############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 11 18:14:52 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_allh40.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb40.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 86.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 31.693) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 86.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 30.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 58.26) Valist_readPDB: Counted 29844 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 23.463) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 0.281) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.609308 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.35533 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.58317 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 168.178 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -104.792 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 111.287 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 111.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.609308 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.35533 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.58317 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 168.178 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -104.792 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 111.287 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 111.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.609308 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.35533 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.58317 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 31.693 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 168.178 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -104.792 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 111.287 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 111.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 82.7076 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 111.81 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, 123.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 12929860 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.859000e+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 = 5.310000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.375000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034800e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.173243e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.586200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.386454e+06 PMG: contraction number = , 4.386454e+06 NEWTON: attempting damping, relres = 1.072682e-01 NEWTON: attempting damping, relres = 5.450563e-01 NEWTON: damping accepted, relres = 1.072682e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.072682e-01 PMG: contraction number = 1.072682e-01 NEWTON: using errtol_s: 4.476561e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.662200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.981208e+05 PMG: contraction number = , 5.981208e+05 PMG: iteration = 2 PMG: relative residual = 1.591304e-02 PMG: contraction number = 1.483482e-01 NEWTON: using errtol_s: 6.640899e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.463000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.150605e+05 PMG: contraction number = , 1.150605e+05 PMG: iteration = 3 PMG: relative residual = 3.067894e-03 PMG: contraction number = 1.927912e-01 NEWTON: using errtol_s: 1.280307e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.359200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.630155e+04 PMG: contraction number = , 2.630155e+04 PMG: iteration = 4 PMG: relative residual = 6.779135e-04 PMG: contraction number = 2.209703e-01 NEWTON: using errtol_s: 2.829098e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.198200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.943944e+03 PMG: contraction number = , 6.943944e+03 PMG: iteration = 5 PMG: relative residual = 1.667826e-04 PMG: contraction number = 2.460234e-01 NEWTON: using errtol_s: 6.960242e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.071800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.063037e+03 PMG: contraction number = , 2.063037e+03 PMG: iteration = 6 PMG: relative residual = 4.599216e-05 PMG: contraction number = 2.757612e-01 NEWTON: using errtol_s: 1.919364e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.858600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.654468e+02 PMG: contraction number = , 6.654468e+02 PMG: iteration = 7 PMG: relative residual = 1.435753e-05 PMG: contraction number = 3.121735e-01 NEWTON: using errtol_s: 5.991746e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.693400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.383119e+02 PMG: contraction number = , 2.383119e+02 PMG: iteration = 8 PMG: relative residual = 5.139735e-06 PMG: contraction number = 3.579818e-01 NEWTON: using errtol_s: 2.144936e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.589900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.121441e+02 PMG: contraction number = , 1.121441e+02 PMG: iteration = 9 PMG: relative residual = 2.418579e-06 PMG: contraction number = 4.705649e-01 NEWTON: using errtol_s: 1.009332e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.379000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.209722e+01 PMG: contraction number = , 5.209722e+01 PMG: iteration = 10 PMG: relative residual = 1.123541e-06 PMG: contraction number = 4.645460e-01 NEWTON: using errtol_s: 4.688810e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.015090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.366384e+01 PMG: contraction number = , 2.366384e+01 PMG: iteration = 11 PMG: relative residual = 5.103391e-07 PMG: contraction number = 4.542238e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.596500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.933600e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -104.792) Vpmg_setPart: upper corner = (141.283, 130.313, 168.178) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.792) Vpmg_setPart: actual maxima = (141.283, 130.313, 168.178) 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 = 2.800315264510E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.754403078925E+05 kT Vpmg_energy: dielEnergy = 4.876746595853E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.277000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 82.7076 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 111.81 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, 123.