############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 11 18:13:14 2014 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path piplc_hsp82_bound_to_pcpg_80_20_allh33.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb33.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 79.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 28.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 79.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 23.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 51.26) 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 28.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 155.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.287 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 104.287 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 28.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 155.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.287 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 104.287 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 28.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 155.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.287 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 104.287 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 = 80.515 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 104.81 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, 116.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13483687 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 = 6.890000e+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 = 2.337000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.036600e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.200769e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.580900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.592429e+06 PMG: contraction number = , 4.592429e+06 NEWTON: attempting damping, relres = 1.129668e-01 NEWTON: attempting damping, relres = 5.471201e-01 NEWTON: damping accepted, relres = 1.129668e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.129668e-01 PMG: contraction number = 1.129668e-01 NEWTON: using errtol_s: 4.745476e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.608600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.332272e+05 PMG: contraction number = , 6.332272e+05 PMG: iteration = 2 PMG: relative residual = 1.720906e-02 PMG: contraction number = 1.523373e-01 NEWTON: using errtol_s: 7.229130e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.357900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.227181e+05 PMG: contraction number = , 1.227181e+05 PMG: iteration = 3 PMG: relative residual = 3.415728e-03 PMG: contraction number = 1.984843e-01 NEWTON: using errtol_s: 1.434869e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.125000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.913626e+04 PMG: contraction number = , 2.913626e+04 PMG: iteration = 4 PMG: relative residual = 7.872689e-04 PMG: contraction number = 2.304835e-01 NEWTON: using errtol_s: 3.307135e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.961800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.147975e+03 PMG: contraction number = , 8.147975e+03 PMG: iteration = 5 PMG: relative residual = 2.024156e-04 PMG: contraction number = 2.571112e-01 NEWTON: using errtol_s: 8.503013e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.960200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.504033e+03 PMG: contraction number = , 2.504033e+03 PMG: iteration = 6 PMG: relative residual = 5.674446e-05 PMG: contraction number = 2.803364e-01 NEWTON: using errtol_s: 2.383704e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.878600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.858714e+02 PMG: contraction number = , 7.858714e+02 PMG: iteration = 7 PMG: relative residual = 1.690643e-05 PMG: contraction number = 2.979397e-01 NEWTON: using errtol_s: 7.102001e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.686800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.486618e+02 PMG: contraction number = , 2.486618e+02 PMG: iteration = 8 PMG: relative residual = 5.328550e-06 PMG: contraction number = 3.151789e-01 NEWTON: using errtol_s: 2.238401e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.450100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.857273e+01 PMG: contraction number = , 9.857273e+01 PMG: iteration = 9 PMG: relative residual = 2.111932e-06 PMG: contraction number = 3.963427e-01 NEWTON: using errtol_s: 8.871739e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.283000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.623875e+01 PMG: contraction number = , 4.623875e+01 PMG: iteration = 10 PMG: relative residual = 9.906650e-07 PMG: contraction number = 4.690800e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.854400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.190300e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.542) Vpmg_setPart: upper corner = (141.283, 130.313, 155.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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 = 2.819130172805E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.003614350407E+06 kT Vpmg_energy: dielEnergy = 5.017613335872E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.389000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 80.515 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 104.81 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, 116.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13483687 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 155.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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, 104.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 155.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0150355 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0184229 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 = 1.269000e+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 = 2.334000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.176290e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.524826e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.881619e+06 PMG: contraction number = , 7.881619e+06 NEWTON: attempting damping, relres = 1.736508e-01 NEWTON: attempting damping, relres = 5.786504e-01 NEWTON: damping accepted, relres = 1.736508e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.736508e-01 PMG: contraction number = 1.736508e-01 NEWTON: using errtol_s: 7.857396e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.359620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.062855e+06 PMG: contraction number = , 1.062855e+06 PMG: iteration = 2 PMG: relative residual = 2.572239e-02 PMG: contraction number = 1.481272e-01 NEWTON: using errtol_s: 1.163894e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.450440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.892841e+05 PMG: contraction number = , 1.892841e+05 PMG: iteration = 3 PMG: relative residual = 4.891370e-03 PMG: contraction number = 1.901600e-01 NEWTON: using errtol_s: 2.213260e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.523200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.334370e+04 PMG: contraction number = , 4.334370e+04 PMG: iteration = 4 PMG: relative residual = 1.151444e-03 PMG: contraction number = 2.354033e-01 NEWTON: using errtol_s: 5.210086e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.618870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.237481e+04 PMG: contraction number = , 1.237481e+04 PMG: iteration = 5 PMG: relative residual = 3.159827e-04 PMG: contraction number = 2.744229e-01 NEWTON: using errtol_s: 1.429767e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.711360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.357749e+03 PMG: contraction number = , 4.357749e+03 PMG: iteration = 6 PMG: relative residual = 9.617587e-05 PMG: contraction number = 3.043707e-01 NEWTON: using errtol_s: 4.351791e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.808300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.466204e+03 PMG: contraction number = , 1.466204e+03 PMG: iteration = 7 PMG: relative residual = 2.926456e-05 PMG: contraction number = 3.042817e-01 NEWTON: using errtol_s: 1.324170e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.899400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.946120e+02 PMG: contraction number = , 4.946120e+02 PMG: iteration = 8 PMG: relative residual = 9.851509e-06 PMG: contraction number = 3.366362e-01 NEWTON: using errtol_s: 4.457637e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.987500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.949487e+02 PMG: contraction number = , 1.949487e+02 PMG: iteration = 9 PMG: relative residual = 3.877119e-06 PMG: contraction number = 3.935559e-01 NEWTON: using errtol_s: 1.754329e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.095750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.539872e+01 PMG: contraction number = , 8.539872e+01 PMG: iteration = 10 PMG: relative residual = 1.699124e-06 PMG: contraction number = 4.382440e-01 NEWTON: using errtol_s: 7.688242e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.172720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.913673e+01 PMG: contraction number = , 3.913673e+01 PMG: iteration = 11 PMG: relative residual = 7.784285e-07 PMG: contraction number = 4.581351e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.069310e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.102080e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.287) 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 = 2.771313917066E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.278812441562E+06 kT Vpmg_energy: dielEnergy = 1.139361193064E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.157000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.0691) 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 = 3.837000e+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 = 5.650000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.940000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.431100e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.957696e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.485950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.266283e+05 PMG: contraction number = , 7.266283e+05 NEWTON: attempting damping, relres = 9.484585e-02 NEWTON: attempting damping, relres = 5.451167e-01 NEWTON: damping accepted, relres = 9.484585e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.484585e-02 PMG: contraction number = 9.484585e-02 NEWTON: using errtol_s: 6.599086e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.593590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.539394e+04 PMG: contraction number = , 9.539394e+04 PMG: iteration = 2 PMG: relative residual = 1.234610e-02 PMG: contraction number = 1.301702e-01 NEWTON: using errtol_s: 8.590042e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.674980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.502457e+04 PMG: contraction number = , 1.502457e+04 PMG: iteration = 3 PMG: relative residual = 1.943520e-03 PMG: contraction number = 1.574197e-01 NEWTON: using errtol_s: 1.352242e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.765610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.626062e+03 PMG: contraction number = , 2.626062e+03 PMG: iteration = 4 PMG: relative residual = 3.396903e-04 PMG: contraction number = 1.747810e-01 NEWTON: using errtol_s: 2.363462e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.848920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.880198e+02 PMG: contraction number = , 4.880198e+02 PMG: iteration = 5 PMG: relative residual = 6.312720e-05 PMG: contraction number = 1.858375e-01 NEWTON: using errtol_s: 4.392199e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.943610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.072006e+02 PMG: contraction number = , 1.072006e+02 PMG: iteration = 6 PMG: relative residual = 1.386675e-05 PMG: contraction number = 2.196636e-01 NEWTON: using errtol_s: 9.648060e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.030400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.595208e+01 PMG: contraction number = , 3.595208e+01 PMG: iteration = 7 PMG: relative residual = 4.650565e-06 PMG: contraction number = 3.353754e-01 NEWTON: using errtol_s: 3.235722e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.114600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.728658e+01 PMG: contraction number = , 1.728658e+01 PMG: iteration = 8 PMG: relative residual = 2.236075e-06 PMG: contraction number = 4.808179e-01 NEWTON: using errtol_s: 1.555793e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.190380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.353614e+00 PMG: contraction number = , 9.353614e+00 PMG: iteration = 9 PMG: relative residual = 1.209931e-06 PMG: contraction number = 5.410959e-01 NEWTON: using errtol_s: 8.418331e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.283310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.769426e+00 PMG: contraction number = , 4.769426e+00 PMG: iteration = 10 PMG: relative residual = 6.169405e-07 PMG: contraction number = 5.098974e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.060700e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.454100e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.542) Vpmg_setPart: upper corner = (141.283, 130.313, 155.