############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Mar 13 15:18:40 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_allh30.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb30.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 417) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 417) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 417) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 76.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 26.693) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 76.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 20.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 48.26) 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 26.693 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 26.693 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.596082 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.358625 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.601637 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 26.693 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 150.678 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -97.292 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 101.287 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 101.287 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 26.693 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 26.693 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.596082 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.358625 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.601637 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 26.693 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 150.678 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -97.292 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 101.287 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 101.287 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 26.693 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 26.693 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.596082 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.358625 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.601637 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 26.693 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 150.678 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -97.292 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 101.287 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 101.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 79.6047 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 101.81 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, 113.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13738827 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.720000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 4.890000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.168000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.909000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.184207e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.517100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.459487e+06 PMG: contraction number = , 4.459487e+06 NEWTON: attempting damping, relres = 1.125011e-01 NEWTON: attempting damping, relres = 5.458121e-01 NEWTON: damping accepted, relres = 1.125011e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.125011e-01 PMG: contraction number = 1.125011e-01 NEWTON: using errtol_s: 4.707278e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.406100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.169706e+05 PMG: contraction number = , 6.169706e+05 PMG: iteration = 2 PMG: relative residual = 1.759901e-02 PMG: contraction number = 1.564341e-01 NEWTON: using errtol_s: 7.363789e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.054400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.223211e+05 PMG: contraction number = , 1.223211e+05 PMG: iteration = 3 PMG: relative residual = 3.618642e-03 PMG: contraction number = 2.056163e-01 NEWTON: using errtol_s: 1.514115e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.698200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.011773e+04 PMG: contraction number = , 3.011773e+04 PMG: iteration = 4 PMG: relative residual = 8.586479e-04 PMG: contraction number = 2.372845e-01 NEWTON: using errtol_s: 3.592760e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.344000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.720522e+03 PMG: contraction number = , 8.720522e+03 PMG: iteration = 5 PMG: relative residual = 2.208444e-04 PMG: contraction number = 2.572002e-01 NEWTON: using errtol_s: 9.240587e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.992100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.618848e+03 PMG: contraction number = , 2.618848e+03 PMG: iteration = 6 PMG: relative residual = 5.863679e-05 PMG: contraction number = 2.655118e-01 NEWTON: using errtol_s: 2.453484e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.648500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.542165e+02 PMG: contraction number = , 7.542165e+02 PMG: iteration = 7 PMG: relative residual = 1.624728e-05 PMG: contraction number = 2.770834e-01 NEWTON: using errtol_s: 6.798199e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.468900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.311656e+02 PMG: contraction number = , 2.311656e+02 PMG: iteration = 8 PMG: relative residual = 4.972619e-06 PMG: contraction number = 3.060585e-01 NEWTON: using errtol_s: 2.080647e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.112400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.066655e+02 PMG: contraction number = , 1.066655e+02 PMG: iteration = 9 PMG: relative residual = 2.294479e-06 PMG: contraction number = 4.614226e-01 NEWTON: using errtol_s: 9.600574e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.760900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.803924e+01 PMG: contraction number = , 4.803924e+01 