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 12929860 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, 111.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -104.792 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 168.178 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 111.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.792) Vpmg_setPart: actual maxima = (141.283, 130.313, 168.178) 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, 111.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -104.792) VPMG::extEnergy Old upper corner = (141.283, 130.313, 168.178) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0135624 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0166591 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 = 1.214200e+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 = 3.625000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.302000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.283460e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.523200e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.342240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.810910e+06 PMG: contraction number = , 7.810910e+06 NEWTON: attempting damping, relres = 1.711990e-01 NEWTON: attempting damping, relres = 5.779028e-01 NEWTON: damping accepted, relres = 1.711990e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.711990e-01 PMG: contraction number = 1.711990e-01 NEWTON: using errtol_s: 7.743674e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.056314e+06 PMG: contraction number = , 1.056314e+06 PMG: iteration = 2 PMG: relative residual = 2.527391e-02 PMG: contraction number = 1.476288e-01 NEWTON: using errtol_s: 1.143189e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.540900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.868733e+05 PMG: contraction number = , 1.868733e+05 PMG: iteration = 3 PMG: relative residual = 4.775235e-03 PMG: contraction number = 1.889393e-01 NEWTON: using errtol_s: 2.159934e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.624910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.143088e+04 PMG: contraction number = , 4.143088e+04 PMG: iteration = 4 PMG: relative residual = 1.107991e-03 PMG: contraction number = 2.320285e-01 NEWTON: using errtol_s: 5.011662e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.702390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.144659e+04 PMG: contraction number = , 1.144659e+04 PMG: iteration = 5 PMG: relative residual = 2.984474e-04 PMG: contraction number = 2.693592e-01 NEWTON: using errtol_s: 1.349937e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.783010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.926386e+03 PMG: contraction number = , 3.926386e+03 PMG: iteration = 6 PMG: relative residual = 8.786986e-05 PMG: contraction number = 2.944233e-01 NEWTON: using errtol_s: 3.974529e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.871820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.271484e+03 PMG: contraction number = , 1.271484e+03 PMG: iteration = 7 PMG: relative residual = 2.552969e-05 PMG: contraction number = 2.905398e-01 NEWTON: using errtol_s: 1.154759e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.958870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.296148e+02 PMG: contraction number = , 4.296148e+02 PMG: iteration = 8 PMG: relative residual = 8.566757e-06 PMG: contraction number = 3.355606e-01 NEWTON: using errtol_s: 3.874915e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.049440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.795933e+02 PMG: contraction number = , 1.795933e+02 PMG: iteration = 9 PMG: relative residual = 3.573464e-06 PMG: contraction number = 4.171314e-01 NEWTON: using errtol_s: 1.616349e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.136480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.301442e+01 PMG: contraction number = , 8.301442e+01 PMG: iteration = 10 PMG: relative residual = 1.652416e-06 PMG: contraction number = 4.624130e-01 NEWTON: using errtol_s: 7.474208e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.216020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.061493e+01 PMG: contraction number = , 4.061493e+01 PMG: iteration = 11 PMG: relative residual = 8.081398e-07 PMG: contraction number = 4.890656e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.961200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.069870e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 111.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 111.287) 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 = 2.748050053669E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.221974618454E+06 kT Vpmg_energy: dielEnergy = 1.110942622137E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.147000e+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, 23.