############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Mar 13 15:31:51 2014 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path piplc_hsp82_bound_to_pcpg_80_20_allh31.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb31.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, 417) 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, 417) 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, 417) 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, 77.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 27.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 77.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 21.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 49.26) 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 27.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 27.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.602091 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.361029 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.599625 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 27.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 152.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -98.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 102.287 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 102.287 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 27.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 27.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.602091 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.361029 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.599625 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 27.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 152.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -98.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 102.287 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 102.287 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 27.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 27.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.602091 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.361029 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.599625 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 27.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 152.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -98.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 102.287 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 102.287 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 = 79.9061 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 102.81 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, 114.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13650168 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 = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, 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 = 6.723000e+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 = 5.430000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.575000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.046700e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.179041e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.610300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.456937e+06 PMG: contraction number = , 4.456937e+06 NEWTON: attempting damping, relres = 1.113651e-01 NEWTON: attempting damping, relres = 5.458130e-01 NEWTON: damping accepted, relres = 1.113651e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.113651e-01 PMG: contraction number = 1.113651e-01 NEWTON: using errtol_s: 4.653992e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.547100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.179944e+05 PMG: contraction number = , 6.179944e+05 PMG: iteration = 2 PMG: relative residual = 1.721209e-02 PMG: contraction number = 1.545556e-01 NEWTON: using errtol_s: 7.193005e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.240600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.217442e+05 PMG: contraction number = , 1.217442e+05 PMG: iteration = 3 PMG: relative residual = 3.475326e-03 PMG: contraction number = 2.019119e-01 NEWTON: using errtol_s: 1.452353e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.978300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.922924e+04 PMG: contraction number = , 2.922924e+04 PMG: iteration = 4 PMG: relative residual = 8.014024e-04 PMG: contraction number = 2.305978e-01 NEWTON: using errtol_s: 3.349094e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.780900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.112446e+03 PMG: contraction number = , 8.112446e+03 PMG: iteration = 5 PMG: relative residual = 1.988294e-04 PMG: contraction number = 2.481019e-01 NEWTON: using errtol_s: 8.309164e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.476800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.308928e+03 PMG: contraction number = , 2.308928e+03 PMG: iteration = 6 PMG: relative residual = 5.106817e-05 PMG: contraction number = 2.568441e-01 NEWTON: using errtol_s: 2.134160e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.167300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.854783e+02 PMG: contraction number = , 6.854783e+02 PMG: iteration = 7 PMG: relative residual = 1.477176e-05 PMG: contraction number = 2.892557e-01 NEWTON: using errtol_s: 6.173178e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.857200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.375955e+02 PMG: contraction number = , 2.375955e+02 PMG: iteration = 8 PMG: relative residual = 5.117098e-06 PMG: contraction number = 3.464109e-01 NEWTON: using errtol_s: 2.138456e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.556100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.147751e+02 PMG: contraction number = , 1.147751e+02 PMG: iteration = 9 PMG: relative residual = 2.472044e-06 PMG: contraction number = 4.830950e-01 NEWTON: using errtol_s: 1.033078e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.253100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.906823e+01 PMG: contraction number = , 4.906823e+01 PMG: iteration = 10 PMG: relative residual = 1.056754e-06 PMG: contraction number = 4.274818e-01 NEWTON: using errtol_s: 4.416218e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.970100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.284641e+01 PMG: contraction number = , 2.284641e+01 PMG: iteration = 11 PMG: relative residual = 4.920308e-07 PMG: contraction number = 4.656059e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.454100e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.816700e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -98.042) Vpmg_setPart: upper corner = (141.283, 130.313, 152.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -98.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 152.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.836629732443E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.753028747022E+05 kT Vpmg_energy: dielEnergy = 4.876051014851E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.121000e+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 = 79.9061 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 102.81 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, 114.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13650168 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 = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, 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, 102.