############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Mar 13 08:17:51 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_allh37.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb37.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, 83.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 30.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 83.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 27.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 55.26) 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 30.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 30.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.592567 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.348634 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.588345 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 30.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 162.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -102.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 108.287 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 108.287 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 30.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 30.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.592567 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.348634 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.588345 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 30.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 162.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -102.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 108.287 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 108.287 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 30.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 30.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.592567 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.348634 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.588345 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 30.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 162.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -102.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 108.287 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 108.287 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 = 81.7565 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 108.81 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, 120.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13155484 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 = 6.869000e+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 = 5.220000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.337000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026200e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.187201e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.564700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.461019e+06 PMG: contraction number = , 4.461019e+06 NEWTON: attempting damping, relres = 1.089064e-01 NEWTON: attempting damping, relres = 5.457271e-01 NEWTON: damping accepted, relres = 1.089064e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.089064e-01 PMG: contraction number = 1.089064e-01 NEWTON: using errtol_s: 4.560129e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.499100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.083250e+05 PMG: contraction number = , 6.083250e+05 PMG: iteration = 2 PMG: relative residual = 1.620387e-02 PMG: contraction number = 1.487872e-01 NEWTON: using errtol_s: 6.784888e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.181800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.170906e+05 PMG: contraction number = , 1.170906e+05 PMG: iteration = 3 PMG: relative residual = 3.136806e-03 PMG: contraction number = 1.935837e-01 NEWTON: using errtol_s: 1.313444e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.862900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.692798e+04 PMG: contraction number = , 2.692798e+04 PMG: iteration = 4 PMG: relative residual = 6.996229e-04 PMG: contraction number = 2.230367e-01 NEWTON: using errtol_s: 2.929462e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.543700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.210939e+03 PMG: contraction number = , 7.210939e+03 PMG: iteration = 5 PMG: relative residual = 1.734732e-04 PMG: contraction number = 2.479525e-01 NEWTON: using errtol_s: 7.263673e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.224500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.146762e+03 PMG: contraction number = , 2.146762e+03 PMG: iteration = 6 PMG: relative residual = 4.758111e-05 PMG: contraction number = 2.742851e-01 NEWTON: using errtol_s: 1.992317e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.906500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.286235e+02 PMG: contraction number = , 7.286235e+02 PMG: iteration = 7 PMG: relative residual = 1.567065e-05 PMG: contraction number = 3.293460e-01 NEWTON: using errtol_s: 6.561617e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.600400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.998784e+02 PMG: contraction number = , 2.998784e+02 PMG: iteration = 8 PMG: relative residual = 6.445935e-06 PMG: contraction number = 4.113381e-01 NEWTON: using errtol_s: 2.699043e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.292100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.486563e+02 PMG: contraction number = , 1.486563e+02 PMG: iteration = 9 PMG: relative residual = 3.195495e-06 PMG: contraction number = 4.957381e-01 NEWTON: using errtol_s: 1.338018e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.070200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.379204e+01 PMG: contraction number = , 6.379204e+01 PMG: iteration = 10 PMG: relative residual = 1.371185e-06 PMG: contraction number = 4.290992e-01 NEWTON: using errtol_s: 5.741426e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.172700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.907668e+01 PMG: contraction number = , 2.907668e+01 PMG: iteration = 11 PMG: relative residual = 6.249862e-07 PMG: contraction number = 4.558002e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.767700e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.095300e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -102.542) Vpmg_setPart: upper corner = (141.283, 130.313, 162.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -102.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 162.928) 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 = 2.801932612072E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.814842069190E+05 kT Vpmg_energy: dielEnergy = 4.906966473277E+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 = 81.7565 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 108.81 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, 120.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13155484 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, 108.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -102.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 162.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 108.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -102.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 162.928) 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, 108.