,151 +16708,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.306074 │ │ │ +Vacc_SASA: Time elapsed: 0.558037 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.963950e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.408188e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.931700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.761200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.475340e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.159219e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.403050e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.719212e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2208581.508242 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.865610e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.288396e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.858538e+05 │ │ │ Vprtstp: contraction number = 2.858538e+05 │ │ │ Vnewton: Attempting damping, relres = 0.131715 │ │ │ Vnewton: Attempting damping, relres = 0.556234 │ │ │ Vnewton: Damping accepted, relres = 0.131715 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.317149e-01 │ │ │ Vprtstp: contraction number = 1.317149e-01 │ │ │ Vnewton: Using errtol_s: 290903.178824 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.309755e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.928848e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.143090e+04 │ │ │ Vprtstp: contraction number = 5.143090e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.336960e-02 │ │ │ Vprtstp: contraction number = 1.774256e-01 │ │ │ Vnewton: Using errtol_s: 51613.668608 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.559391e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.603007e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.206326e+04 │ │ │ Vprtstp: contraction number = 1.206326e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.129225e-03 │ │ │ Vprtstp: contraction number = 2.194828e-01 │ │ │ Vnewton: Using errtol_s: 11328.310511 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.808978e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.072744e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.187128e+03 │ │ │ Vprtstp: contraction number = 3.187128e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.301872e-03 │ │ │ Vprtstp: contraction number = 2.538146e-01 │ │ │ Vnewton: Using errtol_s: 2875.290058 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.059088e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.058971e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.922285e+02 │ │ │ Vprtstp: contraction number = 8.922285e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.635897e-04 │ │ │ Vprtstp: contraction number = 2.792822e-01 │ │ │ Vnewton: Using errtol_s: 803.017471 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.309241e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.310867e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.591681e+02 │ │ │ Vprtstp: contraction number = 2.591681e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.056114e-04 │ │ │ Vprtstp: contraction number = 2.904687e-01 │ │ │ Vnewton: Using errtol_s: 233.251428 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.558838e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.563251e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.682702e+01 │ │ │ Vprtstp: contraction number = 7.682702e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.130712e-05 │ │ │ Vprtstp: contraction number = 2.964369e-01 │ │ │ Vnewton: Using errtol_s: 69.144331 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.808468e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.806837e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.309726e+01 │ │ │ Vprtstp: contraction number = 2.309726e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.412165e-06 │ │ │ Vprtstp: contraction number = 3.006398e-01 │ │ │ Vnewton: Using errtol_s: 20.787535 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.058017e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.038476e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.019037e+00 │ │ │ Vprtstp: contraction number = 7.019037e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.860267e-06 │ │ │ Vprtstp: contraction number = 3.038904e-01 │ │ │ Vnewton: Using errtol_s: 6.317133 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.295663e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.252435e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.152093e+00 │ │ │ Vprtstp: contraction number = 2.152093e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.769810e-07 │ │ │ Vprtstp: contraction number = 3.066081e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.649622e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.868728e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.414566e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.427263e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -16862,17 +16862,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.850378362352E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.566988443868E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282832279800E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.039600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.119400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.3 │ │ │ Vpbe_ctor2: xkappa = 0.178353 │ │ │ @@ -16919,160 +16919,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0167285 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.301835 │ │ │ +Vacc_SASA: Time elapsed: 0.473721 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.526940e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.270581e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.908900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.226200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.441590e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.064127e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.401551e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.467117e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2261526.211377 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.554836e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.494844e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.556600e+05 │ │ │ Vprtstp: contraction number = 3.556600e+05 │ │ │ Vnewton: Attempting damping, relres = 0.156191 │ │ │ Vnewton: Attempting damping, relres = 0.568968 │ │ │ Vnewton: Damping accepted, relres = 0.156191 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.561910e-01 │ │ │ Vprtstp: contraction number = 1.561910e-01 │ │ │ Vnewton: Using errtol_s: 353229.985787 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.876574e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.729672e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.049885e+04 │ │ │ Vprtstp: contraction number = 7.049885e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.038701e-02 │ │ │ Vprtstp: contraction number = 1.945503e-01 │ │ │ Vnewton: Using errtol_s: 68721.012670 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.126903e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.947981e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.762526e+04 │ │ │ Vprtstp: contraction number = 1.762526e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.209079e-03 │ │ │ Vprtstp: contraction number = 2.372422e-01 │ │ │ Vnewton: Using errtol_s: 16303.521422 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.377375e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.163499e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.877060e+03 │ │ │ Vprtstp: contraction number = 4.877060e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.943013e-03 │ │ │ Vprtstp: contraction number = 2.695230e-01 │ │ │ Vnewton: Using errtol_s: 4394.173812 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.627115e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.381716e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.426343e+03 │ │ │ Vprtstp: contraction number = 1.426343e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.676342e-04 │ │ │ Vprtstp: contraction number = 2.921413e-01 │ │ │ Vnewton: Using errtol_s: 1283.719712 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.876469e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.592915e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.339166e+02 │ │ │ Vprtstp: contraction number = 4.339166e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.726822e-04 │ │ │ Vprtstp: contraction number = 3.042139e-01 │ │ │ Vnewton: Using errtol_s: 390.525321 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.142246e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.828077e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.354221e+02 │ │ │ Vprtstp: contraction number = 1.354221e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.389279e-05 │ │ │ Vprtstp: contraction number = 3.120924e-01 │ │ │ Vnewton: Using errtol_s: 121.879967 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.392527e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.046670e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.309648e+01 │ │ │ Vprtstp: contraction number = 4.309648e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.715074e-05 │ │ │ Vprtstp: contraction number = 3.182380e-01 │ │ │ Vnewton: Using errtol_s: 38.786838 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.630865e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.267409e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.394777e+01 │ │ │ Vprtstp: contraction number = 1.394777e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.550675e-06 │ │ │ Vprtstp: contraction number = 3.236406e-01 │ │ │ Vnewton: Using errtol_s: 12.552997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.880774e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.498502e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.577150e+00 │ │ │ Vprtstp: contraction number = 4.577150e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.821529e-06 │ │ │ Vprtstp: contraction number = 3.281635e-01 │ │ │ Vnewton: Using errtol_s: 4.119435 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.131260e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.753453e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.519139e+00 │ │ │ Vprtstp: contraction number = 1.519139e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.045585e-07 │ │ │ Vprtstp: contraction number = 3.318962e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.920092e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.131290e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.532886e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.544899e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -17082,17 +17082,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.837128515027E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951603256216E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475141098473E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.027500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.605600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -17119,151 +17119,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108759 │ │ │ +Vacc_SASA: Time elapsed: 0.238008 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.554450e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.109250e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.959800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.794000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.417010e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.323537e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.824637e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.046212e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 654975.595106 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.969567e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.077563e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.825232e+04 │ │ │ Vprtstp: contraction number = 8.825232e+04 │ │ │ Vnewton: Attempting damping, relres = 0.129536 │ │ │ Vnewton: Attempting damping, relres = 0.558179 │ │ │ Vnewton: Damping accepted, relres = 0.129536 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.295360e-01 │ │ │ Vprtstp: contraction number = 1.295360e-01 │ │ │ Vnewton: Using errtol_s: 84842.899807 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.290784e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.267184e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.656273e+04 │ │ │ Vprtstp: contraction number = 1.656273e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.304324e-02 │ │ │ Vprtstp: contraction number = 1.778907e-01 │ │ │ Vnewton: Using errtol_s: 15092.761763 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.562119e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.421814e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.788125e+03 │ │ │ Vprtstp: contraction number = 3.788125e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.206395e-03 │ │ │ Vprtstp: contraction number = 2.259402e-01 │ │ │ Vnewton: Using errtol_s: 3410.061436 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.812383e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.579108e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.653659e+02 │ │ │ Vprtstp: contraction number = 9.653659e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.326515e-03 │ │ │ Vprtstp: contraction number = 2.547856e-01 │ │ │ Vnewton: Using errtol_s: 868.834666 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005008e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.739403e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.601053e+02 │ │ │ Vprtstp: contraction number = 2.601053e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.574104e-04 │ │ │ Vprtstp: contraction number = 2.694357e-01 │ │ │ Vnewton: Using errtol_s: 234.095066 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.029998e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.905131e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.225806e+01 │ │ │ Vprtstp: contraction number = 7.225806e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.928962e-05 │ │ │ Vprtstp: contraction number = 2.778029e-01 │ │ │ Vnewton: Using errtol_s: 65.032277 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.054932e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.061347e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.049231e+01 │ │ │ Vprtstp: contraction number = 2.049231e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.815843e-05 │ │ │ Vprtstp: contraction number = 2.835989e-01 │ │ │ Vnewton: Using errtol_s: 18.443082 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.080001e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.215086e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.907221e+00 │ │ │ Vprtstp: contraction number = 5.907221e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.117095e-06 │ │ │ Vprtstp: contraction number = 2.882652e-01 │ │ │ Vnewton: Using errtol_s: 5.316499 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.106093e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.370266e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.726518e+00 │ │ │ Vprtstp: contraction number = 1.726518e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.372403e-06 │ │ │ Vprtstp: contraction number = 2.922725e-01 │ │ │ Vnewton: Using errtol_s: 1.553866 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.131083e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.526797e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.104456e-01 │ │ │ Vprtstp: contraction number = 5.104456e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.014018e-07 │ │ │ Vprtstp: contraction number = 2.956503e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.673030e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.883227e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.615616e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.630092e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -17273,17 +17273,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.824785455447E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.831245180939E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.413552848131E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.392600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.393000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.3 │ │ │ Vpbe_ctor2: xkappa = 0.178353 │ │ │ @@ -17330,160 +17330,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00286585 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.111200 │ │ │ +Vacc_SASA: Time elapsed: 0.181981 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.941440e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.979030e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.974300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.223400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.451730e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.092888e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.205806e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.682220e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 681119.647673 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.220367e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.708646e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.097058e+05 │ │ │ Vprtstp: contraction number = 1.097058e+05 │ │ │ Vnewton: Attempting damping, relres = 0.152443 │ │ │ Vnewton: Attempting damping, relres = 0.570128 │ │ │ Vnewton: Damping accepted, relres = 0.152443 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.524432e-01 │ │ │ Vprtstp: contraction number = 1.524432e-01 │ │ │ Vnewton: Using errtol_s: 103832.028377 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.252639e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.889540e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.238938e+04 │ │ │ Vprtstp: contraction number = 2.238938e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.984124e-02 │ │ │ Vprtstp: contraction number = 1.957533e-01 │ │ │ Vnewton: Using errtol_s: 20325.457528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.277549e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.054737e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.463136e+03 │ │ │ Vprtstp: contraction number = 5.463136e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.220083e-03 │ │ │ Vprtstp: contraction number = 2.419498e-01 │ │ │ Vnewton: Using errtol_s: 4917.740487 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.302480e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.224335e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.437458e+03 │ │ │ Vprtstp: contraction number = 1.437458e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.899412e-03 │ │ │ Vprtstp: contraction number = 2.630734e-01 │ │ │ Vnewton: Using errtol_s: 1293.726521 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.327414e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.383395e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.972446e+02 │ │ │ Vprtstp: contraction number = 3.972446e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.249023e-04 │ │ │ Vprtstp: contraction number = 2.763499e-01 │ │ │ Vnewton: Using errtol_s: 357.521241 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.352324e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.545092e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.134401e+02 │ │ │ Vprtstp: contraction number = 1.134401e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.498946e-04 │ │ │ Vprtstp: contraction number = 2.855667e-01 │ │ │ Vnewton: Using errtol_s: 102.096166 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.377300e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.709617e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.318595e+01 │ │ │ Vprtstp: contraction number = 3.318595e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.385040e-05 │ │ │ Vprtstp: contraction number = 2.925415e-01 │ │ │ Vnewton: Using errtol_s: 29.867366 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.402232e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.877109e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.910309e+00 │ │ │ Vprtstp: contraction number = 9.910309e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.309503e-05 │ │ │ Vprtstp: contraction number = 2.986296e-01 │ │ │ Vnewton: Using errtol_s: 8.919279 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427095e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.040584e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.018558e+00 │ │ │ Vprtstp: contraction number = 3.018558e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.988583e-06 │ │ │ Vprtstp: contraction number = 3.045877e-01 │ │ │ Vnewton: Using errtol_s: 2.716702 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452041e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.194216e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.355568e-01 │ │ │ Vprtstp: contraction number = 9.355568e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.236201e-06 │ │ │ Vprtstp: contraction number = 3.099350e-01 │ │ │ Vnewton: Using errtol_s: 0.842001 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.478001e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.353215e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.941742e-01 │ │ │ Vprtstp: contraction number = 2.941742e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.887082e-07 │ │ │ Vprtstp: contraction number = 3.144376e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.907816e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.122687e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.812956e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.825699e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -17493,17 +17493,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.816506018339E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.063774350048E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.029829357702E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.245000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.615900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -17530,162 +17530,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.175103 │ │ │ +Vacc_SASA: Time elapsed: 0.259980 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.966020e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.771010e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.976300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.821400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.422990e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.164137e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.663257e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.533163e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1525884.348969 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.677160e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.558375e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.167719e+05 │ │ │ Vprtstp: contraction number = 2.167719e+05 │ │ │ Vnewton: Attempting damping, relres = 0.176913 │ │ │ Vnewton: Attempting damping, relres = 0.564272 │ │ │ Vnewton: Damping accepted, relres = 0.176913 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.769126e-01 │ │ │ Vprtstp: contraction number = 1.769126e-01 │ │ │ Vnewton: Using errtol_s: 269948.173272 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.710413e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.736404e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.092694e+04 │ │ │ Vprtstp: contraction number = 4.092694e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.387341e-02 │ │ │ Vprtstp: contraction number = 1.914697e-01 │ │ │ Vnewton: Using errtol_s: 51686.903490 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.735290e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.934150e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.034780e+04 │ │ │ Vprtstp: contraction number = 1.034780e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.283807e-03 │ │ │ Vprtstp: contraction number = 2.150302e-01 │ │ │ Vnewton: Using errtol_s: 11114.247135 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.760213e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.106986e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.862719e+03 │ │ │ Vprtstp: contraction number = 2.862719e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.717625e-03 │ │ │ Vprtstp: contraction number = 2.358142e-01 │ │ │ Vnewton: Using errtol_s: 2620.897639 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.785119e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.264856e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.092476e+02 │ │ │ Vprtstp: contraction number = 8.092476e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.773796e-04 │ │ │ Vprtstp: contraction number = 2.779300e-01 │ │ │ Vnewton: Using errtol_s: 728.426056 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.810091e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.419570e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.405150e+02 │ │ │ Vprtstp: contraction number = 2.405150e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.418612e-04 │ │ │ Vprtstp: contraction number = 2.971664e-01 │ │ │ Vnewton: Using errtol_s: 216.463714 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.839162e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.573421e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.272000e+01 │ │ │ Vprtstp: contraction number = 7.272000e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.289186e-05 │ │ │ Vprtstp: contraction number = 3.023510e-01 │ │ │ Vnewton: Using errtol_s: 65.448016 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.864149e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.742658e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.214460e+01 │ │ │ Vprtstp: contraction number = 2.214460e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.306137e-05 │ │ │ Vprtstp: contraction number = 3.045186e-01 │ │ │ Vnewton: Using errtol_s: 19.930141 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.889115e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.909038e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.772692e+00 │ │ │ Vprtstp: contraction number = 6.772692e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.994682e-06 │ │ │ Vprtstp: contraction number = 3.058394e-01 │ │ │ Vnewton: Using errtol_s: 6.095423 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.912840e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.006965e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.077475e+00 │ │ │ Vprtstp: contraction number = 2.077475e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.225341e-06 │ │ │ Vprtstp: contraction number = 3.067429e-01 │ │ │ Vnewton: Using errtol_s: 1.869728 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.937730e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023163e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.386558e-01 │ │ │ Vprtstp: contraction number = 6.386558e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.766932e-07 │ │ │ Vprtstp: contraction number = 3.074192e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.931545e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.146712e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.869928e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.882481e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -17695,17 +17695,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.069846752513E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.873729752993E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.358408005729E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.181200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.664500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.3 │ │ │ Vpbe_ctor2: xkappa = 0.178353 │ │ │ @@ -17752,160 +17752,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00434174 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.174278 │ │ │ +Vacc_SASA: Time elapsed: 0.282617 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.422980e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.039812e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.926700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.986400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.418230e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.303773e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.027090e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042853e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1557370.209900 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.041172e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.045928e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.714539e+05 │ │ │ Vprtstp: contraction number = 2.714539e+05 │ │ │ Vnewton: Attempting damping, relres = 0.204551 │ │ │ Vnewton: Attempting damping, relres = 0.578965 │ │ │ Vnewton: Damping accepted, relres = 0.204551 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.045506e-01 │ │ │ Vprtstp: contraction number = 2.045506e-01 │ │ │ Vnewton: Using errtol_s: 318560.936336 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.074498e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065411e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.592903e+04 │ │ │ Vprtstp: contraction number = 5.592903e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.183467e-02 │ │ │ Vprtstp: contraction number = 2.045200e-01 │ │ │ Vnewton: Using errtol_s: 65152.068354 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.099528e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085903e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.489191e+04 │ │ │ Vprtstp: contraction number = 1.489191e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.724338e-03 │ │ │ Vprtstp: contraction number = 2.324469e-01 │ │ │ Vnewton: Using errtol_s: 15144.393716 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.124511e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102982e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.311238e+03 │ │ │ Vprtstp: contraction number = 4.311238e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.516326e-03 │ │ │ Vprtstp: contraction number = 2.587658e-01 │ │ │ Vnewton: Using errtol_s: 3918.850513 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.149546e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119891e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.290056e+03 │ │ │ Vprtstp: contraction number = 1.290056e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.455704e-04 │ │ │ Vprtstp: contraction number = 2.962933e-01 │ │ │ Vnewton: Using errtol_s: 1161.129054 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.173335e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137357e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.045979e+02 │ │ │ Vprtstp: contraction number = 4.045979e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.338163e-04 │ │ │ Vprtstp: contraction number = 3.136073e-01 │ │ │ Vnewton: Using errtol_s: 364.138497 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.198341e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.154602e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.295599e+02 │ │ │ Vprtstp: contraction number = 1.295599e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.487232e-05 │ │ │ Vprtstp: contraction number = 3.202186e-01 │ │ │ Vnewton: Using errtol_s: 116.603918 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.223367e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.172291e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.202377e+01 │ │ │ Vprtstp: contraction number = 4.202377e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.428543e-05 │ │ │ Vprtstp: contraction number = 3.243579e-01 │ │ │ Vnewton: Using errtol_s: 37.821402 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.248395e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.190132e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.376584e+01 │ │ │ Vprtstp: contraction number = 1.376584e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 7.955244e-06 │ │ │ Vprtstp: contraction number = 3.275727e-01 │ │ │ Vnewton: Using errtol_s: 12.389260 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273448e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.207580e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.544810e+00 │ │ │ Vprtstp: contraction number = 4.544810e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.626434e-06 │ │ │ Vprtstp: contraction number = 3.301512e-01 │ │ │ Vnewton: Using errtol_s: 4.090329 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.298462e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.224518e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.509859e+00 │ │ │ Vprtstp: contraction number = 1.509859e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.725435e-07 │ │ │ Vprtstp: contraction number = 3.322161e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.898264e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.113568e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.971097e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.985252e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -17915,29 +17915,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 8.058985499757E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.135468016715E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066711397255E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.061600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.347200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.420578e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.241934e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:09:08 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 02:13:29 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -18207,151 +18207,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.302685 │ │ │ +Vacc_SASA: Time elapsed: 0.686159 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.886320e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.623506e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.911600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.683100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.435000e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.270475e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.329870e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.075832e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2191468.217175 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.801000e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.982847e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.835462e+05 │ │ │ Vprtstp: contraction number = 2.835462e+05 │ │ │ Vnewton: Attempting damping, relres = 0.130770 │ │ │ Vnewton: Attempting damping, relres = 0.556143 │ │ │ Vnewton: Damping accepted, relres = 0.130770 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.307700e-01 │ │ │ Vprtstp: contraction number = 1.307700e-01 │ │ │ Vnewton: Using errtol_s: 286578.355364 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.302349e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.240620e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.106806e+04 │ │ │ Vprtstp: contraction number = 5.106806e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.314467e-02 │ │ │ Vprtstp: contraction number = 1.769876e-01 │ │ │ Vnewton: Using errtol_s: 50720.810223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.552497e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.653965e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.199262e+04 │ │ │ Vprtstp: contraction number = 1.199262e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.100754e-03 │ │ │ Vprtstp: contraction number = 2.203857e-01 │ │ │ Vnewton: Using errtol_s: 11178.140515 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.789739e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.905789e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.172798e+03 │ │ │ Vprtstp: contraction number = 3.172798e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.305202e-03 │ │ │ Vprtstp: contraction number = 2.558841e-01 │ │ │ Vnewton: Using errtol_s: 2860.308039 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.039817e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013055e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.902300e+02 │ │ │ Vprtstp: contraction number = 8.902300e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.656064e-04 │ │ │ Vprtstp: contraction number = 2.801149e-01 │ │ │ Vnewton: Using errtol_s: 801.214793 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.289162e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.235288e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.587695e+02 │ │ │ Vprtstp: contraction number = 2.587695e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.062725e-04 │ │ │ Vprtstp: contraction number = 2.906745e-01 │ │ │ Vnewton: Using errtol_s: 232.892741 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.550193e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.447208e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.672901e+01 │ │ │ Vprtstp: contraction number = 7.672901e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.151135e-05 │ │ │ Vprtstp: contraction number = 2.965147e-01 │ │ │ Vnewton: Using errtol_s: 69.056118 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.787251e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.659785e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.307099e+01 │ │ │ Vprtstp: contraction number = 2.307099e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.474878e-06 │ │ │ Vprtstp: contraction number = 3.006815e-01 │ │ │ Vnewton: Using errtol_s: 20.763894 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.037048e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.869998e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.011582e+00 │ │ │ Vprtstp: contraction number = 7.011582e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.879541e-06 │ │ │ Vprtstp: contraction number = 3.039133e-01 │ │ │ Vnewton: Using errtol_s: 6.310424 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.286704e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.076412e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.149903e+00 │ │ │ Vprtstp: contraction number = 2.149903e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.829299e-07 │ │ │ Vprtstp: contraction number = 3.066217e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.661589e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.878877e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.257203e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.271299e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -18361,17 +18361,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.760186349323E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.566917500477E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282812157004E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.150000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.448400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.325 │ │ │ Vpbe_ctor2: xkappa = 0.185636 │ │ │ @@ -18418,160 +18418,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0160678 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.305381 │ │ │ +Vacc_SASA: Time elapsed: 0.483621 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.609740e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.332477e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.892900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.072980e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.443980e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.102285e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.424111e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.315111e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2243053.741102 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.560180e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.339130e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.528083e+05 │ │ │ Vprtstp: contraction number = 3.528083e+05 │ │ │ Vnewton: Attempting damping, relres = 0.155339 │ │ │ Vnewton: Attempting damping, relres = 0.568910 │ │ │ Vnewton: Damping accepted, relres = 0.155339 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.553392e-01 │ │ │ Vprtstp: contraction number = 1.553392e-01 │ │ │ Vnewton: Using errtol_s: 348434.112950 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.893637e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.571083e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.998444e+04 │ │ │ Vprtstp: contraction number = 6.998444e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.017800e-02 │ │ │ Vprtstp: contraction number = 1.942717e-01 │ │ │ Vnewton: Using errtol_s: 67690.878524 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.142713e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.782959e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.750872e+04 │ │ │ Vprtstp: contraction number = 1.750872e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.184752e-03 │ │ │ Vprtstp: contraction number = 2.380791e-01 │ │ │ Vnewton: Using errtol_s: 16115.784303 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.379775e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.995866e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.850206e+03 │ │ │ Vprtstp: contraction number = 4.850206e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.947538e-03 │ │ │ Vprtstp: contraction number = 2.710655e-01 │ │ │ Vnewton: Using errtol_s: 4368.432326 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.629349e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.238519e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.421336e+03 │ │ │ Vprtstp: contraction number = 1.421336e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.702989e-04 │ │ │ Vprtstp: contraction number = 2.928307e-01 │ │ │ Vnewton: Using errtol_s: 1279.211122 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.877844e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.494027e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.327691e+02 │ │ │ Vprtstp: contraction number = 4.327691e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.736439e-04 │ │ │ Vprtstp: contraction number = 3.044787e-01 │ │ │ Vnewton: Using errtol_s: 389.492590 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.127533e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.733146e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.351326e+02 │ │ │ Vprtstp: contraction number = 1.351326e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.422045e-05 │ │ │ Vprtstp: contraction number = 3.122508e-01 │ │ │ Vnewton: Using errtol_s: 121.619374 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.377713e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.974143e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.301940e+01 │ │ │ Vprtstp: contraction number = 4.301940e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.726105e-05 │ │ │ Vprtstp: contraction number = 3.183495e-01 │ │ │ Vnewton: Using errtol_s: 38.717465 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.627570e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.219457e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.392593e+01 │ │ │ Vprtstp: contraction number = 1.392593e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.587625e-06 │ │ │ Vprtstp: contraction number = 3.237129e-01 │ │ │ Vnewton: Using errtol_s: 12.533342 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.891873e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.466856e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.570574e+00 │ │ │ Vprtstp: contraction number = 4.570574e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.833891e-06 │ │ │ Vprtstp: contraction number = 3.282059e-01 │ │ │ Vnewton: Using errtol_s: 4.113517 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.143144e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.706646e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.517041e+00 │ │ │ Vprtstp: contraction number = 1.517041e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.086957e-07 │ │ │ Vprtstp: contraction number = 3.319148e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.923934e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.141020e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.614379e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.627452e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -18581,15 +18581,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.747143888593E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951532357684E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475121024223E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.146600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.058300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ @@ -18618,151 +18618,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108152 │ │ │ +Vacc_SASA: Time elapsed: 0.239401 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.547320e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.239390e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.892000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.706400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.433530e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.234357e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.851758e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.972167e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 651047.049796 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.002732e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.998705e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.764819e+04 │ │ │ Vprtstp: contraction number = 8.764819e+04 │ │ │ Vnewton: Attempting damping, relres = 0.129306 │ │ │ Vnewton: Attempting damping, relres = 0.558102 │ │ │ Vnewton: Damping accepted, relres = 0.129306 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.293065e-01 │ │ │ Vprtstp: contraction number = 1.293065e-01 │ │ │ Vnewton: Using errtol_s: 84184.596649 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.325269e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.203906e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.647823e+04 │ │ │ Vprtstp: contraction number = 1.647823e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.304786e-02 │ │ │ Vprtstp: contraction number = 1.782421e-01 │ │ │ Vnewton: Using errtol_s: 15005.240621 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.574699e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.372330e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.775815e+03 │ │ │ Vprtstp: contraction number = 3.775815e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.220699e-03 │ │ │ Vprtstp: contraction number = 2.265156e-01 │ │ │ Vnewton: Using errtol_s: 3398.920946 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.823726e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.541181e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.635341e+02 │ │ │ Vprtstp: contraction number = 9.635341e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.331987e-03 │ │ │ Vprtstp: contraction number = 2.551357e-01 │ │ │ Vnewton: Using errtol_s: 867.186094 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007367e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.703470e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.598155e+02 │ │ │ Vprtstp: contraction number = 2.598155e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.591665e-04 │ │ │ Vprtstp: contraction number = 2.696472e-01 │ │ │ Vnewton: Using errtol_s: 233.834272 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.032312e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.886484e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.221080e+01 │ │ │ Vprtstp: contraction number = 7.221080e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 9.982341e-05 │ │ │ Vprtstp: contraction number = 2.779308e-01 │ │ │ Vnewton: Using errtol_s: 64.989737 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057320e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.063059e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.048426e+01 │ │ │ Vprtstp: contraction number = 2.048426e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.831721e-05 │ │ │ Vprtstp: contraction number = 2.836731e-01 │ │ │ Vnewton: Using errtol_s: 18.435838 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082301e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.225109e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.905744e+00 │ │ │ Vprtstp: contraction number = 5.905744e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.164034e-06 │ │ │ Vprtstp: contraction number = 2.883064e-01 │ │ │ Vnewton: Using errtol_s: 5.315170 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.108258e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.380130e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.726219e+00 │ │ │ Vprtstp: contraction number = 1.726219e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.386306e-06 │ │ │ Vprtstp: contraction number = 2.922949e-01 │ │ │ Vnewton: Using errtol_s: 1.553597 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.133225e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.541042e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.103781e-01 │ │ │ Vprtstp: contraction number = 5.103781e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.055409e-07 │ │ │ Vprtstp: contraction number = 2.956624e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.675237e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.884908e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.728263e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.741954e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -18772,15 +18772,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.829422361663E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.830982023597E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.413426199926E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.278300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.013200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ @@ -18829,160 +18829,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00263165 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.111037 │ │ │ +Vacc_SASA: Time elapsed: 0.237238 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.931840e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.206400e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.176100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.910900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.465020e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.462549e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.209390e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.724913e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 676873.511924 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.223367e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.751640e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.089080e+05 │ │ │ Vprtstp: contraction number = 1.089080e+05 │ │ │ Vnewton: Attempting damping, relres = 0.152173 │ │ │ Vnewton: Attempting damping, relres = 0.570027 │ │ │ Vnewton: Damping accepted, relres = 0.152173 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.521734e-01 │ │ │ Vprtstp: contraction number = 1.521734e-01 │ │ │ Vnewton: Using errtol_s: 103002.176045 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.256946e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.950376e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.224678e+04 │ │ │ Vprtstp: contraction number = 2.224678e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.982235e-02 │ │ │ Vprtstp: contraction number = 1.959760e-01 │ │ │ Vnewton: Using errtol_s: 20185.957327 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.280672e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.125488e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.434268e+03 │ │ │ Vprtstp: contraction number = 5.434268e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.226895e-03 │ │ │ Vprtstp: contraction number = 2.423315e-01 │ │ │ Vnewton: Using errtol_s: 4891.693818 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305625e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.309943e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.431460e+03 │ │ │ Vprtstp: contraction number = 1.431460e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.903352e-03 │ │ │ Vprtstp: contraction number = 2.633707e-01 │ │ │ Vnewton: Using errtol_s: 1288.328715 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330648e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.483339e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.959616e+02 │ │ │ Vprtstp: contraction number = 3.959616e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.264891e-04 │ │ │ Vprtstp: contraction number = 2.766115e-01 │ │ │ Vnewton: Using errtol_s: 356.366550 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355648e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.663440e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.131619e+02 │ │ │ Vprtstp: contraction number = 1.131619e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.504650e-04 │ │ │ Vprtstp: contraction number = 2.857895e-01 │ │ │ Vnewton: Using errtol_s: 101.845804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.379457e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.834145e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.312512e+01 │ │ │ Vprtstp: contraction number = 3.312512e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.404458e-05 │ │ │ Vprtstp: contraction number = 2.927230e-01 │ │ │ Vnewton: Using errtol_s: 29.812613 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.404450e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.039706e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.896913e+00 │ │ │ Vprtstp: contraction number = 9.896913e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.315936e-05 │ │ │ Vprtstp: contraction number = 2.987736e-01 │ │ │ Vnewton: Using errtol_s: 8.907223 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.428264e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.246795e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.015572e+00 │ │ │ Vprtstp: contraction number = 3.015572e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.009634e-06 │ │ │ Vprtstp: contraction number = 3.046983e-01 │ │ │ Vnewton: Using errtol_s: 2.714015 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.453217e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.432147e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.348798e-01 │ │ │ Vprtstp: contraction number = 9.348798e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.243056e-06 │ │ │ Vprtstp: contraction number = 3.100174e-01 │ │ │ Vnewton: Using errtol_s: 0.841392 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.478213e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.611309e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.940173e-01 │ │ │ Vprtstp: contraction number = 2.940173e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.909380e-07 │ │ │ Vprtstp: contraction number = 3.144974e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.871576e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.095129e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.053017e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.068816e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -18992,15 +18992,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.821085170706E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.063512300781E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.029703319589E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.162400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.217700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ @@ -19029,162 +19029,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.178193 │ │ │ +Vacc_SASA: Time elapsed: 0.309459 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.372890e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.891080e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.957300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.588800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.661430e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.103294e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.666800e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.816780e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1509004.572180 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.688522e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.842731e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.143767e+05 │ │ │ Vprtstp: contraction number = 2.143767e+05 │ │ │ Vnewton: Attempting damping, relres = 0.173607 │ │ │ Vnewton: Attempting damping, relres = 0.564075 │ │ │ Vnewton: Damping accepted, relres = 0.173607 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.736069e-01 │ │ │ Vprtstp: contraction number = 1.736069e-01 │ │ │ Vnewton: Using errtol_s: 261973.588074 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.720727e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.012883e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.041338e+04 │ │ │ Vprtstp: contraction number = 4.041338e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.283481e-02 │ │ │ Vprtstp: contraction number = 1.891331e-01 │ │ │ Vnewton: Using errtol_s: 49547.880487 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.745753e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.205037e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.021814e+04 │ │ │ Vprtstp: contraction number = 1.021814e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.057379e-03 │ │ │ Vprtstp: contraction number = 2.149359e-01 │ │ │ Vnewton: Using errtol_s: 10649.617829 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.769463e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.380313e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.824157e+03 │ │ │ Vprtstp: contraction number = 2.824157e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.703748e-03 │ │ │ Vprtstp: contraction number = 2.414137e-01 │ │ │ Vnewton: Using errtol_s: 2570.963479 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.794373e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.549651e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.035455e+02 │ │ │ Vprtstp: contraction number = 8.035455e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.792870e-04 │ │ │ Vprtstp: contraction number = 2.813133e-01 │ │ │ Vnewton: Using errtol_s: 723.246303 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.819340e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.723561e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.394281e+02 │ │ │ Vprtstp: contraction number = 2.394281e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.427997e-04 │ │ │ Vprtstp: contraction number = 2.979420e-01 │ │ │ Vnewton: Using errtol_s: 215.485426 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.844261e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.898854e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.242618e+01 │ │ │ Vprtstp: contraction number = 7.242618e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.319641e-05 │ │ │ Vprtstp: contraction number = 3.024964e-01 │ │ │ Vnewton: Using errtol_s: 65.183576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.869222e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007131e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.205930e+01 │ │ │ Vprtstp: contraction number = 2.205930e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.315660e-05 │ │ │ Vprtstp: contraction number = 3.045762e-01 │ │ │ Vnewton: Using errtol_s: 19.853369 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.894047e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024764e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.747262e+00 │ │ │ Vprtstp: contraction number = 6.747262e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.024200e-06 │ │ │ Vprtstp: contraction number = 3.058693e-01 │ │ │ Vnewton: Using errtol_s: 6.072536 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.917774e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042353e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.069809e+00 │ │ │ Vprtstp: contraction number = 2.069809e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.234475e-06 │ │ │ Vprtstp: contraction number = 3.067629e-01 │ │ │ Vnewton: Using errtol_s: 1.862829 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.942590e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.061048e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.363291e-01 │ │ │ Vprtstp: contraction number = 6.363291e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.795192e-07 │ │ │ Vprtstp: contraction number = 3.074337e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.950749e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.182634e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.951401e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.963401e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -19194,17 +19194,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.932901630700E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.873629019341E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.358152654068E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.164000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.664700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.325 │ │ │ Vpbe_ctor2: xkappa = 0.185636 │ │ │ @@ -19251,160 +19251,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00380956 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173365 │ │ │ +Vacc_SASA: Time elapsed: 0.368121 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.374310e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.124115e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.941800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.672900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.436670e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.180023e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.031163e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079329e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1539412.424593 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.045820e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081951e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.684916e+05 │ │ │ Vprtstp: contraction number = 2.684916e+05 │ │ │ Vnewton: Attempting damping, relres = 0.201455 │ │ │ Vnewton: Attempting