############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Mar 14 15:28:48 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_hse82_bound_to_pcpg_80_20_allh35.pdb NOsh: Storing molecule 1 path piplc_hse82_memb35.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 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 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 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 34598 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 81.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 29.193) Valist_readPDB: Counted 4754 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 81.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 25.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 53.26) 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 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 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 106.287 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 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 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 106.287 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 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 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 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -59.15 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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306722 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 = 7.736000e+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 = 9.860000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.799000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.298400e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.193854e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.570100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.531897e+06 PMG: contraction number = , 4.531897e+06 NEWTON: attempting damping, relres = 1.117671e-01 NEWTON: attempting damping, relres = 5.465064e-01 NEWTON: damping accepted, relres = 1.117671e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.117671e-01 PMG: contraction number = 1.117671e-01 NEWTON: using errtol_s: 4.687349e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.522700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.238432e+05 PMG: contraction number = , 6.238432e+05 PMG: iteration = 2 PMG: relative residual = 1.697829e-02 PMG: contraction number = 1.519077e-01 NEWTON: using errtol_s: 7.120446e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.967400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.214950e+05 PMG: contraction number = , 1.214950e+05 PMG: iteration = 3 PMG: relative residual = 3.358666e-03 PMG: contraction number = 1.978212e-01 NEWTON: using errtol_s: 1.408575e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.410300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.859196e+04 PMG: contraction number = , 2.859196e+04 PMG: iteration = 4 PMG: relative residual = 7.640410e-04 PMG: contraction number = 2.274835e-01 NEWTON: using errtol_s: 3.204276e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.847500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.797939e+03 PMG: contraction number = , 7.797939e+03 PMG: iteration = 5 PMG: relative residual = 1.920489e-04 PMG: contraction number = 2.513595e-01 NEWTON: using errtol_s: 8.054251e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.338711e+03 PMG: contraction number = , 2.338711e+03 PMG: iteration = 6 PMG: relative residual = 5.233084e-05 PMG: contraction number = 2.724870e-01 NEWTON: using errtol_s: 2.194679e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.173090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.409908e+02 PMG: contraction number = , 7.409908e+02 PMG: iteration = 7 PMG: relative residual = 1.592152e-05 PMG: contraction number = 3.042474e-01 NEWTON: using errtol_s: 6.677252e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.316940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.628877e+02 PMG: contraction number = , 2.628877e+02 PMG: iteration = 8 PMG: relative residual = 5.642171e-06 PMG: contraction number = 3.543739e-01 NEWTON: using errtol_s: 2.366244e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.461110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.302156e+02 PMG: contraction number = , 1.302156e+02 PMG: iteration = 9 PMG: relative residual = 2.794628e-06 PMG: contraction number = 4.953107e-01 NEWTON: using errtol_s: 1.172026e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.605360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.635682e+01 PMG: contraction number = , 5.635682e+01 PMG: iteration = 10 PMG: relative residual = 1.209431e-06 PMG: contraction number = 4.327698e-01 NEWTON: using errtol_s: 5.072175e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.749640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.575360e+01 PMG: contraction number = , 2.575360e+01 PMG: iteration = 11 PMG: relative residual = 5.526828e-07 PMG: contraction number = 4.569777e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.710260e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.761930e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) 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 = 2.869936618303E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.949118235597E+05 kT Vpmg_energy: dielEnergy = 4.974091335434E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.546000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -59.15 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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306722 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, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) 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, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0136372 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0166995 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 = 1.601700e+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 = 9.880000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.795000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.103270e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.523765e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.230380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.851431e+06 PMG: contraction number = , 7.851431e+06 NEWTON: attempting damping, relres = 1.740881e-01 NEWTON: attempting damping, relres = 5.783754e-01 NEWTON: damping accepted, relres = 1.740881e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.740881e-01 PMG: contraction number = 1.740881e-01 NEWTON: using errtol_s: 