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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 = 2.577527936684E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.465268152113E+05 kT Vpmg_energy: dielEnergy = 7.326037994920E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.285000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.0691) 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, 104.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 155.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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, 104.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 155.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000173882 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000246939 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 = 6.621000e+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 = 2.328000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.460620e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.466830e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.522930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.348421e+06 PMG: contraction number = , 1.348421e+06 NEWTON: attempting damping, relres = 1.633404e-01 NEWTON: attempting damping, relres = 5.811488e-01 NEWTON: damping accepted, relres = 1.633404e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.633404e-01 PMG: contraction number = 1.633404e-01 NEWTON: using errtol_s: 1.219635e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.639980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.742933e+05 PMG: contraction number = , 1.742933e+05 PMG: iteration = 2 PMG: relative residual = 2.101578e-02 PMG: contraction number = 1.286625e-01 NEWTON: using errtol_s: 1.569213e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.722760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.582218e+04 PMG: contraction number = , 2.582218e+04 PMG: iteration = 3 PMG: relative residual = 3.112455e-03 PMG: contraction number = 1.481009e-01 NEWTON: using errtol_s: 2.324017e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.797700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.207963e+03 PMG: contraction number = , 4.207963e+03 PMG: iteration = 4 PMG: relative residual = 5.071997e-04 PMG: contraction number = 1.629581e-01 NEWTON: using errtol_s: 3.787174e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.891970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.252604e+02 PMG: contraction number = , 7.252604e+02 PMG: iteration = 5 PMG: relative residual = 8.741821e-05 PMG: contraction number = 1.723546e-01 NEWTON: using errtol_s: 6.527369e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.003980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.537733e+02 PMG: contraction number = , 1.537733e+02 PMG: iteration = 6 PMG: relative residual = 1.853478e-05 PMG: contraction number = 2.120243e-01 NEWTON: using errtol_s: 1.383961e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.081980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.953648e+01 PMG: contraction number = , 6.953648e+01 PMG: iteration = 7 PMG: relative residual = 8.381717e-06 PMG: contraction number = 4.522156e-01 NEWTON: using errtol_s: 6.258486e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.193660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.444483e+01 PMG: contraction number = , 3.444483e+01 PMG: iteration = 8 PMG: relative residual = 4.151750e-06 PMG: contraction number = 4.953340e-01 NEWTON: using errtol_s: 3.100041e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.285000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.452612e+01 PMG: contraction number = , 1.452612e+01 PMG: iteration = 9 PMG: relative residual = 1.750936e-06 PMG: contraction number = 4.217346e-01 NEWTON: using errtol_s: 1.307394e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.379980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.739898e+00 PMG: contraction number = , 6.739898e+00 PMG: iteration = 10 PMG: relative residual = 8.123811e-07 PMG: contraction number = 4.639695e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.865600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.019270e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.287) 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 = 2.507366130507E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.445716491001E+05 kT Vpmg_energy: dielEnergy = 1.722828957029E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.309000e+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 = 7.134000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.300000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.420000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.661100e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.505746e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.717210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.870093e+06 PMG: contraction number = , 3.870093e+06 NEWTON: attempting damping, relres = 1.150191e-01 NEWTON: attempting damping, relres = 5.475092e-01 NEWTON: damping accepted, relres = 1.150191e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.150191e-01 PMG: contraction number = 1.150191e-01 NEWTON: using errtol_s: 4.032279e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.832940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.353751e+05 PMG: contraction number = , 5.353751e+05 PMG: iteration = 2 PMG: relative residual = 1.757508e-02 PMG: contraction number = 1.528014e-01 NEWTON: using errtol_s: 6.161377e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.920510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.055551e+05 PMG: contraction number = , 1.055551e+05 PMG: iteration = 3 PMG: relative residual = 3.506498e-03 PMG: contraction number = 1.995153e-01 NEWTON: using errtol_s: 1.229289e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.001530e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.490597e+04 PMG: contraction number = , 2.490597e+04 PMG: iteration = 4 PMG: relative residual = 8.077896e-04 PMG: contraction number = 2.303693e-01 NEWTON: using errtol_s: 2.831906e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.080780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.939309e+03 PMG: contraction number = , 6.939309e+03 PMG: iteration = 5 PMG: relative residual = 2.102217e-04 PMG: contraction number = 2.602431e-01 NEWTON: using errtol_s: 7.369838e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.161860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.205198e+03 PMG: contraction number = , 2.205198e+03 PMG: iteration = 6 PMG: relative residual = 6.102208e-05 PMG: contraction number = 2.902750e-01 NEWTON: using errtol_s: 2.139280e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.243100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.220538e+02 PMG: contraction number = , 7.220538e+02 PMG: iteration = 7 PMG: relative residual = 1.868429e-05 PMG: contraction number = 3.061889e-01 NEWTON: using errtol_s: 6.550238e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.332050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.346067e+02 PMG: contraction number = , 2.346067e+02 PMG: iteration = 8 PMG: relative residual = 6.023579e-06 PMG: contraction number = 3.223874e-01 NEWTON: using errtol_s: 2.111714e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.418680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.844869e+01 PMG: contraction number = , 8.844869e+01 PMG: iteration = 9 PMG: relative residual = 2.270696e-06 PMG: contraction number = 3.769679e-01 NEWTON: using errtol_s: 7.960484e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.497760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.174068e+01 PMG: contraction number = , 4.174068e+01 PMG: iteration = 10 PMG: relative residual = 1.071594e-06 PMG: contraction number = 4.719232e-01 NEWTON: using errtol_s: 3.756737e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.581990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.108620e+01 PMG: contraction number = , 2.108620e+01 PMG: iteration = 11 PMG: relative residual = 5.413304e-07 PMG: contraction number = 5.051637e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.743900e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.008970e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.542) Vpmg_setPart: upper corner = (141.283, 130.313, 155.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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 = 2.557898245141E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.570893758881E+05 kT Vpmg_energy: dielEnergy = 4.285020668887E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.429000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 155.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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, 104.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 155.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0152143 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0183283 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 = 1.219900e+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 = 5.320000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.730000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.823460e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.778147e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.878660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.535046e+06 PMG: contraction number = , 6.535046e+06 NEWTON: attempting damping, relres = 1.736557e-01 NEWTON: attempting damping, relres = 5.781215e-01 NEWTON: damping accepted, relres = 1.736557e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.736557e-01 PMG: contraction number = 1.736557e-01 NEWTON: using errtol_s: 6.560969e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.986190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.838716e+05 PMG: contraction number = , 8.838716e+05 PMG: iteration = 2 PMG: relative residual = 2.585637e-02 PMG: contraction number = 1.488944e-01 NEWTON: using errtol_s: 9.768918e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.063070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.594408e+05 PMG: contraction number = , 1.594408e+05 PMG: iteration = 3 PMG: relative residual = 4.958660e-03 PMG: contraction number = 1.917771e-01 NEWTON: using errtol_s: 1.873455e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.142560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.651314e+04 PMG: contraction number = , 3.651314e+04 PMG: iteration = 4 PMG: relative residual = 1.175701e-03 PMG: contraction number = 2.371006e-01 NEWTON: using errtol_s: 4.441973e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.243950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.053772e+04 PMG: contraction number = , 1.053772e+04 PMG: iteration = 5 PMG: relative residual = 3.263858e-04 PMG: contraction number = 2.776094e-01 NEWTON: using errtol_s: 1.233133e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.344770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.783664e+03 PMG: contraction number = , 3.783664e+03 PMG: iteration = 6 PMG: relative residual = 9.994096e-05 PMG: contraction number = 3.062050e-01 NEWTON: using errtol_s: 3.775917e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.442100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.260841e+03 PMG: contraction number = , 1.260841e+03 PMG: iteration = 7 PMG: relative residual = 3.008587e-05 PMG: contraction number = 3.010364e-01 NEWTON: using errtol_s: 1.136688e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.523390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.240162e+02 PMG: contraction number = , 4.240162e+02 PMG: iteration = 8 PMG: relative residual = 1.011348e-05 PMG: contraction number = 3.361539e-01 NEWTON: using errtol_s: 3.821023e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.605450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.700688e+02 PMG: contraction number = , 1.700688e+02 PMG: iteration = 9 PMG: relative residual = 4.050688e-06 PMG: contraction number = 4.005235e-01 NEWTON: using errtol_s: 1.530409e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.702330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.414522e+01 PMG: contraction number = , 7.414522e+01 PMG: iteration = 10 PMG: relative residual = 1.766627e-06 PMG: contraction number = 4.361301e-01 NEWTON: using errtol_s: 6.674576e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.794250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.446737e+01 PMG: contraction number = , 3.446737e+01 PMG: iteration = 11 PMG: relative residual = 8.210416e-07 PMG: contraction number = 4.647510e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.035130e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.072810e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.287) 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 = 2.514578387393E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.934242795836E+06 kT Vpmg_energy: dielEnergy = 9.670795251519E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.117000e+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 = 6.966450e+03 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 11 20:47:13 2014 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path piplc_hsp82_bound_to_pcpg_80_20_allh33.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb33.