############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 18 15:08:23 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_allh36.23.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb36.23.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, 82.517) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 29.808) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 82.517) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 26.463) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 54.49) 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 29.808 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.808 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.58827 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.346915 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.589721 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 29.808 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 161.581 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.965 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 107.517 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 107.517 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 29.808 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.808 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.58827 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.346915 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.589721 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 29.808 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 161.581 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.965 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 107.517 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 107.517 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 29.808 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.808 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.58827 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.346915 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.589721 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 29.808 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 161.581 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.965 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 107.517 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 107.517 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 = 81.5151 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 108.04 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, 119.746) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13215728 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 = 6.924000e+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 = 5.420000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.449000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052000e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.188955e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.625100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.477248e+06 PMG: contraction number = , 4.477248e+06 NEWTON: attempting damping, relres = 1.094884e-01 NEWTON: attempting damping, relres = 5.459046e-01 NEWTON: damping accepted, relres = 1.094884e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.094884e-01 PMG: contraction number = 1.094884e-01 NEWTON: using errtol_s: 4.586421e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.771000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.107246e+05 PMG: contraction number = , 6.107246e+05 PMG: iteration = 2 PMG: relative residual = 1.632965e-02 PMG: contraction number = 1.491449e-01 NEWTON: using errtol_s: 6.840415e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.597700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.176217e+05 PMG: contraction number = , 1.176217e+05 PMG: iteration = 3 PMG: relative residual = 3.171749e-03 PMG: contraction number = 1.942326e-01 NEWTON: using errtol_s: 1.328631e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.319200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.733894e+04 PMG: contraction number = , 2.733894e+04 PMG: iteration = 4 PMG: relative residual = 7.136594e-04 PMG: contraction number = 2.250050e-01 NEWTON: using errtol_s: 2.989487e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.064300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.408159e+03 PMG: contraction number = , 7.408159e+03 PMG: iteration = 5 PMG: relative residual = 1.788525e-04 PMG: contraction number = 2.506133e-01 NEWTON: using errtol_s: 7.492051e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.841300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.204987e+03 PMG: contraction number = , 2.204987e+03 PMG: iteration = 6 PMG: relative residual = 4.913559e-05 PMG: contraction number = 2.747269e-01 NEWTON: using errtol_s: 2.058268e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.608900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.183474e+02 PMG: contraction number = , 7.183474e+02 PMG: iteration = 7 PMG: relative residual = 1.544359e-05 PMG: contraction number = 3.143056e-01 NEWTON: using errtol_s: 6.469250e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.509400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.672155e+02 PMG: contraction number = , 2.672155e+02 PMG: iteration = 8 PMG: relative residual = 5.741627e-06 PMG: contraction number = 3.717806e-01 NEWTON: using errtol_s: 2.405142e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.276100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.351177e+02 PMG: contraction number = , 1.351177e+02 PMG: iteration = 9 PMG: relative residual = 2.903167e-06 PMG: contraction number = 5.056349e-01 NEWTON: using errtol_s: 1.216124e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.029700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.092630e+01 PMG: contraction number = , 6.092630e+01 PMG: iteration = 10 PMG: relative residual = 1.309031e-06 PMG: contraction number = 4.508977e-01 