7.875337e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.424080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.063524e+06 PMG: contraction number = , 1.063524e+06 PMG: iteration = 2 PMG: relative residual = 2.608491e-02 PMG: contraction number = 1.498374e-01 NEWTON: using errtol_s: 1.180020e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.567270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.912816e+05 PMG: contraction number = , 1.912816e+05 PMG: iteration = 3 PMG: relative residual = 5.046152e-03 PMG: contraction number = 1.934510e-01 NEWTON: using errtol_s: 2.282760e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.710260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.360991e+04 PMG: contraction number = , 4.360991e+04 PMG: iteration = 4 PMG: relative residual = 1.203413e-03 PMG: contraction number = 2.384814e-01 NEWTON: using errtol_s: 5.443959e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.853880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.233096e+04 PMG: contraction number = , 1.233096e+04 PMG: iteration = 5 PMG: relative residual = 3.318588e-04 PMG: contraction number = 2.757646e-01 NEWTON: using errtol_s: 1.501251e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.997000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.353204e+03 PMG: contraction number = , 4.353204e+03 PMG: iteration = 6 PMG: relative residual = 1.003240e-04 PMG: contraction number = 3.023093e-01 NEWTON: using errtol_s: 4.538422e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.140430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.494582e+03 PMG: contraction number = , 1.494582e+03 PMG: iteration = 7 PMG: relative residual = 3.008940e-05 PMG: contraction number = 2.999223e-01 NEWTON: using errtol_s: 1.361174e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.283590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.159946e+02 PMG: contraction number = , 5.159946e+02 PMG: iteration = 8 PMG: relative residual = 1.027140e-05 PMG: contraction number = 3.413628e-01 NEWTON: using errtol_s: 4.646540e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.426780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.846238e+02 PMG: contraction number = , 1.846238e+02 PMG: iteration = 9 PMG: relative residual = 3.673089e-06 PMG: contraction number = 3.576036e-01 NEWTON: using errtol_s: 1.661619e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.570170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.357907e+01 PMG: contraction number = , 8.357907e+01 PMG: iteration = 10 PMG: relative residual = 1.663201e-06 PMG: contraction number = 4.528072e-01 NEWTON: using errtol_s: 7.523932e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.713720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.763929e+01 PMG: contraction number = , 3.763929e+01 PMG: iteration = 11 PMG: relative residual = 7.488323e-07 PMG: contraction number = 4.502355e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.700640e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.752300e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) 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 = 2.821902190771E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.246447408346E+06 kT Vpmg_energy: dielEnergy = 1.123177905295E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.145000e+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 = -7.15 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, 18.0691) Vclist_assignAtoms: Have 7368701 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 = 5.058000e+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 = 9.850000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.787000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.953380e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.939730e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.079990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.130056e+05 PMG: contraction number = , 7.130056e+05 NEWTON: attempting damping, relres = 9.362717e-02 NEWTON: attempting damping, relres = 5.443275e-01 NEWTON: damping accepted, relres = 9.362717e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.362717e-02 PMG: contraction number = 9.362717e-02 NEWTON: using errtol_s: 6.497473e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.275330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.280104e+04 PMG: contraction number = , 9.280104e+04 PMG: iteration = 2 PMG: relative residual = 1.207047e-02 PMG: contraction number = 1.289206e-01 NEWTON: using errtol_s: 8.376583e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.419760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.453049e+04 PMG: contraction number = , 1.453049e+04 PMG: iteration = 3 PMG: relative residual = 1.885310e-03 PMG: contraction number = 1.561919e-01 NEWTON: using errtol_s: 1.308354e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.564570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.556012e+03 PMG: contraction number = , 2.556012e+03 PMG: iteration = 4 PMG: relative residual = 3.314852e-04 PMG: contraction number = 1.758253e-01 NEWTON: using errtol_s: 2.300418e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.709130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.804394e+02 PMG: contraction number = , 4.804394e+02 PMG: iteration = 5 PMG: relative residual = 6.230746e-05 PMG: contraction number = 1.879645e-01 NEWTON: using errtol_s: 4.323970e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.853700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.030883e+02 PMG: contraction number = , 1.030883e+02 PMG: iteration = 6 PMG: relative residual = 1.336932e-05 PMG: contraction number = 2.145702e-01 NEWTON: using errtol_s: 9.277949e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.998550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.340232e+01 PMG: contraction number = , 3.340232e+01 PMG: iteration = 7 PMG: relative residual = 4.331912e-06 PMG: contraction number = 3.240188e-01 NEWTON: using errtol_s: 3.006230e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.143390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.607601e+01 PMG: contraction number = , 1.607601e+01 PMG: iteration = 8 PMG: relative residual = 2.084867e-06 PMG: contraction number = 4.812812e-01 NEWTON: using errtol_s: 1.446842e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.287950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.956283e+00 PMG: contraction number = , 8.956283e+00 PMG: iteration = 9 PMG: relative residual = 1.161531e-06 PMG: contraction number = 5.571246e-01 NEWTON: using errtol_s: 8.060711e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.432200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.377854e+00 