PMG: iteration = 10 PMG: relative residual = 1.033301e-06 PMG: contraction number = 4.503423e-01 NEWTON: using errtol_s: 4.323545e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.418900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.235151e+01 PMG: contraction number = , 2.235151e+01 PMG: iteration = 11 PMG: relative residual = 4.807813e-07 PMG: contraction number = 4.652868e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.018800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.326000e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -97.292) Vpmg_setPart: upper corner = (141.283, 130.313, 150.678) Vpmg_setPart: actual minima = (-143.597, -129.429, -97.292) Vpmg_setPart: actual maxima = (141.283, 130.313, 150.678) 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 = 2.843322655302E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.797692109979E+05 kT Vpmg_energy: dielEnergy = 4.898381666521E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.080000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 79.6047 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 101.81 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, 113.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13738827 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 101.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -97.292 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 150.678 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 101.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -97.292) Vpmg_setPart: actual maxima = (141.283, 130.313, 150.678) 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, 101.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -97.292) VPMG::extEnergy Old upper corner = (141.283, 130.313, 150.678) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.014561 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0177577 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 = 1.188700e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 4.930000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.182000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073380e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.522917e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.127950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.794954e+06 PMG: contraction number = , 7.794954e+06 NEWTON: attempting damping, relres = 1.757814e-01 NEWTON: attempting damping, relres = 5.778308e-01 NEWTON: damping accepted, relres = 1.757814e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.757814e-01 PMG: contraction number = 1.757814e-01 NEWTON: using errtol_s: 7.950449e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.230890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.066098e+06 PMG: contraction number = , 1.066098e+06 PMG: iteration = 2 PMG: relative residual = 2.712679e-02 PMG: contraction number = 1.543211e-01 NEWTON: using errtol_s: 1.226922e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.311030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.949494e+05 PMG: contraction number = , 1.949494e+05 PMG: iteration = 3 PMG: relative residual = 5.448014e-03 PMG: contraction number = 2.008352e-01 NEWTON: using errtol_s: 2.464091e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.382780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.623030e+04 PMG: contraction number = , 4.623030e+04 PMG: iteration = 4 PMG: relative residual = 1.351377e-03 PMG: contraction number = 2.480494e-01 NEWTON: using errtol_s: 6.112165e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.358183e+04 PMG: contraction number = , 1.358183e+04 PMG: iteration = 5 PMG: relative residual = 3.817569e-04 PMG: contraction number = 2.824948e-01 NEWTON: using errtol_s: 1.726655e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.522510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.764378e+03 PMG: contraction number = , 4.764378e+03 PMG: iteration = 6 PMG: relative residual = 1.149493e-04 PMG: contraction number = 3.011060e-01 NEWTON: using errtol_s: 5.199061e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.595970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.644349e+03 PMG: contraction number = , 1.644349e+03 PMG: iteration = 7 PMG: relative residual = 3.363018e-05 PMG: contraction number = 2.925653e-01 NEWTON: using errtol_s: 1.521065e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.671260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.501561e+02 PMG: contraction number = , 5.501561e+02 PMG: iteration = 8 PMG: relative residual = 1.094983e-05 PMG: contraction number = 3.255954e-01 NEWTON: using errtol_s: 4.952518e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.746560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.923970e+02 PMG: contraction number = , 1.923970e+02 PMG: iteration = 9 PMG: relative residual = 3.828442e-06 PMG: contraction number = 3.496347e-01 NEWTON: using errtol_s: 1.731572e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.819710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.997324e+01 PMG: contraction number = , 8.997324e+01 PMG: iteration = 10 PMG: relative residual = 1.790898e-06 PMG: contraction number = 4.677878e-01 NEWTON: using errtol_s: 8.100084e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.893060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.118112e+01 PMG: contraction number = , 4.118112e+01 PMG: iteration = 11 PMG: relative residual = 8.194496e-07 PMG: contraction number = 4.575635e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.694200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.006500e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 101.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 101.287) 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 = 2.796019541303E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.222440361785E+06 kT Vpmg_energy: dielEnergy = 1.111174553745E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.985000e+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, 13.