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653 lines (647 loc) · 27.9 KB
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##############################################################################
# MC-shell I/O capture file.
# Creation Date and Time: Tue Mar 17 21:21:33 2026
##############################################################################
Hello world from PE 0
Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..
##############################################################################
# MC-shell I/O capture file.
# Creation Date and Time: Sun Mar 22 15:18:09 2026
##############################################################################
Hello world from PE 0
Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..
##############################################################################
# MC-shell I/O capture file.
# Creation Date and Time: Sun Mar 22 15:26:22 2026
##############################################################################
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 structures/pcv2_capsid.pqr
NOsh: Done parsing READ section
NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0)
NOsh: Parsing ELEC section
NOsh_parseMG: Parsing parameters for MG calculation
NOsh_parseMG: Parsing dime...
PBEparm_parseToken: trying dime...
MGparm_parseToken: trying dime...
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 mol...
PBEparm_parseToken: trying mol...
NOsh_parseMG: Parsing lpbe...
PBEparm_parseToken: trying lpbe...
NOsh: parsed lpbe
NOsh_parseMG: Parsing bcfl...
PBEparm_parseToken: trying bcfl...
NOsh_parseMG: Parsing pdie...
PBEparm_parseToken: trying pdie...
NOsh_parseMG: Parsing sdie...
PBEparm_parseToken: trying sdie...
NOsh_parseMG: Parsing chgm...
PBEparm_parseToken: trying chgm...
MGparm_parseToken: trying chgm...
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 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.
##############################################################################
# MC-shell I/O capture file.
# Creation Date and Time: Sun Mar 22 15:40:00 2026
##############################################################################
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 structures/pcv2_capsid.pqr
NOsh: Done parsing READ section
NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0)
NOsh: Parsing ELEC section
NOsh_parseMG: Parsing parameters for MG calculation
NOsh_parseMG: Parsing dime...
PBEparm_parseToken: trying dime...
MGparm_parseToken: trying dime...
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 cgcent...
PBEparm_parseToken: trying cgcent...
MGparm_parseToken: trying cgcent...
NOsh_parseMG: Parsing fgcent...
PBEparm_parseToken: trying fgcent...
MGparm_parseToken: trying fgcent...
NOsh_parseMG: Parsing mol...
PBEparm_parseToken: trying mol...
NOsh_parseMG: Parsing lpbe...
PBEparm_parseToken: trying lpbe...
NOsh: parsed lpbe
NOsh_parseMG: Parsing bcfl...
PBEparm_parseToken: trying bcfl...
NOsh_parseMG: Parsing pdie...
PBEparm_parseToken: trying pdie...
NOsh_parseMG: Parsing sdie...
PBEparm_parseToken: trying sdie...
NOsh_parseMG: Parsing chgm...
PBEparm_parseToken: trying chgm...
MGparm_parseToken: trying chgm...
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 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 = (65, 65, 65)
##############################################################################
# MC-shell I/O capture file.
# Creation Date and Time: Sun Mar 22 15:44:32 2026
##############################################################################
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 structures/pcv2_capsid.pqr
NOsh: Done parsing READ section
NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0)
NOsh: Parsing ELEC section
NOsh_parseMG: Parsing parameters for MG calculation
NOsh_parseMG: Parsing dime...
PBEparm_parseToken: trying dime...
MGparm_parseToken: trying dime...
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 cgcent...
PBEparm_parseToken: trying cgcent...
MGparm_parseToken: trying cgcent...
NOsh_parseMG: Parsing fgcent...
PBEparm_parseToken: trying fgcent...
MGparm_parseToken: trying fgcent...
NOsh_parseMG: Parsing mol...
PBEparm_parseToken: trying mol...
NOsh_parseMG: Parsing lpbe...
PBEparm_parseToken: trying lpbe...
NOsh: parsed lpbe
NOsh_parseMG: Parsing bcfl...
PBEparm_parseToken: trying bcfl...
NOsh_parseMG: Parsing pdie...
