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2.59 MB
/srv/reproducible-results/rbuild-debian/r-b-build.PxhV4VLr/b1/apbs_3.0.0+dfsg1-3_armhf.changes vs.
/srv/reproducible-results/rbuild-debian/r-b-build.PxhV4VLr/b2/apbs_3.0.0+dfsg1-3_armhf.changes
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878 B
Files
    
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1 ·efe39fb66072236bbd44b855bd6adfd1·226054036·science·optional·apbs-data_3.0.0+dfsg1-3_all.deb1 ·8e0bd964794838aabf020cad9382382f·226051632·science·optional·apbs-data_3.0.0+dfsg1-3_all.deb
2 ·aec9e52af137eebf716292f3f873b8e1·150680·debug·optional·apbs-dbgsym_3.0.0+dfsg1-3_armhf.deb2 ·aec9e52af137eebf716292f3f873b8e1·150680·debug·optional·apbs-dbgsym_3.0.0+dfsg1-3_armhf.deb
3 ·f6b368384fdb2d7a36d6154b5e846a86·78452·science·optional·apbs_3.0.0+dfsg1-3_armhf.deb3 ·f6b368384fdb2d7a36d6154b5e846a86·78452·science·optional·apbs_3.0.0+dfsg1-3_armhf.deb
4 ·686fd59d452b8837e34a0f61fa49a2c4·66312·libdevel·optional·libapbs-dev_3.0.0+dfsg1-3_armhf.deb4 ·686fd59d452b8837e34a0f61fa49a2c4·66312·libdevel·optional·libapbs-dev_3.0.0+dfsg1-3_armhf.deb
5 ·1c0731a6357931f15ddde136c32d8a01·517500·debug·optional·libapbs3-dbgsym_3.0.0+dfsg1-3_armhf.deb5 ·1c0731a6357931f15ddde136c32d8a01·517500·debug·optional·libapbs3-dbgsym_3.0.0+dfsg1-3_armhf.deb
6 ·c5f7e47c9c4fc893e4306febf64268d2·215104·libs·optional·libapbs3_3.0.0+dfsg1-3_armhf.deb6 ·c5f7e47c9c4fc893e4306febf64268d2·215104·libs·optional·libapbs3_3.0.0+dfsg1-3_armhf.deb
7 ·acca7639e805699d8399027302dac4e4·157116·debug·optional·python3-apbslib-dbgsym_3.0.0+dfsg1-3_armhf.deb7 ·acca7639e805699d8399027302dac4e4·157116·debug·optional·python3-apbslib-dbgsym_3.0.0+dfsg1-3_armhf.deb
8 ·4770e2f8ce8b8319254161c605116a44·98876·python·optional·python3-apbslib_3.0.0+dfsg1-3_armhf.deb8 ·4770e2f8ce8b8319254161c605116a44·98876·python·optional·python3-apbslib_3.0.0+dfsg1-3_armhf.deb
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2.59 MB
apbs-data_3.0.0+dfsg1-3_all.deb
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369 B
file list
    
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1 -rw-r--r--···0········0········0········4·2020-07-23·09:35:23.000000·debian-binary1 -rw-r--r--···0········0········0········4·2020-07-23·09:35:23.000000·debian-binary
2 -rw-r--r--···0········0········0····13240·2020-07-23·09:35:23.000000·control.tar.xz2 -rw-r--r--···0········0········0····13240·2020-07-23·09:35:23.000000·control.tar.xz
3 -rw-r--r--···0········0········0·226040604·2020-07-23·09:35:23.000000·data.tar.xz3 -rw-r--r--···0········0········0·226038200·2020-07-23·09:35:23.000000·data.tar.xz
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98.0 B
control.tar.xz
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control.tar
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48.0 B
./md5sums
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30.0 B
./md5sums
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2.59 MB
data.tar.xz
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2.59 MB
data.tar
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169 KB
./usr/share/apbs/examples/FKBP/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:31:41·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:06:15·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·1d7h-dmso-complex.pqr9 NOsh:·Storing·molecule·0·path·1d7h-dmso-complex.pqr
Offset 637, 32 lines modifiedOffset 637, 32 lines modified
637 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1637 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
638 Setting·PDE·center·to·local·center...638 Setting·PDE·center·to·local·center...
639 Vpmg_fillco:··filling·in·source·term.639 Vpmg_fillco:··filling·in·source·term.
640 fillcoCharge:··Calling·fillcoChargeSpline1...640 fillcoCharge:··Calling·fillcoChargeSpline1...
