############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 11 18:14:05 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_allh35.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb35.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 81.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 29.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 81.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 25.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 53.26) Valist_readPDB: Counted 29844 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 23.463) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 0.281) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.864000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.910000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.388000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.162900e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.194270e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.745200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.532553e+06 PMG: contraction number = , 4.532553e+06 NEWTON: attempting damping, relres = 1.110366e-01 NEWTON: attempting damping, relres = 5.464844e-01 NEWTON: damping accepted, relres = 1.110366e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.110366e-01 PMG: contraction number = 1.110366e-01 NEWTON: using errtol_s: 4.657174e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.805200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.227057e+05 PMG: contraction number = , 6.227057e+05 PMG: iteration = 2 PMG: relative residual = 1.673706e-02 PMG: contraction number = 1.507347e-01 NEWTON: using errtol_s: 7.019977e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.588800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.203781e+05 PMG: contraction number = , 1.203781e+05 PMG: iteration = 3 PMG: relative residual = 3.281525e-03 PMG: contraction number = 1.960634e-01 NEWTON: using errtol_s: 1.376360e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.424300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.799430e+04 PMG: contraction number = , 2.799430e+04 PMG: iteration = 4 PMG: relative residual = 7.395324e-04 PMG: contraction number = 2.253624e-01 NEWTON: using errtol_s: 3.101799e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.241200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.562729e+03 PMG: contraction number = , 7.562729e+03 PMG: iteration = 5 PMG: relative residual = 1.845581e-04 PMG: contraction number = 2.495605e-01 NEWTON: using errtol_s: 7.740865e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.030700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.249390e+03 PMG: contraction number = , 2.249390e+03 PMG: iteration = 6 PMG: relative residual = 5.010831e-05 PMG: contraction number = 2.715042e-01 NEWTON: using errtol_s: 2.101678e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.798100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.245877e+02 PMG: contraction number = , 7.245877e+02 PMG: iteration = 7 PMG: relative residual = 1.556172e-05 PMG: contraction number = 3.105618e-01 NEWTON: using errtol_s: 6.527007e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.578200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.678540e+02 PMG: contraction number = , 2.678540e+02 PMG: iteration = 8 PMG: relative residual = 5.748005e-06 PMG: contraction number = 3.693682e-01 NEWTON: using errtol_s: 2.410869e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.305800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.344206e+02 PMG: contraction number = , 1.344206e+02 PMG: iteration = 9 PMG: relative residual = 2.884573e-06 PMG: contraction number = 5.018390e-01 NEWTON: using errtol_s: 1.209868e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.107200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.709076e+01 PMG: contraction number = , 5.709076e+01 PMG: iteration = 10 PMG: relative residual = 1.225064e-06 PMG: contraction number = 4.246950e-01 NEWTON: using errtol_s: 5.138248e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.888900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.612651e+01 PMG: contraction number = , 2.612651e+01 PMG: iteration = 11 PMG: relative residual = 5.606277e-07 PMG: contraction number = 4.576314e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.296200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.761000e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.809431581915E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.949605090681E+05 kT Vpmg_energy: dielEnergy = 4.974345457710E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.375000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0136297 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0166919 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 = 1.257200e+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 = 5.250000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.336000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232320e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.524216e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.287380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.852491e+06 PMG: contraction number = , 7.852491e+06 NEWTON: attempting damping, relres = 1.732143e-01 NEWTON: attempting damping, relres = 5.783538e-01 NEWTON: damping accepted, relres = 1.732143e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.732143e-01 PMG: contraction number = 1.732143e-01 NEWTON: using errtol_s: 7.836588e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.391980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.061555e+06 PMG: contraction number = , 1.061555e+06 PMG: iteration = 2 PMG: relative residual = 2.577303e-02 PMG: contraction number = 1.487928e-01 NEWTON: using errtol_s: 1.166028e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.473620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.894966e+05 PMG: contraction number = , 1.894966e+05 PMG: iteration = 3 PMG: relative residual = 4.941158e-03 PMG: contraction number = 1.917181e-01 NEWTON: using errtol_s: 2.235487e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.552430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.269994e+04 PMG: contraction number = , 4.269994e+04 PMG: iteration = 4 PMG: relative residual = 1.168895e-03 PMG: contraction number = 2.365629e-01 NEWTON: using errtol_s: 5.288333e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.643430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.202156e+04 PMG: contraction number = , 1.202156e+04 PMG: iteration = 5 PMG: relative residual = 3.210073e-04 PMG: contraction number = 2.746247e-01 NEWTON: using errtol_s: 1.452307e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.720240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.224272e+03 PMG: contraction number = , 4.224272e+03 PMG: iteration = 6 PMG: relative residual = 9.658380e-05 PMG: contraction number = 3.008772e-01 NEWTON: using errtol_s: 4.369660e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.808740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.435657e+03 PMG: contraction number = , 1.435657e+03 PMG: iteration = 7 PMG: relative residual = 2.884704e-05 PMG: contraction number = 2.986737e-01 NEWTON: using errtol_s: 1.305102e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.891010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.959551e+02 PMG: contraction number = , 4.959551e+02 PMG: iteration = 8 PMG: relative residual = 9.872876e-06 PMG: contraction number = 3.422492e-01 NEWTON: using errtol_s: 4.466703e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.964500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.816811e+02 PMG: contraction number = , 1.816811e+02 PMG: iteration = 9 PMG: relative residual = 3.614184e-06 PMG: contraction number = 3.660720e-01 NEWTON: using errtol_s: 1.635135e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.043220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.211116e+01 PMG: contraction number = , 8.211116e+01 PMG: iteration = 10 PMG: relative residual = 1.633856e-06 PMG: contraction number = 4.520678e-01 NEWTON: using errtol_s: 7.391919e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.116100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.724917e+01 PMG: contraction number = , 3.724917e+01 PMG: iteration = 11 PMG: relative residual = 7.409971e-07 PMG: contraction number = 4.535265e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.318100e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.650500e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.760838632749E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.246597482164E+06 kT Vpmg_energy: dielEnergy = 1.123254009296E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.200000e+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, 18.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.818000e+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 = 5.550000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.609000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.342720e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.944059e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.398110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.137913e+05 PMG: contraction number = , 7.137913e+05 NEWTON: attempting damping, relres = 9.337025e-02 NEWTON: attempting damping, relres = 5.443408e-01 NEWTON: damping accepted, relres = 9.337025e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.337025e-02 PMG: contraction number = 9.337025e-02 NEWTON: using errtol_s: 6.483686e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.501500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.299055e+04 PMG: contraction number = , 9.299055e+04 PMG: iteration = 2 PMG: relative residual = 1.205864e-02 PMG: contraction number = 1.291487e-01 NEWTON: using errtol_s: 8.373593e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.586700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.450690e+04 PMG: contraction number = , 1.450690e+04 PMG: iteration = 3 PMG: relative residual = 1.880248e-03 PMG: contraction number = 1.559254e-01 NEWTON: using errtol_s: 1.305656e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.667770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.526149e+03 PMG: contraction number = , 2.526149e+03 PMG: iteration = 4 PMG: relative residual = 3.274081e-04 PMG: contraction number = 1.741303e-01 NEWTON: using errtol_s: 2.273541e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.751710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.725291e+02 PMG: contraction number = , 4.725291e+02 PMG: iteration = 5 PMG: relative residual = 6.124356e-05 PMG: contraction number = 1.870557e-01 NEWTON: using errtol_s: 4.252789e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.838810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.079851e+02 PMG: contraction number = , 1.079851e+02 PMG: iteration = 6 PMG: relative residual = 1.399566e-05 PMG: contraction number = 2.285246e-01 NEWTON: using errtol_s: 9.718668e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.923080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.797115e+01 PMG: contraction number = , 3.797115e+01 PMG: iteration = 7 PMG: relative residual = 4.921409e-06 PMG: contraction number = 3.516383e-01 NEWTON: using errtol_s: 3.417456e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.998460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.936340e+01 PMG: contraction number = , 1.936340e+01 PMG: iteration = 8 PMG: relative residual = 2.509638e-06 PMG: contraction number = 5.099429e-01 NEWTON: using errtol_s: 1.742707e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.082930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.018245e+01 PMG: contraction number = , 1.018245e+01 PMG: iteration = 9 PMG: relative residual = 1.319735e-06 PMG: contraction number = 5.258668e-01 NEWTON: using errtol_s: 9.164319e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.169600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.626762e+00 PMG: contraction number = , 4.626762e+00 PMG: iteration = 10 PMG: relative residual = 5.996618e-07 PMG: contraction number = 4.543804e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.806900e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.165000e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.575159635803E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.447972081922E+05 kT Vpmg_energy: dielEnergy = 7.239558043731E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.298000e+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, 18.