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -102.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 162.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0139009 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0170561 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 = 1.200600e+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 = 5.430000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.342000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.157050e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.523734e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.211550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.827346e+06 PMG: contraction number = , 7.827346e+06 NEWTON: attempting damping, relres = 1.715299e-01 NEWTON: attempting damping, relres = 5.780786e-01 NEWTON: damping accepted, relres = 1.715299e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.715299e-01 PMG: contraction number = 1.715299e-01 NEWTON: using errtol_s: 7.759558e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.055454e+06 PMG: contraction number = , 1.055454e+06 PMG: iteration = 2 PMG: relative residual = 2.523999e-02 PMG: contraction number = 1.471463e-01 NEWTON: using errtol_s: 1.141790e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.377900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.867896e+05 PMG: contraction number = , 1.867896e+05 PMG: iteration = 3 PMG: relative residual = 4.755804e-03 PMG: contraction number = 1.884234e-01 NEWTON: using errtol_s: 2.151399e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.464570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.179261e+04 PMG: contraction number = , 4.179261e+04 PMG: iteration = 4 PMG: relative residual = 1.105917e-03 PMG: contraction number = 2.325404e-01 NEWTON: using errtol_s: 5.002873e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.533710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.168368e+04 PMG: contraction number = , 1.168368e+04 PMG: iteration = 5 PMG: relative residual = 2.989849e-04 PMG: contraction number = 2.703504e-01 NEWTON: using errtol_s: 1.352528e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.602680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.070583e+03 PMG: contraction number = , 4.070583e+03 PMG: iteration = 6 PMG: relative residual = 8.945906e-05 PMG: contraction number = 2.992092e-01 NEWTON: using errtol_s: 4.046890e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.674880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.368685e+03 PMG: contraction number = , 1.368685e+03 PMG: iteration = 7 PMG: relative residual = 2.731387e-05 PMG: contraction number = 3.053226e-01 NEWTON: using errtol_s: 1.235607e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.761530e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.819960e+02 PMG: contraction number = , 4.819960e+02 PMG: iteration = 8 PMG: relative residual = 9.607867e-06 PMG: contraction number = 3.517578e-01 NEWTON: using errtol_s: 4.346344e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.830130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.062504e+02 PMG: contraction number = , 2.062504e+02 PMG: iteration = 9 PMG: relative residual = 4.103476e-06 PMG: contraction number = 4.270954e-01 NEWTON: using errtol_s: 1.856303e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.899080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.684090e+01 PMG: contraction number = , 9.684090e+01 PMG: iteration = 10 PMG: relative residual = 1.927338e-06 PMG: contraction number = 4.696842e-01 NEWTON: using errtol_s: 8.718764e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.968070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.799168e+01 PMG: contraction number = , 4.799168e+01 PMG: iteration = 11 PMG: relative residual = 9.548058e-07 PMG: contraction number = 4.954014e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.569900e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.901800e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 108.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 108.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.754366729194E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.239214087176E+06 kT Vpmg_energy: dielEnergy = 1.119562283169E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.264000e+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, 20.0691) 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 = 3.902000e+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 = 2.916000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.195490e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.927526e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.253940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.057612e+05 PMG: contraction number = , 7.057612e+05 NEWTON: attempting damping, relres = 9.254127e-02 NEWTON: attempting damping, relres = 5.438990e-01 NEWTON: damping accepted, relres = 9.254127e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.254127e-02 PMG: contraction number = 9.254127e-02 NEWTON: using errtol_s: 6.410821e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.374460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.219909e+04 PMG: contraction number = , 9.219909e+04 PMG: iteration = 2 PMG: relative residual = 1.198447e-02 PMG: contraction number = 1.295041e-01 NEWTON: using errtol_s: 8.302273e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.464740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.452368e+04 PMG: contraction number = , 1.452368e+04 PMG: iteration = 3 PMG: relative residual = 1.886925e-03 PMG: contraction number = 1.574475e-01 NEWTON: using errtol_s: 1.307172e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.554400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.585002e+03 PMG: contraction number = , 2.585002e+03 PMG: iteration = 4 PMG: relative residual = 3.358359e-04 PMG: contraction number = 1.779805e-01 NEWTON: using errtol_s: 2.326512e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.644850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.040753e+02 PMG: contraction number = , 5.040753e+02 PMG: iteration = 5 PMG: relative residual = 6.548831e-05 PMG: contraction number = 1.950009e-01 NEWTON: using errtol_s: 4.536720e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.734850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.245815e+02 PMG: contraction number = , 1.245815e+02 PMG: iteration = 6 PMG: relative residual = 1.618521e-05 PMG: contraction number = 2.471465e-01 NEWTON: using errtol_s: 1.121234e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.825410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.368363e+01 PMG: contraction number = , 4.368363e+01 PMG: iteration = 7 PMG: relative residual = 5.675313e-06 PMG: contraction number = 3.506482e-01 NEWTON: using errtol_s: 3.931588e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.916110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.059824e+01 PMG: contraction number = , 2.059824e+01 PMG: iteration = 8 PMG: relative residual = 2.676053e-06 PMG: contraction number = 4.715252e-01 NEWTON: using errtol_s: 1.853843e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.004800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.061093e+01 PMG: contraction number = , 1.061093e+01 PMG: iteration = 9 PMG: relative residual = 1.378551e-06 PMG: contraction number = 5.151433e-01 NEWTON: using errtol_s: 9.549947e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.094490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.330116e+00 PMG: contraction number = , 5.330116e+00 PMG: iteration = 10 PMG: relative residual = 6.924702e-07 PMG: contraction number = 5.023175e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.619900e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.000720e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -102.542) Vpmg_setPart: upper corner = (141.283, 130.313, 162.