############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 18 15:26:00 2014 ############################################################################## 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 piplc_hsp82_bound_to_pcpg_80_20_allh33.23.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb33.23.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 79.517) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 28.308) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 79.517) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 23.463) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 51.49) Valist_readPDB: Counted 29844 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 23.463) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 0.281) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.571529 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.340219 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595278 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 156.331 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.7145 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.517 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 104.517 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.571529 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.340219 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595278 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 156.331 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.7145 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.517 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 104.517 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.571529 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.340219 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595278 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.308 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 156.331 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.7145 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.517 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 104.517 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 80.5855 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 105.04 Vpbe_ctor2: solute charge = -58.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 116.746) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13455509 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... 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 = 7.400000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.300000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.366000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087900e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.199735e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.636000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.582780e+06 PMG: contraction number = , 4.582780e+06 NEWTON: attempting damping, relres = 1.128657e-01 NEWTON: attempting damping, relres = 5.470355e-01 NEWTON: damping accepted, relres = 1.128657e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.128657e-01 PMG: contraction number = 1.128657e-01 NEWTON: using errtol_s: 4.740062e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.780100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.316590e+05 PMG: contraction number = , 6.316590e+05 PMG: iteration = 2 PMG: relative residual = 1.720569e-02 PMG: contraction number = 1.524439e-01 NEWTON: using errtol_s: 7.225933e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.529600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.225054e+05 PMG: contraction number = , 1.225054e+05 PMG: iteration = 3 PMG: relative residual = 3.419945e-03 PMG: contraction number = 1.987683e-01 NEWTON: using errtol_s: 1.436287e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.379000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.910783e+04 PMG: contraction number = , 2.910783e+04 PMG: iteration = 4 PMG: relative residual = 7.901443e-04 PMG: contraction number = 2.310400e-01 NEWTON: using errtol_s: 3.318397e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.135100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.152051e+03 PMG: contraction number = , 8.152051e+03 PMG: iteration = 5 PMG: relative residual = 2.032219e-04 PMG: contraction number = 2.571959e-01 NEWTON: using errtol_s: 8.534781e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.985100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.487492e+03 PMG: contraction number = , 2.487492e+03 PMG: iteration = 6 PMG: relative residual = 5.629301e-05 PMG: contraction number = 2.770027e-01 NEWTON: using errtol_s: 2.364157e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.764900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.679782e+02 PMG: contraction number = , 7.679782e+02 PMG: iteration = 7 PMG: relative residual = 1.652744e-05 PMG: contraction number = 2.935967e-01 NEWTON: using errtol_s: 6.941088e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.528700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.428411e+02 PMG: contraction number = , 2.428411e+02 PMG: iteration = 8 PMG: relative residual = 5.204882e-06 PMG: contraction number = 3.149236e-01 NEWTON: using errtol_s: 2.185913e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.354700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.011790e+02 PMG: contraction number = , 1.011790e+02 PMG: iteration = 9 PMG: relative residual = 2.168324e-06 PMG: contraction number = 4.165942e-01 NEWTON: using errtol_s: 9.106387e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.144500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.827717e+01 PMG: contraction number = , 4.827717e+01 PMG: iteration = 10 PMG: relative residual = 1.034589e-06 PMG: contraction number = 4.771376e-01 NEWTON: using errtol_s: 4.344999e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.902500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.404648e+01 