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000156134 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000220592 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 = 7.811000e+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 = 5.290000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.597000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.362170e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.466455e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.419260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.343122e+06 PMG: contraction number = , 1.343122e+06 NEWTON: attempting damping, relres = 1.627096e-01 NEWTON: attempting damping, relres = 5.808269e-01 NEWTON: damping accepted, relres = 1.627096e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.627096e-01 PMG: contraction number = 1.627096e-01 NEWTON: using errtol_s: 1.214864e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.536860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.727353e+05 PMG: contraction number = , 1.727353e+05 PMG: iteration = 2 PMG: relative residual = 2.082961e-02 PMG: contraction number = 1.280171e-01 NEWTON: using errtol_s: 1.555234e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.626040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.535193e+04 PMG: contraction number = , 2.535193e+04 PMG: iteration = 3 PMG: relative residual = 3.055925e-03 PMG: contraction number = 1.467106e-01 NEWTON: using errtol_s: 2.281692e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.718850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.078724e+03 PMG: contraction number = , 4.078724e+03 PMG: iteration = 4 PMG: relative residual = 4.916467e-04 PMG: contraction number = 1.608831e-01 NEWTON: using errtol_s: 3.670858e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.804210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.011530e+02 PMG: contraction number = , 7.011530e+02 PMG: iteration = 5 PMG: relative residual = 8.451660e-05 PMG: contraction number = 1.719051e-01 NEWTON: using errtol_s: 6.310394e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.878780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.435137e+02 PMG: contraction number = , 1.435137e+02 PMG: iteration = 6 PMG: relative residual = 1.729902e-05 PMG: contraction number = 2.046819e-01 NEWTON: using errtol_s: 1.291624e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.969350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.390377e+01 PMG: contraction number = , 6.390377e+01 PMG: iteration = 7 PMG: relative residual = 7.703066e-06 PMG: contraction number = 4.452891e-01 NEWTON: using errtol_s: 5.751459e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.055340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.404488e+01 PMG: contraction number = , 3.404488e+01 PMG: iteration = 8 PMG: relative residual = 4.103746e-06 PMG: contraction number = 5.327419e-01 NEWTON: using errtol_s: 3.064044e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.145000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.407083e+01 PMG: contraction number = , 1.407083e+01 PMG: iteration = 9 PMG: relative residual = 1.696134e-06 PMG: contraction number = 4.133136e-01 NEWTON: using errtol_s: 1.266411e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.219900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.737799e+00 PMG: contraction number = , 6.737799e+00 PMG: iteration = 10 PMG: relative residual = 8.121689e-07 PMG: contraction number = 4.788354e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.191800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.549500e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.508071317668E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.423901777264E+05 kT Vpmg_energy: dielEnergy = 1.711921591701E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.307000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.810000e+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 = 5.280000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.341000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.496780e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.500453e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.551370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.822126e+06 PMG: contraction number = , 3.822126e+06 NEWTON: attempting damping, relres = 1.138053e-01 NEWTON: attempting damping, relres = 5.469154e-01 NEWTON: damping accepted, relres = 1.138053e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.138053e-01 PMG: contraction number = 1.138053e-01 NEWTON: using errtol_s: 3.983703e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.653070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.288184e+05 PMG: contraction number = , 5.288184e+05 PMG: iteration = 2 PMG: relative residual = 1.737420e-02 PMG: contraction number = 1.526660e-01 NEWTON: using errtol_s: 6.081759e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.738920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.049674e+05 PMG: contraction number = , 1.049674e+05 PMG: iteration = 3 PMG: relative residual = 3.466591e-03 PMG: contraction number = 1.995252e-01 NEWTON: using errtol_s: 1.213464e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.817720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.467381e+04 PMG: contraction number = , 2.467381e+04 PMG: iteration = 4 PMG: relative residual = 7.899710e-04 PMG: contraction number = 2.278812e-01 NEWTON: using errtol_s: 2.765257e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.898020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.743223e+03 PMG: contraction number = , 6.743223e+03 PMG: iteration = 5 PMG: relative residual = 2.002338e-04 PMG: contraction number = 2.534698e-01 NEWTON: using errtol_s: 7.009090e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.977750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.053001e+03 PMG: contraction number = , 2.053001e+03 PMG: iteration = 6 PMG: relative residual = 5.543985e-05 PMG: contraction number = 2.768756e-01 NEWTON: using errtol_s: 1.940646e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.053620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.693316e+02 PMG: contraction number = , 6.693316e+02 PMG: iteration = 7 PMG: relative residual = 1.723694e-05 PMG: contraction number = 3.109125e-01 NEWTON: using errtol_s: 6.033710e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.127970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.417797e+02 PMG: contraction number = , 2.417797e+02 PMG: iteration = 8 PMG: relative residual = 6.217515e-06 PMG: contraction number = 3.607088e-01 NEWTON: using errtol_s: 2.176412e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.204600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.209100e+02 PMG: contraction number = , 1.209100e+02 PMG: iteration = 9 PMG: relative residual = 3.108833e-06 PMG: contraction number = 5.000122e-01 NEWTON: using errtol_s: 1.088233e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.287690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.308125e+01 PMG: contraction number = , 5.308125e+01 PMG: iteration = 10 PMG: relative residual = 1.364806e-06 PMG: contraction number = 4.390091e-01 NEWTON: using errtol_s: 4.777440e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.370270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.376173e+01 PMG: contraction number = , 2.376173e+01 PMG: iteration = 11 PMG: relative residual = 6.109428e-07 PMG: contraction number = 4.476407e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.246200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.580300e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.558884626495E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.501651881935E+05 kT Vpmg_energy: dielEnergy = 4.250398526709E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.309000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0137259 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.016576 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.135900e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 3.121000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.541000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.631640e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.777570e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.689990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.510744e+06 PMG: contraction number = , 6.510744e+06 NEWTON: attempting damping, relres = 1.743795e-01 NEWTON: attempting damping, relres = 5.778484e-01 NEWTON: damping accepted, relres = 1.743795e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.743795e-01 PMG: contraction number = 1.743795e-01 NEWTON: using errtol_s: 6.587309e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.800480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.861794e+05 PMG: contraction number = , 8.861794e+05 PMG: iteration = 2 PMG: relative residual = 2.637852e-02 PMG: contraction number = 1.512707e-01 NEWTON: using errtol_s: 9.964671e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.876380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.616956e+05 PMG: contraction number = , 1.616956e+05 PMG: iteration = 3 PMG: relative residual = 5.179745e-03 PMG: contraction number = 1.963622e-01 NEWTON: using errtol_s: 1.956685e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.964440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.709296e+04 PMG: contraction number = , 3.709296e+04 PMG: iteration = 4 PMG: relative residual = 1.253535e-03 PMG: contraction number = 2.420072e-01 NEWTON: using errtol_s: 4.735318e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.046420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.071987e+04 PMG: contraction number = , 1.071987e+04 PMG: iteration = 5 PMG: relative residual = 3.519840e-04 PMG: contraction number = 2.807931e-01 NEWTON: using errtol_s: 1.329644e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.124090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.850932e+03 PMG: contraction number = , 3.850932e+03 PMG: iteration = 6 PMG: relative residual = 1.069379e-04 PMG: contraction number = 3.038146e-01 NEWTON: using errtol_s: 4.039654e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.199290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.313893e+03 PMG: contraction number = , 1.313893e+03 PMG: iteration = 7 PMG: relative residual = 3.177439e-05 PMG: contraction number = 2.971294e-01 NEWTON: using errtol_s: 1.200300e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.301410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.530186e+02 PMG: contraction number = , 4.530186e+02 PMG: iteration = 8 PMG: relative residual = 1.079637e-05 PMG: contraction number = 3.397821e-01 NEWTON: using errtol_s: 4.078405e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.401210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.579920e+02 PMG: contraction number = , 1.579920e+02 PMG: iteration = 9 PMG: relative residual = 3.764137e-06 PMG: contraction number = 3.486483e-01 NEWTON: using errtol_s: 1.421929e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.484890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.157951e+01 PMG: contraction number = , 7.157951e+01 PMG: iteration = 10 PMG: relative residual = 1.705633e-06 PMG: contraction number = 4.531274e-01 NEWTON: using errtol_s: 6.443150e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.564690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.213075e+01 PMG: contraction number = , 3.213075e+01 PMG: iteration = 11 PMG: relative residual = 7.655109e-07 PMG: contraction number = 4.488132e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.867500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.058160e+03 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.514742034797E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.904209211624E+06 kT Vpmg_energy: dielEnergy = 9.520627821288E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.243000e+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 = 6.726880e+03 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 11 21:06:12 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_allh35.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb35.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 449, 449) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34599 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 81.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 29.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 81.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 25.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 53.26) Valist_readPDB: Counted 29844 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 23.463) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 0.281) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.4425 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.4425 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.4425 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.314 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.391 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.506 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.391 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.506 -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 = -2.5935 -0.8825 53.26 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -2.5935 -0.8825 53.26 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -2.5935 -0.8825 53.26 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 139.846 128.989 183.495 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -145.034 -130.754 -76.975 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 79.3825 76.066 130.354 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -84.5695 -77.831 -23.834 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 79.3825 76.066 130.354 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -84.5695 -77.831 -23.834 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 0.4425 0.281 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.4425 0.281 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.5935, 0.579781, 0.581406 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.341567, 0.34352, 0.34417 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.4425 0.281 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.314 130.516 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -129.954 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.391 77.375 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.506 -76.813 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.391 77.375 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.506 -76.813 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.879000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.270000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.348000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033300e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.194264e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.579700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.532600e+06 PMG: contraction number = , 4.532600e+06 NEWTON: attempting damping, relres = 1.110357e-01 NEWTON: attempting damping, relres = 5.464850e-01 NEWTON: damping accepted, relres = 1.110357e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.110357e-01 PMG: contraction number = 1.110357e-01 NEWTON: using errtol_s: 4.657130e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.632200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.227692e+05 PMG: contraction number = , 6.227692e+05 PMG: iteration = 2 PMG: relative residual = 1.673756e-02 PMG: contraction number = 1.507404e-01 NEWTON: using errtol_s: 7.020174e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.480800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.204033e+05 PMG: contraction number = , 1.204033e+05 PMG: iteration = 3 PMG: relative residual = 3.281723e-03 PMG: contraction number = 1.960694e-01 NEWTON: using errtol_s: 1.376441e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.329100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.799914e+04 PMG: contraction number = , 2.799914e+04 PMG: iteration = 4 PMG: relative residual = 7.395121e-04 PMG: contraction number = 2.253427e-01 NEWTON: using errtol_s: 3.101709e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.175700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.562741e+03 PMG: contraction number = , 7.562741e+03 PMG: iteration = 5 PMG: relative residual = 1.844906e-04 PMG: contraction number = 2.494761e-01 NEWTON: using errtol_s: 7.738023e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.022300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.248411e+03 PMG: contraction number = , 2.248411e+03 PMG: iteration = 6 PMG: relative residual = 5.006709e-05 PMG: contraction number = 2.713802e-01 NEWTON: using errtol_s: 2.099946e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.872000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.243790e+02 PMG: contraction number = , 7.243790e+02 PMG: iteration = 7 PMG: relative residual = 1.555685e-05 PMG: contraction number = 3.107200e-01 NEWTON: using errtol_s: 6.524952e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.714700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.682155e+02 PMG: contraction number = , 2.682155e+02 PMG: iteration = 8 PMG: relative residual = 5.755755e-06 PMG: contraction number = 3.699821e-01 NEWTON: using errtol_s: 2.414116e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.455200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.345644e+02 PMG: contraction number = , 1.345644e+02 PMG: iteration = 9 PMG: relative residual = 2.887664e-06 PMG: contraction number = 5.017003e-01 NEWTON: using errtol_s: 1.211163e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.201600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.707119e+01 PMG: contraction number = , 5.707119e+01 PMG: iteration = 10 PMG: relative residual = 1.224646e-06 PMG: contraction number = 4.240956e-01 NEWTON: using errtol_s: 5.136487e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.962300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.612426e+01 PMG: contraction number = , 2.612426e+01 PMG: iteration = 11 PMG: relative residual = 5.605802e-07 PMG: contraction number = 4.577489e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.499600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.833300e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.314, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.314, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.809434959577E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.949600091319E+05 kT Vpmg_energy: dielEnergy = 4.974342958442E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.370000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.506, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.391, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.314, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.506, -47.901) Vpmg_setPart: upper corner = (80.819, 77.391, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.314, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.506, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.391, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.314, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0136303 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0166927 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 = 1.234000e+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 = 5.230000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.338000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237190e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.524216e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.294760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.852459e+06 PMG: contraction number = , 7.852459e+06 NEWTON: attempting damping, relres = 1.732091e-01 NEWTON: attempting damping, relres = 5.783535e-01 NEWTON: damping accepted, relres = 1.732091e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.732091e-01 PMG: contraction number = 1.732091e-01 NEWTON: using errtol_s: 7.836353e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.410090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.061376e+06 PMG: contraction number = , 1.061376e+06 PMG: iteration = 2 PMG: relative residual = 2.576751e-02 PMG: contraction number = 1.487653e-01 NEWTON: using errtol_s: 1.165778e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.484640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.894610e+05 PMG: contraction number = , 1.894610e+05 PMG: iteration = 3 PMG: relative residual = 4.939925e-03 PMG: contraction number = 1.917114e-01 NEWTON: using errtol_s: 2.234929e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.559710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.268397e+04 PMG: contraction number = , 4.268397e+04 PMG: iteration = 4 PMG: relative residual = 1.168429e-03 PMG: contraction number = 2.365277e-01 NEWTON: using errtol_s: 5.286227e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.633270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.201559e+04 PMG: contraction number = , 1.201559e+04 PMG: iteration = 5 PMG: relative residual = 3.208345e-04 PMG: contraction number = 2.745861e-01 NEWTON: using errtol_s: 1.451525e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.708570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.223818e+03 PMG: contraction number = , 4.223818e+03 PMG: iteration = 6 PMG: relative residual = 9.656209e-05 PMG: contraction number = 3.009717e-01 NEWTON: using errtol_s: 4.368677e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.780240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.435944e+03 PMG: contraction number = , 1.435944e+03 PMG: iteration = 7 PMG: relative residual = 2.885217e-05 PMG: contraction number = 2.987940e-01 NEWTON: using errtol_s: 1.305334e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.872090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.962393e+02 PMG: contraction number = , 4.962393e+02 PMG: iteration = 8 PMG: relative residual = 9.878567e-06 PMG: contraction number = 3.423856e-01 NEWTON: using errtol_s: 4.469277e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.947470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.818481e+02 PMG: contraction number = , 1.818481e+02 PMG: iteration = 9 PMG: relative residual = 3.617508e-06 PMG: contraction number = 3.661976e-01 NEWTON: using errtol_s: 1.636639e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.023100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.217174e+01 PMG: contraction number = , 8.217174e+01 PMG: iteration = 10 PMG: relative residual = 1.635064e-06 PMG: contraction number = 4.519862e-01 NEWTON: using errtol_s: 7.397380e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.106240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.727392e+01 PMG: contraction number = , 3.727392e+01 PMG: iteration = 11 PMG: relative residual = 7.414894e-07 PMG: contraction number = 4.534927e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.309000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.641500e+02 Vpmg_setPart: lower corner = (-83.133, -76.506, -47.901) Vpmg_setPart: upper corner = (80.819, 77.391, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.506, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.391, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.760777438520E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.246581632740E+06 kT Vpmg_energy: dielEnergy = 1.123246089137E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.117000e+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, 18.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.820000e+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 = 5.250000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.347000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.263300e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.938271e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.318260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.106813e+05 PMG: contraction number = , 7.106813e+05 NEWTON: attempting damping, relres = 9.303716e-02 NEWTON: attempting damping, relres = 5.440781e-01 NEWTON: damping accepted, relres = 9.303716e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.303716e-02 PMG: contraction number = 9.303716e-02 NEWTON: using errtol_s: 6.455171e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.427830e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.208056e+04 PMG: contraction number = , 9.208056e+04 PMG: iteration = 2 PMG: relative residual = 1.195109e-02 PMG: contraction number = 1.284550e-01 NEWTON: using errtol_s: 8.291991e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.513790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.434972e+04 PMG: contraction number = , 1.434972e+04 PMG: iteration = 3 PMG: relative residual = 1.861430e-03 PMG: contraction number = 1.557540e-01 NEWTON: using errtol_s: 1.291511e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.591930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.512514e+03 PMG: contraction number = , 2.512514e+03 PMG: iteration = 4 PMG: relative residual = 3.259123e-04 PMG: contraction number = 1.750870e-01 NEWTON: using errtol_s: 2.261268e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.671980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.721042e+02 PMG: contraction number = , 4.721042e+02 PMG: iteration = 5 PMG: relative residual = 6.123938e-05 PMG: contraction number = 1.879014e-01 NEWTON: using errtol_s: 4.248954e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.744010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.004248e+02 PMG: contraction number = , 1.004248e+02 PMG: iteration = 6 PMG: relative residual = 1.302664e-05 PMG: contraction number = 2.127167e-01 NEWTON: using errtol_s: 9.038233e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.821200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.675624e+01 PMG: contraction number = , 2.675624e+01 PMG: iteration = 7 PMG: relative residual = 3.470707e-06 PMG: contraction number = 2.664316e-01 NEWTON: using errtol_s: 2.408071e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.913870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.021931e+00 PMG: contraction number = , 9.021931e+00 PMG: iteration = 8 PMG: relative residual = 1.170283e-06 PMG: contraction number = 3.371886e-01 NEWTON: using errtol_s: 8.119739e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.988820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.471962e+00 PMG: contraction number = , 3.471962e+00 PMG: iteration = 9 PMG: relative residual = 4.503676e-07 PMG: contraction number = 3.848366e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.737500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.070800e+02 Vpmg_setPart: lower corner = (-145.034, -130.754, -76.975) Vpmg_setPart: upper corner = (139.846, 128.989, 183.495) Vpmg_setPart: actual minima = (-145.034, -130.754, -76.975) Vpmg_setPart: actual maxima = (139.846, 128.989, 183.495) 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 = 2.586149765061E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.450911097075E+05 kT Vpmg_energy: dielEnergy = 7.254251362297E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.323000e+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, 18.0691) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -84.5695, -77.831, -23.834 VPMG::focusFillBound -- New mesh maxs = 79.3825, 76.066, 130.354 VPMG::focusFillBound -- Old mesh mins = -145.034, -130.754, -76.975 VPMG::focusFillBound -- Old mesh maxs = 139.846, 128.989, 183.495 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-84.5695, -77.831, -23.834) Vpmg_setPart: upper corner = (79.3825, 76.066, 130.354) Vpmg_setPart: actual minima = (-145.034, -130.754, -76.975) Vpmg_setPart: actual maxima = (139.846, 128.989, 183.495) 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 = (-84.5695, -77.831, -23.834) VPMG::extEnergy Disj part upper corner = (79.3825, 76.066, 130.354) VPMG::extEnergy Old lower corner = (-145.034, -130.754, -76.975) VPMG::extEnergy Old upper corner = (139.846, 128.989, 183.495) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 2.62727e-06 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 3.40574e-06 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 = 7.465000e+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 = 5.260000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.635000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.173370e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.455034e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.232620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.339576e+06 PMG: contraction number = , 1.339576e+06 NEWTON: attempting damping, relres = 1.625326e-01 NEWTON: attempting damping, relres = 5.807225e-01 NEWTON: damping accepted, relres = 1.625326e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.625326e-01 PMG: contraction number = 1.625326e-01 NEWTON: using errtol_s: 1.211686e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.350390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.720271e+05 PMG: contraction number = , 1.720271e+05 PMG: iteration = 2 PMG: relative residual = 2.077571e-02 PMG: contraction number = 1.278249e-01 NEWTON: using errtol_s: 1.548836e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.430660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.521807e+04 PMG: contraction number = , 2.521807e+04 PMG: iteration = 3 PMG: relative residual = 3.044446e-03 PMG: contraction number = 1.465387e-01 NEWTON: using errtol_s: 2.269644e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.518170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.058195e+03 PMG: contraction number = , 4.058195e+03 PMG: iteration = 4 PMG: relative residual = 4.899216e-04 PMG: contraction number = 1.609231e-01 NEWTON: using errtol_s: 3.652382e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.601200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.923620e+02 PMG: contraction number = , 6.923620e+02 PMG: iteration = 5 PMG: relative residual = 8.358491e-05 PMG: contraction number = 1.706088e-01 NEWTON: using errtol_s: 6.231283e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.681350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.485410e+02 PMG: contraction number = , 1.485410e+02 PMG: iteration = 6 PMG: relative residual = 1.793245e-05 PMG: contraction number = 2.145417e-01 NEWTON: using errtol_s: 1.336870e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.763770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.475676e+01 PMG: contraction number = , 6.475676e+01 PMG: iteration = 7 PMG: relative residual = 7.817922e-06 PMG: contraction number = 4.359650e-01 NEWTON: using errtol_s: 5.828287e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.866000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.095906e+01 