641 Vpmg_fillco:··filling·in·source·term.641 Vpmg_fillco:··filling·in·source·term.
642 Vpmg_fillco:··marking·ion·and·solvent·accessibility.642 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
643 fillcoCoef:··Calling·fillcoCoefMol...643 fillcoCoef:··Calling·fillcoCoefMol...
644 Vacc_SASA:·Time·elapsed:·2.747532644 Vacc_SASA:·Time·elapsed:·2.800800
645 Vpmg_fillco:··done·filling·coefficient·arrays645 Vpmg_fillco:··done·filling·coefficient·arrays
646 Vpmg_fillco:··filling·boundary·arrays646 Vpmg_fillco:··filling·boundary·arrays
647 Vpmg_fillco:··done·filling·boundary·arrays647 Vpmg_fillco:··done·filling·boundary·arrays
648 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·6.440030e+00648 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·6.495752e+00
649 Vnm_tstart:·starting·timer·28·(Solver·timer)..649 Vnm_tstart:·starting·timer·28·(Solver·timer)..
650 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..650 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
651 Vbuildops:·Fine:·(065,·065,·065)651 Vbuildops:·Fine:·(065,·065,·065)
652 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)652 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
653 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.120000e-02653 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.139600e-02
654 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..654 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
655 Vbuildops:·Galer:·(033,·033,·033)655 Vbuildops:·Galer:·(033,·033,·033)
656 Vbuildops:·Galer:·(017,·017,·017)656 Vbuildops:·Galer:·(017,·017,·017)
657 Vbuildops:·Galer:·(009,·009,·009)657 Vbuildops:·Galer:·(009,·009,·009)
658 Vbuildops:·Galer:·(005,·005,·005)658 Vbuildops:·Galer:·(005,·005,·005)
659 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.212330e-01659 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.427620e-01
660 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..660 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
661 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·6.778378e+00661 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·6.866708e+00
662 Vprtstp:·iteration·=·0662 Vprtstp:·iteration·=·0
663 Vprtstp:·relative·residual·=·1.000000e+00663 Vprtstp:·relative·residual·=·1.000000e+00
664 Vprtstp:·contraction·number·=·1.000000e+00664 Vprtstp:·contraction·number·=·1.000000e+00
665 Vprtstp:·iteration·=·1665 Vprtstp:·iteration·=·1
666 Vprtstp:·relative·residual·=·6.211746e-02666 Vprtstp:·relative·residual·=·6.211746e-02
667 Vprtstp:·contraction·number·=·6.211746e-02667 Vprtstp:·contraction·number·=·6.211746e-02
668 Vprtstp:·iteration·=·2668 Vprtstp:·iteration·=·2
Offset 736, 32 lines modifiedOffset 736, 32 lines modified
736 Vprtstp:·contraction·number·=·6.956346e-01736 Vprtstp:·contraction·number·=·6.956346e-01
737 Vprtstp:·iteration·=·25737 Vprtstp:·iteration·=·25
738 Vprtstp:·relative·residual·=·1.302234e-06738 Vprtstp:·relative·residual·=·1.302234e-06
739 Vprtstp:·contraction·number·=·6.974500e-01739 Vprtstp:·contraction·number·=·6.974500e-01
740 Vprtstp:·iteration·=·26740 Vprtstp:·iteration·=·26
741 Vprtstp:·relative·residual·=·9.101840e-07741 Vprtstp:·relative·residual·=·9.101840e-07