NEWTON: using errtol_s: 5.483474e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.810100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.779511e+01 PMG: contraction number = , 2.779511e+01 PMG: iteration = 11 PMG: relative residual = 5.971884e-07 PMG: contraction number = 4.562063e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.329400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.677200e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.965) Vpmg_setPart: upper corner = (141.283, 130.313, 161.581) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.965) Vpmg_setPart: actual maxima = (141.283, 130.313, 161.581) 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 = 2.807187862074E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.850610380579E+05 kT Vpmg_energy: dielEnergy = 4.924848752951E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.341000e+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 = 81.5151 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 108.04 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, 119.746) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13215728 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, 107.517 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.965 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 161.581 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 107.517) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.965) Vpmg_setPart: actual maxima = (141.283, 130.313, 161.581) 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, 107.517) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.965) VPMG::extEnergy Old upper corner = (141.283, 130.313, 161.581) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0143901 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0176635 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 = 1.291500e+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 = 5.300000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.351000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.226790e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.523942e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.281930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.838840e+06 PMG: contraction number = , 7.838840e+06 NEWTON: attempting damping, relres = 1.722778e-01 NEWTON: attempting damping, relres = 5.782004e-01 NEWTON: damping accepted, relres = 1.722778e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.722778e-01 PMG: contraction number = 1.722778e-01 NEWTON: using errtol_s: 7.793750e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.386400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.057511e+06 PMG: contraction number = , 1.057511e+06 PMG: iteration = 2 PMG: relative residual = 2.546170e-02 PMG: contraction number = 1.477944e-01 NEWTON: using errtol_s: 1.151873e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.460020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.878030e+05 PMG: contraction number = , 1.878030e+05 PMG: iteration = 3 PMG: relative residual = 4.833613e-03 PMG: contraction number = 1.898386e-01 NEWTON: using errtol_s: 2.186699e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.541040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.237747e+04 PMG: contraction number = , 4.237747e+04 PMG: iteration = 4 PMG: relative residual = 1.135088e-03 PMG: contraction number = 2.348323e-01 NEWTON: using errtol_s: 5.135075e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.624270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.195201e+04 PMG: contraction number = , 1.195201e+04 PMG: iteration = 5 PMG: relative residual = 3.095599e-04 PMG: contraction number = 2.727188e-01 NEWTON: using errtol_s: 1.400431e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.703780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.159104e+03 PMG: contraction number = , 4.159104e+03 PMG: iteration = 6 PMG: relative residual = 9.277568e-05 PMG: contraction number = 2.997018e-01 NEWTON: using errtol_s: 4.197118e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.791440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.378793e+03 PMG: contraction number = , 1.378793e+03 PMG: iteration = 7 PMG: relative residual = 2.759909e-05 PMG: contraction number = 2.974819e-01 NEWTON: using errtol_s: 1.248567e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.874600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.747713e+02 PMG: contraction number = , 4.747713e+02 PMG: iteration = 8 PMG: relative residual = 9.456975e-06 PMG: contraction number = 3.426554e-01 NEWTON: using errtol_s: 4.278281e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.952010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.804264e+02 PMG: contraction number = , 1.804264e+02 PMG: iteration = 9 PMG: relative residual = 3.589474e-06 PMG: contraction number = 3.795584e-01 NEWTON: using errtol_s: 1.623858e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.029330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.308597e+01 PMG: contraction number = , 8.308597e+01 PMG: iteration = 10 PMG: relative residual = 1.653520e-06 PMG: contraction number = 4.606579e-01 NEWTON: using errtol_s: 7.480429e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.107800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.836409e+01 PMG: contraction number = , 3.836409e+01 PMG: iteration = 11 PMG: relative residual = 7.632254e-07 PMG: contraction number = 4.615762e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.446300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.781700e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 107.517) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 107.517) 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 = 2.756838438154E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.256567640422E+06 kT Vpmg_energy: dielEnergy = 