PMG: contraction number = , 3.095906e+01 PMG: iteration = 8 PMG: relative residual = 3.737502e-06 PMG: contraction number = 4.780685e-01 NEWTON: using errtol_s: 2.786321e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.952950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.286074e+01 PMG: contraction number = , 1.286074e+01 PMG: iteration = 9 PMG: relative residual = 1.552643e-06 PMG: contraction number = 4.154225e-01 NEWTON: using errtol_s: 1.157500e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.035890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.871380e+00 PMG: contraction number = , 5.871380e+00 PMG: iteration = 10 PMG: relative residual = 7.088156e-07 PMG: contraction number = 4.565221e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.172000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.531300e+02 Vpmg_setPart: lower corner = (-84.5695, -77.831, -23.834) Vpmg_setPart: upper corner = (79.3825, 76.066, 130.354) Vpmg_setPart: actual minima = (-84.5695, -77.831, -23.834) Vpmg_setPart: actual maxima = (79.3825, 76.066, 130.354) 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 = 2.510530277444E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.422261545488E+05 kT Vpmg_energy: dielEnergy = 1.711101434278E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.298000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.746000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.190000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.204000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.226970e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.499163e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.284860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.806548e+06 PMG: contraction number = , 3.806548e+06 NEWTON: attempting damping, relres = 1.132306e-01 NEWTON: attempting damping, relres = 5.467544e-01 NEWTON: damping accepted, relres = 1.132306e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.132306e-01 PMG: contraction number = 1.132306e-01 NEWTON: using errtol_s: 3.962125e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.394190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.238754e+05 PMG: contraction number = , 5.238754e+05 PMG: iteration = 2 PMG: relative residual = 1.718961e-02 PMG: contraction number = 1.518106e-01 NEWTON: using errtol_s: 6.014926e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.486830e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.035501e+05 PMG: contraction number = , 1.035501e+05 PMG: iteration = 3 PMG: relative residual = 3.413431e-03 PMG: contraction number = 1.985752e-01 NEWTON: using errtol_s: 1.194415e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.571320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.437583e+04 PMG: contraction number = , 2.437583e+04 PMG: iteration = 4 PMG: relative residual = 7.780497e-04 PMG: contraction number = 2.279377e-01 NEWTON: using errtol_s: 2.722523e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.657550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.699328e+03 PMG: contraction number = , 6.699328e+03 PMG: iteration = 5 PMG: relative residual = 1.985474e-04 PMG: contraction number = 2.551860e-01 NEWTON: using errtol_s: 6.947496e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.747150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.047543e+03 PMG: contraction number = , 2.047543e+03 PMG: iteration = 6 PMG: relative residual = 5.550677e-05 PMG: contraction number = 2.795643e-01 NEWTON: using errtol_s: 1.942272e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.830750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.564687e+02 PMG: contraction number = , 6.564687e+02 PMG: iteration = 7 PMG: relative residual = 1.692228e-05 PMG: contraction number = 3.048687e-01 NEWTON: using errtol_s: 5.921380e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.920050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.228903e+02 PMG: contraction number = , 2.228903e+02 PMG: iteration = 8 PMG: relative residual = 5.734638e-06 PMG: contraction number = 3.388810e-01 NEWTON: using errtol_s: 2.006643e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.006260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.076906e+02 PMG: contraction number = , 1.076906e+02 PMG: iteration = 9 PMG: relative residual = 2.769952e-06 PMG: contraction number = 4.830212e-01 NEWTON: using errtol_s: 9.692511e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.091120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.209131e+01 PMG: contraction number = , 5.209131e+01 PMG: iteration = 10 PMG: relative residual = 1.339843e-06 PMG: contraction number = 4.837064e-01 NEWTON: using errtol_s: 4.688330e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.175650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.435048e+01 PMG: contraction number = , 2.435048e+01 PMG: iteration = 11 PMG: relative residual = 6.263123e-07 PMG: contraction number = 4.674519e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.006960e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.049860e+03 Vpmg_setPart: lower corner = (-143.597, -129.429, -129.954) Vpmg_setPart: upper corner = (141.283, 130.314, 130.516) Vpmg_setPart: actual minima = (-143.597, -129.429, -129.954) Vpmg_setPart: actual maxima = (141.283, 130.314, 130.516) 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 = 2.558133647175E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.509378351772E+05 kT Vpmg_energy: dielEnergy = 4.254263067439E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.371000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 72.9788 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 48.912 Vpbe_ctor2: solute charge = -52 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (128.28, 118.225, 60.6918) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 19442224 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 449, nz = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 57, nzc = 57 Vpmg_ctor2: PMG chose nf = 96970081, nc = 198189 Vpmg_ctor2: PMG chose narr = 110913944, narrc = 13943863 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1375347257, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.506, -76.813 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.391, 77.375 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -129.954 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.314, 130.516 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.506, -76.813) Vpmg_setPart: upper corner = (80.819, 77.391, 77.375) Vpmg_setPart: actual minima = (-143.597, -129.429, -129.954) Vpmg_setPart: actual maxima = (141.283, 130.314, 130.516) 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, -76.506, -76.813) VPMG::extEnergy Disj part upper corner = (80.819, 77.391, 77.375) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -129.954) VPMG::extEnergy Old upper corner = (141.283, 130.314, 130.516) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.00175514 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.00218059 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 = 1.139300e+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 = 5.240000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.337000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.407890e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.763275e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.462210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.493192e+06 PMG: contraction number = , 6.493192e+06 NEWTON: attempting damping, relres = 1.749143e-01 NEWTON: attempting damping, relres = 5.779301e-01 NEWTON: damping accepted, relres = 1.749143e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.749143e-01 PMG: contraction number = 1.749143e-01 NEWTON: using errtol_s: 6.582505e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.556790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.855925e+05 PMG: contraction number = , 8.855925e+05 PMG: iteration = 2 PMG: relative residual = 2.657209e-02 PMG: contraction number = 1.519149e-01 NEWTON: using errtol_s: 9.999808e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.626090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.612415e+05 PMG: contraction number = , 1.612415e+05 PMG: iteration = 3 PMG: relative residual = 5.232644e-03 PMG: contraction number = 1.969225e-01 NEWTON: using errtol_s: 1.969188e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.703450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.683642e+04 PMG: contraction number = , 3.683642e+04 PMG: iteration = 4 PMG: relative residual = 1.266239e-03 PMG: contraction number = 2.419883e-01 NEWTON: using errtol_s: 4.765204e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.771230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.041778e+04 PMG: contraction number = , 1.041778e+04 PMG: iteration = 5 PMG: relative residual = 3.519166e-04 PMG: contraction number = 2.779228e-01 NEWTON: using errtol_s: 1.324359e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.840560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.623238e+03 PMG: contraction number = , 3.623238e+03 PMG: iteration = 6 PMG: relative residual = 1.039516e-04 PMG: contraction number = 2.953869e-01 NEWTON: using errtol_s: 3.911983e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.909880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.157386e+03 PMG: contraction number = , 1.157386e+03 PMG: iteration = 7 PMG: relative residual = 2.860233e-05 PMG: contraction number = 2.751506e-01 NEWTON: using errtol_s: 1.076384e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.979440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.861996e+02 PMG: contraction number = , 3.861996e+02 PMG: iteration = 8 PMG: relative residual = 9.246666e-06 PMG: contraction number = 3.232837e-01 NEWTON: using errtol_s: 3.479775e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.087130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.423040e+02 PMG: contraction number = , 1.423040e+02 PMG: iteration = 9 PMG: relative residual = 3.403294e-06 PMG: contraction number = 3.680563e-01 NEWTON: using errtol_s: 1.280753e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.156450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.568325e+01 PMG: contraction number = , 6.568325e+01 PMG: iteration = 10 PMG: relative residual = 1.571357e-06 PMG: contraction number = 4.617165e-01 NEWTON: using errtol_s: 5.913448e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.225800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.009204e+01 PMG: contraction number = , 3.009204e+01 PMG: iteration = 11 PMG: relative residual = 7.196647e-07 PMG: contraction number = 4.579894e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.614400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.942400e+02 Vpmg_setPart: lower corner = (-83.133, -76.506, -76.813) Vpmg_setPart: upper corner = (80.819, 77.391, 77.375) Vpmg_setPart: actual minima = (-83.133, -76.506, -76.813) Vpmg_setPart: actual maxima = (80.819, 77.391, 77.375) 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 = 2.514829709600E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.904544147902E+06 kT Vpmg_energy: dielEnergy = 9.522302609129E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.135000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.292430e+03 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Mar 14 12:12:29 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_allh35.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb35.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (321, 321, 321) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (321, 321, 321) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (321, 321, 321) 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, 81.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 29.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 81.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 25.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 53.26) Valist_readPDB: Counted 29844 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 23.463) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 0.281) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.89025, 0.811694, 0.813969 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.51235, 0.480928, 0.481837 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.89025, 0.811694, 0.813969 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.51235, 0.480928, 0.481837 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.89025, 0.811694, 0.813969 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.51235, 0.480928, 0.481837 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 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 = 321, ny = 321, nz = 321 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 21, nyc = 21, nzc = 21 Vpmg_ctor2: PMG chose nf = 33076161, nc = 9261 Vpmg_ctor2: PMG chose narr = 37859065, narrc = 4782904 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 470274760, niwk = 900 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 = 4.270000e+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 = 3.