--- /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 residua