############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Mar 13 09:17:23 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_allh39.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb39.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, 85.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 31.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 85.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 29.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 57.26) 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 31.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 31.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.603728 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.353098 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.584863 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 31.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 166.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -104.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 110.287 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 110.287 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 31.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 31.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.603728 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.353098 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.584863 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 31.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 166.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -104.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 110.287 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 110.287 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 31.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 31.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.603728 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.353098 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.584863 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 31.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 166.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -104.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 110.287 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 110.287 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 = 82.3887 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 110.81 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, 122.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 12998921 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.290000e+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 = 5.340000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.528000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.097500e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.176921e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.698800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.420228e+06 PMG: contraction number = , 4.420228e+06 NEWTON: attempting damping, relres = 1.079376e-01 NEWTON: attempting damping, relres = 5.453742e-01 NEWTON: damping accepted, relres = 1.079376e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.079376e-01 PMG: contraction number = 1.079376e-01 NEWTON: using errtol_s: 4.508468e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.802900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.021952e+05 PMG: contraction number = , 6.021952e+05 PMG: iteration = 2 PMG: relative residual = 1.599097e-02 PMG: contraction number = 1.481502e-01 NEWTON: using errtol_s: 6.679304e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.625100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.158083e+05 PMG: contraction number = , 1.158083e+05 PMG: iteration = 3 PMG: relative residual = 3.082116e-03 PMG: contraction number = 1.927410e-01 NEWTON: using errtol_s: 1.287375e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.450700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.665703e+04 PMG: contraction number = , 2.665703e+04 PMG: iteration = 4 PMG: relative residual = 6.865377e-04 PMG: contraction number = 2.227488e-01 NEWTON: using errtol_s: 2.867614e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.251200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.209282e+03 PMG: contraction number = , 7.209282e+03 PMG: iteration = 5 PMG: relative residual = 1.723740e-04 PMG: contraction number = 2.510772e-01 NEWTON: using errtol_s: 7.199926e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.041300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.174729e+03 PMG: contraction number = , 2.174729e+03 PMG: iteration = 6 PMG: relative residual = 4.795657e-05 PMG: contraction number = 2.782123e-01 NEWTON: using errtol_s: 2.003108e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.923000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.966397e+02 PMG: contraction number = , 6.966397e+02 PMG: iteration = 7 PMG: relative residual = 1.501602e-05 PMG: contraction number = 3.131171e-01 NEWTON: using errtol_s: 6.272075e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.727700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.630707e+02 PMG: contraction number = , 2.630707e+02 PMG: iteration = 8 PMG: relative residual = 5.668533e-06 PMG: contraction number = 3.774989e-01 NEWTON: using errtol_s: 2.367701e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.536600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.286094e+02 PMG: contraction number = , 1.286094e+02 PMG: iteration = 9 PMG: relative residual = 2.771314e-06 PMG: contraction number = 4.888943e-01 NEWTON: using errtol_s: 1.157556e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.343000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.900989e+01 PMG: contraction number = , 5.900989e+01 PMG: iteration = 10 PMG: relative residual = 1.271504e-06 PMG: contraction number = 4.588090e-01 NEWTON: using errtol_s: 5.310971e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.657720e+01 PMG: contraction number = , 2.657720e+01 PMG: iteration = 11 PMG: relative residual = 5.726663e-07 PMG: contraction number = 4.503851e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.538300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.894600e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -104.042) Vpmg_setPart: upper corner = (141.283, 130.313, 166.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 166.428) 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 = 2.798643081797E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.711015701138E+05 kT Vpmg_energy: dielEnergy = 4.855053958692E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.371000e+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 = 82.3887 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 110.81 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, 122.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 12998921 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, 110.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -104.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 166.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 110.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 166.428) 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, 110.