damping, relres = 0.578827 │ │ │ Vnewton: Damping accepted, relres = 0.201455 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.014550e-01 │ │ │ Vprtstp: contraction number = 2.014550e-01 │ │ │ Vnewton: Using errtol_s: 310122.358535 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.078090e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.100932e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.524646e+04 │ │ │ Vprtstp: contraction number = 5.524646e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 4.083558e-02 │ │ │ Vprtstp: contraction number = 2.027032e-01 │ │ │ Vnewton: Using errtol_s: 62862.800070 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.103105e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121901e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.470940e+04 │ │ │ Vprtstp: contraction number = 1.470940e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.510864e-03 │ │ │ Vprtstp: contraction number = 2.329063e-01 │ │ │ Vnewton: Using errtol_s: 14641.142976 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.128181e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141045e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.258026e+03 │ │ │ Vprtstp: contraction number = 4.258026e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.506079e-03 │ │ │ Vprtstp: contraction number = 2.634965e-01 │ │ │ Vnewton: Using errtol_s: 3857.889813 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.151992e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.160020e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.281004e+03 │ │ │ Vprtstp: contraction number = 1.281004e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.489530e-04 │ │ │ Vprtstp: contraction number = 2.988545e-01 │ │ │ Vnewton: Using errtol_s: 1152.947571 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.176667e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.179584e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.026096e+02 │ │ │ Vprtstp: contraction number = 4.026096e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.353814e-04 │ │ │ Vprtstp: contraction number = 3.142806e-01 │ │ │ Vnewton: Using errtol_s: 362.348997 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.201738e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.198138e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.290278e+02 │ │ │ Vprtstp: contraction number = 1.290278e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.543469e-05 │ │ │ Vprtstp: contraction number = 3.204786e-01 │ │ │ Vnewton: Using errtol_s: 116.125091 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.226685e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.216076e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.187301e+01 │ │ │ Vprtstp: contraction number = 4.187301e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.448058e-05 │ │ │ Vprtstp: contraction number = 3.245269e-01 │ │ │ Vnewton: Using errtol_s: 37.685715 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.250140e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.234616e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.372141e+01 │ │ │ Vprtstp: contraction number = 1.372141e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 8.022069e-06 │ │ │ Vprtstp: contraction number = 3.276911e-01 │ │ │ Vnewton: Using errtol_s: 12.349273 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273541e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.252053e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.531250e+00 │ │ │ Vprtstp: contraction number = 4.531250e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.649144e-06 │ │ │ Vprtstp: contraction number = 3.302320e-01 │ │ │ Vnewton: Using errtol_s: 4.078125 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.296994e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.269447e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.505606e+00 │ │ │ Vprtstp: contraction number = 1.505606e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.802356e-07 │ │ │ Vprtstp: contraction number = 3.322717e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.840344e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.048975e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.067472e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.080485e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -19414,29 +19414,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.922197679692E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.135367311591E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066685879920E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.095000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.892600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.417217e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.287686e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:09:20 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 02:41:05 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -19706,151 +19706,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.301935 │ │ │ +Vacc_SASA: Time elapsed: 0.528826 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.928690e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.382076e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.874900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.319300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.426690e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.168197e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.333520e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.737312e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2152094.716706 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.791590e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.237488e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.782066e+05 │ │ │ Vprtstp: contraction number = 2.782066e+05 │ │ │ Vnewton: Attempting damping, relres = 0.128497 │ │ │ Vnewton: Attempting damping, relres = 0.555913 │ │ │ Vnewton: Damping accepted, relres = 0.128497 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.284973e-01 │ │ │ Vprtstp: contraction number = 1.284973e-01 │ │ │ Vnewton: Using errtol_s: 276538.353939 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.300580e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.753563e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.023327e+04 │ │ │ Vprtstp: contraction number = 5.023327e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.262924e-02 │ │ │ Vprtstp: contraction number = 1.761067e-01 │ │ │ Vnewton: Using errtol_s: 48700.264198 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.550510e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.930921e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.183043e+04 │ │ │ Vprtstp: contraction number = 1.183043e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.048628e-03 │ │ │ Vprtstp: contraction number = 2.231020e-01 │ │ │ Vnewton: Using errtol_s: 10865.126461 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.788299e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.055124e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.142996e+03 │ │ │ Vprtstp: contraction number = 3.142996e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.315159e-03 │ │ │ Vprtstp: contraction number = 2.604983e-01 │ │ │ Vnewton: Using errtol_s: 2830.346955 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.037963e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.116283e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.861041e+02 │ │ │ Vprtstp: contraction number = 8.861041e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.705677e-04 │ │ │ Vprtstp: contraction number = 2.817665e-01 │ │ │ Vnewton: Using errtol_s: 797.496893 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.288673e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119779e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.579465e+02 │ │ │ Vprtstp: contraction number = 2.579465e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.078726e-04 │ │ │ Vprtstp: contraction number = 2.911008e-01 │ │ │ Vnewton: Using errtol_s: 232.151972 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.538075e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320028e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.653069e+01 │ │ │ Vprtstp: contraction number = 7.653069e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.200493e-05 │ │ │ Vprtstp: contraction number = 2.966920e-01 │ │ │ Vnewton: Using errtol_s: 68.877633 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.789483e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.517693e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.301874e+01 │ │ │ Vprtstp: contraction number = 2.301874e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.626375e-06 │ │ │ Vprtstp: contraction number = 3.007779e-01 │ │ │ Vnewton: Using errtol_s: 20.716870 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.038511e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.714249e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.996910e+00 │ │ │ Vprtstp: contraction number = 6.996910e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.926088e-06 │ │ │ Vprtstp: contraction number = 3.039658e-01 │ │ │ Vnewton: Using errtol_s: 6.297219 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.276079e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.916706e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.145621e+00 │ │ │ Vprtstp: contraction number = 2.145621e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 8.972926e-07 │ │ │ Vprtstp: contraction number = 3.066526e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.635431e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.850178e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.089818e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.103019e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -19860,17 +19860,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.527227679472E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.566736557939E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282759892518E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.037800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.070600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.4 │ │ │ Vpbe_ctor2: xkappa = 0.205945 │ │ │ @@ -19917,160 +19917,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0146503 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.300692 │ │ │ +Vacc_SASA: Time elapsed: 0.464334 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.527040e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.338966e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.871000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.044370e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.422260e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.246162e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.387667e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.146304e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2200727.622444 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.533863e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.172216e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.461855e+05 │ │ │ Vprtstp: contraction number = 3.461855e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153259 │ │ │ Vnewton: Attempting damping, relres = 0.568747 │ │ │ Vnewton: Damping accepted, relres = 0.153259 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.532593e-01 │ │ │ Vprtstp: contraction number = 1.532593e-01 │ │ │ Vnewton: Using errtol_s: 337281.994589 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.856572e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.414015e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.878964e+04 │ │ │ Vprtstp: contraction number = 6.878964e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.969348e-02 │ │ │ Vprtstp: contraction number = 1.937467e-01 │ │ │ Vnewton: Using errtol_s: 65347.260012 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.106886e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.644138e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.723760e+04 │ │ │ Vprtstp: contraction number = 1.723760e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.139932e-03 │ │ │ Vprtstp: contraction number = 2.404545e-01 │ │ │ Vnewton: Using errtol_s: 15713.045576 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.357183e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.883060e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.791285e+03 │ │ │ Vprtstp: contraction number = 4.791285e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.959957e-03 │ │ │ Vprtstp: contraction number = 2.745064e-01 │ │ │ Vnewton: Using errtol_s: 4313.331787 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.595276e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.124455e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.410218e+03 │ │ │ Vprtstp: contraction number = 1.410218e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.767187e-04 │ │ │ Vprtstp: contraction number = 2.942507e-01 │ │ │ Vnewton: Using errtol_s: 1269.200854 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.857579e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.349381e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.302153e+02 │ │ │ Vprtstp: contraction number = 4.302153e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.759391e-04 │ │ │ Vprtstp: contraction number = 3.050692e-01 │ │ │ Vnewton: Using errtol_s: 387.194118 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.107920e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.583423e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.344961e+02 │ │ │ Vprtstp: contraction number = 1.344961e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.500295e-05 │ │ │ Vprtstp: contraction number = 3.126248e-01 │ │ │ Vnewton: Using errtol_s: 121.046502 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.346227e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.810020e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.285292e+01 │ │ │ Vprtstp: contraction number = 4.285292e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.752495e-05 │ │ │ Vprtstp: contraction number = 3.186183e-01 │ │ │ Vnewton: Using errtol_s: 38.567632 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.596593e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.041371e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.387951e+01 │ │ │ Vprtstp: contraction number = 1.387951e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.676104e-06 │ │ │ Vprtstp: contraction number = 3.238871e-01 │ │ │ Vnewton: Using errtol_s: 12.491560 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.846704e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.289825e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.556799e+00 │ │ │ Vprtstp: contraction number = 4.556799e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.863529e-06 │ │ │ Vprtstp: contraction number = 3.283112e-01 │ │ │ Vnewton: Using errtol_s: 4.101119 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.105647e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.508320e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.512689e+00 │ │ │ Vprtstp: contraction number = 1.512689e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.186225e-07 │ │ │ Vprtstp: contraction number = 3.319630e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.906751e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.122667e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.575765e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.590473e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -20080,17 +20080,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.514675732237E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951351537778E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475068873214E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.007600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.180800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -20117,151 +20117,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108463 │ │ │ +Vacc_SASA: Time elapsed: 0.233175 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.532260e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.726210e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.900500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.059820e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.442230e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.301658e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.795360e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.764295e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 642085.519744 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.942104e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.790495e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.625055e+04 │ │ │ Vprtstp: contraction number = 8.625055e+04 │ │ │ Vnewton: Attempting damping, relres = 0.128656 │ │ │ Vnewton: Attempting damping, relres = 0.557901 │ │ │ Vnewton: Damping accepted, relres = 0.128656 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.286562e-01 │ │ │ Vprtstp: contraction number = 1.286562e-01 │ │ │ Vnewton: Using errtol_s: 82608.252849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.276277e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.965889e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.628118e+04 │ │ │ Vprtstp: contraction number = 1.628118e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.304734e-02 │ │ │ Vprtstp: contraction number = 1.791390e-01 │ │ │ Vnewton: Using errtol_s: 14798.361839 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.513931e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.126760e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.747143e+03 │ │ │ Vprtstp: contraction number = 3.747143e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.253150e-03 │ │ │ Vprtstp: contraction number = 2.279287e-01 │ │ │ Vnewton: Using errtol_s: 3372.971529 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.762368e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.276817e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.592593e+02 │ │ │ Vprtstp: contraction number = 9.592593e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.344585e-03 │ │ │ Vprtstp: contraction number = 2.559579e-01 │ │ │ Vnewton: Using errtol_s: 863.338654 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001202e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.434505e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.591357e+02 │ │ │ Vprtstp: contraction number = 2.591357e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.632264e-04 │ │ │ Vprtstp: contraction number = 2.701401e-01 │ │ │ Vnewton: Using errtol_s: 233.222386 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026195e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.596338e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.209902e+01 │ │ │ Vprtstp: contraction number = 7.209902e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.010600e-04 │ │ │ Vprtstp: contraction number = 2.782286e-01 │ │ │ Vnewton: Using errtol_s: 64.889141 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051166e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.760099e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.046499e+01 │ │ │ Vprtstp: contraction number = 2.046499e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.868541e-05 │ │ │ Vprtstp: contraction number = 2.838455e-01 │ │ │ Vnewton: Using errtol_s: 18.418489 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074930e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.919190e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.902147e+00 │ │ │ Vprtstp: contraction number = 5.902147e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.272935e-06 │ │ │ Vprtstp: contraction number = 2.884022e-01 │ │ │ Vnewton: Using errtol_s: 5.311932 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099847e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.081838e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.725476e+00 │ │ │ Vprtstp: contraction number = 1.725476e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.418570e-06 │ │ │ Vprtstp: contraction number = 2.923472e-01 │ │ │ Vnewton: Using errtol_s: 1.552929 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.124826e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.238508e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.102067e-01 │ │ │ Vprtstp: contraction number = 5.102067e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.151478e-07 │ │ │ Vprtstp: contraction number = 2.956904e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.641784e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.854901e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.615088e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.629527e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -20271,17 +20271,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.836319274152E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.830295346260E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.413099848091E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.191900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.365800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.4 │ │ │ Vpbe_ctor2: xkappa = 0.205945 │ │ │ @@ -20328,160 +20328,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00207488 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.109059 │ │ │ +Vacc_SASA: Time elapsed: 0.165411 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.111900e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.164000e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.051900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.434900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.709330e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.211597e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.204983e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.400895e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 667195.414501 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.227373e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.429048e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.070575e+05 │ │ │ Vprtstp: contraction number = 1.070575e+05 │ │ │ Vnewton: Attempting damping, relres = 0.151420 │ │ │ Vnewton: Attempting damping, relres = 0.569765 │ │ │ Vnewton: Damping accepted, relres = 0.151420 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.514203e-01 │ │ │ Vprtstp: contraction number = 1.514203e-01 │ │ │ Vnewton: Using errtol_s: 101026.941605 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.264539e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.607738e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.191459e+04 │ │ │ Vprtstp: contraction number = 2.191459e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.976400e-02 │ │ │ Vprtstp: contraction number = 1.965654e-01 │ │ │ Vnewton: Using errtol_s: 19858.405232 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289395e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.773007e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.366842e+03 │ │ │ Vprtstp: contraction number = 5.366842e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.240542e-03 │ │ │ Vprtstp: contraction number = 2.432651e-01 │ │ │ Vnewton: Using errtol_s: 4830.856278 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.313213e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.943119e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.417443e+03 │ │ │ Vprtstp: contraction number = 1.417443e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.912054e-03 │ │ │ Vprtstp: contraction number = 2.640761e-01 │ │ │ Vnewton: Using errtol_s: 1275.713735 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.338191e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.113953e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.929589e+02 │ │ │ Vprtstp: contraction number = 3.929589e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.300759e-04 │ │ │ Vprtstp: contraction number = 2.772285e-01 │ │ │ Vnewton: Using errtol_s: 353.664179 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.362005e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.275233e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.125096e+02 │ │ │ Vprtstp: contraction number = 1.125096e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.517678e-04 │ │ │ Vprtstp: contraction number = 2.863133e-01 │ │ │ Vnewton: Using errtol_s: 101.258773 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.387012e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.437076e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.298207e+01 │ │ │ Vprtstp: contraction number = 3.298207e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.449052e-05 │ │ │ Vprtstp: contraction number = 2.931486e-01 │ │ │ Vnewton: Using errtol_s: 29.683870 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.411942e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.605921e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.865288e+00 │ │ │ Vprtstp: contraction number = 9.865288e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.330759e-05 │ │ │ Vprtstp: contraction number = 2.991106e-01 │ │ │ Vnewton: Using errtol_s: 8.878760 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.435685e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.770521e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.008494e+00 │ │ │ Vprtstp: contraction number = 3.008494e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.058248e-06 │ │ │ Vprtstp: contraction number = 3.049575e-01 │ │ │ Vnewton: Using errtol_s: 2.707645 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.460654e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.931159e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.332652e-01 │ │ │ Vprtstp: contraction number = 9.332652e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.258910e-06 │ │ │ Vprtstp: contraction number = 3.102101e-01 │ │ │ Vnewton: Using errtol_s: 0.839939 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.485741e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.086736e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.936402e-01 │ │ │ Vprtstp: contraction number = 2.936402e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.961001e-07 │ │ │ Vprtstp: contraction number = 3.146374e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.997283e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.249728e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.829290e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.842828e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -20491,17 +20491,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.827843084018E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.062828524213E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.029378526105E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.183200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.323700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -20528,162 +20528,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.172994 │ │ │ +Vacc_SASA: Time elapsed: 0.270529 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.886250e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.425760e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.867900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.168000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.440610e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.049013e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.666998e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.265682e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1471319.117079 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.681530e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.293357e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.089888e+05 │ │ │ Vprtstp: contraction number = 2.089888e+05 │ │ │ Vnewton: Attempting damping, relres = 0.165808 │ │ │ Vnewton: Attempting damping, relres = 0.563564 │ │ │ Vnewton: Damping accepted, relres = 0.165808 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.658082e-01 │ │ │ Vprtstp: contraction number = 1.658082e-01 │ │ │ Vnewton: Using errtol_s: 243956.756463 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.713710e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.470262e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.927783e+04 │ │ │ Vprtstp: contraction number = 3.927783e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.048323e-02 │ │ │ Vprtstp: contraction number = 1.838464e-01 │ │ │ Vnewton: Using errtol_s: 44850.563282 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.737440e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.660433e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.923271e+03 │ │ │ Vprtstp: contraction number = 9.923271e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.609400e-03 │ │ │ Vprtstp: contraction number = 2.168208e-01 │ │ │ Vnewton: Using errtol_s: 9724.536863 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.762386e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.829174e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.744656e+03 │ │ │ Vprtstp: contraction number = 2.744656e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.685430e-03 │ │ │ Vprtstp: contraction number = 2.550050e-01 │ │ │ Vnewton: Using errtol_s: 2479.805360 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.787336e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.990218e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.927726e+02 │ │ │ Vprtstp: contraction number = 7.927726e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.849448e-04 │ │ │ Vprtstp: contraction number = 2.877276e-01 │ │ │ Vnewton: Using errtol_s: 713.508521 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.810813e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.153978e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.371902e+02 │ │ │ Vprtstp: contraction number = 2.371902e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.450884e-04 │ │ │ Vprtstp: contraction number = 2.991854e-01 │ │ │ Vnewton: Using errtol_s: 213.471337 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.835725e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.311538e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.181744e+01 │ │ │ Vprtstp: contraction number = 7.181744e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.393045e-05 │ │ │ Vprtstp: contraction number = 3.027840e-01 │ │ │ Vnewton: Using errtol_s: 64.635706 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.860686e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.477725e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.188269e+01 │ │ │ Vprtstp: contraction number = 2.188269e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.338555e-05 │ │ │ Vprtstp: contraction number = 3.046988e-01 │ │ │ Vnewton: Using errtol_s: 19.694422 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.884380e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.642656e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.694672e+00 │ │ │ Vprtstp: contraction number = 6.694672e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.095104e-06 │ │ │ Vprtstp: contraction number = 3.059346e-01 │ │ │ Vnewton: Using errtol_s: 