############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 11 18:15:24 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_allh45.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb45.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, 481) 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, 481) 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, 481) 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, 91.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 34.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 91.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 35.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 63.26) 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 34.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 34.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.594729 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.342058 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.57515 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 34.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 176.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -108.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 116.287 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 116.287 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 34.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 34.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.594729 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.342058 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.57515 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 34.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 176.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -108.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 116.287 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 116.287 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 34.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 34.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.594729 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.342058 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.57515 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 34.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 176.928 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -108.542 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 116.287 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 116.287 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 = 84.3291 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 116.81 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, 128.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 12546792 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 = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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 = 7.216000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.650000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.555000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.095900e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.181929e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.685600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.463365e+06 PMG: contraction number = , 4.463365e+06 NEWTON: attempting damping, relres = 1.084687e-01 NEWTON: attempting damping, relres = 5.458477e-01 NEWTON: damping accepted, relres = 1.084687e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.084687e-01 PMG: contraction number = 1.084687e-01 NEWTON: using errtol_s: 4.536086e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.812000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.078177e+05 PMG: contraction number = , 6.078177e+05 PMG: iteration = 2 PMG: relative residual = 1.601521e-02 PMG: contraction number = 1.476482e-01 NEWTON: using errtol_s: 6.697447e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.641000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.156275e+05 PMG: contraction number = , 1.156275e+05 PMG: iteration = 3 PMG: relative residual = 3.062247e-03 PMG: contraction number = 1.912087e-01 NEWTON: using errtol_s: 1.280610e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.619300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.604347e+04 PMG: contraction number = , 2.604347e+04 PMG: iteration = 4 PMG: relative residual = 6.700069e-04 PMG: contraction number = 2.187958e-01 NEWTON: using errtol_s: 2.801921e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.456600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.829666e+03 PMG: contraction number = , 6.829666e+03 PMG: iteration = 5 PMG: relative residual = 1.630614e-04 PMG: contraction number = 2.433727e-01 NEWTON: using errtol_s: 6.819112e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.286700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.986158e+03 PMG: contraction number = , 1.986158e+03 PMG: iteration = 6 PMG: relative residual = 4.388553e-05 PMG: contraction number = 2.691351e-01 NEWTON: using errtol_s: 1.835262e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.111800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.456451e+02 PMG: contraction number = , 6.456451e+02 PMG: iteration = 7 PMG: relative residual = 1.390291e-05 PMG: contraction number = 3.167993e-01 NEWTON: using errtol_s: 5.814098e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.936200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.491517e+02 PMG: contraction number = , 2.491517e+02 PMG: iteration = 8 PMG: relative residual = 5.362221e-06 PMG: contraction number = 3.856906e-01 NEWTON: using errtol_s: 2.242443e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.794700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.247270e+02 PMG: contraction number = , 1.247270e+02 PMG: iteration = 9 PMG: relative residual = 2.684415e-06 PMG: contraction number = 5.006162e-01 NEWTON: using errtol_s: 1.122603e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.619100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.239542e+01 PMG: contraction number = , 5.239542e+01 PMG: iteration = 10 PMG: relative residual = 1.127629e-06 PMG: contraction number = 4.200653e-01 NEWTON: using errtol_s: 4.715667e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.354425e+01 PMG: contraction number = , 2.354425e+01 PMG: iteration = 11 PMG: relative residual = 5.067054e-07 PMG: contraction number = 4.493545e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.784400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.014690e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -108.542) Vpmg_setPart: upper corner = (141.283, 130.313, 176.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -108.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 176.928) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.796769322370E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.902706694189E+05 kT Vpmg_energy: dielEnergy = 4.950898871027E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.552000e+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 = 84.3291 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 116.81 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, 128.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 12546792 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 = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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, 116.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -108.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 176.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 116.