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 79.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 28.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 79.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 23.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 51.26) 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 0.4425 28.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.4425 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.4425 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.314 155.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.391 104.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.506 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.391 104.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.506 -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 = -2.5935 -0.8825 51.26 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -2.5935 -0.8825 51.26 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -2.5935 -0.8825 51.26 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 139.846 128.989 178.995 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -145.034 -130.754 -76.475 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 79.3825 76.066 127.354 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -84.5695 -77.831 -24.834 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 79.3825 76.066 127.354 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -84.5695 -77.831 -24.834 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 0.4425 0.281 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.4425 0.281 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.4425 0.281 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.314 128.016 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -127.454 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.391 76.375 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.506 -75.813 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.391 76.375 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.506 -75.813 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 80.515 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 104.81 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, 116.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13483687 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 = 6.864000e+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 = 5.230000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.339000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028700e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.200760e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.592565e+06 PMG: contraction number = , 4.592565e+06 NEWTON: attempting damping, relres = 1.129696e-01 NEWTON: attempting damping, relres = 5.471217e-01 NEWTON: damping accepted, relres = 1.129696e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.129696e-01 PMG: contraction number = 1.129696e-01 NEWTON: using errtol_s: 4.745582e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.514600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.332825e+05 PMG: contraction number = , 6.332825e+05 PMG: iteration = 2 PMG: relative residual = 1.721031e-02 PMG: contraction number = 1.523446e-01 NEWTON: using errtol_s: 7.229638e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.208700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.227320e+05 PMG: contraction number = , 1.227320e+05 PMG: iteration = 3 PMG: relative residual = 3.416209e-03 PMG: contraction number = 1.984978e-01 NEWTON: using errtol_s: 1.435067e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.902200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.913833e+04 PMG: contraction number = , 2.913833e+04 PMG: iteration = 4 PMG: relative residual = 7.874423e-04 PMG: contraction number = 2.305018e-01 NEWTON: using errtol_s: 3.307856e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.595900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.150119e+03 PMG: contraction number = , 8.150119e+03 PMG: iteration = 5 PMG: relative residual = 2.024837e-04 PMG: contraction number = 2.571411e-01 NEWTON: using errtol_s: 8.505857e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.289100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.504430e+03 PMG: contraction number = , 2.504430e+03 PMG: iteration = 6 PMG: relative residual = 5.675078e-05 PMG: contraction number = 2.802733e-01 NEWTON: using errtol_s: 2.383964e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.982400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.858813e+02 PMG: contraction number = , 7.858813e+02 PMG: iteration = 7 PMG: relative residual = 1.690636e-05 PMG: contraction number = 2.979053e-01 NEWTON: using errtol_s: 7.101956e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.675800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.487255e+02 PMG: contraction number = , 2.487255e+02 PMG: iteration = 8 PMG: relative residual = 5.329932e-06 PMG: contraction number = 3.152620e-01 NEWTON: using errtol_s: 2.238977e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.369000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.872565e+01 PMG: contraction number = , 9.872565e+01 PMG: iteration = 9 PMG: relative residual = 2.115213e-06 PMG: contraction number = 3.968556e-01 NEWTON: using errtol_s: 8.885504e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.062300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.635616e+01 PMG: contraction number = , 4.635616e+01 PMG: iteration = 10 PMG: relative residual = 9.931827e-07 PMG: contraction number = 4.695426e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.481900e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.812500e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.542) Vpmg_setPart: upper corner = (141.283, 130.314, 155.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.314, 155.928) 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 = 2.819018906464E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.003613934590E+06 kT Vpmg_energy: dielEnergy = 5.017611312401E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.243000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 80.515 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 104.81 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, 116.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13483687 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, -76.506, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.391, 104.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.314, 155.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.506, -47.901) Vpmg_setPart: upper corner = (80.819, 77.391, 104.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.314, 155.928) 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, -76.506, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.391, 104.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.542) VPMG::extEnergy Old upper corner = (141.283, 130.314, 155.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0150371 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0184247 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 = 1.217500e+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 = 5.250000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.341000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.030340e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.524827e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.084690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.881491e+06 PMG: contraction number = , 7.881491e+06 NEWTON: attempting damping, relres = 1.736383e-01 NEWTON: attempting damping, relres = 5.786491e-01 NEWTON: damping accepted, relres = 1.736383e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.736383e-01 PMG: contraction number = 1.736383e-01 NEWTON: using errtol_s: 7.856831e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.184590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.062861e+06 PMG: contraction number = , 1.062861e+06 PMG: iteration = 2 PMG: relative residual = 2.571892e-02 PMG: contraction number = 1.481178e-01 NEWTON: using errtol_s: 1.163737e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.255650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.892654e+05 PMG: contraction number = , 1.892654e+05 PMG: iteration = 3 PMG: relative residual = 4.889906e-03 PMG: contraction number = 1.901287e-01 NEWTON: using errtol_s: 2.212598e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.331690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.333758e+04 PMG: contraction number = , 4.333758e+04 PMG: iteration = 4 PMG: relative residual = 1.150872e-03 PMG: contraction number = 2.353567e-01 NEWTON: using errtol_s: 5.207497e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.418420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.237181e+04 PMG: contraction number = , 1.237181e+04 PMG: iteration = 5 PMG: relative residual = 3.157650e-04 PMG: contraction number = 2.743702e-01 NEWTON: using errtol_s: 1.428782e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.505550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.355840e+03 PMG: contraction number = , 4.355840e+03 PMG: iteration = 6 PMG: relative residual = 9.610227e-05 PMG: contraction number = 3.043475e-01 NEWTON: using errtol_s: 4.348461e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.584880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.465039e+03 PMG: contraction number = , 1.465039e+03 PMG: iteration = 7 PMG: relative residual = 2.923962e-05 PMG: contraction number = 3.042553e-01 NEWTON: using errtol_s: 1.323042e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.675040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.940854e+02 PMG: contraction number = , 4.940854e+02 PMG: iteration = 8 PMG: relative residual = 9.841058e-06 PMG: contraction number = 3.365658e-01 NEWTON: using errtol_s: 4.452909e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.765200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.949287e+02 PMG: contraction number = , 1.949287e+02 PMG: iteration = 9 PMG: relative residual = 3.876720e-06 PMG: contraction number = 3.939332e-01 NEWTON: using errtol_s: 1.754149e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.850840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.537742e+01 PMG: contraction number = , 8.537742e+01 PMG: iteration = 10 PMG: relative residual = 1.698699e-06 PMG: contraction number = 4.381794e-01 NEWTON: using errtol_s: 7.686318e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.936140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.914617e+01 PMG: contraction number = , 3.914617e+01 PMG: iteration = 11 PMG: relative residual = 7.786163e-07 PMG: contraction number = 4.583604e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.522700e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.855000e+02 Vpmg_setPart: lower corner = (-83.133, -76.506, -47.901) Vpmg_setPart: upper corner = (80.819, 77.391, 104.287) Vpmg_setPart: actual minima = (-83.133, -76.506, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.391, 104.287) 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 = 2.771277947349E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.278795476725E+06 kT Vpmg_energy: dielEnergy = 1.139352711649E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.167000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.0691) 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 = 3.818000e+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 = 5.230000e+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 = 2.158570e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.957014e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.218410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.217944e+05 PMG: contraction number = , 7.217944e+05 NEWTON: attempting damping, relres = 9.422468e-02 NEWTON: attempting damping, relres = 5.447364e-01 NEWTON: damping accepted, relres = 9.422468e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.422468e-02 PMG: contraction number = 9.422468e-02 NEWTON: using errtol_s: 6.555224e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.340590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.386234e+04 PMG: contraction number = , 9.386234e+04 PMG: iteration = 2 PMG: relative residual = 1.214890e-02 PMG: contraction number = 1.289354e-01 NEWTON: using errtol_s: 8.452007e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.426020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.464028e+04 PMG: contraction number = , 1.464028e+04 PMG: iteration = 3 PMG: relative residual = 1.894001e-03 PMG: contraction number = 1.558990e-01 NEWTON: using errtol_s: 1.317659e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.509430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.533547e+03 PMG: contraction number = , 2.533547e+03 PMG: iteration = 4 PMG: relative residual = 3.277553e-04 PMG: contraction number = 1.730491e-01 NEWTON: using errtol_s: 2.280198e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.601670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.608561e+02 PMG: contraction number = , 4.608561e+02 PMG: iteration = 5 PMG: relative residual = 5.961934e-05 PMG: contraction number = 1.819020e-01 NEWTON: using errtol_s: 4.147726e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.693510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.525736e+01 PMG: contraction