742 Vprtstp:·contraction·number·=·6.989406e-01742 Vprtstp:·contraction·number·=·6.989406e-01
743 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·6.359739e+00743 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·7.945705e+00
744 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·6.557417e+00744 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·8.164739e+00
745 Vpmg_setPart:··lower·corner·=·(-22.1255,·-29.651,·-28.888)745 Vpmg_setPart:··lower·corner·=·(-22.1255,·-29.651,·-28.888)
746 Vpmg_setPart:··upper·corner·=·(73.8745,·66.349,·67.112)746 Vpmg_setPart:··upper·corner·=·(73.8745,·66.349,·67.112)
747 Vpmg_setPart:··actual·minima·=·(-22.1255,·-29.651,·-28.888)747 Vpmg_setPart:··actual·minima·=·(-22.1255,·-29.651,·-28.888)
748 Vpmg_setPart:··actual·maxima·=·(73.8745,·66.349,·67.112)748 Vpmg_setPart:··actual·maxima·=·(73.8745,·66.349,·67.112)
749 Vpmg_setPart:··bflag[FRONT]·=·0749 Vpmg_setPart:··bflag[FRONT]·=·0
750 Vpmg_setPart:··bflag[BACK]·=·0750 Vpmg_setPart:··bflag[BACK]·=·0
751 Vpmg_setPart:··bflag[LEFT]·=·0751 Vpmg_setPart:··bflag[LEFT]·=·0
752 Vpmg_setPart:··bflag[RIGHT]·=·0752 Vpmg_setPart:··bflag[RIGHT]·=·0
753 Vpmg_setPart:··bflag[UP]·=·0753 Vpmg_setPart:··bflag[UP]·=·0
754 Vpmg_setPart:··bflag[DOWN]·=·0754 Vpmg_setPart:··bflag[DOWN]·=·0
755 Vnm_tstart:·starting·timer·29·(Energy·timer)..755 Vnm_tstart:·starting·timer·29·(Energy·timer)..
756 Vpmg_energy:··calculating·only·q-phi·energy756 Vpmg_energy:··calculating·only·q-phi·energy
757 Vpmg_energy:··qfEnergy·=·8.506409949028E+03·kT757 Vpmg_energy:··qfEnergy·=·8.506409949028E+03·kT
758 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·5.660000e-04758 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·7.600000e-04
759 Vnm_tstart:·starting·timer·30·(Force·timer)..759 Vnm_tstart:·starting·timer·30·(Force·timer)..
760 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·4.000000e-06760 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·5.000000e-06
761 Vnm_tstart:·starting·timer·27·(Setup·timer)..761 Vnm_tstart:·starting·timer·27·(Setup·timer)..
762 Setting·up·PBE·object...762 Setting·up·PBE·object...
763 Vpbe_ctor2:··solute·radius·=·26.5287763 Vpbe_ctor2:··solute·radius·=·26.5287
764 Vpbe_ctor2:··solute·dimensions·=·50.733·x·37.661·x·37.832764 Vpbe_ctor2:··solute·dimensions·=·50.733·x·37.661·x·37.832
765 Vpbe_ctor2:··solute·charge·=·0.991765 Vpbe_ctor2:··solute·charge·=·0.991
766 Vpbe_ctor2:··bulk·ionic·strength·=·0.01766 Vpbe_ctor2:··bulk·ionic·strength·=·0.01
767 Vpbe_ctor2:··xkappa·=·0.0328757767 Vpbe_ctor2:··xkappa·=·0.0328757
Offset 807, 30 lines modifiedOffset 807, 30 lines modified
807 VPMG::extEnergy:·extQfEnergy·=·7766.58·kT807 VPMG::extEnergy:·extQfEnergy·=·7766.58·kT
808 VPMG::extEnergy:·extDiEnergy·=·3755.14·kT808 VPMG::extEnergy:·extDiEnergy·=·3755.14·kT
809 Vpmg_fillco:··filling·in·source·term.809 Vpmg_fillco:··filling·in·source·term.
810 fillcoCharge:··Calling·fillcoChargeSpline1...810 fillcoCharge:··Calling·fillcoChargeSpline1...
811 Vpmg_fillco:··filling·in·source·term.811 Vpmg_fillco:··filling·in·source·term.
812 Vpmg_fillco:··marking·ion·and·solvent·accessibility.812 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
813 fillcoCoef:··Calling·fillcoCoefMol...813 fillcoCoef:··Calling·fillcoCoefMol...