PMG: contraction number = , 2.404648e+01 PMG: iteration = 11 PMG: relative residual = 5.153200e-07 PMG: contraction number = 4.980917e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.317800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.653400e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.7145) Vpmg_setPart: upper corner = (141.283, 130.313, 156.331) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.7145) Vpmg_setPart: actual maxima = (141.283, 130.313, 156.331) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.819506792726E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.006174487340E+06 kT Vpmg_energy: dielEnergy = 5.030413461584E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.314000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 80.5855 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 105.04 Vpbe_ctor2: solute charge = -58.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 116.746) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13455509 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.517 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.7145 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 156.331 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.517) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.7145) Vpmg_setPart: actual maxima = (141.283, 130.313, 156.331) 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 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 104.517) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.7145) VPMG::extEnergy Old upper corner = (141.283, 130.313, 156.331) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0148592 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.018206 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.254800e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.560000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.987000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.231540e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.524741e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.875236e+06 PMG: contraction number = , 7.875236e+06 NEWTON: attempting damping, relres = 1.744396e-01 NEWTON: attempting damping, relres = 5.785902e-01 NEWTON: damping accepted, relres = 1.744396e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.744396e-01 PMG: contraction number = 1.744396e-01 NEWTON: using errtol_s: 7.892939e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.401380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.062520e+06 PMG: contraction number = , 1.062520e+06 PMG: iteration = 2 PMG: relative residual = 2.606053e-02 PMG: contraction number = 1.493957e-01 NEWTON: using errtol_s: 1.179171e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.481570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.891391e+05 PMG: contraction number = , 1.891391e+05 PMG: iteration = 3 PMG: relative residual = 5.017418e-03 PMG: contraction number = 1.925294e-01 NEWTON: using errtol_s: 2.270252e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.560520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.292216e+04 PMG: contraction number = , 4.292216e+04 PMG: iteration = 4 PMG: relative residual = 1.192601e-03 PMG: contraction number = 2.376922e-01 NEWTON: using errtol_s: 5.396210e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.642160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.201259e+04 PMG: contraction number = , 1.201259e+04 PMG: iteration = 5 PMG: relative residual = 3.260376e-04 PMG: contraction number = 2.733836e-01 NEWTON: using errtol_s: 1.475236e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.718380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.131954e+03 PMG: contraction number = , 4.131954e+03 PMG: iteration = 6 PMG: relative residual = 9.611467e-05 PMG: contraction number = 2.947963e-01 NEWTON: using errtol_s: 4.348940e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.806920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.333695e+03 PMG: contraction number = , 1.333695e+03 PMG: iteration = 7 PMG: relative residual = 2.708583e-05 PMG: contraction number = 2.818075e-01 NEWTON: using errtol_s: 1.225564e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.885680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.368617e+02 PMG: contraction number = , 4.368617e+02 PMG: iteration = 8 PMG: relative residual = 8.704021e-06 PMG: contraction number = 3.213496e-01 NEWTON: using errtol_s: 3.938344e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.967040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.575949e+02 PMG: contraction number = , 1.575949e+02 PMG: iteration = 9 PMG: relative residual = 3.134737e-06 PMG: contraction number = 3.601482e-01 NEWTON: using errtol_s: 1.418387e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.049670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.957255e+01 PMG: contraction number = , 6.957255e+01 PMG: iteration = 10 PMG: relative residual = 1.384413e-06 PMG: contraction number = 4.416360e-01 NEWTON: using errtol_s: 6.264108e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.130070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.037457e+01 PMG: contraction number = , 3.037457e+01 PMG: iteration = 11 PMG: relative residual = 6.041724e-07 PMG: contraction number = 4.364106e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.606600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.001290e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.517) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.517) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.770869472038E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.268564718483E+06 kT Vpmg_energy: dielEnergy = 1.134237311512E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.238000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.2991) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... 