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.772000e+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 = 5.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.175000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.114660e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.920563e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.169360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.019059e+05 PMG: contraction number = , 7.019059e+05 NEWTON: attempting damping, relres = 9.213324e-02 NEWTON: attempting damping, relres = 5.436698e-01 NEWTON: damping accepted, relres = 9.213324e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.213324e-02 PMG: contraction number = 9.213324e-02 NEWTON: using errtol_s: 6.376139e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.276510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.176498e+04 PMG: contraction number = , 9.176498e+04 PMG: iteration = 2 PMG: relative residual = 1.193993e-02 PMG: contraction number = 1.295941e-01 NEWTON: using errtol_s: 8.263101e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.358720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.438546e+04 PMG: contraction number = , 1.438546e+04 PMG: iteration = 3 PMG: relative residual = 1.870853e-03 PMG: contraction number = 1.566888e-01 NEWTON: using errtol_s: 1.294736e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.431860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.526455e+03 PMG: contraction number = , 2.526455e+03 PMG: iteration = 4 PMG: relative residual = 3.285599e-04 PMG: contraction number = 1.756204e-01 NEWTON: using errtol_s: 2.273820e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.503150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.828222e+02 PMG: contraction number = , 4.828222e+02 PMG: iteration = 5 PMG: relative residual = 6.279044e-05 PMG: contraction number = 1.911080e-01 NEWTON: using errtol_s: 4.345452e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.576980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.181615e+02 PMG: contraction number = , 1.181615e+02 PMG: iteration = 6 PMG: relative residual = 1.536659e-05 PMG: contraction number = 2.447281e-01 NEWTON: using errtol_s: 1.063454e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.659140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.922045e+01 PMG: contraction number = , 3.922045e+01 PMG: iteration = 7 PMG: relative residual = 5.100591e-06 PMG: contraction number = 3.319274e-01 NEWTON: using errtol_s: 3.529896e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.731290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.670603e+01 PMG: contraction number = , 1.670603e+01 PMG: iteration = 8 PMG: relative residual = 2.172573e-06 PMG: contraction number = 4.259454e-01 NEWTON: using errtol_s: 1.503543e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.797340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.553009e+00 PMG: contraction number = , 7.553009e+00 PMG: iteration = 9 PMG: relative residual = 9.822559e-07 PMG: contraction number = 4.521163e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.308000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.626400e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -97.292) Vpmg_setPart: upper corner = (141.283, 130.313, 150.678) Vpmg_setPart: actual minima = (-143.597, -129.429, -97.292) Vpmg_setPart: actual maxima = (141.283, 130.313, 150.678) 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 = 2.579725375703E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.425829930371E+05 kT Vpmg_energy: dielEnergy = 7.128846581130E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.191000e+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, 13.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 101.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -97.292 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 150.678 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 101.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -97.292) Vpmg_setPart: actual maxima = (141.283, 130.313, 150.678) 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, 101.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -97.292) VPMG::extEnergy Old upper corner = (141.283, 130.313, 150.678) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000167943 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000238109 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.598000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 4.970000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.172000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.968110e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.464932e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.021770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.336002e+06 PMG: contraction number = , 1.336002e+06 NEWTON: attempting damping, relres = 1.618837e-01 NEWTON: attempting damping, relres = 5.803849e-01 NEWTON: damping accepted, relres = 1.618837e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.618837e-01 PMG: contraction number = 1.618837e-01 NEWTON: using errtol_s: 1.208451e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.137260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.734298e+05 PMG: contraction number = , 1.734298e+05 PMG: iteration = 2 PMG: relative residual = 2.091719e-02 PMG: contraction number = 1.292112e-01 NEWTON: using errtol_s: 1.561454e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.219320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.570925e+04 PMG: contraction number = , 2.570925e+04 PMG: iteration = 3 PMG: relative residual = 3.099628e-03 PMG: contraction number = 1.481857e-01 NEWTON: using errtol_s: 2.313852e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.287880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.175427e+03 PMG: contraction number = , 4.175427e+03 PMG: iteration = 4 PMG: relative residual = 5.034059e-04 PMG: contraction number = 1.624085e-01 NEWTON: using errtol_s: 3.757891e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.360970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.279396e+02 PMG: contraction number = , 7.279396e+02 PMG: iteration = 5 PMG: relative residual = 8.776342e-05 PMG: contraction number = 1.743393e-01 NEWTON: using errtol_s: 6.551480e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.440970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.651318e+02 PMG: contraction number = , 1.651318e+02 PMG: iteration = 6 PMG: relative residual = 1.990893e-05 PMG: contraction number = 2.268477e-01 NEWTON: using errtol_s: 1.486188e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.523910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.285406e+01 PMG: contraction number = , 8.285406e+01 PMG: iteration = 7 PMG: relative residual = 9.989518e-06 PMG: contraction number = 5.017607e-01 NEWTON: using errtol_s: 7.457108e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.593510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.378683e+01 PMG: contraction number = , 4.378683e+01 PMG: iteration = 8 PMG: relative residual = 5.279115e-06 PMG: contraction number = 5.284654e-01 NEWTON: using errtol_s: 3.940823e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.669780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.904302e+01 PMG: contraction number = , 1.904302e+01 PMG: iteration = 9 PMG: relative residual = 2.295987e-06 PMG: contraction number = 4.349190e-01 NEWTON: using errtol_s: 1.713939e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.750970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.302950e+00 PMG: contraction number = , 9.302950e+00 PMG: iteration = 10 PMG: relative residual = 1.121599e-06 PMG: contraction number = 4.885041e-01 NEWTON: using errtol_s: 8.372662e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.820620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.288391e+00 PMG: contraction number = , 4.288391e+00 PMG: iteration = 11 PMG: relative residual = 5.170299e-07 PMG: contraction number = 4.609756e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.041300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.358100e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 101.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 101.287) 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 = 2.511055125077E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.361462423397E+05 kT Vpmg_energy: dielEnergy = 1.680701872914E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.168000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.467000e+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 = 5.160000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.525000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.071440e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.493092e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.124970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.763485e+06 PMG: contraction number = , 3.763485e+06 NEWTON: attempting damping, relres = 1.123872e-01 NEWTON: attempting damping, relres = 5.461909e-01 NEWTON: damping accepted, relres = 1.123872e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.123872e-01 PMG: contraction number = 1.123872e-01 NEWTON: using errtol_s: 3.925787e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.216060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.197371e+05 PMG: contraction number = , 5.197371e+05 PMG: iteration = 2 PMG: relative residual = 1.714594e-02 PMG: contraction number = 1.525614e-01 NEWTON: using errtol_s: 5.989235e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.282810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.028550e+05 PMG: contraction number = , 1.028550e+05 PMG: iteration = 3 PMG: relative residual = 3.403096e-03 PMG: contraction number = 1.984782e-01 NEWTON: using errtol_s: 1.188733e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.349000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.398807e+04 PMG: contraction number = , 2.398807e+04 PMG: iteration = 4 PMG: relative residual = 7.683917e-04 PMG: contraction number = 2.257920e-01 NEWTON: using errtol_s: 2.684063e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.415250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.472291e+03 PMG: contraction number = , 6.472291e+03 PMG: iteration = 5 PMG: relative residual = 1.920394e-04 PMG: contraction number = 2.499239e-01 NEWTON: using errtol_s: 6.708113e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.486040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.930155e+03 PMG: contraction number = , 1.930155e+03 PMG: iteration = 6 PMG: relative residual = 5.222553e-05 PMG: contraction number = 2.719521e-01 NEWTON: using errtol_s: 1.824286e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.569930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.146043e+02 PMG: contraction number = , 6.146043e+02 PMG: iteration = 7 PMG: relative residual = 1.586798e-05 PMG: contraction number = 3.038357e-01 NEWTON: using errtol_s: 5.542831e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.636070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.185160e+02 PMG: contraction number = , 2.185160e+02 PMG: iteration = 8 PMG: relative residual = 5.630693e-06 PMG: contraction number = 3.548462e-01 NEWTON: using errtol_s: 1.966853e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.704420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.099144e+02 PMG: contraction number = , 1.099144e+02 PMG: iteration = 9 PMG: relative residual = 2.832120e-06 PMG: contraction number = 5.029790e-01 NEWTON: using errtol_s: 9.892857e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.777860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.925233e+01 PMG: contraction number = , 4.925233e+01 PMG: iteration = 10 PMG: relative residual = 1.269009e-06 PMG: contraction number = 4.480773e-01 NEWTON: using errtol_s: 