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -98.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 152.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 102.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -98.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 152.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 102.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -98.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 152.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0138469 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0168912 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 = 1.167400e+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 = 4.920000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.181000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121400e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.522522e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.172770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.787148e+06 PMG: contraction number = , 7.787148e+06 NEWTON: attempting damping, relres = 1.736194e-01 NEWTON: attempting damping, relres = 5.777354e-01 NEWTON: damping accepted, relres = 1.736194e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.736194e-01 PMG: contraction number = 1.736194e-01 NEWTON: using errtol_s: 7.851978e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.271150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.063109e+06 PMG: contraction number = , 1.063109e+06 PMG: iteration = 2 PMG: relative residual = 2.635468e-02 PMG: contraction number = 1.517957e-01 NEWTON: using errtol_s: 1.191896e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.343940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.928113e+05 PMG: contraction number = , 1.928113e+05 PMG: iteration = 3 PMG: relative residual = 5.166133e-03 PMG: contraction number = 1.960234e-01 NEWTON: using errtol_s: 2.336395e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.416020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.511432e+04 PMG: contraction number = , 4.511432e+04 PMG: iteration = 4 PMG: relative residual = 1.250609e-03 PMG: contraction number = 2.420784e-01 NEWTON: using errtol_s: 5.655909e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.488450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.308071e+04 PMG: contraction number = , 1.308071e+04 PMG: iteration = 5 PMG: relative residual = 3.481877e-04 PMG: contraction number = 2.784144e-01 NEWTON: using errtol_s: 1.574687e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.561440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.593933e+03 PMG: contraction number = , 4.593933e+03 PMG: iteration = 6 PMG: relative residual = 1.057298e-04 PMG: contraction number = 3.036575e-01 NEWTON: using errtol_s: 4.781654e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.633230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.597183e+03 PMG: contraction number = , 1.597183e+03 PMG: iteration = 7 PMG: relative residual = 3.210006e-05 PMG: contraction number = 3.036047e-01 NEWTON: using errtol_s: 1.451733e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.703220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.303495e+02 PMG: contraction number = , 5.303495e+02 PMG: iteration = 8 PMG: relative residual = 1.055762e-05 PMG: contraction number = 3.288971e-01 NEWTON: using errtol_s: 4.774707e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.773150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.816336e+02 PMG: contraction number = , 1.816336e+02 PMG: iteration = 9 PMG: relative residual = 3.614422e-06 PMG: contraction number = 3.423519e-01 NEWTON: using errtol_s: 1.634630e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.845520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.084452e+01 PMG: contraction number = , 8.084452e+01 PMG: iteration = 10 PMG: relative residual = 1.609269e-06 PMG: contraction number = 4.452356e-01 NEWTON: using errtol_s: 7.277955e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.917410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.513511e+01 PMG: contraction number = , 3.513511e+01 PMG: iteration = 11 PMG: relative residual = 6.992000e-07 PMG: contraction number = 4.344830e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.461300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.773800e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 102.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 102.287) 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 = 2.784911039228E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.197492648302E+06 kT Vpmg_energy: dielEnergy = 1.098701122688E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.029000e+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, 14.0691) 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 = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, 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 = 4.295000e+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 = 4.920000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.158000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.141300e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.915578e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.192560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.032841e+05 PMG: contraction number = , 7.032841e+05 NEWTON: attempting damping, relres = 9.238495e-02 NEWTON: attempting damping, relres = 5.437621e-01 NEWTON: damping accepted, relres = 9.238495e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.238495e-02 PMG: contraction number = 9.238495e-02 NEWTON: using errtol_s: 6.388954e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.291680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.217273e+04 PMG: contraction number = , 9.217273e+04 PMG: iteration = 2 PMG: relative residual = 1.200248e-02 PMG: contraction number = 1.299182e-01 NEWTON: using errtol_s: 8.300412e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.358190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.447571e+04 PMG: contraction number = , 1.447571e+04 PMG: iteration = 3 PMG: relative residual = 1.883943e-03 PMG: contraction number = 1.569627e-01 NEWTON: using errtol_s: 1.302855e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.442920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.554134e+03 PMG: contraction number = , 2.554134e+03 PMG: iteration = 4 PMG: relative residual = 3.323988e-04 PMG: contraction number = 1.764379e-01 NEWTON: using errtol_s: 2.298730e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.516100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.938706e+02 PMG: contraction number = , 4.938706e+02 PMG: iteration = 5 PMG: relative residual = 6.427329e-05 PMG: contraction number = 1.933620e-01 NEWTON: using errtol_s: 4.444870e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.589820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.208573e+02 PMG: contraction number = , 1.208573e+02 PMG: iteration = 6 PMG: relative residual = 1.572849e-05 PMG: contraction number = 2.447127e-01 NEWTON: using errtol_s: 1.087716e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.662770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.882180e+01 PMG: contraction number = , 3.882180e+01 PMG: iteration = 7 PMG: relative residual = 5.052349e-06 PMG: contraction number = 3.212228e-01 NEWTON: using errtol_s: 3.493992e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.740970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.548482e+01 PMG: contraction number = , 1.548482e+01 PMG: iteration = 8 PMG: relative residual = 2.015210e-06 PMG: contraction number = 3.988659e-01 NEWTON: using errtol_s: 1.393634e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.822960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.629378e+00 PMG: contraction number = , 6.629378e+00 PMG: iteration = 9 PMG: relative residual = 8.627575e-07 PMG: contraction number = 4.281228e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.318500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.627300e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -98.042) Vpmg_setPart: upper corner = (141.283, 130.313, 152.