number = , 9.525736e+01 PMG: iteration = 6 PMG: relative residual = 1.232306e-05 PMG: contraction number = 2.066957e-01 NEWTON: using errtol_s: 8.573169e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.786120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.782193e+01 PMG: contraction number = , 2.782193e+01 PMG: iteration = 7 PMG: relative residual = 3.599242e-06 PMG: contraction number = 2.920738e-01 NEWTON: using errtol_s: 2.503998e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.895130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.181633e+01 PMG: contraction number = , 1.181633e+01 PMG: iteration = 8 PMG: relative residual = 1.528629e-06 PMG: contraction number = 4.247087e-01 NEWTON: using errtol_s: 1.063470e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.988910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.792862e+00 PMG: contraction number = , 5.792862e+00 PMG: iteration = 9 PMG: relative residual = 7.494035e-07 PMG: contraction number = 4.902453e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.986300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.314400e+02 Vpmg_setPart: lower corner = (-145.034, -130.754, -76.475) Vpmg_setPart: upper corner = (139.846, 128.989, 178.995) Vpmg_setPart: actual minima = (-145.034, -130.754, -76.475) Vpmg_setPart: actual maxima = (139.846, 128.989, 178.995) 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 = 2.583747594526E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.468550517094E+05 kT Vpmg_energy: dielEnergy = 7.342448918035E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.402000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.0691) 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 = -84.5695, -77.831, -24.834 VPMG::focusFillBound -- New mesh maxs = 79.3825, 76.066, 127.354 VPMG::focusFillBound -- Old mesh mins = -145.034, -130.754, -76.475 VPMG::focusFillBound -- Old mesh maxs = 139.846, 128.989, 178.995 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-84.5695, -77.831, -24.834) Vpmg_setPart: upper corner = (79.3825, 76.066, 127.354) Vpmg_setPart: actual minima = (-145.034, -130.754, -76.475) Vpmg_setPart: actual maxima = (139.846, 128.989, 178.995) 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 = (-84.5695, -77.831, -24.834) VPMG::extEnergy Disj part upper corner = (79.3825, 76.066, 127.354) VPMG::extEnergy Old lower corner = (-145.034, -130.754, -76.475) VPMG::extEnergy Old upper corner = (139.846, 128.989, 178.995) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 3.05654e-06 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 3.97372e-06 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 = 6.905000e+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 = 5.280000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.345000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.186500e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.455221e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.240940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.346502e+06 PMG: contraction number = , 1.346502e+06 NEWTON: attempting damping, relres = 1.633654e-01 NEWTON: attempting damping, relres = 5.811656e-01 NEWTON: damping accepted, relres = 1.633654e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.633654e-01 PMG: contraction number = 1.633654e-01 NEWTON: using errtol_s: 1.217925e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.339970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.736956e+05 PMG: contraction number = , 1.736956e+05 PMG: iteration = 2 PMG: relative residual = 2.097662e-02 PMG: contraction number = 1.284031e-01 NEWTON: using errtol_s: 1.563853e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.412540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.567010e+04 PMG: contraction number = , 2.567010e+04 PMG: iteration = 3 PMG: relative residual = 3.098939e-03 PMG: contraction number = 1.477330e-01 NEWTON: using errtol_s: 2.310327e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.489940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.178442e+03 PMG: contraction number = , 4.178442e+03 PMG: iteration = 4 PMG: relative residual = 5.044256e-04 PMG: contraction number = 1.627737e-01 NEWTON: using errtol_s: 3.760604e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.578420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.191941e+02 PMG: contraction number = , 7.191941e+02 PMG: iteration = 5 PMG: relative residual = 8.682200e-05 PMG: contraction number = 1.721205e-01 NEWTON: using errtol_s: 6.472772e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.651230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.507347e+02 PMG: contraction number = , 1.507347e+02 PMG: iteration = 6 PMG: relative residual = 1.819683e-05 PMG: contraction number = 2.095877e-01 NEWTON: using errtol_s: 1.356614e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.723970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.406082e+01 PMG: contraction number = , 6.406082e+01 PMG: iteration = 7 PMG: relative residual = 7.733701e-06 PMG: contraction number = 4.250027e-01 NEWTON: using errtol_s: 5.765645e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.797700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.163693e+01 PMG: contraction number = , 3.163693e+01 PMG: iteration = 8 PMG: relative residual = 3.819241e-06 PMG: contraction number = 4.938439e-01 NEWTON: using errtol_s: 2.847329e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.870380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.308037e+01 PMG: contraction number = , 1.308037e+01 PMG: iteration = 9 PMG: relative residual = 1.579121e-06 PMG: contraction number = 4.134645e-01 NEWTON: using errtol_s: 1.177269e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.943080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.984730e+00 PMG: contraction number = , 5.984730e+00 PMG: iteration = 10 PMG: relative residual = 7.224815e-07 PMG: contraction number = 4.575214e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.042000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.378700e+02 Vpmg_setPart: lower corner = (-84.5695, -77.831, -24.834) Vpmg_setPart: upper corner = (79.3825, 76.066, 127.354) Vpmg_setPart: actual minima = (-84.5695, -77.831, -24.834) Vpmg_setPart: actual maxima = (79.3825, 76.066, 127.354) 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 = 2.508387505207E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.447562330263E+05 kT Vpmg_energy: dielEnergy = 1.723751861563E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.303000e+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 = 6.223000e+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 = 5.230000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.338000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.195360e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.504483e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.250720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.853762e+06 PMG: contraction number = , 3.853762e+06 NEWTON: attempting damping, relres = 1.142227e-01 NEWTON: attempting damping, relres = 5.473430e-01 NEWTON: damping accepted, relres = 1.142227e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.142227e-01 PMG: contraction number = 1.142227e-01 NEWTON: using errtol_s: 4.002914e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.345450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.287467e+05 PMG: contraction number = , 5.287467e+05 PMG: iteration = 2 PMG: relative residual = 1.727524e-02 PMG: contraction number = 1.512418e-01 NEWTON: using errtol_s: 6.054079e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.413720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.032819e+05 PMG: contraction number = , 1.032819e+05 PMG: iteration = 3 PMG: relative residual = 3.401341e-03 PMG: contraction number = 1.968911e-01 NEWTON: using errtol_s: 1.191994e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.482010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.408645e+04 PMG: contraction number = , 2.408645e+04 PMG: iteration = 4 PMG: relative residual = 7.710302e-04 PMG: contraction number = 2.266842e-01 NEWTON: using errtol_s: 2.702062e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.550350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.577148e+03 PMG: contraction number = , 6.577148e+03 PMG: iteration = 5 PMG: relative residual = 1.953024e-04 PMG: contraction number = 2.533005e-01 NEWTON: using errtol_s: 6.844339e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.618600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.007942e+03 PMG: contraction number = , 2.007942e+03 PMG: iteration = 6 PMG: relative residual = 5.437920e-05 PMG: contraction number = 2.784360e-01 NEWTON: using errtol_s: 1.905710e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.686900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.339363e+02 PMG: contraction number = , 6.339363e+02 PMG: iteration = 7 PMG: relative residual = 1.632510e-05 PMG: contraction number = 3.002086e-01 NEWTON: using errtol_s: 5.721106e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.755160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.074624e+02 PMG: contraction number = , 2.074624e+02 PMG: iteration = 8 PMG: relative residual = 5.329253e-06 PMG: contraction number = 3.264452e-01 NEWTON: using errtol_s: 1.867628e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.823410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.311176e+01 PMG: contraction number = , 9.311176e+01 PMG: iteration = 9 PMG: relative residual = 2.391310e-06 PMG: contraction number = 4.487140e-01 NEWTON: using errtol_s: 8.380308e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.891640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.475991e+01 PMG: contraction number = , 4.475991e+01 PMG: iteration = 10 PMG: relative residual = 1.149521e-06 PMG: contraction number = 4.807075e-01 NEWTON: using errtol_s: 4.028476e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.959900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.108342e+01 PMG: contraction number = , 2.108342e+01 PMG: iteration = 11 PMG: relative residual = 5.414562e-07 PMG: contraction number = 4.710277e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.084300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.412100e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -127.454) Vpmg_setPart: upper corner = (141.283, 130.314, 128.016) Vpmg_setPart: actual minima = (-143.597, -129.429, -127.454) Vpmg_setPart: actual maxima = (141.283, 130.314, 128.016) 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 = 2.558513918286E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.568988094815E+05 kT Vpmg_energy: dielEnergy = 4.284067266526E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.250000e+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, -76.506, -75.813 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.391, 76.375 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -127.454 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.314, 128.016 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.506, -75.813) Vpmg_setPart: upper corner = (80.819, 77.391, 76.375) Vpmg_setPart: actual minima = (-143.597, -129.429, -127.454) Vpmg_setPart: actual maxima = (141.283, 130.314, 128.016) 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, -76.506, -75.813) VPMG::extEnergy Disj part upper corner = (80.819, 77.391, 76.375) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -127.454) VPMG::extEnergy Old upper corner = (141.283, 130.314, 128.016) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.00176825 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.00219525 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 = 1.100000e+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 = 5.230000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.338000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.170710e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.763670e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.228680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.516874e+06 PMG: contraction number = , 6.516874e+06 NEWTON: attempting damping, relres = 1.761138e-01 NEWTON: attempting damping, relres = 5.782081e-01 NEWTON: damping accepted, relres = 1.761138e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.761138e-01 PMG: contraction number = 1.761138e-01 NEWTON: using errtol_s: 6.628342e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.367990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.869805e+05 PMG: contraction number = , 8.869805e+05 PMG: iteration = 2 PMG: relative residual = 2.684258e-02 PMG: contraction number = 1.524161e-01 NEWTON: using errtol_s: 1.010266e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.479400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.614175e+05 PMG: contraction number = , 1.614175e+05 PMG: iteration = 3 PMG: relative residual = 5.312659e-03 PMG: contraction number = 1.979191e-01 NEWTON: using errtol_s: 1.999509e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.588750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.743836e+04 PMG: contraction number = , 3.743836e+04 PMG: iteration = 4 PMG: relative residual = 1.302860e-03 PMG: contraction number = 2.452369e-01 NEWTON: using errtol_s: 4.903536e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.675900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.083707e+04 