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.842000e+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 = 6.210000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.247000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.478390e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.905226e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.533190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.947465e+05 PMG: contraction number = , 6.947465e+05 NEWTON: attempting damping, relres = 9.140841e-02 NEWTON: attempting damping, relres = 5.432223e-01 NEWTON: damping accepted, relres = 9.140841e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.140841e-02 PMG: contraction number = 9.140841e-02 NEWTON: using errtol_s: 6.311957e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.634070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.048410e+04 PMG: contraction number = , 9.048410e+04 PMG: iteration = 2 PMG: relative residual = 1.179942e-02 PMG: contraction number = 1.290846e-01 NEWTON: using errtol_s: 8.147763e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.726480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.411179e+04 PMG: contraction number = , 1.411179e+04 PMG: iteration = 3 PMG: relative residual = 1.839338e-03 PMG: contraction number = 1.558838e-01 NEWTON: using errtol_s: 1.270105e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.819400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.464699e+03 PMG: contraction number = , 2.464699e+03 PMG: iteration = 4 PMG: relative residual = 3.212407e-04 PMG: contraction number = 1.746501e-01 NEWTON: using errtol_s: 2.218240e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.891440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.659370e+02 PMG: contraction number = , 4.659370e+02 PMG: iteration = 5 PMG: relative residual = 6.072919e-05 PMG: contraction number = 1.890458e-01 NEWTON: using errtol_s: 4.193488e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.001250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.130627e+02 PMG: contraction number = , 1.130627e+02 PMG: iteration = 6 PMG: relative residual = 1.473617e-05 PMG: contraction number = 2.426538e-01 NEWTON: using errtol_s: 1.017566e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.089540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.057458e+01 PMG: contraction number = , 4.057458e+01 PMG: iteration = 7 PMG: relative residual = 5.288452e-06 PMG: contraction number = 3.588756e-01 NEWTON: using errtol_s: 3.651796e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.159280e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.961789e+01 PMG: contraction number = , 1.961789e+01 PMG: iteration = 8 PMG: relative residual = 2.556920e-06 PMG: contraction number = 4.834912e-01 NEWTON: using errtol_s: 1.765611e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.228060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.066037e+00 PMG: contraction number = , 9.066037e+00 PMG: iteration = 9 PMG: relative residual = 1.181648e-06 PMG: contraction number = 4.621372e-01 NEWTON: using errtol_s: 8.159546e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.299370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.878220e+00 PMG: contraction number = , 3.878220e+00 PMG: iteration = 10 PMG: relative residual = 5.054722e-07 PMG: contraction number = 4.277688e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.836500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.273000e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -104.792) Vpmg_setPart: upper corner = (141.283, 130.313, 168.178) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.792) Vpmg_setPart: actual maxima = (141.283, 130.313, 168.178) 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 = 2.577229584256E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.403916570477E+05 kT Vpmg_energy: dielEnergy = 7.019280317752E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.278000e+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, 23.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 111.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -104.792 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 168.178 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 111.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.792) Vpmg_setPart: actual maxima = (141.283, 130.313, 168.178) 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, 111.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -104.792) VPMG::extEnergy Old upper corner = (141.283, 130.313, 168.178) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000155938 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000220479 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 = 7.184000e+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 = 5.270000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.347000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.491710e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465147e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.552900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.338677e+06 PMG: contraction number = , 1.338677e+06 NEWTON: attempting damping, relres = 1.622071e-01 NEWTON: attempting damping, relres = 5.805508e-01 NEWTON: damping accepted, relres = 1.622071e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.622071e-01 PMG: contraction number = 1.622071e-01 NEWTON: using errtol_s: 1.210900e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.698370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.738902e+05 PMG: contraction number = , 1.738902e+05 PMG: iteration = 2 PMG: relative residual = 2.097184e-02 PMG: contraction number = 1.292905e-01 NEWTON: using errtol_s: 1.565578e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.786920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.580572e+04 PMG: contraction number = , 2.580572e+04 PMG: iteration = 3 PMG: relative residual = 3.111171e-03 PMG: contraction number = 1.483499e-01 NEWTON: using errtol_s: 2.322535e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.869120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.195913e+03 PMG: contraction