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -98.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 152.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.581199093926E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.413873062434E+05 kT Vpmg_energy: dielEnergy = 7.069062081944E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.160000e+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, 14.0691) 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 = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, 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, 102.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -98.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 152.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 102.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -98.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 152.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 102.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -98.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 152.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000157783 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000223361 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 = 6.382000e+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 = 5.020000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.229000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.992560e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.464590e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.045720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.337584e+06 PMG: contraction number = , 1.337584e+06 NEWTON: attempting damping, relres = 1.620818e-01 NEWTON: attempting damping, relres = 5.804727e-01 NEWTON: damping accepted, relres = 1.620818e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.620818e-01 PMG: contraction number = 1.620818e-01 NEWTON: using errtol_s: 1.209874e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.161840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.741115e+05 PMG: contraction number = , 1.741115e+05 PMG: iteration = 2 PMG: relative residual = 2.100032e-02 PMG: contraction number = 1.295662e-01 NEWTON: using errtol_s: 1.567588e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.247860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.582007e+04 PMG: contraction number = , 2.582007e+04 PMG: iteration = 3 PMG: relative residual = 3.113131e-03 PMG: contraction number = 1.482421e-01 NEWTON: using errtol_s: 2.323825e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.331170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.185485e+03 PMG: contraction number = , 4.185485e+03 PMG: iteration = 4 PMG: relative residual = 5.046418e-04 PMG: contraction number = 1.621010e-01 NEWTON: using errtol_s: 3.766944e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.402610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.245595e+02 PMG: contraction number = , 7.245595e+02 PMG: iteration = 5 PMG: relative residual = 8.735994e-05 PMG: contraction number = 1.731128e-01 NEWTON: using errtol_s: 6.521062e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.474590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.644532e+02 PMG: contraction number = , 1.644532e+02 PMG: iteration = 6 PMG: relative residual = 1.982801e-05 PMG: contraction number = 2.269692e-01 NEWTON: using errtol_s: 1.480080e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.545720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.841440e+01 PMG: contraction number = , 7.841440e+01 PMG: iteration = 7 PMG: relative residual = 9.454692e-06 PMG: contraction number = 4.768351e-01 NEWTON: using errtol_s: 7.057540e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.618340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.459752e+01 PMG: contraction number = , 3.459752e+01 PMG: iteration = 8 PMG: relative residual = 4.171406e-06 PMG: contraction number = 4.411996e-01 NEWTON: using errtol_s: 3.113784e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.691010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.518822e+01 PMG: contraction number = , 1.518822e+01 PMG: iteration = 9 PMG: relative residual = 1.831287e-06 PMG: contraction number = 4.390095e-01 NEWTON: using errtol_s: 1.366981e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.761960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.779578e+00 PMG: contraction number = , 6.779578e+00 PMG: iteration = 10 PMG: relative residual = 8.174090e-07 PMG: contraction number = 4.463577e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.154400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.476800e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 102.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 102.287) 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 = 2.511034734286E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.349931724674E+05 kT Vpmg_energy: dielEnergy = 1.674936523769E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.118000e+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 = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, 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 = 6.137000e+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 = 4.910000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.910000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.009330e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.488332e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.063840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.758878e+06 PMG: contraction number = , 3.758878e+06 NEWTON: attempting damping, relres = 1.120086e-01 NEWTON: attempting damping, relres = 5.461878e-01 NEWTON: damping accepted, relres = 1.120086e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.120086e-01 PMG: contraction number = 1.120086e-01 NEWTON: using errtol_s: 3.907233e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.178680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.214285e+05 PMG: contraction number = , 5.214285e+05 PMG: iteration = 2 PMG: relative residual = 1.706029e-02 PMG: contraction number = 1.523123e-01 NEWTON: using errtol_s: 5.951195e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.261750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.033226e+05 PMG: contraction number = , 1.033226e+05 PMG: iteration = 3 PMG: relative residual = 3.370893e-03 PMG: contraction number = 1.975871e-01 NEWTON: using errtol_s: 1.175879e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.330930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.394825e+04 PMG: contraction number = , 2.394825e+04 PMG: iteration = 4 PMG: relative residual = 7.514276e-04 PMG: contraction number = 2.229165e-01 NEWTON: using errtol_s: 2.621229e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.399860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.319718e+03 