PMG: contraction number = , 1.083707e+04 PMG: iteration = 5 PMG: relative residual = 3.684834e-04 PMG: contraction number = 2.828265e-01 NEWTON: using errtol_s: 1.386850e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.788000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.838195e+03 PMG: contraction number = , 3.838195e+03 PMG: iteration = 6 PMG: relative residual = 1.110726e-04 PMG: contraction number = 3.014316e-01 NEWTON: using errtol_s: 4.180405e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.898480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.252907e+03 PMG: contraction number = , 1.252907e+03 PMG: iteration = 7 PMG: relative residual = 3.106244e-05 PMG: contraction number = 2.796590e-01 NEWTON: using errtol_s: 1.169088e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.985340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.268264e+02 PMG: contraction number = , 4.268264e+02 PMG: iteration = 8 PMG: relative residual = 1.022132e-05 PMG: contraction number = 3.290571e-01 NEWTON: using errtol_s: 3.846966e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.061840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.594229e+02 PMG: contraction number = , 1.594229e+02 PMG: iteration = 9 PMG: relative residual = 3.812317e-06 PMG: contraction number = 3.729771e-01 NEWTON: using errtol_s: 1.434830e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.173420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.738999e+01 PMG: contraction number = , 7.738999e+01 PMG: iteration = 10 PMG: relative residual = 1.851309e-06 PMG: contraction number = 4.856125e-01 NEWTON: using errtol_s: 6.967715e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.282960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.666449e+01 PMG: contraction number = , 3.666449e+01 PMG: iteration = 11 PMG: relative residual = 8.767568e-07 PMG: contraction number = 4.735875e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.190270e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.223070e+03 Vpmg_setPart: lower corner = (-83.133, -76.506, -75.813) Vpmg_setPart: upper corner = (80.819, 77.391, 76.375) Vpmg_setPart: actual minima = (-83.133, -76.506, -75.813) Vpmg_setPart: actual maxima = (80.819, 77.391, 76.375) 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 = 2.516186992602E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.927809989088E+06 kT Vpmg_energy: dielEnergy = 9.638629580851E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.202000e+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 = 6.464020e+03 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Mar 12 11:43:35 2014 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path piplc_hsp82_bound_to_pcpg_80_20_allh33.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb33.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 etol... PBEparm_parseToken: trying etol... MGparm_parseToken: trying etol... 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 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 etol... PBEparm_parseToken: trying etol... MGparm_parseToken: trying etol... 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 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 etol... PBEparm_parseToken: trying etol... MGparm_parseToken: trying etol... 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 end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 79.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 28.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 79.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 23.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 51.26) 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 28.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 155.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.287 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 104.287 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 28.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 155.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.287 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 104.287 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 28.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.570246 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.339705 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.595718 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 28.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 155.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -99.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 104.287 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 104.287 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 = 80.515 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 104.81 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, 116.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13483687 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Error tolerance (etol) is now set to user-defined value: 1e-12 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 = 6.855000e+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 = 5.230000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.330000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024100e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.200769e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.560900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.592429e+06 PMG: contraction number = , 4.592429e+06 NEWTON: attempting damping, relres = 1.129668e-01 NEWTON: attempting damping, relres = 5.471201e-01 NEWTON: damping accepted, relres = 1.129668e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.129668e-01 PMG: contraction number = 1.129668e-01 NEWTON: using errtol_s: 4.745476e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.494600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.332272e+05 PMG: contraction number = , 6.332272e+05 PMG: iteration = 2 PMG: relative residual = 1.720906e-02 PMG: contraction number = 1.523373e-01 NEWTON: using errtol_s: 7.229130e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.175200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.227181e+05 PMG: contraction number = , 1.227181e+05 PMG: iteration = 3 PMG: relative residual = 3.415728e-03 PMG: contraction number = 1.984843e-01 NEWTON: using errtol_s: 1.434869e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.855600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.913626e+04 PMG: contraction number = , 2.913626e+04 PMG: iteration = 4 PMG: relative residual = 7.872689e-04 PMG: contraction number = 2.304835e-01 NEWTON: using errtol_s: 3.307135e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.535600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.147975e+03 PMG: contraction number = , 8.147975e+03 PMG: iteration = 5 PMG: relative residual = 2.024156e-04 PMG: contraction number = 2.571112e-01 NEWTON: using errtol_s: 8.503013e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.215300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.504033e+03 PMG: contraction number = , 2.504033e+03 PMG: iteration = 6 PMG: relative residual = 5.674446e-05 PMG: contraction number = 2.803364e-01 NEWTON: using errtol_s: 2.383704e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.895700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.858714e+02 PMG: contraction number = , 7.858714e+02 PMG: iteration = 7 PMG: relative residual = 1.690643e-05 PMG: contraction number = 2.979397e-01 NEWTON: using errtol_s: 7.102001e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.658600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.486618e+02 PMG: contraction number = , 2.486618e+02 PMG: iteration = 8 PMG: relative residual = 5.328550e-06 PMG: contraction number = 3.151789e-01 NEWTON: using errtol_s: 2.238401e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.723200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.857273e+01 PMG: contraction number = , 9.857273e+01 PMG: iteration = 9 PMG: relative residual = 2.111932e-06 PMG: contraction number = 3.963427e-01 NEWTON: using errtol_s: 8.871739e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.403400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.623875e+01 PMG: contraction number = , 4.623875e+01 PMG: iteration = 10 PMG: relative residual = 9.906650e-07 PMG: contraction number = 4.690800e-01 NEWTON: using errtol_s: 4.161555e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.083500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.381818e+01 PMG: contraction number = , 2.381818e+01 PMG: iteration = 11 PMG: relative residual = 5.103004e-07 PMG: contraction number = 5.151090e-01 NEWTON: using errtol_s: 2.143654e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.763500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.126101e+01 PMG: contraction number = , 1.126101e+01 PMG: iteration = 12 PMG: relative residual = 2.412638e-07 PMG: contraction number = 4.727877e-01 NEWTON: using errtol_s: 1.013493e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.044360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.167379e+00 PMG: contraction number = , 5.167379e+00 PMG: iteration = 13 PMG: relative residual = 1.107095e-07 PMG: contraction number = 4.588734e-01 NEWTON: using errtol_s: 4.650652e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.302201e+00 PMG: contraction number = , 2.302201e+00 PMG: iteration = 14 PMG: relative residual = 4.932387e-08 PMG: contraction number = 4.455250e-01 NEWTON: using errtol_s: 2.071982e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.037589e+00 PMG: contraction number = , 1.037589e+00 PMG: iteration = 15 PMG: relative residual = 2.222999e-08 PMG: contraction number = 4.506945e-01 NEWTON: using errtol_s: 9.338308e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.248380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.612142e-01 PMG: contraction number = , 4.612142e-01 PMG: iteration = 16 PMG: relative residual = 9.881354e-09 PMG: contraction number = 4.445055e-01 NEWTON: using errtol_s: 2.127186e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.316380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.071235e-01 PMG: contraction number = , 2.071235e-01 PMG: iteration = 17 PMG: relative residual = 4.437550e-09 PMG: contraction number = 4.490832e-01 NEWTON: using errtol_s: 4.290019e-02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.384400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.219919e-02 PMG: contraction number = , 9.219919e-02 PMG: iteration = 2 PMG: relative residual = , 4.135925e-02 PMG: contraction number = , 4.485858e-01 PMG: iteration = 18 PMG: relative residual = 8.861088e-10 PMG: contraction number = 1.996842e-01 NEWTON: using errtol_s: 1.710593e-03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.844061e-02 PMG: contraction number = , 1.844061e-02 PMG: iteration = 2 PMG: relative residual = , 8.270497e-03 PMG: contraction number = , 4.484937e-01 PMG: iteration = 3 PMG: relative residual = , 3.693122e-03 PMG: contraction number = , 4.465417e-01 PMG: iteration = 4 PMG: relative residual = , 1.656737e-03 PMG: contraction number = , 4.486006e-01 PMG: iteration = 19 PMG: relative residual = 3.549652e-11 PMG: contraction number = 4.005887e-02 NEWTON: using errtol_s: 2.745012e-06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.599110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.407997e-04 PMG: contraction number = , 7.407997e-04 PMG: iteration = 2 PMG: relative residual = , 3.324266e-04 PMG: contraction number = , 4.487402e-01 PMG: iteration = 3 PMG: relative residual = , 1.487876e-04 PMG: contraction number = , 4.475803e-01 PMG: iteration = 4 PMG: relative residual = , 6.678490e-05 PMG: contraction number = , 4.488606e-01 PMG: iteration = 5 PMG: relative residual = , 2.991726e-05 PMG: contraction number = , 4.479645e-01 PMG: iteration = 6 PMG: relative residual = , 1.343346e-05 PMG: contraction number = , 4.490203e-01 PMG: iteration = 7 PMG: relative residual = , 6.023269e-06 PMG: contraction number = , 4.483781e-01 PMG: iteration = 8 PMG: relative residual = , 2.706345e-06 PMG: contraction number = , 4.493150e-01 PMG: iteration = 20 PMG: relative residual = 5.987871e-14 PMG: contraction number = 1.686890e-03 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.678030e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.710720e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.542) Vpmg_setPart: upper corner = (141.283, 130.313, 155.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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 = 2.819159601745E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.003614359893E+06 kT Vpmg_energy: dielEnergy = 5.017613427777E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.234000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 80.515 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 104.81 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, 116.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13483687 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Error tolerance (etol) is now set to user-defined value: 1e-12 Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 155.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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, 104.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 155.