814 Vacc_SASA:·Time·elapsed:·2.679923814 Vacc_SASA:·Time·elapsed:·2.753520
815 Vpmg_fillco:··done·filling·coefficient·arrays815 Vpmg_fillco:··done·filling·coefficient·arrays
816 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.006659e+00816 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.073444e+00
817 Vnm_tstart:·starting·timer·28·(Solver·timer)..817 Vnm_tstart:·starting·timer·28·(Solver·timer)..
818 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..818 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
819 Vbuildops:·Fine:·(065,·065,·065)819 Vbuildops:·Fine:·(065,·065,·065)
820 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)820 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
821 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.197400e-02821 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.934000e-02
822 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..822 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
823 Vbuildops:·Galer:·(033,·033,·033)823 Vbuildops:·Galer:·(033,·033,·033)
824 Vbuildops:·Galer:·(017,·017,·017)824 Vbuildops:·Galer:·(017,·017,·017)
825 Vbuildops:·Galer:·(009,·009,·009)825 Vbuildops:·Galer:·(009,·009,·009)
826 Vbuildops:·Galer:·(005,·005,·005)826 Vbuildops:·Galer:·(005,·005,·005)
827 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.248410e-01827 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·2.304250e-01
828 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..828 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
829 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.635267e+01829 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.821158e+01
830 Vprtstp:·iteration·=·0830 Vprtstp:·iteration·=·0
831 Vprtstp:·relative·residual·=·1.000000e+00831 Vprtstp:·relative·residual·=·1.000000e+00
832 Vprtstp:·contraction·number·=·1.000000e+00832 Vprtstp:·contraction·number·=·1.000000e+00
833 Vprtstp:·iteration·=·1833 Vprtstp:·iteration·=·1
834 Vprtstp:·relative·residual·=·1.221522e-01834 Vprtstp:·relative·residual·=·1.221522e-01
835 Vprtstp:·contraction·number·=·1.221522e-01835 Vprtstp:·contraction·number·=·1.221522e-01
836 Vprtstp:·iteration·=·2836 Vprtstp:·iteration·=·2
Offset 862, 32 lines modifiedOffset 862, 32 lines modified
862 Vprtstp:·contraction·number·=·4.471936e-01862 Vprtstp:·contraction·number·=·4.471936e-01
863 Vprtstp:·iteration·=·11863 Vprtstp:·iteration·=·11
864 Vprtstp:·relative·residual·=·1.248629e-06864 Vprtstp:·relative·residual·=·1.248629e-06
865 Vprtstp:·contraction·number·=·4.746468e-01865 Vprtstp:·contraction·number·=·4.746468e-01
866 Vprtstp:·iteration·=·12866 Vprtstp:·iteration·=·12
867 Vprtstp:·relative·residual·=·6.237535e-07867 Vprtstp:·relative·residual·=·6.237535e-07
868 Vprtstp:·contraction·number·=·4.995506e-01868 Vprtstp:·contraction·number·=·4.995506e-01
869 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.965273e+00869 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·3.851445e+00
870 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.163964e+00870 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·4.166334e+00
871 Vpmg_setPart:··lower·corner·=·(10.551,·10.5695,·13.2915)871 Vpmg_setPart:··lower·corner·=·(10.551,·10.5695,·13.2915)
872 Vpmg_setPart:··upper·corner·=·(24.951,·24.9695,·27.6915)872 Vpmg_setPart:··upper·corner·=·(24.951,·24.9695,·27.6915)
873 Vpmg_setPart:··actual·minima·=·(10.551,·10.5695,·13.2915)873 Vpmg_setPart:··actual·minima·=·(10.551,·10.5695,·13.2915)
874 Vpmg_setPart:··actual·maxima·=·(24.951,·24.9695,·27.6915)874 Vpmg_setPart:··actual·maxima·=·(24.951,·24.9695,·27.6915)
875 Vpmg_setPart:··bflag[FRONT]·=·0875 Vpmg_setPart:··bflag[FRONT]·=·0
876 Vpmg_setPart:··bflag[BACK]·=·0876 Vpmg_setPart:··bflag[BACK]·=·0
877 Vpmg_setPart:··bflag[LEFT]·=·0877 Vpmg_setPart:··bflag[LEFT]·=·0
878 Vpmg_setPart:··bflag[RIGHT]·=·0878 Vpmg_setPart:··bflag[RIGHT]·=·0
879 Vpmg_setPart:··bflag[UP]·=·0879 Vpmg_setPart:··bflag[UP]·=·0
880 Vpmg_setPart:··bflag[DOWN]·=·0880 Vpmg_setPart:··bflag[DOWN]·=·0
Max diff block lines reached; 165906/172848 bytes (95.98%) of diff not shown.