number = , 4.195913e+03 PMG: iteration = 4 PMG: relative residual = 5.058614e-04 PMG: contraction number = 1.625952e-01 NEWTON: using errtol_s: 3.776330e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.959250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.309843e+02 PMG: contraction number = , 7.309843e+02 PMG: iteration = 5 PMG: relative residual = 8.812813e-05 PMG: contraction number = 1.742140e-01 NEWTON: using errtol_s: 6.578895e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.031240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.760789e+02 PMG: contraction number = , 1.760789e+02 PMG: iteration = 6 PMG: relative residual = 2.122815e-05 PMG: contraction number = 2.408782e-01 NEWTON: using errtol_s: 1.584712e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.117190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.238090e+01 PMG: contraction number = , 9.238090e+01 PMG: iteration = 7 PMG: relative residual = 1.113798e-05 PMG: contraction number = 5.246800e-01 NEWTON: using errtol_s: 8.314669e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.205660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.182141e+01 PMG: contraction number = , 4.182141e+01 PMG: iteration = 8 PMG: relative residual = 5.042014e-06 PMG: contraction number = 4.526864e-01 NEWTON: using errtol_s: 3.763938e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.294890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.933436e+01 PMG: contraction number = , 1.933436e+01 PMG: iteration = 9 PMG: relative residual = 2.331050e-06 PMG: contraction number = 4.623251e-01 NEWTON: using errtol_s: 1.740163e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.366470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.993773e+00 PMG: contraction number = , 8.993773e+00 PMG: iteration = 10 PMG: relative residual = 1.084292e-06 PMG: contraction number = 4.651520e-01 NEWTON: using errtol_s: 8.094402e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.446310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.264437e+00 PMG: contraction number = , 4.264437e+00 PMG: iteration = 11 PMG: relative residual = 5.141271e-07 PMG: contraction number = 4.741591e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.016010e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.049270e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 111.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 111.287) 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 = 2.510413909147E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.375441220697E+05 kT Vpmg_energy: dielEnergy = 1.687691284086E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.292000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.222000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.230000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.335000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.713380e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.482993e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.767110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.693765e+06 PMG: contraction number = , 3.693765e+06 NEWTON: attempting damping, relres = 1.106306e-01 NEWTON: attempting damping, relres = 5.454451e-01 NEWTON: damping accepted, relres = 1.106306e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.106306e-01 PMG: contraction number = 1.106306e-01 NEWTON: using errtol_s: 3.853256e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.905090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.082876e+05 PMG: contraction number = , 5.082876e+05 PMG: iteration = 2 PMG: relative residual = 1.679618e-02 PMG: contraction number = 1.518222e-01 NEWTON: using errtol_s: 5.850097e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.015130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.013340e+05 PMG: contraction number = , 1.013340e+05 PMG: iteration = 3 PMG: relative residual = 3.336627e-03 PMG: contraction number = 1.986539e-01 NEWTON: using errtol_s: 1.162145e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.106230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.386533e+04 PMG: contraction number = , 2.386533e+04 PMG: iteration = 4 PMG: relative residual = 7.551883e-04 PMG: contraction number = 2.263329e-01 NEWTON: using errtol_s: 2.630316e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.192440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.480749e+03 PMG: contraction number = , 6.480749e+03 PMG: iteration = 5 PMG: relative residual = 1.901316e-04 PMG: contraction number = 2.517671e-01 NEWTON: using errtol_s: 6.622271e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.264340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.975588e+03 PMG: contraction number = , 1.975588e+03 PMG: iteration = 6 PMG: relative residual = 5.333802e-05 PMG: contraction number = 2.805322e-01 NEWTON: using errtol_s: 1.857760e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.353770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.340634e+02 PMG: contraction number = , 6.340634e+02 PMG: iteration = 7 PMG: relative residual = 1.640204e-05 PMG: contraction number = 3.075111e-01 NEWTON: using errtol_s: 5.712819e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.422500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.154737e+02 PMG: contraction number = , 2.154737e+02 PMG: iteration = 8 PMG: relative residual = 5.568485e-06 PMG: contraction number = 3.394996e-01 NEWTON: using errtol_s: 1.939500e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.494770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.668982e+01 PMG: contraction number = , 9.668982e+01 PMG: iteration = 9 PMG: relative residual = 2.498512e-06 PMG: contraction number = 4.486880e-01 NEWTON: using errtol_s: 8.702302e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.606810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.527289e+01 PMG: contraction