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -102.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 162.928) 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 = 2.576055269634E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.429319732972E+05 kT Vpmg_energy: dielEnergy = 7.146296200363E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.335000e+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, 20.0691) 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, 108.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -102.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 162.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 108.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -102.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 162.928) 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, 108.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -102.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 162.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000159425 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000225622 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 = 6.774000e+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 = 5.250000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.346000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.284040e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.466067e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.338830e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.340732e+06 PMG: contraction number = , 1.340732e+06 NEWTON: attempting damping, relres = 1.624283e-01 NEWTON: attempting damping, relres = 5.806697e-01 NEWTON: damping accepted, relres = 1.624283e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.624283e-01 PMG: contraction number = 1.624283e-01 NEWTON: using errtol_s: 1.212700e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.444350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.731634e+05 PMG: contraction number = , 1.731634e+05 PMG: iteration = 2 PMG: relative residual = 2.088193e-02 PMG: contraction number = 1.285609e-01 NEWTON: using errtol_s: 1.559059e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.514010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.558977e+04 PMG: contraction number = , 2.558977e+04 PMG: iteration = 3 PMG: relative residual = 3.084753e-03 PMG: contraction number = 1.477236e-01 NEWTON: using errtol_s: 2.303097e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.588030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.156455e+03 PMG: contraction number = , 4.156455e+03 PMG: iteration = 4 PMG: relative residual = 5.010424e-04 PMG: contraction number = 1.624255e-01 NEWTON: using errtol_s: 3.740816e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.690540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.029888e+02 PMG: contraction number = , 7.029888e+02 PMG: iteration = 5 PMG: relative residual = 8.474237e-05 PMG: contraction number = 1.691321e-01 NEWTON: using errtol_s: 6.326922e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.798220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.453919e+02 PMG: contraction number = , 1.453919e+02 PMG: iteration = 6 PMG: relative residual = 1.752634e-05 PMG: contraction number = 2.068190e-01 NEWTON: using errtol_s: 1.308528e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.879660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.150474e+01 PMG: contraction number = , 6.150474e+01 PMG: iteration = 7 PMG: relative residual = 7.414299e-06 PMG: contraction number = 4.230376e-01 NEWTON: using errtol_s: 5.535565e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.989560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.093158e+01 PMG: contraction number = , 3.093158e+01 PMG: iteration = 8 PMG: relative residual = 3.728665e-06 PMG: contraction number = 5.029019e-01 NEWTON: using errtol_s: 2.783846e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.059380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.288482e+01 PMG: contraction number = , 1.288482e+01 PMG: iteration = 9 PMG: relative residual = 1.553247e-06 PMG: contraction number = 4.165692e-01 NEWTON: using errtol_s: 1.159665e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.128430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.874690e+00 PMG: contraction number = , 5.874690e+00 PMG: iteration = 10 PMG: relative residual = 7.081673e-07 PMG: contraction number = 4.559270e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.887500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.216700e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 108.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 108.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.510456149012E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.405304391012E+05 kT Vpmg_energy: dielEnergy = 1.702622863301E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.293000e+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 = 6.734000e+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 = 2.367000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.377730e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.494899e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.433120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.757907e+06 PMG: contraction number = , 3.757907e+06 NEWTON: attempting damping, relres = 1.119722e-01 NEWTON: attempting damping, relres = 5.461049e-01 NEWTON: damping accepted, relres = 1.119722e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.119722e-01 PMG: contraction number = 1.119722e-01 NEWTON: using errtol_s: 3.913316e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.544220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.160980e+05 PMG: contraction number = , 5.160980e+05 PMG: iteration = 2 PMG: relative residual = 1.696060e-02 PMG: contraction number = 1.514715e-01 NEWTON: using errtol_s: 5.927560e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.622610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.024278e+05 PMG: contraction number = , 1.024278e+05 PMG: iteration = 3 PMG: relative residual = 3.363049e-03 PMG: contraction number = 1.982859e-01 NEWTON: using errtol_s: 1.175352e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.700510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.402211e+04 PMG: contraction number = , 2.402211e+04 PMG: iteration = 4 PMG: relative residual = 7.632394e-04 PMG: contraction number = 2.269487e-01 NEWTON: using errtol_s: 2.667445e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.778050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.548368e+03 PMG: contraction number = , 6.548368e+03 PMG: iteration = 5 PMG: relative residual = 1.925314e-04 PMG: contraction number = 2.522556e-01 NEWTON: using errtol_s: 6.728780e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.855870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.994031e+03 