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -108.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 176.928) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 116.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -108.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 176.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0142322 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0175226 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 = 1.306900e+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 = 5.660000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.560000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.283240e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.524381e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.341380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.861361e+06 PMG: contraction number = , 7.861361e+06 NEWTON: attempting damping, relres = 1.722792e-01 NEWTON: attempting damping, relres = 5.784069e-01 NEWTON: damping accepted, relres = 1.722792e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.722792e-01 PMG: contraction number = 1.722792e-01 NEWTON: using errtol_s: 7.794566e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.058866e+06 PMG: contraction number = , 1.058866e+06 PMG: iteration = 2 PMG: relative residual = 2.536882e-02 PMG: contraction number = 1.472541e-01 NEWTON: using errtol_s: 1.147782e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.539880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.868103e+05 PMG: contraction number = , 1.868103e+05 PMG: iteration = 3 PMG: relative residual = 4.792651e-03 PMG: contraction number = 1.889190e-01 NEWTON: using errtol_s: 2.168378e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.623410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.133369e+04 PMG: contraction number = , 4.133369e+04 PMG: iteration = 4 PMG: relative residual = 1.119223e-03 PMG: contraction number = 2.335290e-01 NEWTON: using errtol_s: 5.063790e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.710880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.152601e+04 PMG: contraction number = , 1.152601e+04 PMG: iteration = 5 PMG: relative residual = 3.060638e-04 PMG: contraction number = 2.734610e-01 NEWTON: using errtol_s: 1.384749e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.788580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.039999e+03 PMG: contraction number = , 4.039999e+03 PMG: iteration = 6 PMG: relative residual = 9.179030e-05 PMG: contraction number = 2.999058e-01 NEWTON: using errtol_s: 4.152943e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.881320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.340011e+03 PMG: contraction number = , 1.340011e+03 PMG: iteration = 7 PMG: relative residual = 2.692966e-05 PMG: contraction number = 2.933824e-01 NEWTON: using errtol_s: 1.218400e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.978050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.643916e+02 PMG: contraction number = , 4.643916e+02 PMG: iteration = 8 PMG: relative residual = 9.250766e-06 PMG: contraction number = 3.435159e-01 NEWTON: using errtol_s: 4.185399e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.064840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.811233e+02 PMG: contraction number = , 1.811233e+02 PMG: iteration = 9 PMG: relative residual = 3.603007e-06 PMG: contraction number = 3.894821e-01 NEWTON: using errtol_s: 1.630138e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.145000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.414385e+01 PMG: contraction number = , 8.414385e+01 PMG: iteration = 10 PMG: relative residual = 1.674474e-06 PMG: contraction number = 4.647435e-01 NEWTON: using errtol_s: 7.575958e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.227780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.959801e+01 PMG: contraction number = , 3.959801e+01 PMG: iteration = 11 PMG: relative residual = 7.876960e-07 PMG: contraction number = 4.704140e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.000250e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.036480e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 116.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 116.287) 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 = 2.744202383063E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.255037216084E+06 kT Vpmg_energy: dielEnergy = 1.127474054026E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.262000e+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, 28.0691) 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 = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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 = 4.091000e+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 = 5.600000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.554000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.471380e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.919099e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.532430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.037303e+05 PMG: contraction number = , 7.037303e+05 NEWTON: attempting damping, relres = 9.239978e-02 NEWTON: attempting damping, relres = 5.438100e-01 NEWTON: damping accepted, relres = 9.239978e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.239978e-02 PMG: contraction number = 9.239978e-02 NEWTON: using errtol_s: 6.393232e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.656980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.101862e+04 PMG: contraction number = , 9.101862e+04 PMG: iteration = 2 PMG: relative residual = 1.184641e-02 PMG: contraction number = 1.282082e-01 NEWTON: using errtol_s: 8.196650e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.752390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.412842e+04 PMG: contraction number = , 1.412842e+04 PMG: iteration = 3 PMG: relative residual = 1.837792e-03 PMG: contraction number = 1.551349e-01 NEWTON: using errtol_s: 1.271587e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.836340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.461832e+03 PMG: contraction number = , 2.461832e+03 PMG: iteration = 4 PMG: relative residual = 3.202231e-04 PMG: contraction number = 1.742434e-01 NEWTON: using errtol_s: 2.215655e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.920070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.629883e+02 PMG: contraction number = , 4.629883e+02 PMG: iteration = 5 PMG: relative residual = 6.022340e-05 PMG: contraction number = 1.880670e-01 NEWTON: using errtol_s: 4.166917e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.007260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.073770e+02 PMG: contraction number = , 1.073770e+02 PMG: iteration = 6 PMG: relative residual = 1.396704e-05 PMG: contraction number = 2.319205e-01 NEWTON: using errtol_s: 9.663933e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.082050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.555329e+01 PMG: contraction number = , 3.555329e+01 PMG: iteration = 7 PMG: relative residual = 4.624633e-06 PMG: contraction number = 3.311105e-01 NEWTON: using errtol_s: 3.199830e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.166070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.602261e+01 PMG: contraction number = , 1.602261e+01 PMG: iteration = 8 PMG: relative residual = 2.084138e-06 PMG: contraction number = 4.506601e-01 NEWTON: using errtol_s: 1.442036e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.248230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.958491e+00 PMG: contraction number = , 7.958491e+00 PMG: iteration = 9 PMG: relative residual = 1.035207e-06 PMG: contraction number = 4.967075e-01 NEWTON: using errtol_s: 7.162698e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.322970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.756588e+00 PMG: contraction number = , 3.756588e+00 PMG: iteration = 10 PMG: relative residual = 4.886373e-07 PMG: contraction number = 4.720190e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.083300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.439700e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -108.542) Vpmg_setPart: upper corner = (141.283, 130.313, 176.