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.044000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.866000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.381936e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.288784e+06 PMG: contraction number = , 2.288784e+06 NEWTON: attempting damping, relres = 7.875112e-02 NEWTON: attempting damping, relres = 5.248557e-01 NEWTON: damping accepted, relres = 7.875112e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 7.875112e-02 PMG: contraction number = 7.875112e-02 NEWTON: using errtol_s: 2.663313e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.628900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.699363e+05 PMG: contraction number = , 3.699363e+05 PMG: iteration = 2 PMG: relative residual = 1.444417e-02 PMG: contraction number = 1.834155e-01 NEWTON: using errtol_s: 4.884928e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.080200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.478442e+04 PMG: contraction number = , 8.478442e+04 PMG: iteration = 3 PMG: relative residual = 3.273660e-03 PMG: contraction number = 2.266422e-01 NEWTON: using errtol_s: 1.107131e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.530700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.240744e+04 PMG: contraction number = , 2.240744e+04 PMG: iteration = 4 PMG: relative residual = 7.886872e-04 PMG: contraction number = 2.409191e-01 NEWTON: using errtol_s: 2.667290e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.980900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.383338e+03 PMG: contraction number = , 6.383338e+03 PMG: iteration = 5 PMG: relative residual = 1.969716e-04 PMG: contraction number = 2.497462e-01 NEWTON: using errtol_s: 6.661454e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.432100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.917419e+03 PMG: contraction number = , 1.917419e+03 PMG: iteration = 6 PMG: relative residual = 5.365617e-05 PMG: contraction number = 2.724056e-01 NEWTON: using errtol_s: 1.814618e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.883200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.858931e+02 PMG: contraction number = , 5.858931e+02 PMG: iteration = 7 PMG: relative residual = 1.571265e-05 PMG: contraction number = 2.928396e-01 NEWTON: using errtol_s: 5.313919e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.334300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.720782e+02 PMG: contraction number = , 1.720782e+02 PMG: iteration = 8 PMG: relative residual = 4.579367e-06 PMG: contraction number = 2.914446e-01 NEWTON: using errtol_s: 1.548713e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.785500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.997306e+01 PMG: contraction number = , 4.997306e+01 PMG: iteration = 9 PMG: relative residual = 1.329884e-06 PMG: contraction number = 2.904078e-01 NEWTON: using errtol_s: 4.497583e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.236600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.717638e+01 PMG: contraction number = , 1.717638e+01 PMG: iteration = 10 PMG: relative residual = 4.570976e-07 PMG: contraction number = 3.437124e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 4.929500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.080700e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.865454790894E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 4.756510669806E+05 kT Vpmg_energy: dielEnergy = 2.377782966652E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.558000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 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 = 321, ny = 321, nz = 321 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 21, nyc = 21, nzc = 21 Vpmg_ctor2: PMG chose nf = 33076161, nc = 9261 Vpmg_ctor2: PMG chose narr = 37859065, narrc = 4782904 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 470274760, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0129002 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0158557 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 = 6.968000e+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 = 3.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.044000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.537900e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.403475e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.955300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.838436e+06 PMG: contraction number = , 5.838436e+06 NEWTON: attempting damping, relres = 1.312726e-01 NEWTON: attempting damping, relres = 5.586187e-01 NEWTON: damping accepted, relres = 1.312726e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.312726e-01 PMG: contraction number = 1.312726e-01 NEWTON: using errtol_s: 5.780559e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.574400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.072491e+05 PMG: contraction number = , 8.072491e+05 PMG: iteration = 2 PMG: relative residual = 1.934347e-02 PMG: contraction number = 1.473534e-01 NEWTON: using errtol_s: 8.517850e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.021900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.447317e+05 PMG: contraction number = , 1.447317e+05 PMG: iteration = 3 PMG: relative residual = 3.499786e-03 PMG: contraction number = 1.809286e-01 NEWTON: using errtol_s: 1.541122e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.469500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.124207e+04 PMG: contraction number = , 3.124207e+04 PMG: iteration = 4 PMG: relative residual = 7.358336e-04 PMG: contraction number = 2.102510e-01 NEWTON: using errtol_s: 3.240225e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.917000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.950679e+03 PMG: contraction number = , 7.950679e+03 PMG: iteration = 5 PMG: relative residual = 1.792379e-04 PMG: contraction number = 2.435849e-01 NEWTON: using errtol_s: 7.892698e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.364600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.547932e+03 PMG: contraction number = , 2.547932e+03 PMG: iteration = 6 PMG: relative residual = 5.385820e-05 PMG: contraction number = 3.004844e-01 NEWTON: using errtol_s: 2.371633e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.812200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.091815e+03 PMG: contraction number = , 1.091815e+03 PMG: iteration = 7 PMG: relative residual = 2.237215e-05 PMG: contraction number = 4.153899e-01 NEWTON: using errtol_s: 9.851523e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.025970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.713730e+02 PMG: contraction number = , 4.713730e+02 PMG: iteration = 8 PMG: relative residual = 9.635418e-06 PMG: contraction number = 4.306880e-01 NEWTON: using errtol_s: 4.242933e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.070730e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.150325e+02 PMG: contraction number = , 2.150325e+02 PMG: iteration = 9 PMG: relative residual = 4.395894e-06 PMG: contraction number = 4.562225e-01 NEWTON: using errtol_s: 1.935721e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.115490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.673113e+01 PMG: contraction number = , 9.673113e+01 PMG: iteration = 10 PMG: relative residual = 1.977077e-06 PMG: contraction number = 4.497554e-01 NEWTON: using errtol_s: 8.706011e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.160240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.451410e+01 PMG: contraction number = , 4.451410e+01 PMG: iteration = 11 PMG: relative residual = 9.098301e-07 PMG: contraction number = 4.601894e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 5.342400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.493500e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.797087525360E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.334103515727E+06 kT Vpmg_energy: dielEnergy = 6.670057905177E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.418000e+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, 18.0691) 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 = 321, ny = 321, nz = 321 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 21, nyc = 21, nzc = 21 Vpmg_ctor2: PMG chose nf = 33076161, nc = 9261 Vpmg_ctor2: PMG chose narr = 37859065, narrc = 4782904 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 470274760, niwk = 900 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 = 1.879000e+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 = 3.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.044000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237920e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 5.558587e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.279630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.469212e+05 PMG: contraction number = , 3.469212e+05 NEWTON: attempting damping, relres = 5.717865e-02 NEWTON: attempting damping, relres = 5.234692e-01 NEWTON: damping accepted, relres = 5.717865e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 5.717865e-02 PMG: contraction number = 5.717865e-02 NEWTON: using errtol_s: 3.178325e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.342210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.632776e+04 PMG: contraction number = , 4.632776e+04 PMG: iteration = 2 PMG: relative residual = 7.516496e-03 PMG: contraction number = 1.314563e-01 NEWTON: using errtol_s: 4.178110e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.387420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.707504e+03 PMG: contraction number = , 7.707504e+03 PMG: iteration = 3 PMG: relative residual = 1.247986e-03 PMG: contraction number = 1.660330e-01 NEWTON: using errtol_s: 6.937041e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.432560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.469959e+03 PMG: contraction number = , 1.469959e+03 PMG: iteration = 4 PMG: relative residual = 2.380042e-04 PMG: contraction number = 1.907106e-01 NEWTON: using errtol_s: 1.322967e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.477740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.117354e+02 PMG: contraction number = , 3.117354e+02 PMG: iteration = 5 PMG: relative residual = 5.047361e-05 PMG: contraction number = 2.120703e-01 NEWTON: using errtol_s: 2.805620e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.522930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.448980e+01 PMG: contraction number = , 7.448980e+01 PMG: iteration = 6 PMG: relative residual = 1.206077e-05 PMG: contraction number = 2.389519e-01 NEWTON: using errtol_s: 6.704083e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.032459e+01 PMG: contraction number = , 2.032459e+01 PMG: iteration = 7 PMG: relative residual = 3.290788e-06 PMG: contraction number = 2.728506e-01 NEWTON: using errtol_s: 1.829213e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.613310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.260854e+00 PMG: contraction number = , 6.260854e+00 PMG: iteration = 8 PMG: relative residual = 1.013705e-06 PMG: contraction number = 3.080433e-01 NEWTON: using errtol_s: 5.634768e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.658510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.087964e+00 PMG: contraction number = , 2.087964e+00 PMG: iteration = 9 PMG: relative residual = 3.380657e-07 PMG: contraction number = 3.334951e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 4.485800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.636900e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.660429490367E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 6.425417109639E+04 kT Vpmg_energy: dielEnergy = 3.212393623951E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.588000e+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, 18.0691) 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 = 321, ny = 321, nz = 321 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 21, nyc = 21, nzc = 21 Vpmg_ctor2: PMG chose nf = 33076161, nc = 9261 Vpmg_ctor2: PMG chose narr = 37859065, narrc = 4782904 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 470274760, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000150363 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000213187 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 = 3.651000e+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 = 3.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.042000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.755760e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.284954e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.797460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.435134e+05 PMG: contraction number = , 9.435134e+05 NEWTON: attempting damping, relres = 1.173861e-01 NEWTON: attempting damping, relres = 5.570925e-01 NEWTON: damping accepted, relres = 1.173861e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.173861e-01 PMG: contraction number = 1.173861e-01 NEWTON: using errtol_s: 8.551526e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.859990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.238310e+05 PMG: contraction number = , 1.238310e+05 PMG: iteration = 2 PMG: relative residual = 1.530514e-02 PMG: contraction number = 1.303828e-01 NEWTON: using errtol_s: 1.114972e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.905170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.920962e+04 PMG: contraction number = , 1.920962e+04 PMG: iteration = 3 PMG: relative residual = 2.373272e-03 PMG: contraction number = 1.550637e-01 NEWTON: using errtol_s: 1.728917e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.950330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.366562e+03 PMG: contraction number = , 3.366562e+03 PMG: iteration = 4 PMG: relative residual = 4.159150e-04 PMG: contraction number = 1.752496e-01 NEWTON: using errtol_s: 3.029922e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.995500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.516438e+02 PMG: contraction number = , 6.516438e+02 PMG: iteration = 5 PMG: relative residual = 8.050697e-05 PMG: contraction number = 1.935659e-01 NEWTON: using errtol_s: 5.864896e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.040600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.679279e+02 PMG: contraction number = , 1.679279e+02 PMG: iteration = 6 PMG: relative residual = 2.074625e-05 PMG: contraction number = 2.576950e-01 NEWTON: using errtol_s: 1.511355e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.085560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.205668e+01 PMG: contraction number = , 7.205668e+01 PMG: iteration = 7 PMG: relative residual = 8.902397e-06 PMG: contraction number = 4.291088e-01 NEWTON: using errtol_s: 6.485355e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.130340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.995556e+01 PMG: contraction number = , 3.995556e+01 PMG: iteration = 8 PMG: relative residual = 4.936209e-06 PMG: contraction number = 5.544809e-01 NEWTON: using errtol_s: 3.596006e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.175260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.952015e+01 PMG: contraction number = , 1.952015e+01 PMG: iteration = 9 PMG: relative residual = 2.411625e-06 PMG: contraction number = 4.885581e-01 NEWTON: using errtol_s: 1.756858e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.220160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.021265e+00 PMG: contraction number = , 9.021265e+00 PMG: iteration = 10 PMG: relative residual = 1.114509e-06 PMG: contraction number = 4.621401e-01 NEWTON: using errtol_s: 8.119144e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.265090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.140514e+00 PMG: contraction number = , 4.140514e+00 PMG: iteration = 11 PMG: relative residual = 5.115315e-07 