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0150347 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0184216 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 = 1.207300e+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 = 5.220000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.334000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.957870e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.524829e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.011550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.881622e+06 PMG: contraction number = , 7.881622e+06 NEWTON: attempting damping, relres = 1.736507e-01 NEWTON: attempting damping, relres = 5.786504e-01 NEWTON: damping accepted, relres = 1.736507e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.736507e-01 PMG: contraction number = 1.736507e-01 NEWTON: using errtol_s: 7.857398e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.104270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.062892e+06 PMG: contraction number = , 1.062892e+06 PMG: iteration = 2 PMG: relative residual = 2.572316e-02 PMG: contraction number = 1.481316e-01 NEWTON: using errtol_s: 1.163929e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.171840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.892796e+05 PMG: contraction number = , 1.892796e+05 PMG: iteration = 3 PMG: relative residual = 4.891277e-03 PMG: contraction number = 1.901507e-01 NEWTON: using errtol_s: 2.213219e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.239390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.334233e+04 PMG: contraction number = , 4.334233e+04 PMG: iteration = 4 PMG: relative residual = 1.151414e-03 PMG: contraction number = 2.354016e-01 NEWTON: using errtol_s: 5.209953e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.306960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.237445e+04 PMG: contraction number = , 1.237445e+04 PMG: iteration = 5 PMG: relative residual = 3.159753e-04 PMG: contraction number = 2.744236e-01 NEWTON: using errtol_s: 1.429734e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.374510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.357725e+03 PMG: contraction number = , 4.357725e+03 PMG: iteration = 6 PMG: relative residual = 9.617512e-05 PMG: contraction number = 3.043754e-01 NEWTON: using errtol_s: 4.351760e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.442060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.466205e+03 PMG: contraction number = , 1.466205e+03 PMG: iteration = 7 PMG: relative residual = 2.926449e-05 PMG: contraction number = 3.042833e-01 NEWTON: using errtol_s: 1.324168e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.509630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.945994e+02 PMG: contraction number = , 4.945994e+02 PMG: iteration = 8 PMG: relative residual = 9.851253e-06 PMG: contraction number = 3.366283e-01 NEWTON: using errtol_s: 4.457523e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.577190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.949431e+02 PMG: contraction number = , 1.949431e+02 PMG: iteration = 9 PMG: relative residual = 3.877005e-06 PMG: contraction number = 3.935545e-01 NEWTON: using errtol_s: 1.754278e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.644710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.539146e+01 PMG: contraction number = , 8.539146e+01 PMG: iteration = 10 PMG: relative residual = 1.698979e-06 PMG: contraction number = 4.382194e-01 NEWTON: using errtol_s: 7.687589e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.712280e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.913117e+01 PMG: contraction number = , 3.913117e+01 PMG: iteration = 11 PMG: relative residual = 7.783176e-07 PMG: contraction number = 4.581090e-01 NEWTON: using errtol_s: 3.521754e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.779820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.838698e+01 PMG: contraction number = , 1.838698e+01 PMG: iteration = 12 PMG: relative residual = 3.657378e-07 PMG: contraction number = 4.699082e-01 NEWTON: using errtol_s: 1.654901e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.847340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.911911e+00 PMG: contraction number = , 8.911911e+00 PMG: iteration = 13 PMG: relative residual = 1.772599e-07 PMG: contraction number = 4.846639e-01 NEWTON: using errtol_s: 8.020708e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.914870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.358377e+00 PMG: contraction number = , 4.358377e+00 PMG: iteration = 14 PMG: relative residual = 8.668972e-08 PMG: contraction number = 4.890543e-01 NEWTON: using errtol_s: 3.922562e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.982420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.177339e+00 PMG: contraction number = , 2.177339e+00 PMG: iteration = 15 PMG: relative residual = 4.330783e-08 PMG: contraction number = 4.995729e-01 NEWTON: using errtol_s: 1.959605e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.049960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.082806e+00 PMG: contraction number = , 1.082806e+00 PMG: iteration = 16 PMG: relative residual = 2.153731e-08 PMG: contraction number = 4.973076e-01 NEWTON: using errtol_s: 9.745266e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.117500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.417515e-01 PMG: contraction number = , 5.417515e-01 PMG: iteration = 17 PMG: relative residual = 1.077558e-08 PMG: contraction number = 5.003214e-01 NEWTON: using errtol_s: 2.934949e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.185050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.670730e-01 PMG: contraction number = , 2.670730e-01 PMG: iteration = 18 PMG: relative residual = 5.312154e-09 PMG: contraction number = 4.929808e-01 NEWTON: using errtol_s: 7.132810e-02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.252580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.315365e-01 PMG: contraction number = , 1.315365e-01 PMG: iteration = 2 PMG: relative residual = , 6.390740e-02 PMG: contraction number = , 4.858529e-01 PMG: iteration = 19 PMG: relative residual = 1.271138e-09 PMG: contraction number = 2.392887e-01 NEWTON: using errtol_s: 4.084182e-03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.339790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.109899e-02 PMG: contraction number = , 3.109899e-02 PMG: iteration = 2 PMG: relative residual = , 1.500664e-02 PMG: contraction number = , 4.825444e-01 PMG: iteration = 3 PMG: relative residual = , 7.272086e-03 PMG: contraction number = , 4.845911e-01 PMG: iteration = 4 PMG: relative residual = , 3.504721e-03 PMG: contraction number = , 4.819416e-01 PMG: iteration = 20 PMG: relative residual = 6.971391e-11 PMG: contraction number = 5.484367e-02 NEWTON: using errtol_s: 1.228452e-05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.466350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.697332e-03 PMG: contraction number = , 1.697332e-03 PMG: iteration = 2 PMG: relative residual = , 8.184482e-04 PMG: contraction number = , 4.821970e-01 PMG: iteration = 3 PMG: relative residual = , 3.964643e-04 PMG: contraction number = , 4.844097e-01 PMG: iteration = 4 PMG: relative residual = , 1.912992e-04 PMG: contraction number = , 4.825130e-01 PMG: iteration = 5 PMG: relative residual = , 9.268210e-05 PMG: contraction number = , 4.844877e-01 PMG: iteration = 6 PMG: relative residual = , 4.473783e-05 PMG: contraction number = , 4.827020e-01 PMG: iteration = 7 PMG: relative residual = , 2.167427e-05 PMG: contraction number = , 4.844730e-01 PMG: iteration = 8 PMG: relative residual = , 1.046397e-05 PMG: contraction number = , 4.827829e-01 PMG: iteration = 21 PMG: relative residual = 2.127957e-13 PMG: contraction number = 3.052415e-03 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.689610e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.722320e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.287) 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 = 2.771365601767E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.278812452604E+06 kT Vpmg_energy: dielEnergy = 1.139361203587E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.082000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.0691) 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... Error tolerance (etol) is now set to user-defined value: 1e-12 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 = 3.800000e+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 = 2.333000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.740640e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.957696e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.794180e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.266283e+05 PMG: contraction number = , 7.266283e+05 NEWTON: attempting damping, relres = 9.484585e-02 NEWTON: attempting damping, relres = 5.451167e-01 NEWTON: damping accepted, relres = 9.484585e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.484585e-02 PMG: contraction number = 9.484585e-02 NEWTON: using errtol_s: 6.599086e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.887670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.539394e+04 PMG: contraction number = , 9.539394e+04 PMG: iteration = 2 PMG: relative residual = 1.234610e-02 PMG: contraction number = 1.301702e-01 NEWTON: using errtol_s: 8.590042e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.955710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.502457e+04 PMG: contraction number = , 1.502457e+04 PMG: iteration = 3 PMG: relative residual = 1.943520e-03 PMG: contraction number = 1.574197e-01 NEWTON: using errtol_s: 1.352242e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.023690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.626062e+03 PMG: contraction number = , 2.626062e+03 PMG: iteration = 4 PMG: relative residual = 3.396903e-04 PMG: contraction number = 1.747810e-01 NEWTON: using errtol_s: 2.363462e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.091650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.880198e+02 PMG: contraction number = , 4.880198e+02 PMG: iteration = 5 PMG: relative residual = 6.312720e-05 PMG: contraction number = 1.858375e-01 NEWTON: using errtol_s: 4.392199e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.159630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.072006e+02 PMG: contraction number = , 1.072006e+02 PMG: iteration = 6 PMG: relative residual = 1.386675e-05 PMG: contraction number = 2.196636e-01 NEWTON: using errtol_s: 9.648060e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.227620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.595208e+01 PMG: contraction number = , 3.595208e+01 PMG: iteration = 7 PMG: relative residual = 4.650565e-06 PMG: contraction number = 3.353754e-01 NEWTON: using errtol_s: 3.235722e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.295570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.728658e+01 PMG: contraction number = , 1.728658e+01 PMG: iteration = 8 PMG: relative residual = 2.236075e-06 PMG: contraction number = 4.808179e-01 NEWTON: using errtol_s: 1.555793e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.363520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.353614e+00 PMG: contraction number = , 9.353614e+00 PMG: iteration = 9 PMG: relative residual = 1.209931e-06 PMG: contraction number = 5.410959e-01 NEWTON: using errtol_s: 8.418331e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.431500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.769426e+00 PMG: contraction number = , 4.769426e+00 PMG: iteration = 10 PMG: relative residual = 6.169405e-07 PMG: contraction number = 5.098974e-01 NEWTON: using errtol_s: 4.292485e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.499480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.136743e+00 PMG: contraction number = , 2.136743e+00 PMG: iteration = 11 PMG: relative residual = 2.763955e-07 PMG: contraction number = 4.480099e-01 NEWTON: using errtol_s: 1.923076e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.567460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.682890e-01 PMG: contraction number = , 9.682890e-01 PMG: iteration = 12 PMG: relative residual = 1.252513e-07 PMG: contraction number = 4.531596e-01 NEWTON: using errtol_s: 8.714602e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.635420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.282367e-01 PMG: contraction number = , 4.282367e-01 PMG: iteration = 13 PMG: relative residual = 5.539380e-08 PMG: contraction number = 4.422615e-01 NEWTON: using errtol_s: 1.833869e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.703390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.935434e-01 PMG: contraction number = , 1.935434e-01 PMG: iteration = 2 PMG: relative residual = , 8.576435e-02 PMG: contraction number = , 4.431271e-01 PMG: iteration = 14 PMG: relative residual = 1.109389e-08 PMG: contraction number = 2.002732e-01 NEWTON: using errtol_s: 7.355527e-03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.791020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.877911e-02 PMG: contraction number = , 3.877911e-02 PMG: iteration = 2 PMG: relative residual = , 1.722204e-02 PMG: contraction number = , 4.441062e-01 PMG: iteration = 3 PMG: relative residual = , 7.788846e-03 PMG: contraction number = , 4.522602e-01 PMG: iteration = 4 PMG: relative residual = , 3.465095e-03 PMG: contraction number = , 4.448792e-01 PMG: iteration = 15 PMG: relative residual = 4.482225e-10 PMG: contraction number = 4.040264e-02 NEWTON: using errtol_s: 1.200696e-05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.917980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.566979e-03 PMG: contraction number = , 1.566979e-03 PMG: iteration = 2 PMG: relative residual = , 6.980212e-04 PMG: contraction number = , 4.454565e-01 PMG: iteration = 3 PMG: relative residual = , 3.155629e-04 PMG: contraction number = , 4.520822e-01 PMG: iteration = 4 PMG: relative residual = , 1.407013e-04 PMG: contraction number = , 4.458741e-01 PMG: iteration = 5 PMG: relative residual = , 6.358061e-05 PMG: contraction number = , 4.518834e-01 PMG: iteration = 6 PMG: relative residual = , 2.836723e-05 PMG: contraction number = , 4.461617e-01 PMG: iteration = 7 PMG: relative residual = , 1.281169e-05 PMG: contraction number = , 4.516369e-01 PMG: iteration = 8 PMG: relative residual = , 5.718374e-06 PMG: contraction number = , 4.463404e-01 PMG: iteration = 16 PMG: relative residual = 7.411859e-13 PMG: contraction number = 1.653612e-03 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.358620e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.391320e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.542) Vpmg_setPart: upper corner = (141.283, 130.313, 155.