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -108.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 176.928) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.576665890551E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.427617922019E+05 kT Vpmg_energy: dielEnergy = 7.137786941095E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.495000e+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, 28.0691) 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 = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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, 116.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -108.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 176.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 116.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -108.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 176.928) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 116.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -108.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 176.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000165095 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000233974 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 = 7.381000e+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 = 5.730000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.557000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.518040e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.466810e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.579450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.346323e+06 PMG: contraction number = , 1.346323e+06 NEWTON: attempting damping, relres = 1.630863e-01 NEWTON: attempting damping, relres = 5.810121e-01 NEWTON: damping accepted, relres = 1.630863e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.630863e-01 PMG: contraction number = 1.630863e-01 NEWTON: using errtol_s: 1.217734e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.691190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.740946e+05 PMG: contraction number = , 1.740946e+05 PMG: iteration = 2 PMG: relative residual = 2.099227e-02 PMG: contraction number = 1.287188e-01 NEWTON: using errtol_s: 1.567453e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.775190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.576521e+04 PMG: contraction number = , 2.576521e+04 PMG: iteration = 3 PMG: relative residual = 3.105593e-03 PMG: contraction number = 1.479399e-01 NEWTON: using errtol_s: 2.318887e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.865920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.181236e+03 PMG: contraction number = , 4.181236e+03 PMG: iteration = 4 PMG: relative residual = 5.039795e-04 PMG: contraction number = 1.622813e-01 NEWTON: using errtol_s: 3.763119e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.946270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.314098e+02 PMG: contraction number = , 7.314098e+02 PMG: iteration = 5 PMG: relative residual = 8.815957e-05 PMG: contraction number = 1.749269e-01 NEWTON: using errtol_s: 6.582708e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.031600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.592006e+02 PMG: contraction number = , 1.592006e+02 PMG: iteration = 6 PMG: relative residual = 1.918900e-05 PMG: contraction number = 2.176621e-01 NEWTON: using errtol_s: 1.432806e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.110990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.634941e+01 PMG: contraction number = , 7.634941e+01 PMG: iteration = 7 PMG: relative residual = 9.202894e-06 PMG: contraction number = 4.795922e-01 NEWTON: using errtol_s: 6.871626e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.191010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.878842e+01 PMG: contraction number = , 3.878842e+01 PMG: iteration = 8 PMG: relative residual = 4.675308e-06 PMG: contraction number = 5.080259e-01 NEWTON: using errtol_s: 3.490964e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.273640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.678362e+01 PMG: contraction number = , 1.678362e+01 PMG: iteration = 9 PMG: relative residual = 2.023050e-06 PMG: contraction number = 4.327095e-01 NEWTON: using errtol_s: 1.510573e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.357710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.946047e+00 PMG: contraction number = , 7.946047e+00 PMG: iteration = 10 PMG: relative residual = 9.577648e-07 PMG: contraction number = 4.734261e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.969600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.337700e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 116.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 116.287) 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 = 2.508414339476E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.433857841457E+05 kT Vpmg_energy: dielEnergy = 1.716899615707E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.465000e+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 = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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 = 7.309000e+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 = 5.810000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.548000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.642460e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.490082e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.703190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.760706e+06 PMG: contraction number = , 3.760706e+06 NEWTON: attempting damping, relres = 1.120443e-01 NEWTON: attempting damping, relres = 5.462751e-01 NEWTON: damping accepted, relres = 1.120443e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.120443e-01 PMG: contraction number = 1.120443e-01 NEWTON: using errtol_s: 3.910437e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.829130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.177314e+05 PMG: contraction number = , 5.177314e+05 PMG: iteration = 2 PMG: relative residual = 1.697207e-02 PMG: contraction number = 1.514764e-01 NEWTON: using errtol_s: 5.923391e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.914320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.021469e+05 PMG: contraction number = , 1.021469e+05 PMG: iteration = 3 PMG: relative residual = 3.351537e-03 PMG: contraction number = 1.974737e-01 NEWTON: using errtol_s: 1.169714e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.995790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.376032e+04 PMG: contraction number = , 2.376032e+04 PMG: iteration = 4 PMG: relative residual = 7.522048e-04 PMG: contraction number = 2.244358e-01 NEWTON: using errtol_s: 