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -104.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 166.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0141941 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0174452 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 = 1.232800e+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 = 5.370000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.344000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.247930e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.523320e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.810645e+06 PMG: contraction number = , 7.810645e+06 NEWTON: attempting damping, relres = 1.707451e-01 NEWTON: attempting damping, relres = 5.779048e-01 NEWTON: damping accepted, relres = 1.707451e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.707451e-01 PMG: contraction number = 1.707451e-01 NEWTON: using errtol_s: 7.723345e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.411310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.053746e+06 PMG: contraction number = , 1.053746e+06 PMG: iteration = 2 PMG: relative residual = 2.504592e-02 PMG: contraction number = 1.466861e-01 NEWTON: using errtol_s: 1.132907e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.487960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.859489e+05 PMG: contraction number = , 1.859489e+05 PMG: iteration = 3 PMG: relative residual = 4.691231e-03 PMG: contraction number = 1.873052e-01 NEWTON: using errtol_s: 2.121994e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.561790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.114195e+04 PMG: contraction number = , 4.114195e+04 PMG: iteration = 4 PMG: relative residual = 1.080750e-03 PMG: contraction number = 2.303766e-01 NEWTON: using errtol_s: 4.888578e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.638820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.133393e+04 PMG: contraction number = , 1.133393e+04 PMG: iteration = 5 PMG: relative residual = 2.895082e-04 PMG: contraction number = 2.678772e-01 NEWTON: using errtol_s: 1.309538e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.716440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.883174e+03 PMG: contraction number = , 3.883174e+03 PMG: iteration = 6 PMG: relative residual = 8.526776e-05 PMG: contraction number = 2.945262e-01 NEWTON: using errtol_s: 3.856933e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.794370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.278771e+03 PMG: contraction number = , 1.278771e+03 PMG: iteration = 7 PMG: relative residual = 2.552909e-05 PMG: contraction number = 2.993991e-01 NEWTON: using errtol_s: 1.154762e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.880900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.326451e+02 PMG: contraction number = , 4.326451e+02 PMG: iteration = 8 PMG: relative residual = 8.622698e-06 PMG: contraction number = 3.377597e-01 NEWTON: using errtol_s: 3.900322e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.957220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.853183e+02 PMG: contraction number = , 1.853183e+02 PMG: iteration = 9 PMG: relative residual = 3.687295e-06 PMG: contraction number = 4.276266e-01 NEWTON: using errtol_s: 1.667881e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.037140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.443184e+01 PMG: contraction number = , 8.443184e+01 PMG: iteration = 10 PMG: relative residual = 1.680325e-06 PMG: contraction number = 4.557068e-01 NEWTON: using errtol_s: 7.600649e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.115340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.192668e+01 PMG: contraction number = , 4.192668e+01 PMG: iteration = 11 PMG: relative residual = 8.342169e-07 PMG: contraction number = 4.964616e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.202500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.540400e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 110.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 110.287) 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 = 2.749648729932E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.220455363260E+06 kT Vpmg_energy: dielEnergy = 1.110182978297E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.196000e+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, 22.0691) 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 = 3.889000e+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 = 5.260000e+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 = 2.351720e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.900402e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.409210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.983522e+05 PMG: contraction number = , 6.983522e+05 NEWTON: attempting damping, relres = 9.194752e-02 NEWTON: attempting damping, relres = 5.435215e-01 NEWTON: damping accepted, relres = 9.194752e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.194752e-02 PMG: contraction number = 9.194752e-02 NEWTON: using errtol_s: 6.344748e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.521680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.091936e+04 PMG: contraction number = , 9.091936e+04 PMG: iteration = 2 PMG: relative residual = 1.186463e-02 PMG: contraction number = 1.290370e-01 NEWTON: using errtol_s: 8.187074e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.602300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.415793e+04 PMG: contraction number = , 1.415793e+04 PMG: iteration = 3 PMG: relative residual = 1.846643e-03 PMG: contraction number = 1.556426e-01 NEWTON: using errtol_s: 1.274258e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.673620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.457799e+03 PMG: contraction number = , 2.457799e+03 PMG: iteration = 4 PMG: relative residual = 3.205652e-04 PMG: contraction number = 1.735935e-01 NEWTON: using errtol_s: 2.212029e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.757970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.618510e+02 PMG: contraction number = , 4.618510e+02 PMG: iteration = 5 PMG: relative residual = 6.023875e-05 PMG: contraction number = 1.879142e-01 NEWTON: using errtol_s: 4.156716e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.832810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.129036e+02 PMG: contraction number = , 1.129036e+02 PMG: iteration = 6 PMG: relative residual = 1.472572e-05 PMG: contraction number = 2.444559e-01 NEWTON: using errtol_s: 1.016134e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.916030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.013741e+01 PMG: contraction number = , 4.013741e+01 PMG: iteration = 7 PMG: relative residual = 5.235125e-06 PMG: contraction number = 3.555090e-01 NEWTON: using errtol_s: 3.612447e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.997280e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.894267e+01 PMG: contraction number = , 1.894267e+01 PMG: iteration = 8 PMG: relative residual = 2.470641e-06 PMG: contraction number = 4.719354e-01 NEWTON: using errtol_s: 1.704842e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.073380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.871988e+00 PMG: contraction number = , 8.871988e+00 PMG: iteration = 9 PMG: relative residual = 1.157163e-06 PMG: contraction number = 4.683655e-01 NEWTON: using errtol_s: 7.984890e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.153450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.897287e+00 PMG: contraction number = , 3.897287e+00 PMG: iteration = 10 PMG: relative residual = 5.083123e-07 PMG: contraction number = 4.392746e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.560200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.889400e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -104.042) Vpmg_setPart: upper corner = (141.283, 130.313, 166.