PBEparm_parseToken: trying pdie...
NOsh_parseMG: Parsing sdie...
PBEparm_parseToken: trying sdie...
NOsh_parseMG: Parsing chgm...
PBEparm_parseToken: trying chgm...
MGparm_parseToken: trying chgm...
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 sdens...
PBEparm_parseToken: trying sdens...
NOsh_parseMG: Parsing temp...
PBEparm_parseToken: trying temp...
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 = (65, 65, 65)
NOsh: Done parsing ELEC section (nelec = 1)
NOsh: Done parsing file (got QUIT)
Valist_readPQR: Counted 3520 atoms
Valist_getStatistics: Max atom coordinate: (49.486, 52.901, 96.47)
Valist_getStatistics: Min atom coordinate: (2.041, -14.649, 51.898)
Valist_getStatistics: Molecule center: (25.7635, 19.126, 74.184)
NOsh_setupCalcMGAUTO(./src/generic/nosh.c, 1868): coarse grid center = 25.7635 19.126 74.184
NOsh_setupCalcMGAUTO(./src/generic/nosh.c, 1873): fine grid center = 25.7635 19.126 74.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1885): Coarse grid spacing = 1.25, 1.25, 1.25
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1887): Fine grid spacing = 0.9375, 0.9375, 0.9375
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1889): Displacement between fine and coarse grids = 0, 0, 0
NOsh: 2 levels of focusing with 0.75, 0.75, 0.75 reductions
NOsh_setupMGAUTO: Resetting boundary flags
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1983): starting mesh repositioning.
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1985): coarse mesh center = 25.7635 19.126 74.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1990): coarse mesh upper corner = 65.7635 59.126 114.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1995): coarse mesh lower corner = -14.2365 -20.874 34.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2000): initial fine mesh upper corner = 55.7635 49.126 104.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2005): initial fine mesh lower corner = -4.2365 -10.874 44.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2066): final fine mesh upper corner = 55.7635 49.126 104.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2071): final fine mesh lower corner = -4.2365 -10.874 44.184
NOsh_setupMGAUTO: Resetting boundary flags
NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2)
Vnm_tstart: starting timer 27 (Setup timer)..
Setting up PBE object...
Vpbe_ctor2: solute radius = 45.0709
Vpbe_ctor2: solute dimensions = 49.502 x 70.041 x 47.037
Vpbe_ctor2: solute charge = 6
Vpbe_ctor2: bulk ionic strength = 0
Vpbe_ctor2: xkappa = 0
Vpbe_ctor2: Debye length = 0
Vpbe_ctor2: zkappa2 = 0
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 1.9 max radius
Vclist_setupGrid: Grid lengths = (58.521, 78.626, 55.648)
Vclist_setupGrid: Grid lower corner = (-3.497, -20.187, 46.36)
Vclist_assignAtoms: Have 2743682 atom entries
Vacc_storeParms: Surf. density = 10
Vacc_storeParms: Max area = 191.134
Vacc_storeParms: Using 1936-point reference sphere
Setting up PDE object...
Vpmp_ctor2: Using meth = 2, mgsolv = 1
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: 0.393499
Vpmg_fillco: done filling coefficient arrays
Vpmg_fillco: filling boundary arrays
Vpmg_fillco: done filling boundary arrays
Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.332550e-01
Vnm_tstart: starting timer 28 (Solver timer)..
Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
Vbuildops: Fine: (065, 065, 065)
Vbuildops: Operator stencil (lev, numdia) = (1, 4)
Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.813900e-02
Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
Vbuildops: Galer: (033, 033, 033)
Vbuildops: Galer: (017, 017, 017)
Vbuildops: Galer: (009, 009, 009)
Vbuildops: Galer: (005, 005, 005)
Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.847410e-01
Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101742e+00
Vprtstp: iteration = 0
Vprtstp: relative residual = 1.000000e+00
Vprtstp: contraction number = 1.000000e+00
Vprtstp: iteration = 1
Vprtstp: relative residual = 7.472847e-02
Vprtstp: contraction number = 7.472847e-02
Vprtstp: iteration = 2
Vprtstp: relative residual = 8.388325e-03
Vprtstp: contraction number = 1.122507e-01
Vprtstp: iteration = 3
Vprtstp: relative residual = 1.087212e-03
Vprtstp: contraction number = 1.296101e-01
Vprtstp: iteration = 4
Vprtstp: relative residual = 1.726897e-04
Vprtstp: contraction number = 1.588372e-01
Vprtstp: iteration = 5
Vprtstp: relative residual = 3.431623e-05
Vprtstp: contraction number = 1.987161e-01
Vprtstp: iteration = 6
Vprtstp: relative residual = 8.105087e-06
Vprtstp: contraction number = 2.361881e-01
Vprtstp: iteration = 7
Vprtstp: relative residual = 2.145421e-06
Vprtstp: contraction number = 2.647006e-01
Vprtstp: iteration = 8
Vprtstp: relative residual = 6.088597e-07
Vprtstp: contraction number = 2.837949e-01
Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.228260e-01
Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.514790e-01
Vpmg_setPart: lower corner = (-14.2365, -20.874, 34.184)
Vpmg_setPart: upper corner = (65.7635, 59.126, 114.184)
Vpmg_setPart: actual minima = (-14.2365, -20.874, 34.184)
Vpmg_setPart: actual maxima = (65.7635, 59.126, 114.184)
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)..
Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.000000e-06
Vnm_tstart: starting timer 30 (Force timer)..
Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.200000e-05
Vnm_tstart: starting timer 27 (Setup timer)..
Setting up PBE object...
Vpbe_ctor2: solute radius = 45.0709
Vpbe_ctor2: solute dimensions = 49.502 x 70.041 x 47.037
Vpbe_ctor2: solute charge = 6
Vpbe_ctor2: bulk ionic strength = 0
Vpbe_ctor2: xkappa = 0
Vpbe_ctor2: Debye length = 0
Vpbe_ctor2: zkappa2 = 0
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 1.9 max radius
Vclist_setupGrid: Grid lengths = (58.521, 78.626, 55.648)
Vclist_setupGrid: Grid lower corner = (-3.497, -20.187, 46.36)
Vclist_assignAtoms: Have 2743682 atom entries
Vacc_storeParms: Surf. density = 10
Vacc_storeParms: Max area = 191.134
Vacc_storeParms: Using 1936-point reference sphere
Setting up PDE object...
Vpmp_ctor2: Using meth = 2, mgsolv = 1
Setting PDE center to local center...
Vpmg_ctor2: Filling boundary with old solution!
VPMG::focusFillBound -- New mesh mins = -4.2365, -10.874, 44.184
VPMG::focusFillBound -- New mesh maxs = 55.7635, 49.126, 104.184
VPMG::focusFillBound -- Old mesh mins = -14.2365, -20.874, 34.184
VPMG::focusFillBound -- Old mesh maxs = 65.7635, 59.126, 114.184
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: 0.367282
Vpmg_fillco: done filling coefficient arrays
Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.727740e-01
Vnm_tstart: starting timer 28 (Solver timer)..
Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
Vbuildops: Fine: (065, 065, 065)
Vbuildops: Operator stencil (lev, numdia) = (1, 4)
Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.351600e-02
Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
Vbuildops: Galer: (033, 033, 033)
Vbuildops: Galer: (017, 017, 017)
Vbuildops: Galer: (009, 009, 009)
Vbuildops: Galer: (005, 005, 005)
Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.360200e-02
Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.385216e+00
Vprtstp: iteration = 0
Vprtstp: relative residual = 1.000000e+00
Vprtstp: contraction number = 1.000000e+00
Vprtstp: iteration = 1
Vprtstp: relative residual = 7.135679e-02
Vprtstp: contraction number = 7.135679e-02
Vprtstp: iteration = 2
Vprtstp: relative residual = 8.110934e-03
Vprtstp: contraction number = 1.136673e-01
Vprtstp: iteration = 3
Vprtstp: relative residual = 1.064898e-03
Vprtstp: contraction number = 1.312917e-01
Vprtstp: iteration = 4
Vprtstp: relative residual = 1.727645e-04
Vprtstp: contraction number = 1.622357e-01
Vprtstp: iteration = 5
Vprtstp: relative residual = 3.487642e-05
Vprtstp: contraction number = 2.018726e-01
Vprtstp: iteration = 6
Vprtstp: relative residual = 8.546575e-06
Vprtstp: contraction number = 2.450531e-01
Vprtstp: iteration = 7
Vprtstp: relative residual = 2.410197e-06
Vprtstp: contraction number = 2.820073e-01
Vprtstp: iteration = 8
Vprtstp: relative residual = 7.445749e-07
Vprtstp: contraction number = 3.089270e-01
Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.819750e-01
Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.585290e-01
Vpmg_setPart: lower corner = (-4.2365, -10.874, 44.184)
Vpmg_setPart: upper corner = (55.7635, 49.126, 104.184)
Vpmg_setPart: actual minima = (-4.2365, -10.874, 44.184)
Vpmg_setPart: actual maxima = (55.7635, 49.126, 104.184)
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)..
Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.000000e-06
Vnm_tstart: starting timer 30 (Force timer)..
Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.500000e-05
Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.811986e+00
##############################################################################
# MC-shell I/O capture file.
# Creation Date and Time: Sun Mar 22 19:51:34 2026
##############################################################################
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 structures/pcv2_capsid.pqr
NOsh: Done parsing READ section
NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0)
NOsh: Parsing ELEC section
NOsh_parseMG: Parsing parameters for MG calculation
NOsh_parseMG: Parsing dime...
PBEparm_parseToken: trying dime...
MGparm_parseToken: trying dime...
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 cgcent...
PBEparm_parseToken: trying cgcent...
MGparm_parseToken: trying cgcent...
NOsh_parseMG: Parsing fgcent...
PBEparm_parseToken: trying fgcent...
MGparm_parseToken: trying fgcent...
NOsh_parseMG: Parsing mol...
PBEparm_parseToken: trying mol...
NOsh_parseMG: Parsing lpbe...
PBEparm_parseToken: trying lpbe...
NOsh: parsed lpbe
NOsh_parseMG: Parsing bcfl...
PBEparm_parseToken: trying bcfl...
NOsh_parseMG: Parsing pdie...
PBEparm_parseToken: trying pdie...
NOsh_parseMG: Parsing sdie...
PBEparm_parseToken: trying sdie...
NOsh_parseMG: Parsing chgm...
PBEparm_parseToken: trying chgm...
MGparm_parseToken: trying chgm...
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 sdens...
PBEparm_parseToken: trying sdens...
NOsh_parseMG: Parsing temp...
PBEparm_parseToken: trying temp...
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 = (65, 65, 65)
NOsh: Done parsing ELEC section (nelec = 1)
NOsh: Done parsing file (got QUIT)
Valist_readPQR: Counted 3520 atoms
Valist_getStatistics: Max atom coordinate: (49.486, 52.901, 96.47)
Valist_getStatistics: Min atom coordinate: (2.041, -14.649, 51.898)
Valist_getStatistics: Molecule center: (25.7635, 19.126, 74.184)
NOsh_setupCalcMGAUTO(./src/generic/nosh.c, 1868): coarse grid center = 25.7635 19.126 74.184
NOsh_setupCalcMGAUTO(./src/generic/nosh.c, 1873): fine grid center = 25.7635 19.126 74.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1885): Coarse grid spacing = 1.25, 1.25, 1.25
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1887): Fine grid spacing = 0.9375, 0.9375, 0.9375
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1889): Displacement between fine and coarse grids = 0, 0, 0
NOsh: 2 levels of focusing with 0.75, 0.75, 0.75 reductions
NOsh_setupMGAUTO: Resetting boundary flags
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1983): starting mesh repositioning.