2.625256e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.081820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.422529e+03 PMG: contraction number = , 6.422529e+03 PMG: iteration = 5 PMG: relative residual = 1.870378e-04 PMG: contraction number = 2.486528e-01 NEWTON: using errtol_s: 6.527774e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.170220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.900332e+03 PMG: contraction number = , 1.900332e+03 PMG: iteration = 6 PMG: relative residual = 5.070546e-05 PMG: contraction number = 2.710973e-01 NEWTON: using errtol_s: 1.769662e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.252770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.053436e+02 PMG: contraction number = , 6.053436e+02 PMG: iteration = 7 PMG: relative residual = 1.562684e-05 PMG: contraction number = 3.081885e-01 NEWTON: using errtol_s: 5.453895e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.331400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.177930e+02 PMG: contraction number = , 2.177930e+02 PMG: iteration = 8 PMG: relative residual = 5.616667e-06 PMG: contraction number = 3.594244e-01 NEWTON: using errtol_s: 1.960263e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.411750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.082778e+02 PMG: contraction number = , 1.082778e+02 PMG: iteration = 9 PMG: relative residual = 2.792337e-06 PMG: contraction number = 4.971520e-01 NEWTON: using errtol_s: 9.745485e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.511290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.636798e+01 PMG: contraction number = , 4.636798e+01 PMG: iteration = 10 PMG: relative residual = 1.195727e-06 PMG: contraction number = 4.282173e-01 NEWTON: using errtol_s: 4.173186e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.608570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.073467e+01 PMG: contraction number = , 2.073467e+01 PMG: iteration = 11 PMG: relative residual = 5.346988e-07 PMG: contraction number = 4.471746e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.033790e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.069890e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -108.542) Vpmg_setPart: upper corner = (141.283, 130.313, 176.928) Vpmg_setPart: actual minima = (-143.597, -129.429, -108.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 176.928) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.561364444498E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.475094316786E+05 kT Vpmg_energy: dielEnergy = 4.237119756903E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.515000e+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 = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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, 116.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -108.542 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 176.928 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 116.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -108.542) Vpmg_setPart: actual maxima = (141.283, 130.313, 176.928) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 116.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -108.542) VPMG::extEnergy Old upper corner = (141.283, 130.313, 176.928) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0140984 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0172924 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 = 1.264900e+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 = 5.640000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.551000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.867370e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.777700e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.926670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.515092e+06 PMG: contraction number = , 6.515092e+06 NEWTON: attempting damping, relres = 1.744194e-01 NEWTON: attempting damping, relres = 5.778977e-01 NEWTON: damping accepted, relres = 1.744194e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.744194e-01 PMG: contraction number = 1.744194e-01 NEWTON: using errtol_s: 6.589043e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.043050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.842997e+05 PMG: contraction number = , 8.842997e+05 PMG: iteration = 2 PMG: relative residual = 2.631845e-02 PMG: contraction number = 1.508917e-01 NEWTON: using errtol_s: 9.942319e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.117260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.607833e+05 PMG: contraction number = , 1.607833e+05 PMG: iteration = 3 PMG: relative residual = 5.148622e-03 PMG: contraction number = 1.956279e-01 NEWTON: using errtol_s: 1.944995e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.191520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.691357e+04 PMG: contraction number = , 3.691357e+04 PMG: iteration = 4 PMG: relative residual = 1.245216e-03 PMG: contraction number = 2.418543e-01 NEWTON: using errtol_s: 4.704053e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.283970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.067095e+04 PMG: contraction number = , 1.067095e+04 PMG: iteration = 5 PMG: relative residual = 3.497734e-04 PMG: contraction number = 2.808937e-01 NEWTON: using errtol_s: 1.321339e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.370500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.833452e+03 PMG: contraction number = , 3.833452e+03 PMG: iteration = 6 PMG: relative residual = 1.060716e-04 PMG: contraction number = 3.032581e-01 NEWTON: using errtol_s: 4.007068e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.446030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.278835e+03 PMG: contraction number = , 1.278835e+03 PMG: iteration = 7 PMG: relative residual = 3.086942e-05 PMG: contraction number = 2.910243e-01 NEWTON: using errtol_s: 1.166154e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.527760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.396539e+02 PMG: contraction number = , 4.396539e+02 PMG: iteration = 8 PMG: relative residual = 1.048496e-05 PMG: contraction number = 3.396553e-01 NEWTON: using errtol_s: 3.960903e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.608570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.642537e+02 PMG: contraction number = , 1.642537e+02 PMG: iteration = 9 PMG: relative residual = 3.913232e-06 PMG: contraction number = 3.732234e-01 NEWTON: using errtol_s: 1.478302e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.692530e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.589407e+01 PMG: contraction number = , 7.589407e+01 PMG: iteration = 10 PMG: relative residual = 1.808819e-06 PMG: contraction number = 4.622315e-01 NEWTON: using errtol_s: 6.833176e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.773650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.478443e+01 PMG: contraction number = , 3.478443e+01 PMG: iteration = 11 PMG: relative residual = 8.287080e-07 PMG: contraction number = 4.581486e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.554700e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.917100e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 116.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 116.287) 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 = 2.515052171776E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.911651995686E+06 kT Vpmg_energy: dielEnergy = 9.557840641347E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.410000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.937430e+03