1.128238989110E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.119000e+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, 19.2991) 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 = 3.835000e+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 = 6.620000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.513000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.364320e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.934808e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.420650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.059441e+05 PMG: contraction number = , 7.059441e+05 NEWTON: attempting damping, relres = 9.247351e-02 NEWTON: attempting damping, relres = 5.438142e-01 NEWTON: damping accepted, relres = 9.247351e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.247351e-02 PMG: contraction number = 9.247351e-02 NEWTON: using errtol_s: 6.412860e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.529230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.168974e+04 PMG: contraction number = , 9.168974e+04 PMG: iteration = 2 PMG: relative residual = 1.190594e-02 PMG: contraction number = 1.287497e-01 NEWTON: using errtol_s: 8.256539e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.614720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.428291e+04 PMG: contraction number = , 1.428291e+04 PMG: iteration = 3 PMG: relative residual = 1.853694e-03 PMG: contraction number = 1.556949e-01 NEWTON: using errtol_s: 1.285501e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.692570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.500820e+03 PMG: contraction number = , 2.500820e+03 PMG: iteration = 4 PMG: relative residual = 3.245579e-04 PMG: contraction number = 1.750871e-01 NEWTON: using errtol_s: 2.250746e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.772670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.781331e+02 PMG: contraction number = , 4.781331e+02 PMG: iteration = 5 PMG: relative residual = 6.205275e-05 PMG: contraction number = 1.911916e-01 NEWTON: using errtol_s: 4.303239e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.850970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.166342e+02 PMG: contraction number = , 1.166342e+02 PMG: iteration = 6 PMG: relative residual = 1.513681e-05 PMG: contraction number = 2.439346e-01 NEWTON: using errtol_s: 1.049709e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.937110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.213873e+01 PMG: contraction number = , 4.213873e+01 PMG: iteration = 7 PMG: relative residual = 5.468863e-06 PMG: contraction number = 3.612955e-01 NEWTON: using errtol_s: 3.792551e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.015870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.048391e+01 PMG: contraction number = , 2.048391e+01 PMG: iteration = 8 PMG: relative residual = 2.658405e-06 PMG: contraction number = 4.860983e-01 NEWTON: using errtol_s: 1.843553e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.101920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.072627e+01 PMG: contraction number = , 1.072627e+01 PMG: iteration = 9 PMG: relative residual = 1.392073e-06 PMG: contraction number = 5.236498e-01 NEWTON: using errtol_s: 9.653761e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.179880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.377762e+00 PMG: contraction number = , 5.377762e+00 PMG: iteration = 10 PMG: relative residual = 6.979267e-07 PMG: contraction number = 5.013577e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.767800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.236200e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.965) Vpmg_setPart: upper corner = (141.283, 130.313, 161.581) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.965) Vpmg_setPart: actual maxima = (141.283, 130.313, 161.581) 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 = 2.579619123889E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.437351304059E+05 kT Vpmg_energy: dielEnergy = 7.186453338896E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.361000e+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, 19.2991) 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, 107.517 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.965 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 161.581 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 107.517) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.965) Vpmg_setPart: actual maxima = (141.283, 130.313, 161.581) 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, 107.517) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.965) VPMG::extEnergy Old upper corner = (141.283, 130.313, 161.581) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000164901 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000233831 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 = 6.684000e+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 = 5.320000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.730000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.371370e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465807e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.428750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.340394e+06 PMG: contraction number = , 1.340394e+06 NEWTON: attempting damping, relres = 1.623958e-01 NEWTON: attempting damping, relres = 5.806573e-01 NEWTON: damping accepted, relres = 1.623958e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.623958e-01 PMG: contraction number = 1.623958e-01 NEWTON: using errtol_s: 1.212416e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.538650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.729688e+05 PMG: contraction number = , 1.729688e+05 PMG: iteration = 2 PMG: relative residual = 2.085972e-02 PMG: contraction number = 1.284499e-01 NEWTON: using errtol_s: 1.557347e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.611860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.551635e+04 