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 = 3.839000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.290000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.349000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.372360e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.954482e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.428890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.248937e+05 PMG: contraction number = , 7.248937e+05 NEWTON: attempting damping, relres = 9.466343e-02 NEWTON: attempting damping, relres = 5.450042e-01 NEWTON: damping accepted, relres = 9.466343e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.466343e-02 PMG: contraction number = 9.466343e-02 NEWTON: using errtol_s: 6.583351e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.531510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.500825e+04 PMG: contraction number = , 9.500825e+04 PMG: iteration = 2 PMG: relative residual = 1.230212e-02 PMG: contraction number = 1.299564e-01 NEWTON: using errtol_s: 8.555486e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.604630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.493813e+04 PMG: contraction number = , 1.493813e+04 PMG: iteration = 3 PMG: relative residual = 1.933235e-03 PMG: contraction number = 1.571465e-01 NEWTON: using errtol_s: 1.344465e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.694100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.611321e+03 PMG: contraction number = , 2.611321e+03 PMG: iteration = 4 PMG: relative residual = 3.379397e-04 PMG: contraction number = 1.748053e-01 NEWTON: using errtol_s: 2.350196e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.782420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.854004e+02 PMG: contraction number = , 4.854004e+02 PMG: iteration = 5 PMG: relative residual = 6.281742e-05 PMG: contraction number = 1.858835e-01 NEWTON: using errtol_s: 4.368626e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.856230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.080450e+02 PMG: contraction number = , 1.080450e+02 PMG: iteration = 6 PMG: relative residual = 1.398243e-05 PMG: contraction number = 2.225884e-01 NEWTON: using errtol_s: 9.724056e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.929780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.597386e+01 PMG: contraction number = , 3.597386e+01 PMG: iteration = 7 PMG: relative residual = 4.655534e-06 PMG: contraction number = 3.329560e-01 NEWTON: using errtol_s: 3.237683e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.008030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.692951e+01 PMG: contraction number = , 1.692951e+01 PMG: iteration = 8 PMG: relative residual = 2.190899e-06 PMG: contraction number = 4.706010e-01 NEWTON: using errtol_s: 1.523657e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.085670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.962569e+00 PMG: contraction number = , 8.962569e+00 PMG: iteration = 9 PMG: relative residual = 1.159883e-06 PMG: contraction number = 5.294096e-01 NEWTON: using errtol_s: 8.066384e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.166460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.574507e+00 PMG: contraction number = , 4.574507e+00 PMG: iteration = 10 PMG: relative residual = 5.920006e-07 PMG: contraction number = 5.103969e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.437700e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.775000e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.7145) Vpmg_setPart: upper corner = (141.283, 130.313, 156.331) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.7145) Vpmg_setPart: actual maxima = (141.283, 130.313, 156.331) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.573661370686E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.465454264849E+05 kT Vpmg_energy: dielEnergy = 7.326969005994E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.320000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.2991) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.517 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.7145 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 156.331 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.517) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.7145) Vpmg_setPart: actual maxima = (141.283, 130.313, 156.331) 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 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 104.517) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.7145) VPMG::extEnergy Old upper corner = (141.283, 130.313, 156.331) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000172524 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000244881 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.366000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.350000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.795000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.353030e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.466887e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.408600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.346066e+06 PMG: contraction number = , 1.346066e+06 NEWTON: attempting damping, relres = 1.630550e-01 NEWTON: attempting damping, relres = 5.809976e-01 NEWTON: damping accepted, relres = 1.630550e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.630550e-01 PMG: contraction number = 1.630550e-01 NEWTON: using errtol_s: 1.217514e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.522450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.732944e+05 PMG: contraction number = , 1.732944e+05 PMG: iteration = 2 PMG: relative residual = 2.089519e-02 PMG: contraction number = 1.281481e-01 NEWTON: using errtol_s: 1.560220e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.608460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.550447e+04 