PMG: contraction number = 4.589749e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 5.372400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.523000e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.552347038790E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.970670584153E+05 kT Vpmg_energy: dielEnergy = 9.853053749641E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.567000e+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 = 321, ny = 321, nz = 321 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 21, nyc = 21, nzc = 21 Vpmg_ctor2: PMG chose nf = 33076161, nc = 9261 Vpmg_ctor2: PMG chose narr = 37859065, narrc = 4782904 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 470274760, niwk = 900 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 = 3.800000e+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 = 3.350000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.040000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.363500e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 2.826501e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.405070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.945039e+06 PMG: contraction number = , 1.945039e+06 NEWTON: attempting damping, relres = 8.248600e-02 NEWTON: attempting damping, relres = 5.251455e-01 NEWTON: damping accepted, relres = 8.248600e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 8.248600e-02 PMG: contraction number = 8.248600e-02 NEWTON: using errtol_s: 2.331467e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.467410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.230592e+05 PMG: contraction number = , 3.230592e+05 PMG: iteration = 2 PMG: relative residual = 1.560421e-02 PMG: contraction number = 1.891741e-01 NEWTON: using errtol_s: 4.410531e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.512490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.636506e+04 PMG: contraction number = , 7.636506e+04 PMG: iteration = 3 PMG: relative residual = 3.601583e-03 PMG: contraction number = 2.308084e-01 NEWTON: using errtol_s: 1.017988e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.557560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.045182e+04 PMG: contraction number = , 2.045182e+04 PMG: iteration = 4 PMG: relative residual = 8.757684e-04 PMG: contraction number = 2.431621e-01 NEWTON: using errtol_s: 2.475360e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.602600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.927284e+03 PMG: contraction number = , 5.927284e+03 PMG: iteration = 5 PMG: relative residual = 2.235063e-04 PMG: contraction number = 2.552117e-01 NEWTON: using errtol_s: 6.317408e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.647610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.861278e+03 PMG: contraction number = , 1.861278e+03 PMG: iteration = 6 PMG: relative residual = 6.332911e-05 PMG: contraction number = 2.833437e-01 NEWTON: using errtol_s: 1.789998e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.692640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.976945e+02 PMG: contraction number = , 5.976945e+02 PMG: iteration = 7 PMG: relative residual = 1.926706e-05 PMG: contraction number = 3.042369e-01 NEWTON: using errtol_s: 5.445834e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.737640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.819132e+02 PMG: contraction number = , 1.819132e+02 PMG: iteration = 8 PMG: relative residual = 5.793846e-06 PMG: contraction number = 3.007126e-01 NEWTON: using errtol_s: 1.637631e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.782660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.182303e+01 PMG: contraction number = , 5.182303e+01 PMG: iteration = 9 PMG: relative residual = 1.650126e-06 PMG: contraction number = 2.848067e-01 NEWTON: using errtol_s: 4.664083e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.827650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.682303e+01 PMG: contraction number = , 1.682303e+01 PMG: iteration = 10 PMG: relative residual = 5.356705e-07 PMG: contraction number = 3.246239e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 4.920400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.070700e+02 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.608449737473E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 4.113988114467E+05 kT Vpmg_energy: dielEnergy = 2.056552344512E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.565000e+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 = 321, ny = 321, nz = 321 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 21, nyc = 21, nzc = 21 Vpmg_ctor2: PMG chose nf = 33076161, nc = 9261 Vpmg_ctor2: PMG chose narr = 37859065, narrc = 4782904 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 470274760, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.013008 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0157512 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 = 6.302000e+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 = 3.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.035000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.951040e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.674982e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.992690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.897471e+06 PMG: contraction number = , 4.897471e+06 NEWTON: attempting damping, relres = 1.335095e-01 NEWTON: attempting damping, relres = 5.589247e-01 NEWTON: damping accepted, relres = 1.335095e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.335095e-01 PMG: contraction number = 1.335095e-01 NEWTON: using errtol_s: 4.906449e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.054520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.828315e+05 PMG: contraction number = , 6.828315e+05 PMG: iteration = 2 PMG: relative residual = 1.995502e-02 PMG: contraction number = 1.494652e-01 NEWTON: using errtol_s: 7.333434e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.099260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.250380e+05 PMG: contraction number = , 1.250380e+05 PMG: iteration = 3 PMG: relative residual = 3.668859e-03 PMG: contraction number = 1.838564e-01 NEWTON: using errtol_s: 1.348299e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.144070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.738387e+04 PMG: contraction number = , 2.738387e+04 PMG: iteration = 4 PMG: relative residual = 7.842800e-04 PMG: contraction number = 2.137668e-01 NEWTON: using errtol_s: 2.882215e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.188860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.133594e+03 PMG: contraction number = , 7.133594e+03 PMG: iteration = 5 PMG: relative residual = 1.963199e-04 PMG: contraction number = 2.503186e-01 NEWTON: using errtol_s: 7.214721e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.233510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.404810e+03 PMG: contraction number = , 2.404810e+03 PMG: iteration = 6 PMG: relative residual = 6.130844e-05 PMG: contraction number = 3.122885e-01 NEWTON: using errtol_s: 2.253074e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.278180e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.023487e+03 PMG: contraction number = , 1.023487e+03 PMG: iteration = 7 PMG: relative residual = 2.514697e-05 PMG: contraction number = 4.101714e-01 NEWTON: using errtol_s: 9.241466e+02 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 = , 4.433686e+02 PMG: contraction number = , 4.433686e+02 PMG: iteration = 8 PMG: relative residual = 1.086023e-05 PMG: contraction number = 4.318705e-01 NEWTON: using errtol_s: 3.991117e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.367790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.998876e+02 PMG: contraction number = , 1.998876e+02 PMG: iteration = 9 PMG: relative residual = 4.896154e-06 PMG: contraction number = 4.508332e-01 NEWTON: using errtol_s: 1.799328e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.412600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.938767e+01 PMG: contraction number = , 8.938767e+01 PMG: iteration = 10 PMG: relative residual = 2.189185e-06 PMG: contraction number = 4.471235e-01 NEWTON: using errtol_s: 8.045217e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.457400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.067201e+01 PMG: contraction number = , 4.067201e+01 PMG: iteration = 11 PMG: relative residual = 9.960815e-07 PMG: contraction number = 4.550010e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 5.341800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.491800e+02 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.547964441231E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.137038359687E+06 kT Vpmg_energy: dielEnergy = 5.684761609200E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.446000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.502200e+03 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Apr 4 12:41:53 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_allh35.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb35.pdb NOsh: Storing molecule 2 path dmpc_pg_80_20.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (641, 609, 609) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (641, 609, 609) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (641, 609, 609) 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, 81.287) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 29.193) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 81.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 25.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 53.26) Valist_readPDB: Counted 29844 atoms Valist_getStatistics: Max atom coordinate: (55.819, 52.391, 23.463) Valist_getStatistics: Min atom coordinate: (-58.133, -51.506, -22.901) Valist_getStatistics: Molecule center: (-1.157, 0.4425, 0.281) NOsh_setupCalcMGAUTO(/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1723): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1728): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1740): Coarse grid spacing = 0.445125, 0.427207, 0.428405 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1742): Fine grid spacing = 0.256175, 0.25312, 0.253599 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1744): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1838): starting mesh repositioning. NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1840): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1845): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1850): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1855): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1860): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1921): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1926): 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(/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1723): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1728): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1740): Coarse grid spacing = 0.445125, 0.427207, 0.428405 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1742): Fine grid spacing = 0.256175, 0.25312, 0.253599 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1744): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1838): starting mesh repositioning. NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1840): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1845): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1850): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1855): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1860): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1921): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1926): 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(/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1723): coarse grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO(/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1728): fine grid center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1740): Coarse grid spacing = 0.445125, 0.427207, 0.428405 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1742): Fine grid spacing = 0.256175, 0.25312, 0.253599 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1744): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.575512, 0.592499, 0.591961 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1838): starting mesh repositioning. NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1840): coarse mesh center = -1.157 0.442 29.193 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1845): coarse mesh upper corner = 141.283 130.313 159.428 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1850): coarse mesh lower corner = -143.597 -129.429 -101.042 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1855): initial fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1860): initial fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1921): final fine mesh upper corner = 80.819 77.3905 106.287 NOsh_setupCalcMGAUTO (/home/d3x923/apbs-pdb2pqr/apbs/src/generic/nosh.c, 1926): final fine mesh lower corner = -83.133 -76.5065 -47.901 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 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_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vacc_SASA: Time elapsed: 47.040000 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 = 2.020500e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. Vbuildops: Fine: (641, 609, 609) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.690000e+01 Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. Vbuildops: Galer: (321, 305, 305) Vbuildops: Galer: (161, 153, 153) Vbuildops: Galer: (081, 077, 077) Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.037800e+02 Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.515400e+02 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vnewton: Damping enabled Vnewton: Using errtol_s: 44561891.663478 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074780e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 6.562255e+06 Vprtstp: contraction number = 6.562255e+06 Vnewton: Attempting damping, relres = 0.149094 Vnewton: Attempting damping, relres = 0.565842 Vnewton: Damping accepted, relres = 0.149094 Vnewton: Damping disabled Vprtstp: iteration = 1 Vprtstp: relative residual = 1.490941e-01 Vprtstp: contraction number = 1.490941e-01 Vnewton: Using errtol_s: 6643914.970581 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.071590e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 