PMG: contraction number = , 2.551635e+04 PMG: iteration = 3 PMG: relative residual = 3.076010e-03 PMG: contraction number = 1.474617e-01 NEWTON: using errtol_s: 2.296490e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.691430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.136760e+03 PMG: contraction number = , 4.136760e+03 PMG: iteration = 4 PMG: relative residual = 4.986856e-04 PMG: contraction number = 1.621209e-01 NEWTON: using errtol_s: 3.723091e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.764930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.150198e+02 PMG: contraction number = , 7.150198e+02 PMG: iteration = 5 PMG: relative residual = 8.619558e-05 PMG: contraction number = 1.728455e-01 NEWTON: using errtol_s: 6.435196e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.847690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.456738e+02 PMG: contraction number = , 1.456738e+02 PMG: iteration = 6 PMG: relative residual = 1.756092e-05 PMG: contraction number = 2.037334e-01 NEWTON: using errtol_s: 1.311065e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.924200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.013655e+01 PMG: contraction number = , 6.013655e+01 PMG: iteration = 7 PMG: relative residual = 7.249571e-06 PMG: contraction number = 4.128240e-01 NEWTON: using errtol_s: 5.412390e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.000740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.162646e+01 PMG: contraction number = , 3.162646e+01 PMG: iteration = 8 PMG: relative residual = 3.812561e-06 PMG: contraction number = 5.259016e-01 NEWTON: using errtol_s: 2.846385e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.086220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.368258e+01 PMG: contraction number = , 1.368258e+01 PMG: iteration = 9 PMG: relative residual = 1.649468e-06 PMG: contraction number = 4.326404e-01 NEWTON: using errtol_s: 1.231461e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.161390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.183326e+00 PMG: contraction number = , 6.183326e+00 PMG: iteration = 10 PMG: relative residual = 7.453978e-07 PMG: contraction number = 4.519020e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.486600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.860700e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 107.517) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 107.517) 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 = 2.507865588896E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.413038216762E+05 kT Vpmg_energy: dielEnergy = 1.706489807238E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.269000e+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 = 6.229000e+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 = 5.310000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.352000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.430180e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.495976e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.487740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.774236e+06 PMG: contraction number = , 3.774236e+06 NEWTON: attempting damping, relres = 1.125220e-01 NEWTON: attempting damping, relres = 5.463322e-01 NEWTON: damping accepted, relres = 1.125220e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.125220e-01 PMG: contraction number = 1.125220e-01 NEWTON: using errtol_s: 3.933741e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.593490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.187325e+05 PMG: contraction number = , 5.187325e+05 PMG: iteration = 2 PMG: relative residual = 1.706551e-02 PMG: contraction number = 1.516638e-01 NEWTON: using errtol_s: 5.966061e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.669880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.029435e+05 PMG: contraction number = , 1.029435e+05 PMG: iteration = 3 PMG: relative residual = 3.391292e-03 PMG: contraction number = 1.987220e-01 NEWTON: using errtol_s: 1.185588e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.751390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.436251e+04 PMG: contraction number = , 2.436251e+04 PMG: iteration = 4 PMG: relative residual = 7.753502e-04 PMG: contraction number = 2.286297e-01 NEWTON: using errtol_s: 2.710606e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.830970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.713694e+03 PMG: contraction number = , 6.713694e+03 PMG: iteration = 5 PMG: relative residual = 1.977665e-04 PMG: contraction number = 2.550673e-01 NEWTON: using errtol_s: 6.913869e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.914030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.049951e+03 PMG: contraction number = , 2.049951e+03 PMG: iteration = 6 PMG: relative residual = 5.543796e-05 PMG: contraction number = 2.803203e-01 NEWTON: using errtol_s: 1.938098e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.004170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.684626e+02 PMG: contraction number = , 6.684626e+02 PMG: iteration = 7 PMG: relative residual = 1.723457e-05 PMG: contraction number = 3.108804e-01 NEWTON: using errtol_s: 6.025166e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.086210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.380617e+02 PMG: contraction number = , 2.380617e+02 PMG: iteration = 8 PMG: relative residual = 6.129741e-06 PMG: contraction number = 3.556654e-01 NEWTON: using errtol_s: 2.142943e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.164430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.167065e+02 PMG: contraction number = , 1.167065e+02 PMG: iteration = 9 PMG: relative residual = 3.004565e-06 PMG: contraction number = 4.901617e-01 NEWTON: using errtol_s: 1.050389e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.242190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.499797e+01 