PMG: contraction number = , 2.550447e+04 PMG: iteration = 3 PMG: relative residual = 3.074136e-03 PMG: contraction number = 1.471217e-01 NEWTON: using errtol_s: 2.295423e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.693690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.120165e+03 PMG: contraction number = , 4.120165e+03 PMG: iteration = 4 PMG: relative residual = 4.966133e-04 PMG: contraction number = 1.615456e-01 NEWTON: using errtol_s: 3.708155e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.770010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.069303e+02 PMG: contraction number = , 7.069303e+02 PMG: iteration = 5 PMG: relative residual = 8.520820e-05 PMG: contraction number = 1.715786e-01 NEWTON: using errtol_s: 6.362400e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.867310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.543321e+02 PMG: contraction number = , 1.543321e+02 PMG: iteration = 6 PMG: relative residual = 1.860200e-05 PMG: contraction number = 2.183123e-01 NEWTON: using errtol_s: 1.388990e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.954030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.132783e+01 PMG: contraction number = , 7.132783e+01 PMG: iteration = 7 PMG: relative residual = 8.597581e-06 PMG: contraction number = 4.621858e-01 NEWTON: using errtol_s: 6.419716e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.040390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.525289e+01 PMG: contraction number = , 3.525289e+01 PMG: iteration = 8 PMG: relative residual = 4.249116e-06 PMG: contraction number = 4.942223e-01 NEWTON: using errtol_s: 3.172767e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.138800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.493383e+01 PMG: contraction number = , 1.493383e+01 PMG: iteration = 9 PMG: relative residual = 1.800068e-06 PMG: contraction number = 4.236334e-01 NEWTON: using errtol_s: 1.344090e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.212160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.929322e+00 PMG: contraction number = , 6.929322e+00 PMG: iteration = 10 PMG: relative residual = 8.352067e-07 PMG: contraction number = 4.639863e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.315600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.694300e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.517) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.517) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.508713717327E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.444826996867E+05 kT Vpmg_energy: dielEnergy = 1.722384190843E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.358000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... 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 = 6.232000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.330000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.355000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.488800e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.505015e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.545060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.862092e+06 PMG: contraction number = , 3.862092e+06 NEWTON: attempting damping, relres = 1.150186e-01 NEWTON: attempting damping, relres = 5.474322e-01 NEWTON: damping accepted, relres = 1.150186e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.150186e-01 PMG: contraction number = 1.150186e-01 NEWTON: using errtol_s: 4.031418e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.664430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.343521e+05 PMG: contraction number = , 5.343521e+05 PMG: iteration = 2 PMG: relative residual = 1.761040e-02 PMG: contraction number = 1.531092e-01 NEWTON: using errtol_s: 6.172471e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.744550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.055476e+05 PMG: contraction number = , 1.055476e+05 PMG: iteration = 3 PMG: relative residual = 3.524525e-03 PMG: contraction number = 2.001388e-01 NEWTON: using errtol_s: 1.235351e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.824630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.496388e+04 PMG: contraction number = , 2.496388e+04 PMG: iteration = 4 PMG: relative residual = 8.149609e-04 PMG: contraction number = 2.312257e-01 NEWTON: using errtol_s: 2.856450e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.904110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.972133e+03 PMG: contraction number = , 6.972133e+03 PMG: iteration = 5 PMG: relative residual = 2.116219e-04 PMG: contraction number = 2.596712e-01 NEWTON: using errtol_s: 7.417379e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.986070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.178078e+03 PMG: contraction number = , 2.178078e+03 PMG: iteration = 6 PMG: relative residual = 6.005733e-05 PMG: contraction number = 2.837955e-01 NEWTON: using errtol_s: 2.105018e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.066710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.964012e+02 PMG: contraction number = , 6.964012e+02 PMG: iteration = 7 PMG: relative residual = 1.801882e-05 PMG: contraction number = 3.000271e-01 NEWTON: using errtol_s: 6.315625e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.147330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.262646e+02 PMG: contraction number = , 2.262646e+02 PMG: iteration = 8 PMG: relative residual = 5.810789e-06 PMG: contraction number = 3.224844e-01 NEWTON: using errtol_s: 2.036690e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.226130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.054111e+01 PMG: contraction number = , 9.054111e+01 PMG: iteration = 9 PMG: relative residual = 2.324909e-06 PMG: contraction number = 4.001021e-01 NEWTON: using errtol_s: 8.148840e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.304200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.355250e+01 