4.432764e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.852090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.246259e+01 PMG: contraction number = , 2.246259e+01 PMG: iteration = 11 PMG: relative residual = 5.787617e-07 PMG: contraction number = 4.560738e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.389500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.739800e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -97.292) Vpmg_setPart: upper corner = (141.283, 130.313, 150.678) Vpmg_setPart: actual minima = (-143.597, -129.429, -97.292) Vpmg_setPart: actual maxima = (141.283, 130.313, 150.678) 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 = 2.559932458259E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.371613110489E+05 kT Vpmg_energy: dielEnergy = 4.185380094697E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.134000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 417 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 53 Vpmg_ctor2: PMG chose nf = 90059073, nc = 184281 Vpmg_ctor2: PMG chose narr = 103012044, narrc = 12952971 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1277450837, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 101.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -97.292 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 150.678 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 101.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -97.292) Vpmg_setPart: actual maxima = (141.283, 130.313, 150.678) 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, 101.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -97.292) VPMG::extEnergy Old upper corner = (141.283, 130.313, 150.678) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0149715 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0177948 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 = 1.068400e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 4.940000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.168000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.071550e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.776426e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.124210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.464440e+06 PMG: contraction number = , 6.464440e+06 NEWTON: attempting damping, relres = 1.740865e-01 NEWTON: attempting damping, relres = 5.772862e-01 NEWTON: damping accepted, relres = 1.740865e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.740865e-01 PMG: contraction number = 1.740865e-01 NEWTON: using errtol_s: 6.574247e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.221170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.841083e+05 PMG: contraction number = , 8.841083e+05 PMG: iteration = 2 PMG: relative residual = 2.663061e-02 PMG: contraction number = 1.529735e-01 NEWTON: using errtol_s: 1.005685e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.301420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.615750e+05 PMG: contraction number = , 1.615750e+05 PMG: iteration = 3 PMG: relative residual = 5.286014e-03 PMG: contraction number = 1.984939e-01 NEWTON: using errtol_s: 1.996224e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.365380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.709883e+04 PMG: contraction number = , 3.709883e+04 PMG: iteration = 4 PMG: relative residual = 1.292939e-03 PMG: contraction number = 2.445962e-01 NEWTON: using errtol_s: 4.882688e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.445740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.070665e+04 PMG: contraction number = , 1.070665e+04 PMG: iteration = 5 PMG: relative residual = 3.663179e-04 PMG: contraction number = 2.833219e-01 NEWTON: using errtol_s: 1.383372e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.545110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.827744e+03 PMG: contraction number = , 3.827744e+03 PMG: iteration = 6 PMG: relative residual = 1.108397e-04 PMG: contraction number = 3.025779e-01 NEWTON: using errtol_s: 4.185779e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.620250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.277506e+03 PMG: contraction number = , 1.277506e+03 PMG: iteration = 7 PMG: relative residual = 3.149713e-05 PMG: contraction number = 2.841683e-01 NEWTON: using errtol_s: 1.189466e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.724910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.339117e+02 PMG: contraction number = , 4.339117e+02 PMG: iteration = 8 PMG: relative residual = 1.034299e-05 PMG: contraction number = 3.283789e-01 NEWTON: using errtol_s: 3.905954e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.791730e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.546436e+02 PMG: contraction number = , 1.546436e+02 PMG: iteration = 9 PMG: relative residual = 3.685483e-06 PMG: contraction number = 3.563266e-01 NEWTON: using errtol_s: 1.391795e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.855960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.369805e+01 PMG: contraction number = , 7.369805e+01 PMG: iteration = 10 PMG: relative residual = 1.756800e-06 PMG: contraction number = 4.766810e-01 NEWTON: using errtol_s: 6.634423e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.921660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.478710e+01 PMG: contraction number = , 3.478710e+01 PMG: iteration = 11 PMG: relative residual = 8.290502e-07 PMG: contraction number = 4.719094e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.117100e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.424800e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 101.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 101.287) 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 = 2.516548926611E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.886273302197E+06 kT Vpmg_energy: dielEnergy = 9.430947575817E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.007000e+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 = 6.075050e+03