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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 = 2.577603159495E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.465268155171E+05 kT Vpmg_energy: dielEnergy = 7.326038017970E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.268000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 16.0691) 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... Error tolerance (etol) is now set to user-defined value: 1e-12 Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 155.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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, 104.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 155.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000173952 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000247012 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 = 6.450000e+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 = 5.210000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.333000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.220750e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.466834e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.274320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.348421e+06 PMG: contraction number = , 1.348421e+06 NEWTON: attempting damping, relres = 1.633403e-01 NEWTON: attempting damping, relres = 5.811488e-01 NEWTON: damping accepted, relres = 1.633403e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.633403e-01 PMG: contraction number = 1.633403e-01 NEWTON: using errtol_s: 1.219635e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.367810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.742933e+05 PMG: contraction number = , 1.742933e+05 PMG: iteration = 2 PMG: relative residual = 2.101577e-02 PMG: contraction number = 1.286625e-01 NEWTON: using errtol_s: 1.569213e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.435940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.582219e+04 PMG: contraction number = , 2.582219e+04 PMG: iteration = 3 PMG: relative residual = 3.112454e-03 PMG: contraction number = 1.481009e-01 NEWTON: using errtol_s: 2.324018e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.504070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.207964e+03 PMG: contraction number = , 4.207964e+03 PMG: iteration = 4 PMG: relative residual = 5.071994e-04 PMG: contraction number = 1.629580e-01 NEWTON: using errtol_s: 3.787174e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.572160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.252604e+02 PMG: contraction number = , 7.252604e+02 PMG: iteration = 5 PMG: relative residual = 8.741817e-05 PMG: contraction number = 1.723546e-01 NEWTON: using errtol_s: 6.527370e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.640270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.537733e+02 PMG: contraction number = , 1.537733e+02 PMG: iteration = 6 PMG: relative residual = 1.853477e-05 PMG: contraction number = 2.120243e-01 NEWTON: using errtol_s: 1.383961e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.708400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.953650e+01 PMG: contraction number = , 6.953650e+01 PMG: iteration = 7 PMG: relative residual = 8.381714e-06 PMG: contraction number = 4.522156e-01 NEWTON: using errtol_s: 6.258487e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.776610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.444484e+01 PMG: contraction number = , 3.444484e+01 PMG: iteration = 8 PMG: relative residual = 4.151748e-06 PMG: contraction number = 4.953340e-01 NEWTON: using errtol_s: 3.100042e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.844700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.452612e+01 PMG: contraction number = , 1.452612e+01 PMG: iteration = 9 PMG: relative residual = 1.750936e-06 PMG: contraction number = 4.217346e-01 NEWTON: using errtol_s: 1.307395e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.912830e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.739899e+00 PMG: contraction number = , 6.739899e+00 PMG: iteration = 10 PMG: relative residual = 8.123808e-07 PMG: contraction number = 4.639695e-01 NEWTON: using errtol_s: 6.065913e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.980950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.993192e+00 PMG: contraction number = , 2.993192e+00 PMG: iteration = 11 PMG: relative residual = 3.607813e-07 PMG: contraction number = 4.441037e-01 NEWTON: using errtol_s: 2.693895e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.049080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.400199e+00 PMG: contraction number = , 1.400199e+00 PMG: iteration = 12 PMG: relative residual = 1.687703e-07 PMG: contraction number = 4.677910e-01 NEWTON: using errtol_s: 1.260180e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.117200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.357476e-01 PMG: contraction number = , 6.357476e-01 PMG: iteration = 13 PMG: relative residual = 7.662870e-08 PMG: contraction number = 4.540415e-01 NEWTON: using errtol_s: 4.041764e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.185330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.986438e-01 PMG: contraction number = , 2.986438e-01 PMG: iteration = 14 PMG: relative residual = 3.599644e-08 PMG: contraction number = 4.697514e-01 NEWTON: using errtol_s: 8.918814e-02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.261780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.368992e-01 PMG: contraction number = , 1.368992e-01 PMG: iteration = 2 PMG: relative residual = , 6.439260e-02 PMG: contraction number = , 4.703649e-01 PMG: iteration = 15 PMG: relative residual = 7.761437e-09 PMG: contraction number = 2.156168e-01 NEWTON: using errtol_s: 4.146410e-03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.388190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.966120e-02 PMG: contraction number = , 2.966120e-02 PMG: iteration = 2 PMG: relative residual = , 1.395905e-02 PMG: contraction number = , 4.706164e-01 PMG: iteration = 3 PMG: relative residual = , 6.449075e-03 PMG: contraction number = , 4.619996e-01 PMG: iteration = 4 PMG: relative residual = , 3.035923e-03 PMG: contraction number = , 4.707532e-01 PMG: iteration = 16 PMG: relative residual = 3.659325e-10 PMG: contraction number = 4.714752e-02 NEWTON: using errtol_s: 9.217008e-06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.515370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.405424e-03 PMG: contraction number = , 1.405424e-03 PMG: iteration = 2 PMG: relative residual = , 6.616927e-04 PMG: contraction number = , 4.708135e-01 PMG: iteration = 3 PMG: relative residual = , 3.067582e-04 PMG: contraction number = , 4.635962e-01 PMG: iteration = 4 PMG: relative residual = , 1.444246e-04 PMG: contraction number = , 4.708091e-01 PMG: iteration = 5 PMG: relative residual = , 6.702685e-05 PMG: contraction number = , 4.640959e-01 PMG: iteration = 6 PMG: relative residual = , 3.155356e-05 PMG: contraction number = , 4.707600e-01 PMG: iteration = 7 PMG: relative residual = , 1.465635e-05 PMG: contraction number = , 4.644912e-01 PMG: iteration = 8 PMG: relative residual = , 6.898527e-06 PMG: contraction number = , 4.706851e-01 PMG: iteration = 17 PMG: relative residual = 8.354476e-13 PMG: contraction number = 2.283065e-03 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.553270e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.586020e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.287) 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 = 2.507501567832E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.445716497350E+05 kT Vpmg_energy: dielEnergy = 1.722828962023E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.319000e+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... Error tolerance (etol) is now set to user-defined value: 1e-12 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 = 5.220000e+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 = 6.893540e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.505746e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.947110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.870093e+06 PMG: contraction number = , 3.870093e+06 NEWTON: attempting damping, relres = 1.150191e-01 NEWTON: attempting damping, relres = 5.475092e-01 NEWTON: damping accepted, relres = 1.150191e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.150191e-01 PMG: contraction number = 1.150191e-01 NEWTON: using errtol_s: 4.032279e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.040400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.353751e+05 PMG: contraction number = , 5.353751e+05 PMG: iteration = 2 PMG: relative residual = 1.757508e-02 PMG: contraction number = 1.528014e-01 NEWTON: using errtol_s: 6.161377e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.108440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.055551e+05 PMG: contraction number = , 1.055551e+05 PMG: iteration = 3 PMG: relative residual = 3.506498e-03 PMG: contraction number = 1.995153e-01 NEWTON: using errtol_s: 1.229289e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.176430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.490597e+04 PMG: contraction number = , 2.490597e+04 PMG: iteration = 4 PMG: relative residual = 8.077896e-04 PMG: contraction number = 2.303693e-01 NEWTON: using errtol_s: 2.831906e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.244430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.939309e+03 PMG: contraction number = , 6.939309e+03 PMG: iteration = 5 PMG: relative residual = 2.102217e-04 PMG: contraction number = 2.602431e-01 NEWTON: using errtol_s: 7.369838e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.312410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.205198e+03 PMG: contraction number = , 2.205198e+03 PMG: iteration = 6 PMG: relative residual = 6.102208e-05 PMG: contraction number = 2.902750e-01 NEWTON: using errtol_s: 2.139280e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.380390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.220538e+02 PMG: contraction number = , 7.220538e+02 PMG: iteration = 7 PMG: relative residual = 1.868429e-05 PMG: contraction number = 3.061889e-01 NEWTON: using errtol_s: 6.550238e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.448320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.346067e+02 PMG: contraction number = , 2.346067e+02 PMG: iteration = 8 PMG: relative residual = 6.023579e-06 PMG: contraction number = 3.223874e-01 NEWTON: using errtol_s: 2.111714e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.516320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.844869e+01 PMG: contraction number = , 8.844869e+01 PMG: iteration = 9 PMG: relative residual = 2.270696e-06 PMG: contraction number = 3.769679e-01 NEWTON: using errtol_s: 7.960484e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.584380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.174068e+01 PMG: contraction number = , 4.174068e+01 PMG: iteration = 10 PMG: relative residual = 1.071594e-06 PMG: contraction number = 4.719232e-01 NEWTON: using errtol_s: 3.756737e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.660680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.108620e+01 PMG: contraction number = , 2.108620e+01 PMG: iteration = 11 PMG: relative residual = 5.413304e-07 PMG: contraction number = 5.051637e-01 NEWTON: using errtol_s: 1.897767e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.767050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.985517e+00 PMG: contraction number = , 9.985517e+00 PMG: iteration = 12 PMG: relative residual = 2.563508e-07 PMG: contraction number = 4.735569e-01 NEWTON: using errtol_s: 8.987008e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.835010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.487961e+00 PMG: contraction number = , 4.487961e+00 PMG: iteration = 13 PMG: relative residual = 1.152157e-07 PMG: contraction number = 4.494455e-01 NEWTON: using errtol_s: 