PMG: contraction number = , 6.319718e+03 PMG: iteration = 5 PMG: relative residual = 1.835533e-04 PMG: contraction number = 2.442727e-01 NEWTON: using errtol_s: 6.402947e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.474910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.837853e+03 PMG: contraction number = , 1.837853e+03 PMG: iteration = 6 PMG: relative residual = 4.918933e-05 PMG: contraction number = 2.679840e-01 NEWTON: using errtol_s: 1.715887e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.559470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.971627e+02 PMG: contraction number = , 5.971627e+02 PMG: iteration = 7 PMG: relative residual = 1.542291e-05 PMG: contraction number = 3.135419e-01 NEWTON: using errtol_s: 5.380024e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.636780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.275027e+02 PMG: contraction number = , 2.275027e+02 PMG: iteration = 8 PMG: relative residual = 5.870194e-06 PMG: contraction number = 3.806151e-01 NEWTON: using errtol_s: 2.047718e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.706490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.173595e+02 PMG: contraction number = , 1.173595e+02 PMG: iteration = 9 PMG: relative residual = 3.028130e-06 PMG: contraction number = 5.158484e-01 NEWTON: using errtol_s: 1.056312e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.779690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.822364e+01 PMG: contraction number = , 4.822364e+01 PMG: iteration = 10 PMG: relative residual = 1.244203e-06 PMG: contraction number = 4.108817e-01 NEWTON: using errtol_s: 4.340194e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.853640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.237416e+01 PMG: contraction number = , 2.237416e+01 PMG: iteration = 11 PMG: relative residual = 5.772701e-07 PMG: contraction number = 4.639677e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.985600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.367200e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -98.042) Vpmg_setPart: upper corner = (141.283, 130.313, 152.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -98.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 152.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.561594950311E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.339075710092E+05 kT Vpmg_energy: dielEnergy = 4.169110291301E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.199000e+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 = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, 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, 102.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -98.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 152.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 102.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -98.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 152.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 102.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -98.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 152.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0141813 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0168976 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 = 1.142600e+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 = 4.880000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.179000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.078740e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.776064e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.130360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.453576e+06 PMG: contraction number = , 6.453576e+06 NEWTON: attempting damping, relres = 1.723286e-01 NEWTON: attempting damping, relres = 5.771558e-01 NEWTON: damping accepted, relres = 1.723286e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.723286e-01 PMG: contraction number = 1.723286e-01 NEWTON: using errtol_s: 6.507241e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.230230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.812180e+05 PMG: contraction number = , 8.812180e+05 PMG: iteration = 2 PMG: relative residual = 2.600932e-02 PMG: contraction number = 1.509286e-01 NEWTON: using errtol_s: 9.821288e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.298720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.605551e+05 PMG: contraction number = , 1.605551e+05 PMG: iteration = 3 PMG: relative residual = 5.066123e-03 PMG: contraction number = 1.947810e-01 NEWTON: using errtol_s: 1.913001e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.366120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.679440e+04 PMG: contraction number = , 3.679440e+04 PMG: iteration = 4 PMG: relative residual = 1.215169e-03 PMG: contraction number = 2.398616e-01 NEWTON: using errtol_s: 4.588555e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.434710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.057602e+04 PMG: contraction number = , 1.057602e+04 PMG: iteration = 5 PMG: relative residual = 3.393034e-04 PMG: contraction number = 2.792234e-01 NEWTON: using errtol_s: 1.281232e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.507030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.792073e+03 PMG: contraction number = , 3.792073e+03 PMG: iteration = 6 PMG: relative residual = 1.036203e-04 PMG: contraction number = 3.053913e-01 NEWTON: using errtol_s: 3.912769e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.579610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.277585e+03 PMG: contraction number = , 1.277585e+03 PMG: iteration = 7 PMG: relative residual = 3.076888e-05 PMG: contraction number = 2.969387e-01 NEWTON: using errtol_s: 1.161853e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.653920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.302128e+02 PMG: contraction number = , 4.302128e+02 PMG: iteration = 8 PMG: relative residual = 1.025909e-05 PMG: contraction number = 3.334241e-01 NEWTON: using errtol_s: 3.873897e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.731150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.525476e+02 PMG: contraction number = , 1.525476e+02 PMG: iteration = 9 PMG: relative residual = 3.635728e-06 PMG: contraction number = 3.543909e-01 NEWTON: using errtol_s: 1.372874e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.803360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.836523e+01 PMG: contraction number = , 6.836523e+01 PMG: iteration = 10 PMG: relative residual = 1.629894e-06 PMG: contraction number = 4.482993e-01 NEWTON: using errtol_s: 6.154585e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.875530e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.039630e+01 PMG: contraction number = , 3.039630e+01 PMG: iteration = 11 PMG: relative residual = 7.244740e-07 PMG: contraction number = 4.444915e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.453000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.767000e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 102.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 102.287) 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 = 2.514037354237E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.862493595456E+06 kT Vpmg_energy: dielEnergy = 9.312051106733E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.034000e+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 = 6.020750e+03