PMG: contraction number = , 5.499797e+01 PMG: iteration = 10 PMG: relative residual = 1.415899e-06 PMG: contraction number = 4.712493e-01 NEWTON: using errtol_s: 4.949949e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.323000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.492596e+01 PMG: contraction number = , 2.492596e+01 PMG: iteration = 11 PMG: relative residual = 6.416969e-07 PMG: contraction number = 4.532082e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.553500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.894000e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.965) Vpmg_setPart: upper corner = (141.283, 130.313, 161.581) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.965) Vpmg_setPart: actual maxima = (141.283, 130.313, 161.581) 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 = 2.560886520167E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.413275537226E+05 kT Vpmg_energy: dielEnergy = 4.206210079356E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.252000e+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, 107.517 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.965 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 161.581 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 107.517) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.965) Vpmg_setPart: actual maxima = (141.283, 130.313, 161.581) 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, 107.517) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.965) VPMG::extEnergy Old upper corner = (141.283, 130.313, 161.581) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0144296 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.01751 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 = 1.095500e+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 = 5.280000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.352000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.553140e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.777361e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.613280e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.499629e+06 PMG: contraction number = , 6.499629e+06 NEWTON: attempting damping, relres = 1.736948e-01 NEWTON: attempting damping, relres = 5.777069e-01 NEWTON: damping accepted, relres = 1.736948e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.736948e-01 PMG: contraction number = 1.736948e-01 NEWTON: using errtol_s: 6.561080e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.748150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.825995e+05 PMG: contraction number = , 8.825995e+05 PMG: iteration = 2 PMG: relative residual = 2.613909e-02 PMG: contraction number = 1.504886e-01 NEWTON: using errtol_s: 9.873676e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.859890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.606676e+05 PMG: contraction number = , 1.606676e+05 PMG: iteration = 3 PMG: relative residual = 5.098671e-03 PMG: contraction number = 1.950593e-01 NEWTON: using errtol_s: 1.925952e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.974670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.716428e+04 PMG: contraction number = , 3.716428e+04 PMG: iteration = 4 PMG: relative residual = 1.229057e-03 PMG: contraction number = 2.410544e-01 NEWTON: using errtol_s: 4.642593e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.083610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.076918e+04 PMG: contraction number = , 1.076918e+04 PMG: iteration = 5 PMG: relative residual = 3.425037e-04 PMG: contraction number = 2.786719e-01 NEWTON: using errtol_s: 1.293760e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.173650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.835656e+03 PMG: contraction number = , 3.835656e+03 PMG: iteration = 6 PMG: relative residual = 1.037731e-04 PMG: contraction number = 3.029840e-01 NEWTON: using errtol_s: 3.919885e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.260710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.274971e+03 PMG: contraction number = , 1.274971e+03 PMG: iteration = 7 PMG: relative residual = 3.065722e-05 PMG: contraction number = 2.954254e-01 NEWTON: using errtol_s: 1.158034e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.337690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.381964e+02 PMG: contraction number = , 4.381964e+02 PMG: iteration = 8 PMG: relative residual = 1.044812e-05 PMG: contraction number = 3.408046e-01 NEWTON: using errtol_s: 3.946632e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.432330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.598814e+02 PMG: contraction number = , 1.598814e+02 PMG: iteration = 9 PMG: relative residual = 3.809422e-06 PMG: contraction number = 3.646036e-01 NEWTON: using errtol_s: 1.438956e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.513560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.388443e+01 PMG: contraction number = , 7.388443e+01 PMG: iteration = 10 PMG: relative residual = 1.760936e-06 PMG: contraction number = 4.622580e-01 NEWTON: using errtol_s: 6.651690e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.619270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.363533e+01 PMG: contraction number = , 3.363533e+01 PMG: iteration = 11 PMG: relative residual = 8.014053e-07 PMG: contraction number = 4.551020e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.110380e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.143380e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 107.517) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 107.517) 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 = 2.516030351414E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.915265482270E+06 kT Vpmg_energy: dielEnergy = 9.575907086386E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.220000e+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 = 6.772180e+03