6.025205 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.909326e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.800042e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.053963e+00 │ │ │ Vprtstp: contraction number = 2.053963e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.256401e-06 │ │ │ Vprtstp: contraction number = 3.068056e-01 │ │ │ Vnewton: Using errtol_s: 1.848567 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.934271e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.964871e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.315192e-01 │ │ │ Vprtstp: contraction number = 6.315192e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.862977e-07 │ │ │ Vprtstp: contraction number = 3.074637e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.854001e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.063883e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.841092e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.852715e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -20693,17 +20693,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.577297422192E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.873373018987E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.357495652952E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.104400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.066710e-01 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.4 │ │ │ Vpbe_ctor2: xkappa = 0.205945 │ │ │ @@ -20750,160 +20750,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00276825 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173496 │ │ │ +Vacc_SASA: Time elapsed: 0.333127 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.882110e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.127528e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.887600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.008500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.446960e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.176766e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.027405e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013236e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1499432.159358 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.041741e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.015636e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.618100e+05 │ │ │ Vprtstp: contraction number = 2.618100e+05 │ │ │ Vnewton: Attempting damping, relres = 0.194105 │ │ │ Vnewton: Attempting damping, relres = 0.578438 │ │ │ Vnewton: Damping accepted, relres = 0.194105 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.941047e-01 │ │ │ Vprtstp: contraction number = 1.941047e-01 │ │ │ Vnewton: Using errtol_s: 291046.875702 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.074048e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033842e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.372130e+04 │ │ │ Vprtstp: contraction number = 5.372130e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.856178e-02 │ │ │ Vprtstp: contraction number = 1.986648e-01 │ │ │ Vnewton: Using errtol_s: 57820.773992 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.100153e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052480e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.429172e+04 │ │ │ Vprtstp: contraction number = 1.429172e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 9.088822e-03 │ │ │ Vprtstp: contraction number = 2.356951e-01 │ │ │ Vnewton: Using errtol_s: 13628.071398 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.125159e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.069764e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.146951e+03 │ │ │ Vprtstp: contraction number = 4.146951e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.494923e-03 │ │ │ Vprtstp: contraction number = 2.745046e-01 │ │ │ Vnewton: Using errtol_s: 3740.967765 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.148946e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086091e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.262928e+03 │ │ │ Vprtstp: contraction number = 1.262928e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.580508e-04 │ │ │ Vprtstp: contraction number = 3.038374e-01 │ │ │ Vnewton: Using errtol_s: 1136.645774 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.173976e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102503e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.984728e+02 │ │ │ Vprtstp: contraction number = 3.984728e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.391744e-04 │ │ │ Vprtstp: contraction number = 3.155124e-01 │ │ │ Vnewton: Using errtol_s: 358.625830 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.199003e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119169e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.279297e+02 │ │ │ Vprtstp: contraction number = 1.279297e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.678689e-05 │ │ │ Vprtstp: contraction number = 3.210497e-01 │ │ │ Vnewton: Using errtol_s: 115.136728 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.224032e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.135763e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.156614e+01 │ │ │ Vprtstp: contraction number = 4.156614e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.494913e-05 │ │ │ Vprtstp: contraction number = 3.249140e-01 │ │ │ Vnewton: Using errtol_s: 37.409531 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.247875e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.152483e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.363199e+01 │ │ │ Vprtstp: contraction number = 1.363199e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 8.182289e-06 │ │ │ Vprtstp: contraction number = 3.279589e-01 │ │ │ Vnewton: Using errtol_s: 12.268788 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.272912e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.169605e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.504209e+00 │ │ │ Vprtstp: contraction number = 4.504209e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.703549e-06 │ │ │ Vprtstp: contraction number = 3.304147e-01 │ │ │ Vnewton: Using errtol_s: 4.053788 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.297911e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.187063e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.497181e+00 │ │ │ Vprtstp: contraction number = 1.497181e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 8.986490e-07 │ │ │ Vprtstp: contraction number = 3.323961e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.898520e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.109807e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.890828e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.903919e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -20913,29 +20913,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.566888561677E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.135111393094E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066620211340E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.021900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.334400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.418558e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.203959e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:09:31 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 03:06:49 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -21205,151 +21205,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.303359 │ │ │ +Vacc_SASA: Time elapsed: 0.399679 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.926950e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.205949e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.881900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.866400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.439770e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.235125e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.322120e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.619291e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2117021.813584 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.708620e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.129051e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.733993e+05 │ │ │ Vprtstp: contraction number = 2.733993e+05 │ │ │ Vnewton: Attempting damping, relres = 0.126346 │ │ │ Vnewton: Attempting damping, relres = 0.555677 │ │ │ Vnewton: Damping accepted, relres = 0.126346 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.263459e-01 │ │ │ Vprtstp: contraction number = 1.263459e-01 │ │ │ Vnewton: Using errtol_s: 267477.104304 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305877e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.650681e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.948638e+04 │ │ │ Vprtstp: contraction number = 4.948638e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.218275e-02 │ │ │ Vprtstp: contraction number = 1.755716e-01 │ │ │ Vnewton: Using errtol_s: 46961.371226 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.543353e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.780227e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.168877e+04 │ │ │ Vprtstp: contraction number = 1.168877e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.021324e-03 │ │ │ Vprtstp: contraction number = 2.263616e-01 │ │ │ Vnewton: Using errtol_s: 10630.252373 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.793792e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.823681e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.120176e+03 │ │ │ Vprtstp: contraction number = 3.120176e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.326708e-03 │ │ │ Vprtstp: contraction number = 2.642148e-01 │ │ │ Vnewton: Using errtol_s: 2808.669489 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.044041e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.867441e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.828690e+02 │ │ │ Vprtstp: contraction number = 8.828690e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.753310e-04 │ │ │ Vprtstp: contraction number = 2.829040e-01 │ │ │ Vnewton: Using errtol_s: 794.583820 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.306785e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099900e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.573077e+02 │ │ │ Vprtstp: contraction number = 2.573077e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.093881e-04 │ │ │ Vprtstp: contraction number = 2.914445e-01 │ │ │ Vnewton: Using errtol_s: 231.577068 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.568711e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.304131e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.638166e+01 │ │ │ Vprtstp: contraction number = 7.638166e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.247180e-05 │ │ │ Vprtstp: contraction number = 2.968494e-01 │ │ │ Vnewton: Using errtol_s: 68.743505 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.819234e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.506186e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.298047e+01 │ │ │ Vprtstp: contraction number = 2.298047e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.769584e-06 │ │ │ Vprtstp: contraction number = 3.008636e-01 │ │ │ Vnewton: Using errtol_s: 20.682422 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.069318e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.707799e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.986364e+00 │ │ │ Vprtstp: contraction number = 6.986364e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.970082e-06 │ │ │ Vprtstp: contraction number = 3.040131e-01 │ │ │ Vnewton: Using errtol_s: 6.287728 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.319395e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.913251e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.142572e+00 │ │ │ Vprtstp: contraction number = 2.142572e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.108619e-07 │ │ │ Vprtstp: contraction number = 3.066791e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.684078e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.900539e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.074480e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.088314e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -21359,17 +21359,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.282938613188E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.566547142826E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282703574681E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.061200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.331000e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.5 │ │ │ Vpbe_ctor2: xkappa = 0.230253 │ │ │ @@ -21416,160 +21416,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0133684 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.292823 │ │ │ +Vacc_SASA: Time elapsed: 0.426615 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.428370e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.221781e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.941700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.840300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.410430e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.118506e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.419678e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.126732e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2163354.564593 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.553268e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.151104e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.401998e+05 │ │ │ Vprtstp: contraction number = 3.401998e+05 │ │ │ Vnewton: Attempting damping, relres = 0.151250 │ │ │ Vnewton: Attempting damping, relres = 0.568556 │ │ │ Vnewton: Damping accepted, relres = 0.151250 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.512496e-01 │ │ │ Vprtstp: contraction number = 1.512496e-01 │ │ │ Vnewton: Using errtol_s: 327206.577099 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.881723e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.377251e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.770698e+04 │ │ │ Vprtstp: contraction number = 6.770698e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.926462e-02 │ │ │ Vprtstp: contraction number = 1.934856e-01 │ │ │ Vnewton: Using errtol_s: 63309.757927 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.131531e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.584287e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.699399e+04 │ │ │ Vprtstp: contraction number = 1.699399e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.115656e-03 │ │ │ Vprtstp: contraction number = 2.431487e-01 │ │ │ Vnewton: Using errtol_s: 15393.687585 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.381877e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.788426e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.742003e+03 │ │ │ Vprtstp: contraction number = 4.742003e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.972961e-03 │ │ │ Vprtstp: contraction number = 2.772704e-01 │ │ │ Vnewton: Using errtol_s: 4268.214485 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.632302e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.991290e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.400571e+03 │ │ │ Vprtstp: contraction number = 1.400571e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.826678e-04 │ │ │ Vprtstp: contraction number = 2.953265e-01 │ │ │ Vnewton: Using errtol_s: 1260.517005 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.882756e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.195912e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.279978e+02 │ │ │ Vprtstp: contraction number = 4.279978e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.780560e-04 │ │ │ Vprtstp: contraction number = 3.055876e-01 │ │ │ Vnewton: Using errtol_s: 385.198337 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.120907e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.397574e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.339544e+02 │ │ │ Vprtstp: contraction number = 1.339544e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.572782e-05 │ │ │ Vprtstp: contraction number = 3.129791e-01 │ │ │ Vnewton: Using errtol_s: 120.559033 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.371188e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.607966e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.271452e+01 │ │ │ Vprtstp: contraction number = 4.271452e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.777012e-05 │ │ │ Vprtstp: contraction number = 3.188734e-01 │ │ │ Vnewton: Using errtol_s: 38.443069 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.621533e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.814290e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.384186e+01 │ │ │ Vprtstp: contraction number = 1.384186e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.758498e-06 │ │ │ Vprtstp: contraction number = 3.240551e-01 │ │ │ Vnewton: Using errtol_s: 12.457672 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.871717e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.021473e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.545889e+00 │ │ │ Vprtstp: contraction number = 4.545889e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.891183e-06 │ │ │ Vprtstp: contraction number = 3.284161e-01 │ │ │ Vnewton: Using errtol_s: 4.091300 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.121711e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.228100e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.509299e+00 │ │ │ Vprtstp: contraction number = 1.509299e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.278996e-07 │ │ │ Vprtstp: contraction number = 3.320141e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.888306e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.103074e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.293595e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.306578e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -21579,17 +21579,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.270848264537E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951162263981E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.475012659776E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.024000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.651500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -21616,151 +21616,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.111199 │ │ │ +Vacc_SASA: Time elapsed: 0.159883 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.748710e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.407550e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.907200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.452800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.631920e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.077030e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.832820e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.454118e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 634193.792999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.018209e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.478112e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.499222e+04 │ │ │ Vprtstp: contraction number = 8.499222e+04 │ │ │ Vnewton: Attempting damping, relres = 0.127890 │ │ │ Vnewton: Attempting damping, relres = 0.557688 │ │ │ Vnewton: Damping accepted, relres = 0.127890 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.278898e-01 │ │ │ Vprtstp: contraction number = 1.278898e-01 │ │ │ Vnewton: Using errtol_s: 81106.914272 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.352069e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.634240e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.610090e+04 │ │ │ Vprtstp: contraction number = 1.610090e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.303084e-02 │ │ │ Vprtstp: contraction number = 1.800835e-01 │ │ │ Vnewton: Using errtol_s: 14606.018111 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.601530e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.774346e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.721077e+03 │ │ │ Vprtstp: contraction number = 3.721077e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.281325e-03 │ │ │ Vprtstp: contraction number = 2.293153e-01 │ │ │ Vnewton: Using errtol_s: 3349.383286 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.838747e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.921823e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.553498e+02 │ │ │ Vprtstp: contraction number = 9.553498e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.355768e-03 │ │ │ Vprtstp: contraction number = 2.567099e-01 │ │ │ Vnewton: Using errtol_s: 859.819863 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008842e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.061094e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.585067e+02 │ │ │ Vprtstp: contraction number = 2.585067e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.668537e-04 │ │ │ Vprtstp: contraction number = 2.705873e-01 │ │ │ Vnewton: Using errtol_s: 232.656331 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033741e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.201134e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.199407e+01 │ │ │ Vprtstp: contraction number = 7.199407e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.021686e-04 │ │ │ Vprtstp: contraction number = 2.784995e-01 │ │ │ Vnewton: Using errtol_s: 64.794682 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.058714e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.343886e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.044636e+01 │ │ │ Vprtstp: contraction number = 2.044636e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.901594e-05 │ │ │ Vprtstp: contraction number = 2.840006e-01 │ │ │ Vnewton: Using errtol_s: 18.401729 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.083619e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.486654e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.898540e+00 │ │ │ Vprtstp: contraction number = 5.898540e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.370763e-06 │ │ │ Vprtstp: contraction number = 2.884884e-01 │ │ │ Vnewton: Using errtol_s: 5.308686 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.108623e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.626786e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.724703e+00 │ │ │ Vprtstp: contraction number = 1.724703e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.447569e-06 │ │ │ Vprtstp: contraction number = 2.923949e-01 │ │ │ Vnewton: Using errtol_s: 1.552233 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.133572e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.768098e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.100216e-01 │ │ │ Vprtstp: contraction number = 5.100216e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.237842e-07 │ │ │ Vprtstp: contraction number = 2.957156e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.688089e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.924237e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.441979e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.453748e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -21770,17 +21770,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.835376083091E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.829553004280E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.412753768634E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.247200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.603100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.5 │ │ │ Vpbe_ctor2: xkappa = 0.230253 │ │ │ @@ -21827,160 +21827,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00156468 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.121821 │ │ │ +Vacc_SASA: Time elapsed: 0.188545 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.002480e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.419080e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.062000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.816500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.455560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.070005e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.209353e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.915176e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 658696.826144 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.223780e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.939321e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.053855e+05 │ │ │ Vprtstp: contraction number = 1.053855e+05 │ │ │ Vnewton: Attempting damping, relres = 0.150549 │ │ │ Vnewton: Attempting damping, relres = 0.569486 │ │ │ Vnewton: Damping accepted, relres = 0.150549 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.505490e-01 │ │ │ Vprtstp: contraction number = 1.505490e-01 │ │ │ Vnewton: Using errtol_s: 99166.139789 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.256133e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.109196e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.161238e+04 │ │ │ Vprtstp: contraction number = 2.161238e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.969136e-02 │ │ │ Vprtstp: contraction number = 1.972206e-01 │ │ │ Vnewton: Using errtol_s: 19557.601485 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.281022e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.263810e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.305338e+03 │ │ │ Vprtstp: contraction number = 5.305338e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.249717e-03 │ │ │ Vprtstp: contraction number = 2.441693e-01 │ │ │ Vnewton: Using errtol_s: 4775.365541 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305997e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.419393e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.404636e+03 │ │ │ Vprtstp: contraction number = 1.404636e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.919225e-03 │ │ │ Vprtstp: contraction number = 2.647311e-01 │ │ │ Vnewton: Using errtol_s: 1264.187582 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330969e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.570627e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.902078e+02 │ │ │ Vprtstp: contraction number = 3.902078e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.331561e-04 │ │ │ Vprtstp: contraction number = 2.777976e-01 │ │ │ Vnewton: Using errtol_s: 351.188214 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.354790e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.719941e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.119096e+02 │ │ │ Vprtstp: contraction number = 1.119096e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.529061e-04 │ │ │ Vprtstp: contraction number = 2.867943e-01 │ │ │ Vnewton: Using errtol_s: 100.718769 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.379736e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.868987e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.284972e+01 │ │ │ Vprtstp: contraction number = 3.284972e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.488371e-05 │ │ │ Vprtstp: contraction number = 2.935377e-01 │ │ │ Vnewton: Using errtol_s: 29.564758 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.404636e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.019874e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.835792e+00 │ │ │ Vprtstp: contraction number = 9.835792e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.343898e-05 │ │ │ Vprtstp: contraction number = 2.994178e-01 │ │ │ Vnewton: Using errtol_s: 8.852214 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.429664e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.166798e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.001834e+00 │ │ │ Vprtstp: contraction number = 3.001834e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.101508e-06 │ │ │ Vprtstp: contraction number = 3.051949e-01 │ │ │ Vnewton: Using errtol_s: 2.701650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.454612e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.319440e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.317265e-01 │ │ │ Vprtstp: contraction number = 9.317265e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.273050e-06 │ │ │ Vprtstp: contraction number = 3.103858e-01 │ │ │ Vnewton: Using errtol_s: 0.838554 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.478440e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.470516e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.932750e-01 │ │ │ Vprtstp: contraction number = 2.932750e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.007117e-07 │ │ │ Vprtstp: contraction number = 3.147651e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.881869e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.104576e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.694379e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.706453e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -21990,17 +21990,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.826778540566E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.062089331006E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.029034062463E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.155700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.710800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -22027,162 +22027,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.174544 │ │ │ +Vacc_SASA: Time elapsed: 0.334088 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.927890e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.338760e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.888500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.056200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.430580e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.011164e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.659155e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.645669e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1439349.266881 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.674436e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.672504e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.043544e+05 │ │ │ Vprtstp: contraction number = 2.043544e+05 │ │ │ Vnewton: Attempting damping, relres = 0.158631 │ │ │ Vnewton: Attempting damping, relres = 0.563029 │ │ │ Vnewton: Damping accepted, relres = 0.158631 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.586310e-01 │ │ │ Vprtstp: contraction number = 1.586310e-01 │ │ │ Vnewton: Using errtol_s: 228325.431602 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.706580e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.845178e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.831785e+04 │ │ │ Vprtstp: contraction number = 3.831785e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.847279e-02 │ │ │ Vprtstp: contraction number = 1.794907e-01 │ │ │ Vnewton: Using errtol_s: 40982.294833 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.731436e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.012474e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.668291e+03 │ │ │ Vprtstp: contraction number = 9.668291e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.314045e-03 │ │ │ Vprtstp: contraction number = 2.217571e-01 │ │ │ Vnewton: Using errtol_s: 9088.116327 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.755180e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.169737e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.688849e+03 │ │ │ Vprtstp: contraction number = 2.688849e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.683268e-03 │ │ │ Vprtstp: contraction number = 2.665910e-01 │ │ │ Vnewton: Using errtol_s: 2422.810315 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.780209e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.319807e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.856129e+02 │ │ │ Vprtstp: contraction number = 7.856129e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.912324e-04 │ │ │ Vprtstp: contraction number = 2.918326e-01 │ │ │ Vnewton: Using errtol_s: 707.055007 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.804010e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.474735e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.356112e+02 │ │ │ Vprtstp: contraction number = 2.356112e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.473237e-04 │ │ │ Vprtstp: contraction number = 2.999062e-01 │ │ │ Vnewton: Using errtol_s: 212.050207 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.828944e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.628790e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.139103e+01 │ │ │ Vprtstp: contraction number = 7.139103e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.463957e-05 │ │ │ Vprtstp: contraction number = 3.030034e-01 │ │ │ Vnewton: Using errtol_s: 64.251934 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.853875e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.796573e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.175983e+01 │ │ │ Vprtstp: contraction number = 2.175983e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.360604e-05 │ │ │ Vprtstp: contraction number = 3.047978e-01 │ │ │ Vnewton: Using errtol_s: 19.583846 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.877683e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.973208e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.658230e+00 │ │ │ Vprtstp: contraction number = 6.658230e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.163275e-06 │ │ │ Vprtstp: contraction number = 3.059873e-01 │ │ │ Vnewton: Using errtol_s: 5.992407 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.902677e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.133827e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.042996e+00 │ │ │ Vprtstp: contraction number = 2.042996e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.277450e-06 │ │ │ Vprtstp: contraction number = 3.068378e-01 │ │ │ Vnewton: Using errtol_s: 1.838697 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.927650e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.289030e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.281914e-01 │ │ │ Vprtstp: contraction number = 6.281914e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.927971e-07 │ │ │ Vprtstp: contraction number = 3.074853e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.868838e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.076975e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.785677e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.796715e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -22192,17 +22192,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.196840922494E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.873106662838E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.356799948261E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.168300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.702900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.5 │ │ │ Vpbe_ctor2: xkappa = 0.230253 │ │ │ @@ -22249,160 +22249,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00202496 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173305 │ │ │ +Vacc_SASA: Time elapsed: 0.284622 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.481430e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.585800e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.941600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.573000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.426300e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.177639e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.017321e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.454948e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1465724.452340 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.031907e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.481177e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.560590e+05 │ │ │ Vprtstp: contraction number = 2.560590e+05 │ │ │ Vnewton: Attempting damping, relres = 0.187284 │ │ │ Vnewton: Attempting damping, relres = 0.577996 │ │ │ Vnewton: Damping accepted, relres = 0.187284 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.872842e-01 │ │ │ Vprtstp: contraction number = 1.872842e-01 │ │ │ Vnewton: Using errtol_s: 274507.063571 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.064208e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.665869e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.241855e+04 │ │ │ Vprtstp: contraction number = 5.241855e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.660510e-02 │ │ │ Vprtstp: contraction number = 1.954521e-01 │ │ │ Vnewton: Using errtol_s: 53652.984086 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.089277e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.847755e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.392830e+04 │ │ │ Vprtstp: contraction number = 1.392830e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.808972e-03 │ │ │ Vprtstp: contraction number = 2.406488e-01 │ │ │ Vnewton: Using errtol_s: 12911.525544 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.113056e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001293e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.064869e+03 │ │ │ Vprtstp: contraction number = 4.064869e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.497826e-03 │ │ │ Vprtstp: contraction number = 2.835548e-01 │ │ │ Vnewton: Using errtol_s: 3661.124985 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.138065e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018724e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.249555e+03 │ │ │ Vprtstp: contraction number = 1.249555e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.672679e-04 │ │ │ Vprtstp: contraction number = 3.071743e-01 │ │ │ Vnewton: Using errtol_s: 1124.603371 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.163101e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035451e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.953417e+02 │ │ │ Vprtstp: contraction number = 3.953417e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.427522e-04 │ │ │ Vprtstp: contraction number = 3.163852e-01 │ │ │ Vnewton: Using errtol_s: 355.807819 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.186763e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051871e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.271192e+02 │ │ │ Vprtstp: contraction number = 1.271192e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.805515e-05 │ │ │ Vprtstp: contraction number = 3.215425e-01 │ │ │ Vnewton: Using errtol_s: 114.407339 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.211670e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068480e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.134607e+01 │ │ │ Vprtstp: contraction number = 4.134607e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.538777e-05 │ │ │ Vprtstp: contraction number = 3.252542e-01 │ │ │ Vnewton: Using errtol_s: 37.211468 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.237107e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.084400e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.356940e+01 │ │ │ Vprtstp: contraction number = 1.356940e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 8.332028e-06 │ │ │ Vprtstp: contraction number = 3.281907e-01 │ │ │ Vnewton: Using errtol_s: 12.212457 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.261027e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.100240e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.485660e+00 │ │ │ Vprtstp: contraction number = 4.485660e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.754334e-06 │ │ │ Vprtstp: contraction number = 3.305718e-01 │ │ │ Vnewton: Using errtol_s: 4.037094 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.285639e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.116270e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.491490e+00 │ │ │ Vprtstp: contraction number = 1.491490e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 9.158205e-07 │ │ │ Vprtstp: contraction number = 3.325017e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.874086e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.087429e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.851575e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.864589e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -22412,29 +22412,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 7.186606092212E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.134845139455E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066550655218E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.149700e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.822700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.407467e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.132058e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:09:43 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 03:30:58 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -22704,151 +22704,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.297774 │ │ │ +Vacc_SASA: Time elapsed: 0.427790 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.866020e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.133493e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.943900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.599100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.453220e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.100776e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.270740e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.368686e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2093191.031761 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.727990e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.755956e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.700910e+05 │ │ │ Vprtstp: contraction number = 2.700910e+05 │ │ │ Vnewton: Attempting damping, relres = 0.124805 │ │ │ Vnewton: Attempting damping, relres = 0.555496 │ │ │ Vnewton: Damping accepted, relres = 0.124805 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.248046e-01 │ │ │ Vprtstp: contraction number = 1.248046e-01 │ │ │ Vnewton: Using errtol_s: 261239.913592 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.294335e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.527630e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.897400e+04 │ │ │ Vprtstp: contraction number = 4.897400e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.189435e-02 │ │ │ Vprtstp: contraction number = 1.754290e-01 │ │ │ Vnewton: Using errtol_s: 45829.056358 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.544594e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.571567e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.159488e+04 │ │ │ Vprtstp: contraction number = 1.159488e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.014196e-03 │ │ │ Vprtstp: contraction number = 2.290178e-01 │ │ │ Vnewton: Using errtol_s: 10495.669115 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.781283e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.644806e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.106549e+03 │ │ │ Vprtstp: contraction number = 3.106549e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.335806e-03 │ │ │ Vprtstp: contraction number = 2.664048e-01 │ │ │ Vnewton: Using errtol_s: 2796.096256 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.030318e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.751415e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.808235e+02 │ │ │ Vprtstp: contraction number = 8.808235e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.787243e-04 │ │ │ Vprtstp: contraction number = 2.835176e-01 │ │ │ Vnewton: Using errtol_s: 792.742402 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.279373e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.078813e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.569082e+02 │ │ │ Vprtstp: contraction number = 2.569082e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.104617e-04 │ │ │ Vprtstp: contraction number = 2.916679e-01 │ │ │ Vnewton: Using errtol_s: 231.217496 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.527776e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.280596e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.629035e+01 │ │ │ Vprtstp: contraction number = 7.629035e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.280223e-05 │ │ │ Vprtstp: contraction number = 2.969556e-01 │ │ │ Vnewton: Using errtol_s: 68.661328 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.765827e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.486788e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.295748e+01 │ │ │ Vprtstp: contraction number = 2.295748e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.870924e-06 │ │ │ Vprtstp: contraction number = 3.009224e-01 │ │ │ Vnewton: Using errtol_s: 20.661731 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.015390e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.696548e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.980126e+00 │ │ │ Vprtstp: contraction number = 6.980126e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.001214e-06 │ │ │ Vprtstp: contraction number = 3.040459e-01 │ │ │ Vnewton: Using errtol_s: 6.282114 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.264429e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.910592e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.140783e+00 │ │ │ Vprtstp: contraction number = 2.140783e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.204627e-07 │ │ │ Vprtstp: contraction number = 3.066968e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.622044e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.838531e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.079278e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.091197e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -22858,17 +22858,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.091310515028E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.566396275850E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282657451494E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.050600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.739900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.6 │ │ │ Vpbe_ctor2: xkappa = 0.25223 │ │ │ @@ -22915,160 +22915,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0123549 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.299394 │ │ │ +Vacc_SASA: Time elapsed: 0.421320 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.428610e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.197787e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.867900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.944500e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.461560e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 9.941430e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.352391e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.127214e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2138246.077963 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.504238e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.152730e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.360784e+05 │ │ │ Vprtstp: contraction number = 3.360784e+05 │ │ │ Vnewton: Attempting damping, relres = 0.149785 │ │ │ Vnewton: Attempting damping, relres = 0.568394 │ │ │ Vnewton: Damping accepted, relres = 0.149785 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.497849e-01 │ │ │ Vprtstp: contraction number = 1.497849e-01 │ │ │ Vnewton: Using errtol_s: 320277.019000 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.826102e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.369444e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.696106e+04 │ │ │ Vprtstp: contraction number = 6.696106e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.898319e-02 │ │ │ Vprtstp: contraction number = 1.934987e-01 │ │ │ Vnewton: Using errtol_s: 61973.189490 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.075037e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.574089e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.682773e+04 │ │ │ Vprtstp: contraction number = 1.682773e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.107594e-03 │ │ │ Vprtstp: contraction number = 2.452316e-01 │ │ │ Vnewton: Using errtol_s: 15197.785187 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.312860e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.786240e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.709721e+03 │ │ │ Vprtstp: contraction number = 4.709721e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.982435e-03 │ │ │ Vprtstp: contraction number = 2.789179e-01 │ │ │ Vnewton: Using errtol_s: 4238.934308 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.562402e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.992723e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.393997e+03 │ │ │ Vprtstp: contraction number = 1.393997e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.867426e-04 │ │ │ Vprtstp: contraction number = 2.959706e-01 │ │ │ Vnewton: Using errtol_s: 1254.599967 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.812834e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.198806e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.264850e+02 │ │ │ Vprtstp: contraction number = 4.264850e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.795101e-04 │ │ │ Vprtstp: contraction number = 3.059436e-01 │ │ │ Vnewton: Using errtol_s: 383.836806 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.062899e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.415651e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.335898e+02 │ │ │ Vprtstp: contraction number = 1.335898e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.622871e-05 │ │ │ Vprtstp: contraction number = 3.132342e-01 │ │ │ Vnewton: Using errtol_s: 120.230819 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.314250e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.630247e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.262294e+01 │ │ │ Vprtstp: contraction number = 4.262294e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.794024e-05 │ │ │ Vprtstp: contraction number = 3.190584e-01 │ │ │ Vnewton: Using errtol_s: 38.360650 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.563773e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.840206e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.381744e+01 │ │ │ Vprtstp: contraction number = 1.381744e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.815841e-06 │ │ │ Vprtstp: contraction number = 3.241785e-01 │ │ │ Vnewton: Using errtol_s: 12.435699 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.820705e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.058888e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.538963e+00 │ │ │ Vprtstp: contraction number = 4.538963e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.910476e-06 │ │ │ Vprtstp: contraction number = 3.284952e-01 │ │ │ Vnewton: Using errtol_s: 4.085067 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.069233e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.284106e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.507189e+00 │ │ │ Vprtstp: contraction number = 1.507189e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.343844e-07 │ │ │ Vprtstp: contraction number = 3.320557e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.901170e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.113945e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.356436e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.367776e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -23078,17 +23078,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 5.079562127761E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.951011518926E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.474966609512E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.981900e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.891800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -23115,151 +23115,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108305 │ │ │ +Vacc_SASA: Time elapsed: 0.156062 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.525110e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.534490e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.960700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.180200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.459520e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.108993e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.795366e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.519920e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 628877.747769 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.955140e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.545266e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.412647e+04 │ │ │ Vprtstp: contraction number = 8.412647e+04 │ │ │ Vnewton: Attempting damping, relres = 0.127232 │ │ │ Vnewton: Attempting damping, relres = 0.557518 │ │ │ Vnewton: Damping accepted, relres = 0.127232 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.272321e-01 │ │ │ Vprtstp: contraction number = 1.272321e-01 │ │ │ Vnewton: Using errtol_s: 80013.454014 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.288696e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.717640e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.597434e+04 │ │ │ Vprtstp: contraction number = 1.597434e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.300878e-02 │ │ │ Vprtstp: contraction number = 1.808409e-01 │ │ │ Vnewton: Using errtol_s: 14469.707458 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.526280e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.868340e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.702955e+03 │ │ │ Vprtstp: contraction number = 3.702955e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.299891e-03 │ │ │ Vprtstp: contraction number = 2.303422e-01 │ │ │ Vnewton: Using errtol_s: 3332.983791 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.774690e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.027945e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.526036e+02 │ │ │ Vprtstp: contraction number = 9.526036e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.363298e-03 │ │ │ Vprtstp: contraction number = 2.572314e-01 │ │ │ Vnewton: Using errtol_s: 857.348085 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002422e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.190616e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.580584e+02 │ │ │ Vprtstp: contraction number = 2.580584e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.693131e-04 │ │ │ Vprtstp: contraction number = 2.708968e-01 │ │ │ Vnewton: Using errtol_s: 232.252814 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.027059e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.347171e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.191756e+01 │ │ │ Vprtstp: contraction number = 7.191756e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.029227e-04 │ │ │ Vprtstp: contraction number = 2.786869e-01 │ │ │ Vnewton: Using errtol_s: 64.725819 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052009e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.492523e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.043225e+01 │ │ │ Vprtstp: contraction number = 2.043225e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.924102e-05 │ │ │ Vprtstp: contraction number = 2.841066e-01 │ │ │ Vnewton: Using errtol_s: 18.389029 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.076943e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.641070e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.895681e+00 │ │ │ Vprtstp: contraction number = 5.895681e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.437431e-06 │ │ │ Vprtstp: contraction number = 2.885477e-01 │ │ │ Vnewton: Using errtol_s: 5.306113 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101820e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.791340e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.724061e+00 │ │ │ Vprtstp: contraction number = 1.724061e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.467339e-06 │ │ │ Vprtstp: contraction number = 2.924277e-01 │ │ │ Vnewton: Using errtol_s: 1.551655 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126791e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.934739e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.098608e-01 │ │ │ Vprtstp: contraction number = 5.098608e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.296724e-07 │ │ │ Vprtstp: contraction number = 2.957325e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.654757e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.867388e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.544009e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.556465e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -23269,17 +23269,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.828142417011E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.828945138010E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.412475614010E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.236300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.658300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.6 │ │ │ Vpbe_ctor2: xkappa = 0.25223 │ │ │ @@ -23326,160 +23326,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0012176 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108318 │ │ │ +Vacc_SASA: Time elapsed: 0.279604 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.885820e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.735360e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.044200e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.125400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.441240e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.092175e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200887e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.085189e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 653003.444935 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.215738e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.109434e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.042328e+05 │ │ │ Vprtstp: contraction number = 1.042328e+05 │ │ │ Vnewton: Attempting damping, relres = 0.149810 │ │ │ Vnewton: Attempting damping, relres = 0.569263 │ │ │ Vnewton: Damping accepted, relres = 0.149810 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.498099e-01 │ │ │ Vprtstp: contraction number = 1.498099e-01 │ │ │ Vnewton: Using errtol_s: 97826.408096 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.247939e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.283833e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.140231e+04 │ │ │ Vprtstp: contraction number = 2.140231e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.962843e-02 │ │ │ Vprtstp: contraction number = 1.977735e-01 │ │ │ Vnewton: Using errtol_s: 19347.468430 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.272747e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.445975e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.262567e+03 │ │ │ Vprtstp: contraction number = 5.262567e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.253840e-03 │ │ │ Vprtstp: contraction number = 2.448270e-01 │ │ │ Vnewton: Using errtol_s: 4736.782334 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.297753e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.604466e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.395696e+03 │ │ │ Vprtstp: contraction number = 1.395696e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.923638e-03 │ │ │ Vprtstp: contraction number = 2.651889e-01 │ │ │ Vnewton: Using errtol_s: 1256.142167 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322789e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.757591e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.882795e+02 │ │ │ Vprtstp: contraction number = 3.882795e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.351469e-04 │ │ │ Vprtstp: contraction number = 2.781952e-01 │ │ │ Vnewton: Using errtol_s: 349.452740 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.346581e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.916844e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.114868e+02 │ │ │ Vprtstp: contraction number = 1.114868e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.536566e-04 │ │ │ Vprtstp: contraction number = 2.871297e-01 │ │ │ Vnewton: Using errtol_s: 100.338262 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.371758e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.078411e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.275571e+01 │ │ │ Vprtstp: contraction number = 3.275571e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.514547e-05 │ │ │ Vprtstp: contraction number = 2.938077e-01 │ │ │ Vnewton: Using errtol_s: 29.480150 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.396804e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.245588e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.814633e+00 │ │ │ Vprtstp: contraction number = 9.814633e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.352699e-05 │ │ │ Vprtstp: contraction number = 2.996311e-01 │ │ │ Vnewton: Using errtol_s: 8.833170 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.421785e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.408763e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.996998e+00 │ │ │ Vprtstp: contraction number = 2.996998e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.130604e-06 │ │ │ Vprtstp: contraction number = 3.053602e-01 │ │ │ Vnewton: Using errtol_s: 2.697298 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.445277e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.572533e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.305904e-01 │ │ │ Vprtstp: contraction number = 9.305904e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.282583e-06 │ │ │ Vprtstp: contraction number = 3.105075e-01 │ │ │ Vnewton: Using errtol_s: 0.837531 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.468675e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.736993e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.929997e-01 │ │ │ Vprtstp: contraction number = 2.929997e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.038259e-07 │ │ │ Vprtstp: contraction number = 3.148535e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.852264e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.072957e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.790863e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.803255e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -23489,15 +23489,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.819478148872E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.061484049390E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.028757163114E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.107800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.098900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ @@ -23526,162 +23526,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.170425 │ │ │ +Vacc_SASA: Time elapsed: 0.204789 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.897750e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.485420e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.961500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.030400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.433120e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.088720e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.646616e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.910412e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1418682.220089 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.660518e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.935766e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.013102e+05 │ │ │ Vprtstp: contraction number = 2.013102e+05 │ │ │ Vnewton: Attempting damping, relres = 0.153624 │ │ │ Vnewton: Attempting damping, relres = 0.562616 │ │ │ Vnewton: Damping accepted, relres = 0.153624 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.536244e-01 │ │ │ Vprtstp: contraction number = 1.536244e-01 │ │ │ Vnewton: Using errtol_s: 217944.143405 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.692768e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.103344e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.768720e+04 │ │ │ Vprtstp: contraction number = 3.768720e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.718554e-02 │ │ │ Vprtstp: contraction number = 1.769611e-01 │ │ │ Vnewton: Using errtol_s: 38567.641801 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.717746e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.270142e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.503404e+03 │ │ │ Vprtstp: contraction number = 9.503404e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.173770e-03 │ │ │ Vprtstp: contraction number = 2.270976e-01 │ │ │ Vnewton: Using errtol_s: 8758.617788 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.741441e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.431975e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.660166e+03 │ │ │ Vprtstp: contraction number = 2.660166e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.688330e-03 │ │ │ Vprtstp: contraction number = 2.734683e-01 │ │ │ Vnewton: Using errtol_s: 2395.204376 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.766378e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.607393e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.818054e+02 │ │ │ Vprtstp: contraction number = 7.818054e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.959721e-04 │ │ │ Vprtstp: contraction number = 2.937648e-01 │ │ │ Vnewton: Using errtol_s: 703.626776 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.792722e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.770581e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.347603e+02 │ │ │ Vprtstp: contraction number = 2.347603e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.489300e-04 │ │ │ Vprtstp: contraction number = 3.002790e-01 │ │ │ Vnewton: Using errtol_s: 211.284321 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.816566e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.947067e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.116445e+01 │ │ │ Vprtstp: contraction number = 7.116445e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.514613e-05 │ │ │ Vprtstp: contraction number = 3.031366e-01 │ │ │ Vnewton: Using errtol_s: 64.048016 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.841548e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.113418e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.169522e+01 │ │ │ Vprtstp: contraction number = 2.169522e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.376326e-05 │ │ │ Vprtstp: contraction number = 3.048603e-01 │ │ │ Vnewton: Using errtol_s: 19.525698 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.865228e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.277414e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.639132e+00 │ │ │ Vprtstp: contraction number = 6.639132e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.211809e-06 │ │ │ Vprtstp: contraction number = 3.060182e-01 │ │ │ Vnewton: Using errtol_s: 5.975219 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.890196e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.437896e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.037255e+00 │ │ │ Vprtstp: contraction number = 2.037255e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.292417e-06 │ │ │ Vprtstp: contraction number = 3.068556e-01 │ │ │ Vnewton: Using errtol_s: 1.833530 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.915177e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.612604e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.264492e-01 │ │ │ Vprtstp: contraction number = 6.264492e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 3.974141e-07 │ │ │ Vprtstp: contraction number = 3.074967e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.868816e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.083743e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.857300e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.869121e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -23691,17 +23691,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.888929472568E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.872895947241E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.356241018508E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.227200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.312600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.6 │ │ │ Vpbe_ctor2: xkappa = 0.25223 │ │ │ @@ -23748,160 +23748,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00159488 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173044 │ │ │ +Vacc_SASA: Time elapsed: 0.310067 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.368980e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.079473e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.882600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.722800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.413380e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.194520e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.002649e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.793099e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1444108.030883 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.017038e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.821199e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.522925e+05 │ │ │ Vprtstp: contraction number = 2.522925e+05 │ │ │ Vnewton: Attempting damping, relres = 0.182497 │ │ │ Vnewton: Attempting damping, relres = 0.577636 │ │ │ Vnewton: Damping accepted, relres = 0.182497 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.824967e-01 │ │ │ Vprtstp: contraction number = 1.824967e-01 │ │ │ Vnewton: Using errtol_s: 263544.898395 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.049267e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001961e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.156495e+04 │ │ │ Vprtstp: contraction number = 5.156495e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.534743e-02 │ │ │ Vprtstp: contraction number = 1.936881e-01 │ │ │ Vnewton: Using errtol_s: 51045.503065 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.074266e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022273e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.369160e+04 │ │ │ Vprtstp: contraction number = 1.369160e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.672608e-03 │ │ │ Vprtstp: contraction number = 2.453533e-01 │ │ │ Vnewton: Using errtol_s: 12524.182385 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.099285e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040376e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.019157e+03 │ │ │ Vprtstp: contraction number = 4.019157e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.505566e-03 │ │ │ Vprtstp: contraction number = 2.889057e-01 │ │ │ Vnewton: Using errtol_s: 3618.307619 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.123297e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057378e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.241608e+03 │ │ │ Vprtstp: contraction number = 1.241608e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.737990e-04 │ │ │ Vprtstp: contraction number = 3.088321e-01 │ │ │ Vnewton: Using errtol_s: 1117.449365 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.148158e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073750e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.934907e+02 │ │ │ Vprtstp: contraction number = 3.934907e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.452323e-04 │ │ │ Vprtstp: contraction number = 3.169199e-01 │ │ │ Vnewton: Using errtol_s: 354.141922 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.172004e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089949e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.266527e+02 │ │ │ Vprtstp: contraction number = 1.266527e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.893280e-05 │ │ │ Vprtstp: contraction number = 3.218695e-01 │ │ │ Vnewton: Using errtol_s: 113.987497 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.197037e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107365e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.122303e+01 │ │ │ Vprtstp: contraction number = 4.122303e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.569111e-05 │ │ │ Vprtstp: contraction number = 3.254807e-01 │ │ │ Vnewton: Using errtol_s: 37.100733 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.222001e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123790e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.353532e+01 │ │ │ Vprtstp: contraction number = 1.353532e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 8.435513e-06 │ │ │ Vprtstp: contraction number = 3.283437e-01 │ │ │ Vnewton: Using errtol_s: 12.181792 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.247047e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140219e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.475781e+00 │ │ │ Vprtstp: contraction number = 4.475781e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.789406e-06 │ │ │ Vprtstp: contraction number = 3.306741e-01 │ │ │ Vnewton: Using errtol_s: 4.028203 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.270885e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156877e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.488509e+00 │ │ │ Vprtstp: contraction number = 1.488509e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 9.276717e-07 │ │ │ Vprtstp: contraction number = 3.325696e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.872656e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.079459e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.927962e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.941860e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -23911,29 +23911,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.878772494899E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.134634520141E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066494761685E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.021400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.591400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.390296e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.173784e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:09:54 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 03:55:57 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -24203,151 +24203,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.304195 │ │ │ +Vacc_SASA: Time elapsed: 0.409339 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.993420e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.211059e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.985400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.441100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.464420e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.079967e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.386380e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.446403e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2075985.759525 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.807080e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.905327e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.676742e+05 │ │ │ Vprtstp: contraction number = 2.676742e+05 │ │ │ Vnewton: Attempting damping, relres = 0.123645 │ │ │ Vnewton: Attempting damping, relres = 0.555352 │ │ │ Vnewton: Damping accepted, relres = 0.123645 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.236446e-01 │ │ │ Vprtstp: contraction number = 1.236446e-01 │ │ │ Vnewton: Using errtol_s: 256684.416130 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.327680e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.689139e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.859973e+04 │ │ │ Vprtstp: contraction number = 4.859973e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.169836e-02 │ │ │ Vprtstp: contraction number = 1.754897e-01 │ │ │ Vnewton: Using errtol_s: 45045.483798 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.590938e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.771821e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.152870e+04 │ │ │ Vprtstp: contraction number = 1.152870e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.014779e-03 │ │ │ Vprtstp: contraction number = 2.311133e-01 │ │ │ Vnewton: Using errtol_s: 10410.609915 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.840266e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.773532e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.097422e+03 │ │ │ Vprtstp: contraction number = 3.097422e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.342870e-03 │ │ │ Vprtstp: contraction number = 2.677824e-01 │ │ │ Vnewton: Using errtol_s: 2787.778355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.102431e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.751487e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.793803e+02 │ │ │ Vprtstp: contraction number = 8.793803e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.812374e-04 │ │ │ Vprtstp: contraction number = 2.838975e-01 │ │ │ Vnewton: Using errtol_s: 791.443333 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.362151e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074789e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.566243e+02 │ │ │ Vprtstp: contraction number = 2.566243e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.112541e-04 │ │ │ Vprtstp: contraction number = 2.918238e-01 │ │ │ Vnewton: Using errtol_s: 230.962017 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.621662e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.272622e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.622598e+01 │ │ │ Vprtstp: contraction number = 7.622598e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.304618e-05 │ │ │ Vprtstp: contraction number = 2.970332e-01 │ │ │ Vnewton: Using errtol_s: 68.603390 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.870439e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.474015e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.294139e+01 │ │ │ Vprtstp: contraction number = 2.294139e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 9.945756e-06 │ │ │ Vprtstp: contraction number = 3.009654e-01 │ │ │ Vnewton: Using errtol_s: 20.647248 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.141643e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.684263e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.975781e+00 │ │ │ Vprtstp: contraction number = 6.975781e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.024203e-06 │ │ │ Vprtstp: contraction number = 3.040697e-01 │ │ │ Vnewton: Using errtol_s: 6.278203 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.403627e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.890301e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.139542e+00 │ │ │ Vprtstp: contraction number = 2.139542e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.275536e-07 │ │ │ Vprtstp: contraction number = 3.067101e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.755591e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.969893e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.055189e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.066981e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24357,15 +24357,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.936418090820E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.566271448852E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282618425876E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.510600e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.739800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ @@ -24414,160 +24414,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0114665 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.302119 │ │ │ +Vacc_SASA: Time elapsed: 0.435414 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.653760e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.316300e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.034100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.036400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.489180e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.130287e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.532645e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.106206e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2120327.174672 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.676175e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.131221e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.330788e+05 │ │ │ Vprtstp: contraction number = 3.330788e+05 │ │ │ Vnewton: Attempting damping, relres = 0.148670 │ │ │ Vnewton: Attempting damping, relres = 0.568259 │ │ │ Vnewton: Damping accepted, relres = 0.148670 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.486698e-01 │ │ │ Vprtstp: contraction number = 1.486698e-01 │ │ │ Vnewton: Using errtol_s: 315228.684259 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.007362e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.349415e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.641464e+04 │ │ │ Vprtstp: contraction number = 6.641464e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.878895e-02 │ │ │ Vprtstp: contraction number = 1.936435e-01 │ │ │ Vnewton: Using errtol_s: 61041.990934 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.257714e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.557993e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.670744e+04 │ │ │ Vprtstp: contraction number = 1.670744e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.105637e-03 │ │ │ Vprtstp: contraction number = 2.468182e-01 │ │ │ Vnewton: Using errtol_s: 15066.274957 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.520323e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.765168e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.686665e+03 │ │ │ Vprtstp: contraction number = 4.686665e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.989361e-03 │ │ │ Vprtstp: contraction number = 2.799694e-01 │ │ │ Vnewton: Using errtol_s: 4218.095910 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.769591e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.969348e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.389137e+03 │ │ │ Vprtstp: contraction number = 1.389137e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.896382e-04 │ │ │ Vprtstp: contraction number = 2.963958e-01 │ │ │ Vnewton: Using errtol_s: 1250.225849 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.083061e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.174083e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.253662e+02 │ │ │ Vprtstp: contraction number = 4.253662e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.805523e-04 │ │ │ Vprtstp: contraction number = 3.062086e-01 │ │ │ Vnewton: Using errtol_s: 382.829903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.341788e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.378033e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.333214e+02 │ │ │ Vprtstp: contraction number = 1.333214e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.659001e-05 │ │ │ Vprtstp: contraction number = 3.134273e-01 │ │ │ Vnewton: Using errtol_s: 119.989327 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.590965e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.598401e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.255612e+01 │ │ │ Vprtstp: contraction number = 4.255612e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.806349e-05 │ │ │ Vprtstp: contraction number = 3.191993e-01 │ │ │ Vnewton: Using errtol_s: 38.300511 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.852140e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.817865e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.379985e+01 │ │ │ Vprtstp: contraction number = 1.379985e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.857525e-06 │ │ │ Vprtstp: contraction number = 3.242742e-01 │ │ │ Vnewton: Using errtol_s: 12.419869 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.102553e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.050519e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.534043e+00 │ │ │ Vprtstp: contraction number = 4.534043e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.924533e-06 │ │ │ Vprtstp: contraction number = 3.285573e-01 │ │ │ Vnewton: Using errtol_s: 4.080639 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.362723e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.282184e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.505713e+00 │ │ │ Vprtstp: contraction number = 1.505713e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.391193e-07 │ │ │ Vprtstp: contraction number = 3.320906e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.019740e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.242071e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.380794e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.393540e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24577,15 +24577,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.924946278586E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.950886798741E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.474927636785E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.044400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.813200e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ @@ -24614,151 +24614,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.110843 │ │ │ +Vacc_SASA: Time elapsed: 0.204622 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.736680e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.933400e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.894000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.102400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.629700e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.099792e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.095829e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.520477e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 625058.556229 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.289931e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.546406e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.349434e+04 │ │ │ Vprtstp: contraction number = 8.349434e+04 │ │ │ Vnewton: Attempting damping, relres = 0.126666 │ │ │ Vnewton: Attempting damping, relres = 0.557380 │ │ │ Vnewton: Damping accepted, relres = 0.126666 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.266665e-01 │ │ │ Vprtstp: contraction number = 1.266665e-01 │ │ │ Vnewton: Using errtol_s: 79173.978566 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.610964e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.716230e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.587988e+04 │ │ │ Vprtstp: contraction number = 1.587988e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.298610e-02 │ │ │ Vprtstp: contraction number = 1.814695e-01 │ │ │ Vnewton: Using errtol_s: 14367.659528 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.860376e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.861981e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.689543e+03 │ │ │ Vprtstp: contraction number = 3.689543e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.312865e-03 │ │ │ Vprtstp: contraction number = 2.311338e-01 │ │ │ Vnewton: Using errtol_s: 3320.851989 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.011100e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.012801e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.505518e+02 │ │ │ Vprtstp: contraction number = 9.505518e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.368674e-03 │ │ │ Vprtstp: contraction number = 2.576150e-01 │ │ │ Vnewton: Using errtol_s: 855.501271 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.036154e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.166625e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.577170e+02 │ │ │ Vprtstp: contraction number = 2.577170e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.710781e-04 │ │ │ Vprtstp: contraction number = 2.711224e-01 │ │ │ Vnewton: Using errtol_s: 231.945545 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.061159e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.319055e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.185767e+01 │ │ │ Vprtstp: contraction number = 7.185767e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.034654e-04 │ │ │ Vprtstp: contraction number = 2.788237e-01 │ │ │ Vnewton: Using errtol_s: 64.671921 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086213e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.468054e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.042074e+01 │ │ │ Vprtstp: contraction number = 2.042074e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.940311e-05 │ │ │ Vprtstp: contraction number = 2.841831e-01 │ │ │ Vnewton: Using errtol_s: 18.378664 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111145e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.616637e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.893233e+00 │ │ │ Vprtstp: contraction number = 5.893233e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.485461e-06 │ │ │ Vprtstp: contraction number = 2.885906e-01 │ │ │ Vnewton: Using errtol_s: 5.303910 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.138873e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.764752e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.723486e+00 │ │ │ Vprtstp: contraction number = 1.723486e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.481587e-06 │ │ │ Vprtstp: contraction number = 2.924517e-01 │ │ │ Vnewton: Using errtol_s: 1.551137 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.163814e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.911591e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.097109e-01 │ │ │ Vprtstp: contraction number = 5.097109e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.339149e-07 │ │ │ Vprtstp: contraction number = 2.957442e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.732001e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.960947e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.518902e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.531026e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24768,17 +24768,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.817512164844E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.828431655726E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.412244339074E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.629200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.554500e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.7 │ │ │ Vpbe_ctor2: xkappa = 0.272439 │ │ │ @@ -24825,160 +24825,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.000971631 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.109014 │ │ │ +Vacc_SASA: Time elapsed: 0.156021 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.907590e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.212010e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.890800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.089700e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.435090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.090316e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238316e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.059615e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 648940.820048 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.253532e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.083573e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.033896e+05 │ │ │ Vprtstp: contraction number = 1.033896e+05 │ │ │ Vnewton: Attempting damping, relres = 0.149178 │ │ │ Vnewton: Attempting damping, relres = 0.569081 │ │ │ Vnewton: Damping accepted, relres = 0.149178 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.491779e-01 │ │ │ Vprtstp: contraction number = 1.491779e-01 │ │ │ Vnewton: Using errtol_s: 96807.596825 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.285839e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.258473e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.124753e+04 │ │ │ Vprtstp: contraction number = 2.124753e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.957488e-02 │ │ │ Vprtstp: contraction number = 1.982525e-01 │ │ │ Vnewton: Using errtol_s: 19192.349469 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.309638e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.416909e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.231045e+03 │ │ │ Vprtstp: contraction number = 5.231045e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.255435e-03 │ │ │ Vprtstp: contraction number = 2.453242e-01 │ │ │ Vnewton: Using errtol_s: 4708.348197 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.340778e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.573139e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.389072e+03 │ │ │ Vprtstp: contraction number = 1.389072e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.926494e-03 │ │ │ Vprtstp: contraction number = 2.655242e-01 │ │ │ Vnewton: Using errtol_s: 1250.180442 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.367021e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.728765e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.868439e+02 │ │ │ Vprtstp: contraction number = 3.868439e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.365061e-04 │ │ │ Vprtstp: contraction number = 2.784884e-01 │ │ │ Vnewton: Using errtol_s: 348.160728 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.392015e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.888082e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.111703e+02 │ │ │ Vprtstp: contraction number = 1.111703e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.541795e-04 │ │ │ Vprtstp: contraction number = 2.873769e-01 │ │ │ Vnewton: Using errtol_s: 100.053355 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.416883e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.052241e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.268464e+01 │ │ │ Vprtstp: contraction number = 3.268464e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.532954e-05 │ │ │ Vprtstp: contraction number = 2.940050e-01 │ │ │ Vnewton: Using errtol_s: 29.416189 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.441924e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.222384e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.798450e+00 │ │ │ Vprtstp: contraction number = 9.798450e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.358923e-05 │ │ │ Vprtstp: contraction number = 2.997875e-01 │ │ │ Vnewton: Using errtol_s: 8.818606 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.468313e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.396414e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.993247e+00 │ │ │ Vprtstp: contraction number = 2.993247e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.151261e-06 │ │ │ Vprtstp: contraction number = 3.054817e-01 │ │ │ Vnewton: Using errtol_s: 2.693923 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.493663e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.556040e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.296932e-01 │ │ │ Vprtstp: contraction number = 9.296932e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.289368e-06 │ │ │ Vprtstp: contraction number = 3.105968e-01 │ │ │ Vnewton: Using errtol_s: 0.836724 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.520077e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.718762e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.927772e-01 │ │ │ Vprtstp: contraction number = 2.927772e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.060455e-07 │ │ │ Vprtstp: contraction number = 3.149181e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.004286e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.215361e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.807592e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.819941e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -24988,17 +24988,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.808821595407E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.060972751461E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.028526891385E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.137500e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.314100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -25025,162 +25025,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.172020 │ │ │ +Vacc_SASA: Time elapsed: 0.322668 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.943640e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.282370e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.918600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.094950e-01 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.422700e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.192081e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.699753e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.906135e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1404398.831107 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.713778e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.931277e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.991752e+05 │ │ │ Vprtstp: contraction number = 1.991752e+05 │ │ │ Vnewton: Attempting damping, relres = 0.149937 │ │ │ Vnewton: Attempting damping, relres = 0.562289 │ │ │ Vnewton: Damping accepted, relres = 0.149937 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.499366e-01 │ │ │ Vprtstp: contraction number = 1.499366e-01 │ │ │ Vnewton: Using errtol_s: 210570.777586 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.748492e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.106456e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.724441e+04 │ │ │ Vprtstp: contraction number = 3.724441e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.631656e-02 │ │ │ Vprtstp: contraction number = 1.755180e-01 │ │ │ Vnewton: Using errtol_s: 36958.952617 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.774500e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.266931e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.392042e+03 │ │ │ Vprtstp: contraction number = 9.392042e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.102282e-03 │ │ │ Vprtstp: contraction number = 2.318799e-01 │ │ │ Vnewton: Using errtol_s: 8570.037199 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.799687e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.416878e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.643900e+03 │ │ │ Vprtstp: contraction number = 2.643900e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.694653e-03 │ │ │ Vprtstp: contraction number = 2.777081e-01 │ │ │ Vnewton: Using errtol_s: 2379.968912 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.824676e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.570504e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.795002e+02 │ │ │ Vprtstp: contraction number = 7.795002e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 4.995386e-04 │ │ │ Vprtstp: contraction number = 2.947734e-01 │ │ │ Vnewton: Using errtol_s: 701.551412 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.849669e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.720048e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.342462e+02 │ │ │ Vprtstp: contraction number = 2.342462e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.501153e-04 │ │ │ Vprtstp: contraction number = 3.005079e-01 │ │ │ Vnewton: Using errtol_s: 210.821708 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.874656e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.872127e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.102938e+01 │ │ │ Vprtstp: contraction number = 7.102938e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.551873e-05 │ │ │ Vprtstp: contraction number = 3.032252e-01 │ │ │ Vnewton: Using errtol_s: 63.926447 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.899630e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.028054e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.165701e+01 │ │ │ Vprtstp: contraction number = 2.165701e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.387876e-05 │ │ │ Vprtstp: contraction number = 3.049021e-01 │ │ │ Vnewton: Using errtol_s: 19.491311 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.924766e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.188158e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.627865e+00 │ │ │ Vprtstp: contraction number = 6.627865e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.247425e-06 │ │ │ Vprtstp: contraction number = 3.060378e-01 │ │ │ Vnewton: Using errtol_s: 5.965078 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.949505e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.345129e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.033869e+00 │ │ │ Vprtstp: contraction number = 2.033869e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.303392e-06 │ │ │ Vprtstp: contraction number = 3.068664e-01 │ │ │ Vnewton: Using errtol_s: 1.830482 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.974464e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.500168e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.254212e-01 │ │ │ Vprtstp: contraction number = 6.254212e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.007972e-07 │ │ │ Vprtstp: contraction number = 3.075032e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.939620e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.153435e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.736795e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.750115e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -25190,17 +25190,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.631424094606E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.872722745686E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.355776117184E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.236100e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.835800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.7 │ │ │ Vpbe_ctor2: xkappa = 0.272439 │ │ │ @@ -25247,160 +25247,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00130951 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.171906 │ │ │ +Vacc_SASA: Time elapsed: 0.269330 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.447300e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.793750e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.888400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.610400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.418770e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.119226e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.064539e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.664653e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1429289.662203 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.078734e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.690429e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.496624e+05 │ │ │ Vprtstp: contraction number = 2.496624e+05 │ │ │ Vnewton: Attempting damping, relres = 0.178955 │ │ │ Vnewton: Attempting damping, relres = 0.577343 │ │ │ Vnewton: Damping accepted, relres = 0.178955 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.789551e-01 │ │ │ Vprtstp: contraction number = 1.789551e-01 │ │ │ Vnewton: Using errtol_s: 255778.622825 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.112245e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.871962e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.096661e+04 │ │ │ Vprtstp: contraction number = 5.096661e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.449699e-02 │ │ │ Vprtstp: contraction number = 1.927690e-01 │ │ │ Vnewton: Using errtol_s: 49306.188432 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.136002e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004828e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.352983e+04 │ │ │ Vprtstp: contraction number = 1.352983e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.601027e-03 │ │ │ Vprtstp: contraction number = 2.493269e-01 │ │ │ Vnewton: Using errtol_s: 12293.359097 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.161014e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021345e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.990835e+03 │ │ │ Vprtstp: contraction number = 3.990835e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.513298e-03 │ │ │ Vprtstp: contraction number = 2.922090e-01 │ │ │ Vnewton: Using errtol_s: 3592.230783 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.185967e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038121e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.236351e+03 │ │ │ Vprtstp: contraction number = 1.236351e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.785110e-04 │ │ │ Vprtstp: contraction number = 3.097567e-01 │ │ │ Vnewton: Using errtol_s: 1112.717700 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.209790e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.054831e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.922762e+02 │ │ │ Vprtstp: contraction number = 3.922762e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.470100e-04 │ │ │ Vprtstp: contraction number = 3.172852e-01 │ │ │ Vnewton: Using errtol_s: 353.048870 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.234705e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.071943e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.263525e+02 │ │ │ Vprtstp: contraction number = 1.263525e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 7.956210e-05 │ │ │ Vprtstp: contraction number = 3.221007e-01 │ │ │ Vnewton: Using errtol_s: 113.717282 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.259974e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.091203e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.114546e+01 │ │ │ Vprtstp: contraction number = 4.114546e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.590862e-05 │ │ │ Vprtstp: contraction number = 3.256402e-01 │ │ │ Vnewton: Using errtol_s: 37.030918 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.284946e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111021e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.351428e+01 │ │ │ Vprtstp: contraction number = 1.351428e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 8.509716e-06 │ │ │ Vprtstp: contraction number = 3.284512e-01 │ │ │ Vnewton: Using errtol_s: 12.162848 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.309885e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.130336e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.469783e+00 │ │ │ Vprtstp: contraction number = 4.469783e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.814548e-06 │ │ │ Vprtstp: contraction number = 3.307453e-01 │ │ │ Vnewton: Using errtol_s: 4.022804 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.334894e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.147584e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.486721e+00 │ │ │ Vprtstp: contraction number = 1.486721e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 9.361638e-07 │ │ │ Vprtstp: contraction number = 3.326161e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.886642e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.100441e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.966946e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.979214e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -25410,29 +25410,29 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.621321814807E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.134461409198E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066448263473E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.033000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.467300e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.453475e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.164930e+03 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:10:06 2020 │ │ │ +# Creation Date and Time: Tue Oct 19 04:20:41 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ @@ -25702,151 +25702,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.312119 │ │ │ +Vacc_SASA: Time elapsed: 0.476348 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.134220e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.260981e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.890700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.249800e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.589030e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.072690e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.686610e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.512236e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2063009.659222 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085338e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.077217e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.658306e+05 │ │ │ Vprtstp: contraction number = 2.658306e+05 │ │ │ Vnewton: Attempting damping, relres = 0.122739 │ │ │ Vnewton: Attempting damping, relres = 0.555235 │ │ │ Vnewton: Damping accepted, relres = 0.122739 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.227391e-01 │ │ │ Vprtstp: contraction number = 1.227391e-01 │ │ │ Vnewton: Using errtol_s: 253211.880914 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.471510e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.040327e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.831485e+04 │ │ │ Vprtstp: contraction number = 4.831485e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.156033e-02 │ │ │ Vprtstp: contraction number = 1.756599e-01 │ │ │ Vnewton: Using errtol_s: 44479.169236 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.762557e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.363383e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.148001e+04 │ │ │ Vprtstp: contraction number = 1.148001e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.018325e-03 │ │ │ Vprtstp: contraction number = 2.327573e-01 │ │ │ Vnewton: Using errtol_s: 10352.852780 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.054204e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.457174e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.090763e+03 │ │ │ Vprtstp: contraction number = 3.090763e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.348386e-03 │ │ │ Vprtstp: contraction number = 2.686924e-01 │ │ │ Vnewton: Using errtol_s: 2781.733245 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.347598e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.534964e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.782780e+02 │ │ │ Vprtstp: contraction number = 8.782780e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.831544e-04 │ │ │ Vprtstp: contraction number = 2.841578e-01 │ │ │ Vnewton: Using errtol_s: 790.451228 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.586910e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.159492e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.564053e+02 │ │ │ Vprtstp: contraction number = 2.564053e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.118584e-04 │ │ │ Vprtstp: contraction number = 2.919407e-01 │ │ │ Vnewton: Using errtol_s: 230.764871 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.838119e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.362454e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.617617e+01 │ │ │ Vprtstp: contraction number = 7.617617e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 3.323230e-05 │ │ │ Vprtstp: contraction number = 2.970927e-01 │ │ │ Vnewton: Using errtol_s: 68.558559 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.113026e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.571623e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.292888e+01 │ │ │ Vprtstp: contraction number = 2.292888e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.000286e-05 │ │ │ Vprtstp: contraction number = 3.009981e-01 │ │ │ Vnewton: Using errtol_s: 20.635996 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.422944e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.796023e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.972403e+00 │ │ │ Vprtstp: contraction number = 6.972403e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 3.041752e-06 │ │ │ Vprtstp: contraction number = 3.040882e-01 │ │ │ Vnewton: Using errtol_s: 6.275163 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.673405e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.043859e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.138578e+00 │ │ │ Vprtstp: contraction number = 2.138578e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 9.329670e-07 │ │ │ Vprtstp: contraction number = 3.067203e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.018877e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.250539e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.220066e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.232072e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -25856,17 +25856,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.808172570835E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.566165331536E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.282584652691E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.085800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.179700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.8 │ │ │ Vpbe_ctor2: xkappa = 0.29125 │ │ │ @@ -25913,160 +25913,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.0106595 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.302237 │ │ │ +Vacc_SASA: Time elapsed: 0.479036 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.156470e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.199158e+00 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.898100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.555100e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.442830e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.136564e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.870818e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.270277e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 2106967.008420 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.012211e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.293903e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.308151e+05 │ │ │ Vprtstp: contraction number = 3.308151e+05 │ │ │ Vnewton: Attempting damping, relres = 0.147795 │ │ │ Vnewton: Attempting damping, relres = 0.568147 │ │ │ Vnewton: Damping accepted, relres = 0.147795 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.477951e-01 │ │ │ Vprtstp: contraction number = 1.477951e-01 │ │ │ Vnewton: Using errtol_s: 311399.390533 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.346555e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.520197e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.599748e+04 │ │ │ Vprtstp: contraction number = 6.599748e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.864948e-02 │ │ │ Vprtstp: contraction number = 1.938459e-01 │ │ │ Vnewton: Using errtol_s: 60363.499136 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.596764e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.722685e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.661676e+04 │ │ │ Vprtstp: contraction number = 1.661676e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.106188e-03 │ │ │ Vprtstp: contraction number = 2.480390e-01 │ │ │ Vnewton: Using errtol_s: 14972.503442 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.846982e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.930396e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.669116e+03 │ │ │ Vprtstp: contraction number = 4.669116e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.994461e-03 │ │ │ Vprtstp: contraction number = 2.806653e-01 │ │ │ Vnewton: Using errtol_s: 4202.262595 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.109541e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.144088e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.385353e+03 │ │ │ Vprtstp: contraction number = 1.385353e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.917609e-04 │ │ │ Vprtstp: contraction number = 2.967022e-01 │ │ │ Vnewton: Using errtol_s: 1246.820661 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.360228e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.384683e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.244924e+02 │ │ │ Vprtstp: contraction number = 4.244924e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.813239e-04 │ │ │ Vprtstp: contraction number = 3.064141e-01 │ │ │ Vnewton: Using errtol_s: 382.043458 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.643671e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.630431e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.331120e+02 │ │ │ Vprtstp: contraction number = 1.331120e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.685939e-05 │ │ │ Vprtstp: contraction number = 3.135792e-01 │ │ │ Vnewton: Using errtol_s: 119.800865 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.893892e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.863157e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.250410e+01 │ │ │ Vprtstp: contraction number = 4.250410e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.815581e-05 │ │ │ Vprtstp: contraction number = 3.193107e-01 │ │ │ Vnewton: Using errtol_s: 38.253693 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.143956e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.085018e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.378625e+01 │ │ │ Vprtstp: contraction number = 1.378625e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 5.888858e-06 │ │ │ Vprtstp: contraction number = 3.243511e-01 │ │ │ Vnewton: Using errtol_s: 12.407629 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.392765e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.300262e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.530276e+00 │ │ │ Vprtstp: contraction number = 4.530276e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.935127e-06 │ │ │ Vprtstp: contraction number = 3.286082e-01 │ │ │ Vnewton: Using errtol_s: 4.077249 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.643116e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.527701e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.504596e+00 │ │ │ Vprtstp: contraction number = 1.504596e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.426945e-07 │ │ │ Vprtstp: contraction number = 3.321201e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.968887e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.187017e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.462295e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.474686e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -26076,17 +26076,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 4.796939220773E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.950780776080E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.474893902492E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.027200e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.388100e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -26113,151 +26113,151 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.107003 │ │ │ +Vacc_SASA: Time elapsed: 0.236009 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.555780e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.004950e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.901300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 6.863200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.447090e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.258690e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.318792e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.771905e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 622184.484743 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.462124e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.797653e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 8.301310e+04 │ │ │ Vprtstp: contraction number = 8.301310e+04 │ │ │ Vnewton: Attempting damping, relres = 0.126177 │ │ │ Vnewton: Attempting damping, relres = 0.557265 │ │ │ Vnewton: Damping accepted, relres = 0.126177 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.261770e-01 │ │ │ Vprtstp: contraction number = 1.261770e-01 │ │ │ Vnewton: Using errtol_s: 78505.344097 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.797098e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.971571e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.580629e+04 │ │ │ Vprtstp: contraction number = 1.580629e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.296474e-02 │ │ │ Vprtstp: contraction number = 1.820042e-01 │ │ │ Vnewton: Using errtol_s: 14288.305999 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004744e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.127052e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.679149e+03 │ │ │ Vprtstp: contraction number = 3.679149e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 5.322303e-03 │ │ │ Vprtstp: contraction number = 2.317597e-01 │ │ │ Vnewton: Using errtol_s: 3311.454085 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031318e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.279888e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.489453e+02 │ │ │ Vprtstp: contraction number = 9.489453e+02 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.372672e-03 │ │ │ Vprtstp: contraction number = 2.579095e-01 │ │ │ Vnewton: Using errtol_s: 854.055318 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056324e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.433557e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.574445e+02 │ │ │ Vprtstp: contraction number = 2.574445e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 3.723980e-04 │ │ │ Vprtstp: contraction number = 2.712942e-01 │ │ │ Vnewton: Using errtol_s: 231.700267 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082599e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.594219e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.180833e+01 │ │ │ Vprtstp: contraction number = 7.180833e+01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.038719e-04 │ │ │ Vprtstp: contraction number = 2.789272e-01 │ │ │ Vnewton: Using errtol_s: 64.627514 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107550e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.752259e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.041084e+01 │ │ │ Vprtstp: contraction number = 2.041084e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.952461e-05 │ │ │ Vprtstp: contraction number = 2.842404e-01 │ │ │ Vnewton: Using errtol_s: 18.369753 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.132578e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.909184e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.891035e+00 │ │ │ Vprtstp: contraction number = 5.891035e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 8.521479e-06 │ │ │ Vprtstp: contraction number = 2.886229e-01 │ │ │ Vnewton: Using errtol_s: 5.301932 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158556e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.056450e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.722947e+00 │ │ │ Vprtstp: contraction number = 1.722947e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 2.492271e-06 │ │ │ Vprtstp: contraction number = 2.924694e-01 │ │ │ Vnewton: Using errtol_s: 1.550653 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183507e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.205401e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.095658e-01 │ │ │ Vprtstp: contraction number = 5.095658e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 7.370953e-07 │ │ │ Vprtstp: contraction number = 2.957524e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.708351e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.920139e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.566173e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.579707e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -26267,17 +26267,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.805001041922E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 6.827988101886E+03 kT │ │ │ Vpmg_energy: dielEnergy = 3.412047294485E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.199000e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.802800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ Vpbe_ctor2: bulk ionic strength = 0.8 │ │ │ Vpbe_ctor2: xkappa = 0.29125 │ │ │ @@ -26324,160 +26324,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.000791536 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.108000 │ │ │ +Vacc_SASA: Time elapsed: 0.144524 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.918060e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.149480e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 5.018800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.112600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.448540e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.156430e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.258861e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.359035e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 645906.037357 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.272371e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.385394e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.027473e+05 │ │ │ Vprtstp: contraction number = 1.027473e+05 │ │ │ Vnewton: Attempting damping, relres = 0.148634 │ │ │ Vnewton: Attempting damping, relres = 0.568930 │ │ │ Vnewton: Damping accepted, relres = 0.148634 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.486339e-01 │ │ │ Vprtstp: contraction number = 1.486339e-01 │ │ │ Vnewton: Using errtol_s: 96003.523693 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305903e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.555567e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.112857e+04 │ │ │ Vprtstp: contraction number = 2.112857e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.952923e-02 │ │ │ Vprtstp: contraction number = 1.986709e-01 │ │ │ Vnewton: Using errtol_s: 19073.107408 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329624e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.709966e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.206787e+03 │ │ │ Vprtstp: contraction number = 5.206787e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 7.255653e-03 │ │ │ Vprtstp: contraction number = 2.457109e-01 │ │ │ Vnewton: Using errtol_s: 4686.469778 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.354646e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.867641e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.383944e+03 │ │ │ Vprtstp: contraction number = 1.383944e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.928400e-03 │ │ │ Vprtstp: contraction number = 2.657790e-01 │ │ │ Vnewton: Using errtol_s: 1245.565289 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.379743e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.023195e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.857274e+02 │ │ │ Vprtstp: contraction number = 3.857274e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.374712e-04 │ │ │ Vprtstp: contraction number = 2.787135e-01 │ │ │ Vnewton: Using errtol_s: 347.155903 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.403517e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.191201e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.109221e+02 │ │ │ Vprtstp: contraction number = 1.109221e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.545581e-04 │ │ │ Vprtstp: contraction number = 2.875654e-01 │ │ │ Vnewton: Using errtol_s: 99.830021 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.428499e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.363981e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.262844e+01 │ │ │ Vprtstp: contraction number = 3.262844e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.546421e-05 │ │ │ Vprtstp: contraction number = 2.941561e-01 │ │ │ Vnewton: Using errtol_s: 29.365605 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452271e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.557055e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.785490e+00 │ │ │ Vprtstp: contraction number = 9.785490e+00 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.363502e-05 │ │ │ Vprtstp: contraction number = 2.999067e-01 │ │ │ Vnewton: Using errtol_s: 8.806942 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.477189e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.749291e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.990197e+00 │ │ │ Vprtstp: contraction number = 2.990197e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.166516e-06 │ │ │ Vprtstp: contraction number = 3.055746e-01 │ │ │ Vnewton: Using errtol_s: 2.691178 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.502191e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.920185e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.289503e-01 │ │ │ Vprtstp: contraction number = 9.289503e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.294392e-06 │ │ │ Vprtstp: contraction number = 3.106652e-01 │ │ │ Vnewton: Using errtol_s: 0.836055 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.525977e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.079284e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.925887e-01 │ │ │ Vprtstp: contraction number = 2.925887e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.076906e-07 │ │ │ Vprtstp: contraction number = 3.149670e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.865843e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.085791e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.858220e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.871220e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -26487,17 +26487,17 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 1.796314557167E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 8.060531082527E+03 kT │ │ │ Vpmg_energy: dielEnergy = 4.028330665485E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.177800e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.235700e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ @@ -26524,162 +26524,162 @@ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.177203 │ │ │ +Vacc_SASA: Time elapsed: 0.269313 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.017830e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.483820e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.981900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.172400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.440940e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.088559e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.709582e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.252773e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1394036.370554 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.723793e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.277185e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.976078e+05 │ │ │ Vprtstp: contraction number = 1.976078e+05 │ │ │ Vnewton: Attempting damping, relres = 0.147111 │ │ │ Vnewton: Attempting damping, relres = 0.562025 │ │ │ Vnewton: Damping accepted, relres = 0.147111 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.471110e-01 │ │ │ Vprtstp: contraction number = 1.471110e-01 │ │ │ Vnewton: Using errtol_s: 205078.018083 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.758755e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.442535e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.691787e+04 │ │ │ Vprtstp: contraction number = 3.691787e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 2.570682e-02 │ │ │ Vprtstp: contraction number = 1.747444e-01 │ │ │ Vnewton: Using errtol_s: 35836.239165 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.783690e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.601236e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 9.313783e+03 │ │ │ Vprtstp: contraction number = 9.313783e+03 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 6.063883e-03 │ │ │ Vprtstp: contraction number = 2.358862e-01 │ │ │ Vnewton: Using errtol_s: 8453.273025 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.808650e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.754751e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.633660e+03 │ │ │ Vprtstp: contraction number = 2.633660e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 1.700470e-03 │ │ │ Vprtstp: contraction number = 2.804259e-01 │ │ │ Vnewton: Using errtol_s: 2370.516473 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.832381e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.912695e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.779603e+02 │ │ │ Vprtstp: contraction number = 7.779603e+02 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 5.022576e-04 │ │ │ Vprtstp: contraction number = 2.953640e-01 │ │ │ Vnewton: Using errtol_s: 700.165343 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.857421e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.063269e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.339032e+02 │ │ │ Vprtstp: contraction number = 2.339032e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.510097e-04 │ │ │ Vprtstp: contraction number = 3.006618e-01 │ │ │ Vnewton: Using errtol_s: 210.512957 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.882412e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.219339e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 7.094002e+01 │ │ │ Vprtstp: contraction number = 7.094002e+01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 4.579940e-05 │ │ │ Vprtstp: contraction number = 3.032879e-01 │ │ │ Vnewton: Using errtol_s: 63.846030 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.906168e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.378097e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.163184e+01 │ │ │ Vprtstp: contraction number = 2.163184e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 1.396567e-05 │ │ │ Vprtstp: contraction number = 3.049313e-01 │ │ │ Vnewton: Using errtol_s: 19.468652 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.931153e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.533121e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.620444e+00 │ │ │ Vprtstp: contraction number = 6.620444e+00 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 4.274207e-06 │ │ │ Vprtstp: contraction number = 3.060510e-01 │ │ │ Vnewton: Using errtol_s: 5.958400 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.956170e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.687884e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.031637e+00 │ │ │ Vprtstp: contraction number = 2.031637e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 1.311640e-06 │ │ │ Vprtstp: contraction number = 3.068733e-01 │ │ │ Vnewton: Using errtol_s: 1.828474 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.979859e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.841012e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 6.247427e-01 │ │ │ Vprtstp: contraction number = 6.247427e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 4.033384e-07 │ │ │ Vprtstp: contraction number = 3.075070e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.914607e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.125961e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.732641e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.744722e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -26689,15 +26689,15 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.410814502422E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 1.872576445438E+04 kT │ │ │ Vpmg_energy: dielEnergy = 9.355379703968E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.112400e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.006600e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ @@ -26746,160 +26746,160 @@ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ VPMG::extEnergy: extDiEnergy = 0.00110224 kT │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.173118 │ │ │ +Vacc_SASA: Time elapsed: 0.255850 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.604050e-01 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.392910e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 4.908400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.150200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.433700e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.061810e+00 │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.073154e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000774e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vnewton: Damping enabled │ │ │ Vnewton: Using errtol_s: 1418623.682815 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.087684e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003364e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.477376e+05 │ │ │ Vprtstp: contraction number = 2.477376e+05 │ │ │ Vnewton: Attempting damping, relres = 0.176231 │ │ │ Vnewton: Attempting damping, relres = 0.577102 │ │ │ Vnewton: Damping accepted, relres = 0.176231 │ │ │ Vnewton: Damping disabled │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.762312e-01 │ │ │ Vprtstp: contraction number = 1.762312e-01 │ │ │ Vnewton: Using errtol_s: 250005.771686 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.119876e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021472e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 5.052668e+04 │ │ │ Vprtstp: contraction number = 5.052668e+04 │ │ │ Vprtstp: iteration = 2 │ │ │ Vprtstp: relative residual = 3.389791e-02 │ │ │ Vprtstp: contraction number = 1.923491e-01 │ │ │ Vnewton: Using errtol_s: 48088.378660 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.144902e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039413e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.341451e+04 │ │ │ Vprtstp: contraction number = 1.341451e+04 │ │ │ Vprtstp: iteration = 3 │ │ │ Vprtstp: relative residual = 8.561128e-03 │ │ │ Vprtstp: contraction number = 2.525562e-01 │ │ │ Vnewton: Using errtol_s: 12145.019085 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.169952e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056694e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.971688e+03 │ │ │ Vprtstp: contraction number = 3.971688e+03 │ │ │ Vprtstp: iteration = 4 │ │ │ Vprtstp: relative residual = 2.519877e-03 │ │ │ Vprtstp: contraction number = 2.943394e-01 │ │ │ Vnewton: Using errtol_s: 3574.757814 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.194922e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073184e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.232605e+03 │ │ │ Vprtstp: contraction number = 1.232605e+03 │ │ │ Vprtstp: iteration = 5 │ │ │ Vprtstp: relative residual = 7.819875e-04 │ │ │ Vprtstp: contraction number = 3.103276e-01 │ │ │ Vnewton: Using errtol_s: 1109.346049 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.218736e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090239e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 3.914134e+02 │ │ │ Vprtstp: contraction number = 3.914134e+02 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 2.483197e-04 │ │ │ Vprtstp: contraction number = 3.175495e-01 │ │ │ Vnewton: Using errtol_s: 352.272271 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.243697e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.106774e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.261412e+02 │ │ │ Vprtstp: contraction number = 1.261412e+02 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 8.002626e-05 │ │ │ Vprtstp: contraction number = 3.222710e-01 │ │ │ Vnewton: Using errtol_s: 113.527152 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.268752e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123361e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.109151e+01 │ │ │ Vprtstp: contraction number = 4.109151e+01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 2.606919e-05 │ │ │ Vprtstp: contraction number = 3.257579e-01 │ │ │ Vnewton: Using errtol_s: 36.982365 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.293702e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.139722e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.349979e+01 │ │ │ Vprtstp: contraction number = 1.349979e+01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 8.564509e-06 │ │ │ Vprtstp: contraction number = 3.285300e-01 │ │ │ Vnewton: Using errtol_s: 12.149816 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.317451e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156967e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 4.465689e+00 │ │ │ Vprtstp: contraction number = 4.465689e+00 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.833112e-06 │ │ │ Vprtstp: contraction number = 3.307968e-01 │ │ │ Vnewton: Using errtol_s: 4.019120 │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.342458e+01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174329e+03 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.485509e+00 │ │ │ Vprtstp: contraction number = 1.485509e+00 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 9.424331e-07 │ │ │ Vprtstp: contraction number = 3.326494e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.887573e+00 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.095760e+00 │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.898917e+02 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.910816e+02 │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ @@ -26909,19 +26909,19 @@ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ Vpmg_energy: qmEnergy = 6.400773657781E+00 kT │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ Vpmg_energy: qfEnergy = 2.134315194179E+04 kT │ │ │ Vpmg_energy: dielEnergy = 1.066408609760E+04 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.090300e-02 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.379900e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.462570e+01 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.192394e+03 │ │ ├── ./usr/share/apbs/examples/solv/io.mc │ │ │ @@ -1,10 +1,10 @@ │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:47 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 20:57:00 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path methanol.pqr │ │ │ @@ -245,32 +245,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000421 │ │ │ +Vacc_SASA: Time elapsed: 0.000987 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.837000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.688690e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.170900e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.722200e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.195500e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.214006e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060670e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.578442e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.930795e-01 │ │ │ Vprtstp: contraction number = 2.930795e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -299,32 +299,32 @@ │ │ │ Vprtstp: contraction number = 3.064107e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 2.158998e-06 │ │ │ Vprtstp: contraction number = 3.114698e-01 │ │ │ Vprtstp: iteration = 11 │ │ │ Vprtstp: relative residual = 6.836605e-07 │ │ │ Vprtstp: contraction number = 3.166565e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.589220e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.375280e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.230364e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.453608e+01 │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.481476875907E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.190000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 2.83039 │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.8153 │ │ │ Vpbe_ctor2: solute charge = 5.55112e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -345,32 +345,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000380 │ │ │ +Vacc_SASA: Time elapsed: 0.001352 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.165300e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.168320e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.188300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.030000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.606600e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.307439e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.791340e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.756206e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.518468e-01 │ │ │ Vprtstp: contraction number = 1.518468e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -387,32 +387,32 @@ │ │ │ Vprtstp: contraction number = 1.057725e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.782567e-06 │ │ │ Vprtstp: contraction number = 1.074900e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.936135e-07 │ │ │ Vprtstp: contraction number = 1.086150e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.869350e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.729900e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.761243e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.992830e+01 │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.510541428496E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.280000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -433,32 +433,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000249 │ │ │ +Vacc_SASA: Time elapsed: 0.004266 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.818500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.246960e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 7.613000e-03 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.273000e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.996700e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.303356e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067365e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.803620e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.228747e-01 │ │ │ Vprtstp: contraction number = 1.228747e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -484,32 +484,32 @@ │ │ │ Vprtstp: contraction number = 3.196112e-01 │ │ │ Vprtstp: iteration = 9 │ │ │ Vprtstp: relative residual = 1.915327e-06 │ │ │ Vprtstp: contraction number = 3.214910e-01 │ │ │ Vprtstp: iteration = 10 │ │ │ Vprtstp: relative residual = 6.179105e-07 │ │ │ Vprtstp: contraction number = 3.226135e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.119880e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.801060e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.148140e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.396715e+01 │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.191047608004E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.700000e-05 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -530,32 +530,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000244 │ │ │ +Vacc_SASA: Time elapsed: 0.001016 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.201700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.261520e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 7.744000e-03 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.382400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.164800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.283430e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.572989e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.220837e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.134958e-01 │ │ │ Vprtstp: contraction number = 1.134958e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -572,42 +572,42 @@ │ │ │ Vprtstp: contraction number = 1.069805e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.498256e-06 │ │ │ Vprtstp: contraction number = 1.078455e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.625625e-07 │ │ │ Vprtstp: contraction number = 1.085012e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.860910e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.676050e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.762336e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.983264e+01 │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.504084363930E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.871286e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.497680e+02 │ │ │ ############################################################################## │ │ │ # MC-shell I/O capture file. │ │ │ -# Creation Date and Time: Thu Jul 23 11:06:48 2020 │ │ │ +# Creation Date and Time: Mon Oct 18 21:00:12 2021 │ │ │ │ │ │ ############################################################################## │ │ │ Hello world from PE 0 │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ NOsh: Parsing READ section │ │ │ NOsh: Storing molecule 0 path methanol.pqr │ │ │ @@ -848,32 +848,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000422 │ │ │ +Vacc_SASA: Time elapsed: 0.000630 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.458100e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.606040e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.239300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.350400e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.401400e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.204787e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.856870e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.669978e+00 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 2.392714e-01 │ │ │ Vprtstp: contraction number = 2.392714e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -893,32 +893,32 @@ │ │ │ Vprtstp: contraction number = 1.556589e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 2.217054e-06 │ │ │ Vprtstp: contraction number = 1.639311e-01 │ │ │ Vprtstp: iteration = 8 │ │ │ Vprtstp: relative residual = 3.821154e-07 │ │ │ Vprtstp: contraction number = 1.723528e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.396730e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.226480e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.357563e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.576025e+01 │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.481634746029E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.380000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 2.83039 │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.8153 │ │ │ Vpbe_ctor2: solute charge = 5.55112e-17 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -939,32 +939,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000383 │ │ │ +Vacc_SASA: Time elapsed: 0.003118 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.046700e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.755320e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.090300e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.536600e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.727100e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.239200e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.654400e-01 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.892050e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.514442e-01 │ │ │ Vprtstp: contraction number = 1.514442e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -981,32 +981,32 @@ │ │ │ Vprtstp: contraction number = 1.045560e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.694780e-06 │ │ │ Vprtstp: contraction number = 1.061179e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.817099e-07 │ │ │ Vprtstp: contraction number = 1.072174e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.847930e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.637860e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.840031e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.068784e+01 │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 1.511763544580E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.477800e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1027,32 +1027,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000276 │ │ │ +Vacc_SASA: Time elapsed: 0.000793 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.318500e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.934930e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 7.831000e-03 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.947900e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.566800e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.196258e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121341e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.002817e+01 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.159916e-01 │ │ │ Vprtstp: contraction number = 1.159916e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1069,32 +1069,32 @@ │ │ │ Vprtstp: contraction number = 1.378576e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 3.539643e-06 │ │ │ Vprtstp: contraction number = 1.515814e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 5.760895e-07 │ │ │ Vprtstp: contraction number = 1.627536e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.817690e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.445410e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.835916e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.053957e+01 │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.192183682119E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.200000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.339400e-02 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ Setting up PBE object... │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ @@ -1115,32 +1115,32 @@ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ Setting PDE center to local center... │ │ │ Vpmg_fillco: filling in source term. │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ Vpmg_fillco: filling in source term. │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ -Vacc_SASA: Time elapsed: 0.000245 │ │ │ +Vacc_SASA: Time elapsed: 0.003093 │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.789000e-02 │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.855440e-01 │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 8.247000e-03 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.505300e-02 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 4.548000e-02 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.378180e+00 │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.537460e+00 │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.011544e+02 │ │ │ Vprtstp: iteration = 0 │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ Vprtstp: iteration = 1 │ │ │ Vprtstp: relative residual = 1.128724e-01 │ │ │ Vprtstp: contraction number = 1.128724e-01 │ │ │ Vprtstp: iteration = 2 │ │ │ @@ -1157,32 +1157,32 @@ │ │ │ Vprtstp: contraction number = 1.067766e-01 │ │ │ Vprtstp: iteration = 6 │ │ │ Vprtstp: relative residual = 1.477665e-06 │ │ │ Vprtstp: contraction number = 1.075719e-01 │ │ │ Vprtstp: iteration = 7 │ │ │ Vprtstp: relative residual = 1.598211e-07 │ │ │ Vprtstp: contraction number = 1.081578e-01 │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.924020e-01 │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.540520e-01 │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.822130e+01 │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.060381e+01 │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ Vpmg_energy: qfEnergy = 2.505883286802E+03 kT │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-05 │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.140000e-04 │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ printEnergy: Performing global reduction (sum) │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.834330e+00 │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.294399e+02