9.141893e+05 Vprtstp: contraction number = 9.141893e+05 Vprtstp: iteration = 2 Vprtstp: relative residual = 2.301631e-02 Vprtstp: contraction number = 1.543744e-01 Vnewton: Using errtol_s: 1025650.130741 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.621560e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.663121e+05 Vprtstp: contraction number = 1.663121e+05 Vprtstp: iteration = 3 Vprtstp: relative residual = 4.497325e-03 Vprtstp: contraction number = 1.953973e-01 Vnewton: Using errtol_s: 200409.297838 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.173370e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.756709e+04 Vprtstp: contraction number = 3.756709e+04 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.061051e-03 Vprtstp: contraction number = 2.359293e-01 Vnewton: Using errtol_s: 47282.432211 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.744950e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.028441e+04 Vprtstp: contraction number = 1.028441e+04 Vprtstp: iteration = 5 Vprtstp: relative residual = 2.817207e-04 Vprtstp: contraction number = 2.655110e-01 Vnewton: Using errtol_s: 12554.007627 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.310130e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.333353e+03 Vprtstp: contraction number = 3.333353e+03 Vprtstp: iteration = 6 Vprtstp: relative residual = 7.828362e-05 Vprtstp: contraction number = 2.778767e-01 Vnewton: Using errtol_s: 3488.466207 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085717e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.018368e+03 Vprtstp: contraction number = 1.018368e+03 Vprtstp: iteration = 7 Vprtstp: relative residual = 2.109377e-05 Vprtstp: contraction number = 2.694531e-01 Vnewton: Using errtol_s: 939.978098 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238312e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.231218e+02 Vprtstp: contraction number = 3.231218e+02 Vprtstp: iteration = 8 Vprtstp: relative residual = 6.533413e-06 Vprtstp: contraction number = 3.097319e-01 Vnewton: Using errtol_s: 291.141235 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.396176e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.284977e+02 Vprtstp: contraction number = 1.284977e+02 Vprtstp: iteration = 9 Vprtstp: relative residual = 2.595300e-06 Vprtstp: contraction number = 3.972350e-01 Vnewton: Using errtol_s: 115.651483 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.550568e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.917127e+01 Vprtstp: contraction number = 5.917127e+01 Vprtstp: iteration = 10 Vprtstp: relative residual = 1.195132e-06 Vprtstp: contraction number = 4.604985e-01 Vnewton: Using errtol_s: 53.257338 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.705620e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.985845e+01 Vprtstp: contraction number = 2.985845e+01 Vprtstp: iteration = 11 Vprtstp: relative residual = 6.030478e-07 Vprtstp: contraction number = 5.045868e-01 Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.789276e+04 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.814100e+04 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.783650546666E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.612108285058E+06 kT Vpmg_energy: dielEnergy = 8.060085980605E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.979000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.1319 Vpbe_ctor2: solute dimensions = 116.705 x 106.577 x 106.81 Vpbe_ctor2: solute charge = -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, 118.516) Vclist_setupGrid: Grid lower corner = (-65.2969, -58.6699, -30.0649) Vclist_assignAtoms: Have 13306902 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: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0145601 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0178234 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... Vacc_SASA: Time elapsed: 47.030000 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.597000e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. Vbuildops: Fine: (641, 609, 609) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.473000e+01 Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. Vbuildops: Galer: (321, 305, 305) Vbuildops: Galer: (161, 153, 153) Vbuildops: Galer: (081, 077, 077) Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.116200e+02 Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.903010e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vnewton: Damping enabled Vnewton: Using errtol_s: 45419478.561970 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.959216e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 9.549623e+06 Vprtstp: contraction number = 9.549623e+06 Vnewton: Attempting damping, relres = 0.211477 Vnewton: Attempting damping, relres = 0.595110 Vnewton: Damping accepted, relres = 0.211477 Vnewton: Damping disabled Vprtstp: iteration = 1 Vprtstp: relative residual = 2.114768e-01 Vprtstp: contraction number = 2.114768e-01 Vnewton: Using errtol_s: 9605167.628149 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.137302e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.314398e+06 Vprtstp: contraction number = 1.314398e+06 Vprtstp: iteration = 2 Vprtstp: relative residual = 3.262398e-02 Vprtstp: contraction number = 1.542674e-01 Vnewton: Using errtol_s: 1481764.231072 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.280208e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.426912e+05 Vprtstp: contraction number = 2.426912e+05 Vprtstp: iteration = 3 Vprtstp: relative residual = 6.625635e-03 Vprtstp: contraction number = 2.030909e-01 Vnewton: Using errtol_s: 300932.899422 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.420955e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.621399e+04 Vprtstp: contraction number = 5.621399e+04 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.662104e-03 Vprtstp: contraction number = 2.508596e-01 Vnewton: Using errtol_s: 75491.909476 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.563102e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.550268e+04 Vprtstp: contraction number = 1.550268e+04 Vprtstp: iteration = 5 Vprtstp: relative residual = 4.656453e-04 Vprtstp: contraction number = 2.801541e-01 Vnewton: Using errtol_s: 21149.365732 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.707139e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.454000e+03 Vprtstp: contraction number = 5.454000e+03 Vprtstp: iteration = 6 Vprtstp: relative residual = 1.412876e-04 Vprtstp: contraction number = 3.034232e-01 Vnewton: Using errtol_s: 6417.207389 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.849856e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.126050e+03 Vprtstp: contraction number = 2.126050e+03 Vprtstp: iteration = 7 Vprtstp: relative residual = 4.623616e-05 Vprtstp: contraction number = 3.272486e-01 Vnewton: Using errtol_s: 2100.022173 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.990858e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 8.546562e+02 Vprtstp: contraction number = 8.546562e+02 Vprtstp: iteration = 8 Vprtstp: relative residual = 1.738145e-05 Vprtstp: contraction number = 3.759275e-01 Vnewton: Using errtol_s: 789.456170 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.132784e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.753456e+02 Vprtstp: contraction number = 3.753456e+02 Vprtstp: iteration = 9 Vprtstp: relative residual = 7.451041e-06 Vprtstp: contraction number = 4.286779e-01 Vnewton: Using errtol_s: 338.422418 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.275789e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.709365e+02 Vprtstp: contraction number = 1.709365e+02 Vprtstp: iteration = 10 Vprtstp: relative residual = 3.391729e-06 Vprtstp: contraction number = 4.552020e-01 Vnewton: Using errtol_s: 154.050550 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.420172e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 7.914844e+01 Vprtstp: contraction number = 7.914844e+01 Vprtstp: iteration = 11 Vprtstp: relative residual = 1.568419e-06 Vprtstp: contraction number = 4.624248e-01 Vnewton: Using errtol_s: 71.236789 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.564299e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.823192e+01 Vprtstp: contraction number = 3.823192e+01 Vprtstp: iteration = 12 Vprtstp: relative residual = 7.576902e-07 Vprtstp: contraction number = 4.830916e-01 Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.777287e+04 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.803021e+04 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.744500600623E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.328094332494E+06 kT Vpmg_energy: dielEnergy = 1.664002626031E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.469000e+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, 18.0691) 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_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vacc_SASA: Time elapsed: 22.540000 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 = 1.473900e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. Vbuildops: Fine: (641, 609, 609) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.469000e+01 Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. Vbuildops: Galer: (321, 305, 305) Vbuildops: Galer: (161, 153, 153) Vbuildops: Galer: (081, 077, 077) Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.132400e+02 Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.726735e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vnewton: Damping enabled Vnewton: Using errtol_s: 7386840.054763 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.785775e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.087009e+06 Vprtstp: contraction number = 1.087009e+06 Vnewton: Attempting damping, relres = 0.133257 Vnewton: Attempting damping, relres = 0.565494 Vnewton: Damping accepted, relres = 0.133257 Vnewton: Damping disabled Vprtstp: iteration = 1 Vprtstp: relative residual = 1.332573e-01 Vprtstp: contraction number = 1.332573e-01 Vnewton: Using errtol_s: 984350.395127 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.959597e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.415819e+05 Vprtstp: contraction number = 1.415819e+05 Vprtstp: iteration = 2 Vprtstp: relative residual = 1.725847e-02 Vprtstp: contraction number = 1.295124e-01 Vnewton: Using errtol_s: 127485.585279 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.105420e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.130048e+04 Vprtstp: contraction number = 2.130048e+04 Vprtstp: iteration = 3 Vprtstp: relative residual = 2.595247e-03 Vprtstp: contraction number = 1.503752e-01 Vnewton: Using errtol_s: 19170.676401 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.249067e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.520204e+03 Vprtstp: contraction number = 3.520204e+03 Vprtstp: iteration = 4 Vprtstp: relative residual = 4.288970e-04 Vprtstp: contraction number = 1.652625e-01 Vnewton: Using errtol_s: 3168.193249 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.394403e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 6.078921e+02 Vprtstp: contraction number = 6.078921e+02 Vprtstp: iteration = 5 Vprtstp: relative residual = 7.406495e-05 Vprtstp: contraction number = 1.726870e-01 Vnewton: Using errtol_s: 547.105946 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.538476e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.238829e+02 Vprtstp: contraction number = 1.238829e+02 Vprtstp: iteration = 6 Vprtstp: relative residual = 1.509369e-05 Vprtstp: contraction number = 2.037899e-01 Vnewton: Using errtol_s: 111.494692 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.682733e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 4.604797e+01 Vprtstp: contraction number = 4.604797e+01 Vprtstp: iteration = 7 Vprtstp: relative residual = 5.610559e-06 Vprtstp: contraction number = 3.717155e-01 Vnewton: Using errtol_s: 41.444305 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.825596e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.361281e+01 Vprtstp: contraction number = 2.361281e+01 Vprtstp: iteration = 8 Vprtstp: relative residual = 2.876948e-06 Vprtstp: contraction number = 5.127738e-01 Vnewton: Using errtol_s: 21.251555 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.969487e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 9.272800e+00 Vprtstp: contraction number = 9.272800e+00 Vprtstp: iteration = 9 Vprtstp: relative residual = 1.129810e-06 Vprtstp: contraction number = 3.927115e-01 Vnewton: Using errtol_s: 8.345729 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.114564e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 4.277161e+00 Vprtstp: contraction number = 4.277161e+00 Vprtstp: iteration = 10 Vprtstp: relative residual = 5.211223e-07 Vprtstp: contraction number = 4.612475e-01 Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.507966e+04 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.533723e+04 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.537584395269E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.425272506386E+05 kT Vpmg_energy: dielEnergy = 1.212606528340E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.198000e+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, 18.0691) 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: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.00016726 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000236634 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... Vacc_SASA: Time elapsed: 22.020000 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.433100e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. Vbuildops: Fine: (641, 609, 609) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.472000e+01 Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. Vbuildops: Galer: (321, 305, 305) Vbuildops: Galer: (161, 153, 153) Vbuildops: Galer: (081, 077, 077) Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.035200e+02 Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.291655e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vnewton: Damping enabled Vnewton: Using errtol_s: 7476305.974338 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.353486e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.628896e+06 Vprtstp: contraction number = 1.628896e+06 Vnewton: Attempting damping, relres = 0.196928 Vnewton: Attempting damping, relres = 0.598117 Vnewton: Damping accepted, relres = 0.196928 Vnewton: Damping disabled