PMG: contraction number = , 4.355250e+01 PMG: iteration = 10 PMG: relative residual = 1.118341e-06 PMG: contraction number = 4.810257e-01 NEWTON: using errtol_s: 3.919801e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.385100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.146474e+01 PMG: contraction number = , 2.146474e+01 PMG: iteration = 11 PMG: relative residual = 5.511642e-07 PMG: contraction number = 4.928410e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.502200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.842400e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.7145) Vpmg_setPart: upper corner = (141.283, 130.313, 156.331) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.7145) Vpmg_setPart: actual maxima = (141.283, 130.313, 156.331) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.559857432433E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.596310885234E+05 kT Vpmg_energy: dielEnergy = 4.297728277474E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.283000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.517 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.7145 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 156.331 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.517) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.7145) Vpmg_setPart: actual maxima = (141.283, 130.313, 156.331) 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 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 104.517) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.7145) VPMG::extEnergy Old upper corner = (141.283, 130.313, 156.331) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0150271 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.018109 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.242400e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.738000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.625390e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.778051e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.681510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.530900e+06 PMG: contraction number = , 6.530900e+06 NEWTON: attempting damping, relres = 1.748706e-01 NEWTON: attempting damping, relres = 5.780810e-01 NEWTON: damping accepted, relres = 1.748706e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.748706e-01 PMG: contraction number = 1.748706e-01 NEWTON: using errtol_s: 6.606700e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.789810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.849737e+05 PMG: contraction number = , 8.849737e+05 PMG: iteration = 2 PMG: relative residual = 2.636861e-02 PMG: contraction number = 1.507893e-01 NEWTON: using errtol_s: 9.962196e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.872780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.597771e+05 PMG: contraction number = , 1.597771e+05 PMG: iteration = 3 PMG: relative residual = 5.145021e-03 PMG: contraction number = 1.951192e-01 NEWTON: using errtol_s: 1.943815e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.954190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.633416e+04 PMG: contraction number = , 3.633416e+04 PMG: iteration = 4 PMG: relative residual = 1.237153e-03 PMG: contraction number = 2.404564e-01 NEWTON: using errtol_s: 4.674029e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.035600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.031138e+04 PMG: contraction number = , 1.031138e+04 PMG: iteration = 5 PMG: relative residual = 3.433270e-04 PMG: contraction number = 2.775137e-01 NEWTON: using errtol_s: 1.297107e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.117020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.607084e+03 PMG: contraction number = , 3.607084e+03 PMG: iteration = 6 PMG: relative residual = 1.015186e-04 PMG: contraction number = 2.956908e-01 NEWTON: using errtol_s: 3.835427e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.198300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.147185e+03 PMG: contraction number = , 1.147185e+03 PMG: iteration = 7 PMG: relative residual = 2.801647e-05 PMG: contraction number = 2.759736e-01 NEWTON: using errtol_s: 1.058477e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.279450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.734723e+02 PMG: contraction number = , 3.734723e+02 PMG: iteration = 8 PMG: relative residual = 8.907413e-06 PMG: contraction number = 3.179349e-01 NEWTON: using errtol_s: 3.365266e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.360220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.331216e+02 PMG: contraction number = , 1.331216e+02 PMG: iteration = 9 PMG: relative residual = 3.171229e-06 PMG: contraction number = 3.560214e-01 NEWTON: using errtol_s: 1.198107e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.441380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.897579e+01 PMG: contraction number = , 5.897579e+01 PMG: iteration = 10 PMG: relative residual = 1.405383e-06 PMG: contraction number = 4.431666e-01 NEWTON: using errtol_s: 5.309609e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.522400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.594651e+01 PMG: contraction number = , 2.594651e+01 PMG: iteration = 11 PMG: relative residual = 6.180949e-07 PMG: contraction number = 4.398053e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.537500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.914000e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.517) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.517) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.515375425537E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.924084138451E+06 kT Vpmg_energy: dielEnergy = 9.620001455589E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.238000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.685150e+03