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 166.428) 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 = 2.581901202802E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.414310584389E+05 kT Vpmg_energy: dielEnergy = 7.071249356863E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.311000e+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, 22.0691) 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, 110.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -104.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 166.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 110.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 166.428) 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, 110.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -104.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 166.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000163275 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000231374 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 = 6.739000e+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 = 2.332000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.334550e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465433e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.391250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.338455e+06 PMG: contraction number = , 1.338455e+06 NEWTON: attempting damping, relres = 1.621743e-01 NEWTON: attempting damping, relres = 5.805299e-01 NEWTON: damping accepted, relres = 1.621743e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.621743e-01 PMG: contraction number = 1.621743e-01 NEWTON: using errtol_s: 1.210702e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.503750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.733563e+05 PMG: contraction number = , 1.733563e+05 PMG: iteration = 2 PMG: relative residual = 2.090647e-02 PMG: contraction number = 1.289135e-01 NEWTON: using errtol_s: 1.560758e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.573520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.566076e+04 PMG: contraction number = , 2.566076e+04 PMG: iteration = 3 PMG: relative residual = 3.093577e-03 PMG: contraction number = 1.479723e-01 NEWTON: using errtol_s: 2.309489e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.643300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.181501e+03 PMG: contraction number = , 4.181501e+03 PMG: iteration = 4 PMG: relative residual = 5.041046e-04 PMG: contraction number = 1.629520e-01 NEWTON: using errtol_s: 3.763359e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.713010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.248170e+02 PMG: contraction number = , 7.248170e+02 PMG: iteration = 5 PMG: relative residual = 8.738141e-05 PMG: contraction number = 1.733398e-01 NEWTON: using errtol_s: 6.523400e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.799370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.758428e+02 PMG: contraction number = , 1.758428e+02 PMG: iteration = 6 PMG: relative residual = 2.119888e-05 PMG: contraction number = 2.426017e-01 NEWTON: using errtol_s: 1.582588e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.869050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.661973e+01 PMG: contraction number = , 8.661973e+01 PMG: iteration = 7 PMG: relative residual = 1.044309e-05 PMG: contraction number = 4.926244e-01 NEWTON: using errtol_s: 7.796216e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.938580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.768395e+01 PMG: contraction number = , 3.768395e+01 PMG: iteration = 8 PMG: relative residual = 4.543024e-06 PMG: contraction number = 4.350269e-01 NEWTON: using errtol_s: 3.391564e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.007840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.707786e+01 PMG: contraction number = , 1.707786e+01 PMG: iteration = 9 PMG: relative residual = 2.058915e-06 PMG: contraction number = 4.532037e-01 NEWTON: using errtol_s: 1.537069e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.077630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.724658e+00 PMG: contraction number = , 7.724658e+00 PMG: iteration = 10 PMG: relative residual = 9.312517e-07 PMG: contraction number = 4.523021e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.878100e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.205500e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 110.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 110.287) 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 = 2.510243298712E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.383005665522E+05 kT Vpmg_energy: dielEnergy = 1.691473501921E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.298000e+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 = 6.199000e+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 = 2.351000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.320370e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.487210e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.375320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.724041e+06 PMG: contraction number = , 3.724041e+06 NEWTON: attempting damping, relres = 1.111883e-01 NEWTON: attempting damping, relres = 5.457623e-01 NEWTON: damping accepted, relres = 1.111883e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.111883e-01 PMG: contraction number = 1.111883e-01 NEWTON: using errtol_s: 3.877368e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.480920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.117491e+05 PMG: contraction number = , 5.117491e+05 PMG: iteration = 2 PMG: relative residual = 1.682874e-02 PMG: contraction number = 1.513536e-01 NEWTON: using errtol_s: 5.868535e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.559850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.018682e+05 PMG: contraction number = , 1.018682e+05 PMG: iteration = 3 PMG: relative residual = 3.336147e-03 PMG: contraction number = 1.982411e-01 NEWTON: using errtol_s: 1.163385e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.647800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.412151e+04 PMG: contraction number = , 2.412151e+04 PMG: iteration = 4 PMG: relative residual = 7.602584e-04 PMG: contraction number = 2.278851e-01 NEWTON: using errtol_s: 2.651180e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.723790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.696564e+03 PMG: contraction number = , 6.696564e+03 PMG: iteration = 5 PMG: relative residual = 1.949925e-04 PMG: contraction number = 2.564819e-01 NEWTON: using errtol_s: 6.799799e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.800380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.067291e+03 PMG: contraction number = , 2.067291e+03 PMG: iteration = 6 PMG: relative residual = 5.502286e-05 PMG: contraction number = 2.821793e-01 NEWTON: using errtol_s: 1.918763e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.874890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.605372e+02 PMG: contraction number = , 6.605372e+02 PMG: iteration = 7 PMG: relative residual = 1.705805e-05 PMG: contraction number = 3.100175e-01 NEWTON: using errtol_s: 5.948500e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.948990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.369917e+02 PMG: contraction number = , 2.369917e+02 PMG: iteration = 8 PMG: relative residual = 6.116650e-06 PMG: contraction number = 3.585785e-01 NEWTON: using errtol_s: 2.133004e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.025590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.151786e+02 PMG: contraction number = , 1.151786e+02 PMG: iteration = 9 PMG: relative residual = 2.972728e-06 PMG: contraction number = 4.860059e-01 NEWTON: using errtol_s: 1.036653e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.100090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.321353e+01 PMG: contraction number = , 5.321353e+01 PMG: iteration = 10 PMG: relative residual = 1.373389e-06 PMG: contraction number = 4.619963e-01 NEWTON: using errtol_s: 4.789297e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.174190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.410177e+01 PMG: contraction number = , 2.410177e+01 PMG: iteration = 11 PMG: relative residual = 6.220404e-07 PMG: contraction number = 4.529235e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.047800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.381900e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -104.042) Vpmg_setPart: upper corner = (141.283, 130.313, 166.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 166.428) 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 = 2.559384190872E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.296716939278E+05 kT Vpmg_energy: dielEnergy = 4.147932070646E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.283000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 110.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -104.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 166.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 110.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 166.428) 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, 110.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -104.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 166.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0141545 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0172566 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 = 1.082300e+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 = 5.270000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.340000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.390710e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.776776e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.445090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.473125e+06 PMG: contraction number = , 6.473125e+06 NEWTON: attempting damping, relres = 1.724447e-01 NEWTON: attempting damping, relres = 5.773906e-01 NEWTON: damping accepted, relres = 1.724447e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.724447e-01 PMG: contraction number = 1.724447e-01 NEWTON: using errtol_s: 6.512851e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.540000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.790767e+05 PMG: contraction number = , 8.790767e+05 PMG: iteration = 2 PMG: relative residual = 2.582483e-02 PMG: contraction number = 1.497571e-01 NEWTON: using errtol_s: 9.753459e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.608710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.595094e+05 PMG: contraction number = , 1.595094e+05 PMG: iteration = 3 PMG: relative residual = 4.991107e-03 PMG: contraction number = 1.932678e-01 NEWTON: using errtol_s: 1.885029e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.677520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.639794e+04 PMG: contraction number = , 3.639794e+04 PMG: iteration = 4 PMG: relative residual = 1.185836e-03 PMG: contraction number = 2.375898e-01 NEWTON: using errtol_s: 4.478637e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.749300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.034124e+04 PMG: contraction number = , 1.034124e+04 PMG: iteration = 5 PMG: relative residual = 3.255169e-04 PMG: contraction number = 2.745042e-01 NEWTON: using errtol_s: 1.229405e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.836220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.625573e+03 PMG: contraction number = , 3.625573e+03 PMG: iteration = 6 PMG: relative residual = 9.678924e-05 PMG: contraction number = 2.973401e-01 NEWTON: using errtol_s: 3.655513e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.905330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.190854e+03 PMG: contraction number = , 1.190854e+03 PMG: iteration = 7 PMG: relative residual = 2.850475e-05 PMG: contraction number = 2.945032e-01 NEWTON: using errtol_s: 1.076560e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.973780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.045853e+02 PMG: contraction number = , 4.045853e+02 PMG: iteration = 8 PMG: relative residual = 9.656318e-06 PMG: contraction number = 3.387618e-01 NEWTON: using errtol_s: 3.646975e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.042920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.666782e+02 PMG: contraction number = , 1.666782e+02 PMG: iteration = 9 PMG: relative residual = 3.971911e-06 PMG: contraction number = 4.113277e-01 NEWTON: using errtol_s: 1.500102e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.111590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.524555e+01 PMG: contraction number = , 7.524555e+01 PMG: iteration = 10 PMG: relative residual = 1.793559e-06 PMG: contraction number = 4.515608e-01 NEWTON: using errtol_s: 6.773872e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.180730e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.624533e+01 PMG: contraction number = , 3.624533e+01 PMG: iteration = 11 PMG: relative residual = 8.637245e-07 PMG: contraction number = 4.815701e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.338800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.667300e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 110.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 110.287) 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 = 2.516521646361E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.882155991939E+06 kT Vpmg_energy: dielEnergy = 9.410359539905E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.230000e+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 = 6.326700e+03