PMG: contraction number = , 4.377854e+00 PMG: iteration = 10 PMG: relative residual = 5.677554e-07 PMG: contraction number = 4.887992e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.569400e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.620910e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) 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 = 2.805510205462E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.447482268228E+05 kT Vpmg_energy: dielEnergy = 7.237061319561E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.628000e+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 = -7.15 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, 18.0691) Vclist_assignAtoms: Have 7368701 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, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) 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, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000158869 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000224002 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 = 1.036600e+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 = 9.860000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.786000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.730200e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.461940e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.857540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.342007e+06 PMG: contraction number = , 1.342007e+06 NEWTON: attempting damping, relres = 1.631241e-01 NEWTON: attempting damping, relres = 5.808291e-01 NEWTON: damping accepted, relres = 1.631241e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.631241e-01 PMG: contraction number = 1.631241e-01 NEWTON: using errtol_s: 1.217222e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.052710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.726410e+05 PMG: contraction number = , 1.726410e+05 PMG: iteration = 2 PMG: relative residual = 2.091650e-02 PMG: contraction number = 1.282245e-01 NEWTON: using errtol_s: 1.560776e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.197010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.541210e+04 PMG: contraction number = , 2.541210e+04 PMG: iteration = 3 PMG: relative residual = 3.070788e-03 PMG: contraction number = 1.468118e-01 NEWTON: using errtol_s: 2.291403e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.341760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.104838e+03 PMG: contraction number = , 4.104838e+03 PMG: iteration = 4 PMG: relative residual = 4.950977e-04 PMG: contraction number = 1.612282e-01 NEWTON: using errtol_s: 3.694389e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.486470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.143460e+02 PMG: contraction number = , 7.143460e+02 PMG: iteration = 5 PMG: relative residual = 8.616079e-05 PMG: contraction number = 1.740279e-01 NEWTON: using errtol_s: 6.429266e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.631210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.484733e+02 PMG: contraction number = , 1.484733e+02 PMG: iteration = 6 PMG: relative residual = 1.790767e-05 PMG: contraction number = 2.078401e-01 NEWTON: using errtol_s: 1.336260e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.775960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.534624e+01 PMG: contraction number = , 6.534624e+01 PMG: iteration = 7 PMG: relative residual = 7.882453e-06 PMG: contraction number = 4.401719e-01 NEWTON: using errtol_s: 5.881839e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.920700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.991634e+01 PMG: contraction number = , 2.991634e+01 PMG: iteration = 8 PMG: relative residual = 3.608272e-06 PMG: contraction number = 4.577601e-01 NEWTON: using errtol_s: 2.692471e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.065350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.390010e+01 PMG: contraction number = , 1.390010e+01 PMG: iteration = 9 PMG: relative residual = 1.676613e-06 PMG: contraction number = 4.646581e-01 NEWTON: using errtol_s: 1.251078e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.209820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.633126e+00 PMG: contraction number = , 6.633126e+00 PMG: iteration = 10 PMG: relative residual = 8.000352e-07 PMG: contraction number = 4.771736e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.570450e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.621980e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) 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 = 2.734197134420E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.422397805862E+05 kT Vpmg_energy: dielEnergy = 1.711165007321E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.569000e+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_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 = 7.334000e+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 = 9.820000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.780000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.477030e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.500453e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.604240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.822126e+06 PMG: contraction number = , 3.822126e+06 NEWTON: attempting damping, relres = 1.138053e-01 NEWTON: attempting damping, relres = 5.469154e-01 NEWTON: damping accepted, relres = 1.138053e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.138053e-01 PMG: contraction number = 1.138053e-01 NEWTON: using errtol_s: 3.983703e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.799710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.288184e+05 PMG: contraction number = , 5.288184e+05 PMG: iteration = 2 PMG: relative residual = 1.737420e-02 PMG: contraction number = 1.526660e-01 NEWTON: using errtol_s: 6.081759e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.944400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.049674e+05 PMG: contraction number = , 1.049674e+05 PMG: iteration = 3 PMG: relative residual = 3.466591e-03 PMG: contraction number = 1.995252e-01 NEWTON: using errtol_s: 1.213464e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.089080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.467381e+04 PMG: contraction number = , 2.467381e+04 PMG: iteration = 4 PMG: relative residual = 7.899710e-04 PMG: contraction number = 2.278812e-01 NEWTON: using errtol_s: 2.765257e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.233850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.743223e+03 PMG: contraction number = , 6.743223e+03 PMG: iteration = 5 PMG: relative