4.039170e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.902990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.996498e+00 PMG: contraction number = , 1.996498e+00 PMG: iteration = 14 PMG: relative residual = 5.125442e-08 PMG: contraction number = 4.448563e-01 NEWTON: using errtol_s: 1.796850e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.970920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.887693e-01 PMG: contraction number = , 8.887693e-01 PMG: iteration = 15 PMG: relative residual = 2.281661e-08 PMG: contraction number = 4.451638e-01 NEWTON: using errtol_s: 7.899112e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.038890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.950819e-01 PMG: contraction number = , 3.950819e-01 PMG: iteration = 16 PMG: relative residual = 1.014260e-08 PMG: contraction number = 4.445269e-01 NEWTON: using errtol_s: 1.560898e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.106890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.762639e-01 PMG: contraction number = , 1.762639e-01 PMG: iteration = 2 PMG: relative residual = , 7.860469e-02 PMG: contraction number = , 4.459489e-01 PMG: iteration = 17 PMG: relative residual = 2.017952e-09 PMG: contraction number = 1.989581e-01 NEWTON: using errtol_s: 6.178708e-03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.194530e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.514444e-02 PMG: contraction number = , 3.514444e-02 PMG: iteration = 2 PMG: relative residual = , 1.571045e-02 PMG: contraction number = , 4.470252e-01 PMG: iteration = 3 PMG: relative residual = , 7.033028e-03 PMG: contraction number = , 4.476656e-01 PMG: iteration = 4 PMG: relative residual = , 3.148471e-03 PMG: contraction number = , 4.476694e-01 PMG: iteration = 18 PMG: relative residual = 8.082959e-11 PMG: contraction number = 4.005526e-02 NEWTON: using errtol_s: 9.913265e-06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.321480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.410538e-03 PMG: contraction number = , 1.410538e-03 PMG: iteration = 2 PMG: relative residual = , 6.321292e-04 PMG: contraction number = , 4.481475e-01 PMG: iteration = 3 PMG: relative residual = , 2.833867e-04 PMG: contraction number = , 4.483051e-01 PMG: iteration = 4 PMG: relative residual = , 1.271194e-04 PMG: contraction number = , 4.485723e-01 PMG: iteration = 5 PMG: relative residual = , 5.702927e-05 PMG: contraction number = , 4.486274e-01 PMG: iteration = 6 PMG: relative residual = , 2.560632e-05 PMG: contraction number = , 4.490032e-01 PMG: iteration = 7 PMG: relative residual = , 1.149777e-05 PMG: contraction number = , 4.490206e-01 PMG: iteration = 8 PMG: relative residual = , 5.168102e-06 PMG: contraction number = , 4.494874e-01 PMG: iteration = 19 PMG: relative residual = 1.345303e-13 PMG: contraction number = 1.664370e-03 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.645130e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.677820e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -99.542) Vpmg_setPart: upper corner = (141.283, 130.313, 155.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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 = 2.557904076536E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.570893791090E+05 kT Vpmg_energy: dielEnergy = 4.285020700512E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.239000e+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... Error tolerance (etol) is now set to user-defined value: 1e-12 Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 104.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -99.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 155.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -99.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 155.928) 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, 104.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -99.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 155.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0152154 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0183298 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 = 1.098600e+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 = 5.230000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.333000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.705280e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.778146e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.758930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.535044e+06 PMG: contraction number = , 6.535044e+06 NEWTON: attempting damping, relres = 1.736557e-01 NEWTON: attempting damping, relres = 5.781215e-01 NEWTON: damping accepted, relres = 1.736557e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.736557e-01 PMG: contraction number = 1.736557e-01 NEWTON: using errtol_s: 6.560968e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.851640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.839089e+05 PMG: contraction number = , 8.839089e+05 PMG: iteration = 2 PMG: relative residual = 2.585721e-02 PMG: contraction number = 1.488993e-01 NEWTON: using errtol_s: 9.769232e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.919270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.594401e+05 PMG: contraction number = , 1.594401e+05 PMG: iteration = 3 PMG: relative residual = 4.958662e-03 PMG: contraction number = 1.917710e-01 NEWTON: using errtol_s: 1.873455e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.986900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.651390e+04 PMG: contraction number = , 3.651390e+04 PMG: iteration = 4 PMG: relative residual = 1.175720e-03 PMG: contraction number = 2.371042e-01 NEWTON: using errtol_s: 4.442041e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.062800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.053759e+04 PMG: contraction number = , 1.053759e+04 PMG: iteration = 5 PMG: relative residual = 3.263827e-04 PMG: contraction number = 2.776025e-01 NEWTON: using errtol_s: 1.233122e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.168840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.783605e+03 PMG: contraction number = , 3.783605e+03 PMG: iteration = 6 PMG: relative residual = 9.993959e-05 PMG: contraction number = 3.062037e-01 NEWTON: using errtol_s: 3.775864e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.236460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.260768e+03 PMG: contraction number = , 1.260768e+03 PMG: iteration = 7 PMG: relative residual = 3.008415e-05 PMG: contraction number = 3.010233e-01 NEWTON: using errtol_s: 1.136623e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.304070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.239635e+02 PMG: contraction number = , 4.239635e+02 PMG: iteration = 8 PMG: relative residual = 1.011223e-05 PMG: contraction number = 3.361315e-01 NEWTON: using errtol_s: 3.820548e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.371710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.700161e+02 PMG: contraction number = , 1.700161e+02 PMG: iteration = 9 PMG: relative residual = 4.049434e-06 PMG: contraction number = 4.004491e-01 NEWTON: using errtol_s: 1.529935e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.467560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.410761e+01 PMG: contraction number = , 7.410761e+01 PMG: iteration = 10 PMG: relative residual = 1.765731e-06 PMG: contraction number = 4.360440e-01 NEWTON: using errtol_s: 6.671191e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.535180e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.443696e+01 PMG: contraction number = , 3.443696e+01 PMG: iteration = 11 PMG: relative residual = 8.203174e-07 PMG: contraction number = 4.645766e-01 NEWTON: using errtol_s: 3.099279e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.602790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.628778e+01 PMG: contraction number = , 1.628778e+01 PMG: iteration = 12 PMG: relative residual = 3.880063e-07 PMG: contraction number = 4.729953e-01 NEWTON: using errtol_s: 1.465945e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.670420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.020098e+00 PMG: contraction number = , 8.020098e+00 PMG: iteration = 13 PMG: relative residual = 1.910482e-07 PMG: contraction number = 4.923843e-01 NEWTON: using errtol_s: 7.218082e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.738040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.930937e+00 PMG: contraction number = , 3.930937e+00 PMG: iteration = 14 PMG: relative residual = 9.364005e-08 PMG: contraction number = 4.901383e-01 NEWTON: using errtol_s: 3.537858e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.805610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.965090e+00 PMG: contraction number = , 1.965090e+00 PMG: iteration = 15 PMG: relative residual = 4.681084e-08 PMG: contraction number = 4.999019e-01 NEWTON: using errtol_s: 1.768582e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.873210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.638545e-01 PMG: contraction number = , 9.638545e-01 PMG: iteration = 16 PMG: relative residual = 2.296019e-08 PMG: contraction number = 4.904888e-01 NEWTON: using errtol_s: 8.674697e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.940810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.757559e-01 PMG: contraction number = , 4.757559e-01 PMG: iteration = 17 PMG: relative residual = 1.133309e-08 PMG: contraction number = 4.935971e-01 NEWTON: using errtol_s: 2.263439e-01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000842e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.302553e-01 PMG: contraction number = , 2.302553e-01 PMG: iteration = 2 PMG: relative residual = , 1.121529e-01 PMG: contraction number = , 4.870806e-01 PMG: iteration = 18 PMG: relative residual = 2.671621e-09 PMG: contraction number = 2.357364e-01 NEWTON: using errtol_s: 1.257830e-02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.009571e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.388479e-02 PMG: contraction number = , 5.388479e-02 PMG: iteration = 2 PMG: relative residual = , 2.611742e-02 PMG: contraction number = , 4.846900e-01 PMG: iteration = 3 PMG: relative residual = , 1.253906e-02 PMG: contraction number = , 4.801032e-01 PMG: iteration = 19 PMG: relative residual = 2.986997e-10 PMG: contraction number = 1.118047e-01 NEWTON: using errtol_s: 1.572324e-04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020266e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.074927e-03 PMG: contraction number = , 6.074927e-03 PMG: iteration = 2 PMG: relative residual = , 2.920933e-03 PMG: contraction number = , 4.808177e-01 PMG: iteration = 3 PMG: relative residual = , 1.416229e-03 PMG: contraction number = , 4.848551e-01 PMG: iteration = 4 PMG: relative residual = , 6.821153e-04 PMG: contraction number = , 4.816419e-01 PMG: iteration = 5 PMG: relative residual = , 3.309742e-04 PMG: contraction number = , 4.852174e-01 PMG: iteration = 6 PMG: relative residual = , 1.596289e-04 PMG: contraction number = , 4.823001e-01 PMG: iteration = 7 PMG: relative residual = , 7.749117e-05 PMG: contraction number = , 4.854458e-01 PMG: iteration = 20 PMG: relative residual = 1.850394e-12 PMG: contraction number = 6.194830e-03 NEWTON: using errtol_s: 6.033940e-09 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038841e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.741149e-05 PMG: contraction number = , 3.741149e-05 PMG: iteration = 2 PMG: relative residual = , 1.816604e-05 PMG: contraction number = , 4.855738e-01 PMG: iteration = 3 PMG: relative residual = , 8.776951e-06 PMG: contraction number = , 4.831516e-01 PMG: iteration = 4 PMG: relative residual = , 4.262411e-06 PMG: contraction number = , 4.856369e-01 PMG: iteration = 5 PMG: relative residual = , 2.060521e-06 PMG: contraction number = , 4.834166e-01 PMG: iteration = 6 PMG: relative residual = , 1.000650e-06 PMG: contraction number = , 4.856299e-01 PMG: iteration = 7 PMG: relative residual = , 4.838994e-07 PMG: contraction number = , 4.835848e-01 PMG: iteration = 8 PMG: relative residual = , 2.349615e-07 PMG: contraction number = , 4.855586e-01 PMG: iteration = 9 PMG: relative residual = , 1.136457e-07 PMG: contraction number = , 4.836782e-01 PMG: iteration = 10 PMG: relative residual = , 5.516960e-08 PMG: contraction number = , 4.854524e-01 PMG: iteration = 11 PMG: relative residual = , 2.668662e-08 PMG: contraction number = , 4.837197e-01 PMG: iteration = 12 PMG: relative residual = , 1.295185e-08 PMG: contraction number = , 4.853311e-01 PMG: iteration = 13 PMG: relative residual = , 6.265292e-09 PMG: contraction number = , 4.837374e-01 PMG: iteration = 14 PMG: relative residual = , 3.039960e-09 PMG: contraction number = , 4.852065e-01 PMG: iteration = 21 PMG: relative residual = 8.673724e-15 PMG: contraction number = 4.687501e-03 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.982450e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.015170e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 104.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 104.287) 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 = 2.514621443665E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.934242805623E+06 kT Vpmg_energy: dielEnergy = 9.670795345062E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.086000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 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 = 1.071034e+04