Vprtstp: iteration = 1 Vprtstp: relative residual = 1.969281e-01 Vprtstp: contraction number = 1.969281e-01 Vnewton: Using errtol_s: 1472294.810629 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.535202e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.126503e+05 Vprtstp: contraction number = 2.126503e+05 Vprtstp: iteration = 2 Vprtstp: relative residual = 2.560659e-02 Vprtstp: contraction number = 1.300301e-01 Vnewton: Using errtol_s: 191442.696255 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.677712e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.150235e+04 Vprtstp: contraction number = 3.150235e+04 Vprtstp: iteration = 3 Vprtstp: relative residual = 3.792287e-03 Vprtstp: contraction number = 1.480981e-01 Vnewton: Using errtol_s: 28352.294902 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.820542e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.365524e+03 Vprtstp: contraction number = 5.365524e+03 Vprtstp: iteration = 4 Vprtstp: relative residual = 6.459048e-04 Vprtstp: contraction number = 1.703207e-01 Vnewton: Using errtol_s: 4828.981787 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.959062e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 9.790451e+02 Vprtstp: contraction number = 9.790451e+02 Vprtstp: iteration = 5 Vprtstp: relative residual = 1.178580e-04 Vprtstp: contraction number = 1.824697e-01 Vnewton: Using errtol_s: 881.142720 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.100616e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.631854e+02 Vprtstp: contraction number = 2.631854e+02 Vprtstp: iteration = 6 Vprtstp: relative residual = 3.168236e-05 Vprtstp: contraction number = 2.688180e-01 Vnewton: Using errtol_s: 236.867041 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.245584e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.194877e+02 Vprtstp: contraction number = 1.194877e+02 Vprtstp: iteration = 7 Vprtstp: relative residual = 1.438427e-05 Vprtstp: contraction number = 4.540150e-01 Vnewton: Using errtol_s: 107.541189 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.388033e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.094717e+01 Vprtstp: contraction number = 5.094717e+01 Vprtstp: iteration = 8 Vprtstp: relative residual = 6.133043e-06 Vprtstp: contraction number = 4.263716e-01 Vnewton: Using errtol_s: 45.852506 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.527956e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.606737e+01 Vprtstp: contraction number = 2.606737e+01 Vprtstp: iteration = 9 Vprtstp: relative residual = 3.138046e-06 Vprtstp: contraction number = 5.116622e-01 Vnewton: Using errtol_s: 23.460996 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.666990e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.145163e+01 Vprtstp: contraction number = 1.145163e+01 Vprtstp: iteration = 10 Vprtstp: relative residual = 1.378551e-06 Vprtstp: contraction number = 4.393022e-01 Vnewton: Using errtol_s: 10.306468 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.807292e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.763645e+00 Vprtstp: contraction number = 5.763645e+00 Vprtstp: iteration = 11 Vprtstp: relative residual = 6.938335e-07 Vprtstp: contraction number = 5.033064e-01 Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.634060e+04 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.659846e+04 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.482727111698E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 5.099899946324E+05 kT Vpmg_energy: dielEnergy = 2.549921024225E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.024000e+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_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vacc_SASA: Time elapsed: 41.010000 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 = 1.989000e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. Vbuildops: Fine: (641, 609, 609) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.470000e+01 Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. Vbuildops: Galer: (321, 305, 305) Vbuildops: Galer: (161, 153, 153) Vbuildops: Galer: (081, 077, 077) Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.104300e+02 Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.977974e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vnewton: Damping enabled Vnewton: Using errtol_s: 37183058.443046 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.031498e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.478328e+06 Vprtstp: contraction number = 5.478328e+06 Vnewton: Attempting damping, relres = 0.151469 Vnewton: Attempting damping, relres = 0.565905 Vnewton: Damping accepted, relres = 0.151469 Vnewton: Damping disabled Vprtstp: iteration = 1 Vprtstp: relative residual = 1.514689e-01 Vprtstp: contraction number = 1.514689e-01 Vnewton: Using errtol_s: 5632076.905590 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.188792e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 7.689621e+05 Vprtstp: contraction number = 7.689621e+05 Vprtstp: iteration = 2 Vprtstp: relative residual = 2.379933e-02 Vprtstp: contraction number = 1.571235e-01 Vnewton: Using errtol_s: 884931.742633 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.318965e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.431955e+05 Vprtstp: contraction number = 1.431955e+05 Vprtstp: iteration = 3 Vprtstp: relative residual = 4.764759e-03 Vprtstp: contraction number = 2.002056e-01 Vnewton: Using errtol_s: 177168.306692 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.448884e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.279151e+04 Vprtstp: contraction number = 3.279151e+04 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.146811e-03 Vprtstp: contraction number = 2.406861e-01 Vnewton: Using errtol_s: 42641.940393 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.582906e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 9.169885e+03 Vprtstp: contraction number = 9.169885e+03 Vprtstp: iteration = 5 Vprtstp: relative residual = 3.103770e-04 Vprtstp: contraction number = 2.706436e-01 Vnewton: Using errtol_s: 11540.766621 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.715521e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.022508e+03 Vprtstp: contraction number = 3.022508e+03 Vprtstp: iteration = 6 Vprtstp: relative residual = 8.689211e-05 Vprtstp: contraction number = 2.799567e-01 Vnewton: Using errtol_s: 3230.914410 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.849464e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 9.320908e+02 Vprtstp: contraction number = 9.320908e+02 Vprtstp: iteration = 7 Vprtstp: relative residual = 2.326219e-05 Vprtstp: contraction number = 2.677135e-01 Vnewton: Using errtol_s: 864.959502 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.983933e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.001818e+02 Vprtstp: contraction number = 3.001818e+02 Vprtstp: iteration = 8 Vprtstp: relative residual = 7.274115e-06 Vprtstp: contraction number = 3.127012e-01 Vnewton: Using errtol_s: 270.473855 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.114366e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.144792e+02 Vprtstp: contraction number = 1.144792e+02 Vprtstp: iteration = 9 Vprtstp: relative residual = 2.770988e-06 Vprtstp: contraction number = 3.809381e-01 Vnewton: Using errtol_s: 103.033793 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.244947e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.195138e+01 Vprtstp: contraction number = 5.195138e+01 Vprtstp: iteration = 10 Vprtstp: relative residual = 1.257537e-06 Vprtstp: contraction number = 4.538226e-01 Vnewton: Using errtol_s: 46.759068 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.377691e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.549474e+01 Vprtstp: contraction number = 2.549474e+01 Vprtstp: iteration = 11 Vprtstp: relative residual = 6.170951e-07 Vprtstp: contraction number = 4.907173e-01 Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.509690e+04 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.535121e+04 Vpmg_setPart: lower corner = (-143.597, -129.429, -101.042) Vpmg_setPart: upper corner = (141.283, 130.313, 159.428) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.535544580557E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.369582939887E+06 kT Vpmg_energy: dielEnergy = 6.847488624049E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.115000e+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: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -83.133, -76.5065, -47.901 VPMG::focusFillBound -- New mesh maxs = 80.819, 77.3905, 106.287 VPMG::focusFillBound -- Old mesh mins = -143.597, -129.429, -101.042 VPMG::focusFillBound -- Old mesh maxs = 141.283, 130.313, 159.428 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-143.597, -129.429, -101.042) Vpmg_setPart: actual maxima = (141.283, 130.313, 159.428) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-83.133, -76.5065, -47.901) VPMG::extEnergy Disj part upper corner = (80.819, 77.3905, 106.287) VPMG::extEnergy Old lower corner = (-143.597, -129.429, -101.042) VPMG::extEnergy Old upper corner = (141.283, 130.313, 159.428) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0146406 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0176895 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... Vacc_SASA: Time elapsed: 42.600000 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.475600e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. Vbuildops: Fine: (641, 609, 609) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.477000e+01 Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. Vbuildops: Galer: (321, 305, 305) Vbuildops: Galer: (161, 153, 153) Vbuildops: Galer: (081, 077, 077) Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 1.955200e+02 Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.553292e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vnewton: Damping enabled Vnewton: Using errtol_s: 37943145.798211 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.606880e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 7.923108e+06 Vprtstp: contraction number = 7.923108e+06 Vnewton: Attempting damping, relres = 0.213460 Vnewton: Attempting damping, relres = 0.594513 Vnewton: Damping accepted, relres = 0.213460 Vnewton: Damping disabled Vprtstp: iteration = 1 Vprtstp: relative residual = 2.134603e-01 Vprtstp: contraction number = 2.134603e-01 Vnewton: Using errtol_s: 8099357.162852 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.763197e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.099167e+06 Vprtstp: contraction number = 1.099167e+06 Vprtstp: iteration = 2 Vprtstp: relative residual = 3.363296e-02 Vprtstp: contraction number = 1.575607e-01 Vnewton: Using errtol_s: 1276140.286244 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.891738e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.070541e+05 Vprtstp: contraction number = 2.070541e+05 Vprtstp: iteration = 3 Vprtstp: relative residual = 7.020393e-03 Vprtstp: contraction number = 2.087355e-01 Vnewton: Using errtol_s: 266375.789819 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.021385e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 4.810644e+04 Vprtstp: contraction number = 4.810644e+04 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.786167e-03 Vprtstp: contraction number = 2.544255e-01 Vnewton: Using errtol_s: 67772.789752 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.153051e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.352437e+04 Vprtstp: contraction number = 1.352437e+04 Vprtstp: iteration = 5 Vprtstp: relative residual = 5.097015e-04 Vprtstp: contraction number = 2.853605e-01 Vnewton: Using errtol_s: 19339.679515 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.280476e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 4.899724e+03 Vprtstp: contraction number = 4.899724e+03 Vprtstp: iteration = 6 Vprtstp: relative residual = 1.564365e-04 Vprtstp: contraction number = 3.069179e-01 Vnewton: Using errtol_s: 5935.694378 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.413873e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.920547e+03 Vprtstp: contraction number = 1.920547e+03 Vprtstp: iteration = 7 Vprtstp: relative residual = 5.066764e-05 Vprtstp: contraction number = 3.238862e-01 Vnewton: Using errtol_s: 1922.489683 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.543643e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 7.691487e+02 Vprtstp: contraction number = 7.691487e+02 Vprtstp: iteration = 8 Vprtstp: relative residual = 1.877729e-05 Vprtstp: contraction number = 3.705973e-01 Vnewton: Using errtol_s: 712.469534 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.675921e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.285458e+02 Vprtstp: contraction number = 3.285458e+02 Vprtstp: iteration = 9 Vprtstp: relative residual = 7.810249e-06 Vprtstp: contraction number = 4.159412e-01 Vnewton: Using errtol_s: 296.345412 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.806651e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.489584e+02 Vprtstp: contraction number = 1.489584e+02 Vprtstp: iteration = 10 Vprtstp: relative residual = 3.537982e-06 Vprtstp: contraction number = 4.529922e-01 Vnewton: Using errtol_s: 134.242166 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.943167e+04 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 6.813166e+01 Vprtstp: contraction number = 6.813166e+01 Vprtstp: iteration = 11 Vprtstp: relative residual = 1.616143e-06 Vprtstp: contraction number = 4.567980e-01 Vnewton: Using errtol_s: 61.321548 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007248e+05 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.280516e+01 Vprtstp: contraction number = 3.280516e+01 Vprtstp: iteration = 12 Vprtstp: relative residual = 7.782452e-07 Vprtstp: contraction number = 4.815448e-01 Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.624432e+04 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.648555e+04 Vpmg_setPart: lower corner = (-83.133, -76.5065, -47.901) Vpmg_setPart: upper corner = (80.819, 77.3905, 106.287) Vpmg_setPart: actual minima = (-83.133, -76.5065, -47.901) Vpmg_setPart: actual maxima = (80.819, 77.3905, 106.287) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.500067268526E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.818106242022E+06 kT Vpmg_energy: dielEnergy = 1.409011466448E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.437000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.018407e+05