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1985): coarse mesh center = 25.7635 19.126 74.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1990): coarse mesh upper corner = 65.7635 59.126 114.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 1995): coarse mesh lower corner = -14.2365 -20.874 34.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2000): initial fine mesh upper corner = 55.7635 49.126 104.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2005): initial fine mesh lower corner = -4.2365 -10.874 44.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2066): final fine mesh upper corner = 55.7635 49.126 104.184
NOsh_setupCalcMGAUTO (./src/generic/nosh.c, 2071): final fine mesh lower corner = -4.2365 -10.874 44.184
NOsh_setupMGAUTO: Resetting boundary flags
NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2)
Vnm_tstart: starting timer 27 (Setup timer)..
Setting up PBE object...
Vpbe_ctor2: solute radius = 45.0709
Vpbe_ctor2: solute dimensions = 49.502 x 70.041 x 47.037
Vpbe_ctor2: solute charge = 6
Vpbe_ctor2: bulk ionic strength = 0
Vpbe_ctor2: xkappa = 0
Vpbe_ctor2: Debye length = 0
Vpbe_ctor2: zkappa2 = 0
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 1.9 max radius
Vclist_setupGrid: Grid lengths = (58.521, 78.626, 55.648)
Vclist_setupGrid: Grid lower corner = (-3.497, -20.187, 46.36)
Vclist_assignAtoms: Have 2743682 atom entries
Vacc_storeParms: Surf. density = 10
Vacc_storeParms: Max area = 191.134
Vacc_storeParms: Using 1936-point reference sphere
Setting up PDE object...
Vpmp_ctor2: Using meth = 2, mgsolv = 1
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: 0.385782
Vpmg_fillco: done filling coefficient arrays
Vpmg_fillco: filling boundary arrays
Vpmg_fillco: done filling boundary arrays
Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.424910e-01
Vnm_tstart: starting timer 28 (Solver timer)..
Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
Vbuildops: Fine: (065, 065, 065)
Vbuildops: Operator stencil (lev, numdia) = (1, 4)
Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.408400e-02
Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
Vbuildops: Galer: (033, 033, 033)
Vbuildops: Galer: (017, 017, 017)
Vbuildops: Galer: (009, 009, 009)
Vbuildops: Galer: (005, 005, 005)
Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.145070e-01
Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.793060e-01
Vprtstp: iteration = 0
Vprtstp: relative residual = 1.000000e+00
Vprtstp: contraction number = 1.000000e+00
Vprtstp: iteration = 1
Vprtstp: relative residual = 7.472847e-02
Vprtstp: contraction number = 7.472847e-02
Vprtstp: iteration = 2
Vprtstp: relative residual = 8.388325e-03
Vprtstp: contraction number = 1.122507e-01
Vprtstp: iteration = 3
Vprtstp: relative residual = 1.087212e-03
Vprtstp: contraction number = 1.296101e-01
Vprtstp: iteration = 4
Vprtstp: relative residual = 1.726897e-04
Vprtstp: contraction number = 1.588372e-01
Vprtstp: iteration = 5
Vprtstp: relative residual = 3.431623e-05
Vprtstp: contraction number = 1.987161e-01
Vprtstp: iteration = 6
Vprtstp: relative residual = 8.105087e-06
Vprtstp: contraction number = 2.361881e-01
Vprtstp: iteration = 7
Vprtstp: relative residual = 2.145421e-06
Vprtstp: contraction number = 2.647006e-01
Vprtstp: iteration = 8
Vprtstp: relative residual = 6.088597e-07
Vprtstp: contraction number = 2.837949e-01
Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.955740e-01
Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.851980e-01
Vpmg_setPart: lower corner = (-14.2365, -20.874, 34.184)
Vpmg_setPart: upper corner = (65.7635, 59.126, 114.184)
Vpmg_setPart: actual minima = (-14.2365, -20.874, 34.184)
Vpmg_setPart: actual maxima = (65.7635, 59.126, 114.184)
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)..
Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.000000e-06
Vnm_tstart: starting timer 30 (Force timer)..
Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.100000e-05
Vnm_tstart: starting timer 27 (Setup timer)..
Setting up PBE object...
Vpbe_ctor2: solute radius = 45.0709
Vpbe_ctor2: solute dimensions = 49.502 x 70.041 x 47.037
Vpbe_ctor2: solute charge = 6
Vpbe_ctor2: bulk ionic strength = 0
Vpbe_ctor2: xkappa = 0
Vpbe_ctor2: Debye length = 0
Vpbe_ctor2: zkappa2 = 0
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 1.9 max radius
Vclist_setupGrid: Grid lengths = (58.521, 78.626, 55.648)
Vclist_setupGrid: Grid lower corner = (-3.497, -20.187, 46.36)
Vclist_assignAtoms: Have 2743682 atom entries
Vacc_storeParms: Surf. density = 10
Vacc_storeParms: Max area = 191.134
Vacc_storeParms: Using 1936-point reference sphere
Setting up PDE object...
Vpmp_ctor2: Using meth = 2, mgsolv = 1
Setting PDE center to local center...
Vpmg_ctor2: Filling boundary with old solution!
VPMG::focusFillBound -- New mesh mins = -4.2365, -10.874, 44.184
VPMG::focusFillBound -- New mesh maxs = 55.7635, 49.126, 104.184
VPMG::focusFillBound -- Old mesh mins = -14.2365, -20.874, 34.184
VPMG::focusFillBound -- Old mesh maxs = 65.7635, 59.126, 114.184
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: 0.341476
Vpmg_fillco: done filling coefficient arrays
Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.986710e-01
Vnm_tstart: starting timer 28 (Solver timer)..
Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
Vbuildops: Fine: (065, 065, 065)
Vbuildops: Operator stencil (lev, numdia) = (1, 4)
Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.605900e-02
Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
Vbuildops: Galer: (033, 033, 033)
Vbuildops: Galer: (017, 017, 017)
Vbuildops: Galer: (009, 009, 009)
Vbuildops: Galer: (005, 005, 005)
Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.914300e-02
Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.269474e+00
Vprtstp: iteration = 0
Vprtstp: relative residual = 1.000000e+00
Vprtstp: contraction number = 1.000000e+00
Vprtstp: iteration = 1
Vprtstp: relative residual = 7.135679e-02
Vprtstp: contraction number = 7.135679e-02
Vprtstp: iteration = 2
Vprtstp: relative residual = 8.110934e-03
Vprtstp: contraction number = 1.136673e-01
Vprtstp: iteration = 3
Vprtstp: relative residual = 1.064898e-03
Vprtstp: contraction number = 1.312917e-01
Vprtstp: iteration = 4
Vprtstp: relative residual = 1.727645e-04
Vprtstp: contraction number = 1.622357e-01
Vprtstp: iteration = 5
Vprtstp: relative residual = 3.487642e-05
Vprtstp: contraction number = 2.018726e-01
Vprtstp: iteration = 6
Vprtstp: relative residual = 8.546575e-06
Vprtstp: contraction number = 2.450531e-01
Vprtstp: iteration = 7
Vprtstp: relative residual = 2.410197e-06
Vprtstp: contraction number = 2.820073e-01
Vprtstp: iteration = 8
Vprtstp: relative residual = 7.445749e-07
Vprtstp: contraction number = 3.089270e-01
Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.908040e-01
Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.761720e-01
Vpmg_setPart: lower corner = (-4.2365, -10.874, 44.184)
Vpmg_setPart: upper corner = (55.7635, 49.126, 104.184)
Vpmg_setPart: actual minima = (-4.2365, -10.874, 44.184)
Vpmg_setPart: actual maxima = (55.7635, 49.126, 104.184)
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)..
Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.000000e-06
Vnm_tstart: starting timer 30 (Force timer)..
Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.500000e-05
Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.700000e+00