number = , 4.527289e+01 PMG: iteration = 10 PMG: relative residual = 1.169860e-06 PMG: contraction number = 4.682226e-01 NEWTON: using errtol_s: 4.074614e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.699550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.109894e+01 PMG: contraction number = , 2.109894e+01 PMG: iteration = 11 PMG: relative residual = 5.451983e-07 PMG: contraction number = 4.660373e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.053350e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.086120e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -104.792) Vpmg_setPart: upper corner = (141.283, 130.313, 168.178) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.792) Vpmg_setPart: actual maxima = (141.283, 130.313, 168.178) 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 = 2.563199077723E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.350496940449E+05 kT Vpmg_energy: dielEnergy = 4.174820663802E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.473000e+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, 111.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -104.792 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 168.178 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 111.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -104.792) Vpmg_setPart: actual maxima = (141.283, 130.313, 168.178) 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, 111.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -104.792) VPMG::extEnergy Old upper corner = (141.283, 130.313, 168.178) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0135083 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.016472 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 = 1.268600e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.290000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.339000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.957720e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.776685e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.012780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.473001e+06 PMG: contraction number = , 6.473001e+06 NEWTON: attempting damping, relres = 1.730949e-01 NEWTON: attempting damping, relres = 5.773860e-01 NEWTON: damping accepted, relres = 1.730949e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.730949e-01 PMG: contraction number = 1.730949e-01 NEWTON: using errtol_s: 6.537248e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.135500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.813058e+05 PMG: contraction number = , 8.813058e+05 PMG: iteration = 2 PMG: relative residual = 2.612644e-02 PMG: contraction number = 1.509371e-01 NEWTON: using errtol_s: 9.867134e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.239810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.604350e+05 PMG: contraction number = , 1.604350e+05 PMG: iteration = 3 PMG: relative residual = 5.101025e-03 PMG: contraction number = 1.952437e-01 NEWTON: using errtol_s: 1.926496e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.329610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.676805e+04 PMG: contraction number = , 3.676805e+04 PMG: iteration = 4 PMG: relative residual = 1.222451e-03 PMG: contraction number = 2.396482e-01 NEWTON: using errtol_s: 4.616813e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.420810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.049655e+04 PMG: contraction number = , 1.049655e+04 PMG: iteration = 5 PMG: relative residual = 3.377117e-04 PMG: contraction number = 2.762578e-01 NEWTON: using errtol_s: 1.275430e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.514480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.686770e+03 PMG: contraction number = , 3.686770e+03 PMG: iteration = 6 PMG: relative residual = 1.004272e-04 PMG: contraction number = 2.973755e-01 NEWTON: using errtol_s: 3.792818e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.606900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.190028e+03 PMG: contraction number = , 1.190028e+03 PMG: iteration = 7 PMG: relative residual = 2.868842e-05 PMG: contraction number = 2.856639e-01 NEWTON: using errtol_s: 1.083471e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.696140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.003813e+02 PMG: contraction number = , 4.003813e+02 PMG: iteration = 8 PMG: relative residual = 9.559911e-06 PMG: contraction number = 3.332324e-01 NEWTON: using errtol_s: 3.610477e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.775570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.594455e+02 PMG: contraction number = , 1.594455e+02 PMG: iteration = 9 PMG: relative residual = 3.799685e-06 PMG: contraction number = 3.974603e-01 NEWTON: using errtol_s: 1.435021e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.860900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.305770e+01 PMG: contraction number = , 7.305770e+01 PMG: iteration = 10 PMG: relative residual = 1.741733e-06 PMG: contraction number = 4.583889e-01 NEWTON: using errtol_s: 6.577978e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.934630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.448964e+01 PMG: contraction number = , 3.448964e+01 PMG: iteration = 11 PMG: relative residual = 8.219100e-07 PMG: contraction number = 4.718920e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.032050e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.067710e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 111.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 111.287) 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 = 2.516521539712E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.884431548923E+06 kT Vpmg_energy: dielEnergy = 9.421737250587E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.248000e+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 = 7.096980e+03