residual = 2.002338e-04 PMG: contraction number = 2.534698e-01 NEWTON: using errtol_s: 7.009090e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.378450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.053001e+03 PMG: contraction number = , 2.053001e+03 PMG: iteration = 6 PMG: relative residual = 5.543985e-05 PMG: contraction number = 2.768756e-01 NEWTON: using errtol_s: 1.940646e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.523070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.693316e+02 PMG: contraction number = , 6.693316e+02 PMG: iteration = 7 PMG: relative residual = 1.723694e-05 PMG: contraction number = 3.109125e-01 NEWTON: using errtol_s: 6.033710e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.667180e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.417797e+02 PMG: contraction number = , 2.417797e+02 PMG: iteration = 8 PMG: relative residual = 6.217515e-06 PMG: contraction number = 3.607088e-01 NEWTON: using errtol_s: 2.176412e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.811520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.209100e+02 PMG: contraction number = , 1.209100e+02 PMG: iteration = 9 PMG: relative residual = 3.108833e-06 PMG: contraction number = 5.000122e-01 NEWTON: using errtol_s: 1.088233e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.955890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.308125e+01 PMG: contraction number = , 5.308125e+01 PMG: iteration = 10 PMG: relative residual = 1.364806e-06 PMG: contraction number = 4.390091e-01 NEWTON: using errtol_s: 4.777440e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.100300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.376173e+01 PMG: contraction number = , 2.376173e+01 PMG: iteration = 11 PMG: relative residual = 6.109428e-07 PMG: contraction number = 4.476407e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.714220e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.765640e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) 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 = 2.558884626495E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.501651881935E+05 kT Vpmg_energy: dielEnergy = 4.250398526709E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.556000e+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, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) 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, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0137259 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.016576 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 = 1.493200e+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 = 9.860000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.787000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.443590e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.777570e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.570990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.510744e+06 PMG: contraction number = , 6.510744e+06 NEWTON: attempting damping, relres = 1.743795e-01 NEWTON: attempting damping, relres = 5.778484e-01 NEWTON: damping accepted, relres = 1.743795e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.743795e-01 PMG: contraction number = 1.743795e-01 NEWTON: using errtol_s: 6.587309e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.765290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.861794e+05 PMG: contraction number = , 8.861794e+05 PMG: iteration = 2 PMG: relative residual = 2.637852e-02 PMG: contraction number = 1.512707e-01 NEWTON: using errtol_s: 9.964671e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.908520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.616956e+05 PMG: contraction number = , 1.616956e+05 PMG: iteration = 3 PMG: relative residual = 5.179745e-03 PMG: contraction number = 1.963622e-01 NEWTON: using errtol_s: 1.956685e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005167e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.709296e+04 PMG: contraction number = , 3.709296e+04 PMG: iteration = 4 PMG: relative residual = 1.253535e-03 PMG: contraction number = 2.420072e-01 NEWTON: using errtol_s: 4.735318e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019508e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.071987e+04 PMG: contraction number = , 1.071987e+04 PMG: iteration = 5 PMG: relative residual = 3.519840e-04 PMG: contraction number = 2.807931e-01 NEWTON: using errtol_s: 1.329644e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033861e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.850932e+03 PMG: contraction number = , 3.850932e+03 PMG: iteration = 6 PMG: relative residual = 1.069379e-04 PMG: contraction number = 3.038146e-01 NEWTON: using errtol_s: 4.039654e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048199e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.313893e+03 PMG: contraction number = , 1.313893e+03 PMG: iteration = 7 PMG: relative residual = 3.177439e-05 PMG: contraction number = 2.971294e-01 NEWTON: using errtol_s: 1.200300e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062538e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.530186e+02 PMG: contraction number = , 4.530186e+02 PMG: iteration = 8 PMG: relative residual = 1.079637e-05 PMG: contraction number = 3.397821e-01 NEWTON: using errtol_s: 4.078405e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.076885e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.579920e+02 PMG: contraction number = , 1.579920e+02 PMG: iteration = 9 PMG: relative residual = 3.764137e-06 PMG: contraction number = 3.486483e-01 NEWTON: using errtol_s: 1.421929e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.091274e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.157951e+01 PMG: contraction number = , 7.157951e+01 PMG: iteration = 10 PMG: relative residual = 1.705633e-06 PMG: contraction number = 4.531274e-01 NEWTON: using errtol_s: 6.443150e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.105617e+04 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.213075e+01 PMG: contraction number = , 3.213075e+01 PMG: iteration = 11 PMG: relative residual = 7.655109e-07 PMG: contraction number = 4.488132e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.702470e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.754000e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) 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 = 2.514742034797E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.904209211624E+06 kT Vpmg_energy: dielEnergy = 9.520627821288E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.234000e+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 = 1.119622e+04