PMG: contraction number = , 1.994031e+03 PMG: iteration = 6 PMG: relative residual = 5.358164e-05 PMG: contraction number = 2.783007e-01 NEWTON: using errtol_s: 1.872624e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.938100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.738777e+02 PMG: contraction number = , 6.738777e+02 PMG: iteration = 7 PMG: relative residual = 1.737599e-05 PMG: contraction number = 3.242900e-01 NEWTON: using errtol_s: 6.072734e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.016250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.655048e+02 PMG: contraction number = , 2.655048e+02 PMG: iteration = 8 PMG: relative residual = 6.837770e-06 PMG: contraction number = 3.935183e-01 NEWTON: using errtol_s: 2.389732e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.094020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.355627e+02 PMG: contraction number = , 1.355627e+02 PMG: iteration = 9 PMG: relative residual = 3.491161e-06 PMG: contraction number = 5.105701e-01 NEWTON: using errtol_s: 1.220126e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.185940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.758862e+01 PMG: contraction number = , 5.758862e+01 PMG: iteration = 10 PMG: relative residual = 1.483061e-06 PMG: contraction number = 4.248047e-01 NEWTON: using errtol_s: 5.183150e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.274080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.619233e+01 PMG: contraction number = , 2.619233e+01 PMG: iteration = 11 PMG: relative residual = 6.745070e-07 PMG: contraction number = 4.548072e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.513600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.850200e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -102.542) Vpmg_setPart: upper corner = (141.283, 130.313, 162.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -102.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 162.928) 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 = 2.558685360017E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.385537469408E+05 kT Vpmg_energy: dielEnergy = 4.192342346338E+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 = 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, 108.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -102.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 162.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 108.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -102.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 162.928) 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, 108.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -102.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 162.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0139198 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0168987 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 = 1.218400e+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 = 5.240000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.436000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.511950e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.777127e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.567520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.487666e+06 PMG: contraction number = , 6.487666e+06 NEWTON: attempting damping, relres = 1.730113e-01 NEWTON: attempting damping, relres = 5.775627e-01 NEWTON: damping accepted, relres = 1.730113e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.730113e-01 PMG: contraction number = 1.730113e-01 NEWTON: using errtol_s: 6.534856e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.672600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.805910e+05 PMG: contraction number = , 8.805910e+05 PMG: iteration = 2 PMG: relative residual = 2.594805e-02 PMG: contraction number = 1.499789e-01 NEWTON: using errtol_s: 9.800907e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.751410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.599954e+05 PMG: contraction number = , 1.599954e+05 PMG: iteration = 3 PMG: relative residual = 5.032961e-03 PMG: contraction number = 1.939630e-01 NEWTON: using errtol_s: 1.901013e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.829600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.679384e+04 PMG: contraction number = , 3.679384e+04 PMG: iteration = 4 PMG: relative residual = 1.203932e-03 PMG: contraction number = 2.392095e-01 NEWTON: using errtol_s: 4.547404e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.906470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.059666e+04 PMG: contraction number = , 1.059666e+04 PMG: iteration = 5 PMG: relative residual = 3.332984e-04 PMG: contraction number = 2.768415e-01 NEWTON: using errtol_s: 1.258910e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.983070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.782464e+03 PMG: contraction number = , 3.782464e+03 PMG: iteration = 6 PMG: relative residual = 1.009052e-04 PMG: contraction number = 3.027475e-01 NEWTON: using errtol_s: 3.811319e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.062590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.276114e+03 PMG: contraction number = , 1.276114e+03 PMG: iteration = 7 PMG: relative residual = 3.053620e-05 PMG: contraction number = 3.026225e-01 NEWTON: using errtol_s: 1.153391e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.138320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.517392e+02 PMG: contraction number = , 4.517392e+02 PMG: iteration = 8 PMG: relative residual = 1.078011e-05 PMG: contraction number = 3.530272e-01 NEWTON: using errtol_s: 4.071784e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.215300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.860480e+02 PMG: contraction number = , 1.860480e+02 PMG: iteration = 9 PMG: relative residual = 4.433157e-06 PMG: contraction number = 4.112349e-01 NEWTON: using errtol_s: 1.674460e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.289130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.722306e+01 PMG: contraction number = , 8.722306e+01 PMG: iteration = 10 PMG: relative residual = 2.079056e-06 PMG: contraction number = 4.689786e-01 NEWTON: using errtol_s: 7.852858e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.366610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.237260e+01 PMG: contraction number = , 4.237260e+01 PMG: iteration = 11 PMG: relative residual = 1.009645e-06 PMG: contraction number = 4.856265e-01 NEWTON: using errtol_s: 3.813556e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.440010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.135566e+01 PMG: contraction number = , 2.135566e+01 PMG: iteration = 12 PMG: relative residual = 5.088782e-07 PMG: contraction number = 5.040172e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.833500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.017430e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 108.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 108.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.516046988039E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.898685176855E+06 kT Vpmg_energy: dielEnergy = 9.493005813279E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.339000e+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 = 6.609840e+03