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1020 KB
./usr/share/apbs/examples/actin-dimer/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·15:31:58·20243 #·Creation·Date·and·Time:··Mon·Jan··8·19:34:54·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·mol1.pqr9 NOsh:·Storing·molecule·0·path·mol1.pqr
Offset 262, 217 lines modifiedOffset 262, 217 lines modified
262 Vpmp_ctor2:··Using·meth·=·1,·mgsolv·=·0262 Vpmp_ctor2:··Using·meth·=·1,·mgsolv·=·0
263 Setting·PDE·center·to·local·center...263 Setting·PDE·center·to·local·center...
264 Vpmg_fillco:··filling·in·source·term.264 Vpmg_fillco:··filling·in·source·term.
265 fillcoCharge:··Calling·fillcoChargeSpline1...265 fillcoCharge:··Calling·fillcoChargeSpline1...
266 Vpmg_fillco:··filling·in·source·term.266 Vpmg_fillco:··filling·in·source·term.
267 Vpmg_fillco:··marking·ion·and·solvent·accessibility.267 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
268 fillcoCoef:··Calling·fillcoCoefMol...268 fillcoCoef:··Calling·fillcoCoefMol...
269 Vacc_SASA:·Time·elapsed:·7.359902269 Vacc_SASA:·Time·elapsed:·7.366003
270 Vpmg_fillco:··done·filling·coefficient·arrays270 Vpmg_fillco:··done·filling·coefficient·arrays
271 Vpmg_fillco:··filling·boundary·arrays271 Vpmg_fillco:··filling·boundary·arrays
272 Vpmg_fillco:··done·filling·boundary·arrays272 Vpmg_fillco:··done·filling·boundary·arrays
273 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·8.935742e+00273 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·8.875521e+00
274 Vnm_tstart:·starting·timer·28·(Solver·timer)..274 Vnm_tstart:·starting·timer·28·(Solver·timer)..
275 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·fine·problem·setup)..275 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·fine·problem·setup)..
276 Vbuildops:·Fine:·(161,·161,·161)276 Vbuildops:·Fine:·(161,·161,·161)
277 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)277 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
278 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·fine·problem·setup).··CPU·TIME·=·8.909910e-01278 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·fine·problem·setup).··CPU·TIME·=·8.470670e-01
279 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·coarse·problem·setup)..279 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·coarse·problem·setup)..
280 Vbuildops:·Galer:·(081,·081,·081)280 Vbuildops:·Galer:·(081,·081,·081)
281 Vbuildops:·Galer:·(041,·041,·041)281 Vbuildops:·Galer:·(041,·041,·041)
282 Vbuildops:·Galer:·(021,·021,·021)282 Vbuildops:·Galer:·(021,·021,·021)
283 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·coarse·problem·setup).··CPU·TIME·=·2.760189e+00283 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·coarse·problem·setup).··CPU·TIME·=·3.093672e+00
284 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·solve)..284 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·solve)..
285 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.357596e+01285 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.376956e+01
286 Vprtstp:·iteration·=·0286 Vprtstp:·iteration·=·0
287 Vprtstp:·relative·residual·=·1.000000e+00287 Vprtstp:·relative·residual·=·1.000000e+00
288 Vprtstp:·contraction·number·=·1.000000e+00288 Vprtstp:·contraction·number·=·1.000000e+00
289 Vnewton:·Damping·enabled289 Vnewton:·Damping·enabled
290 Vnewton:·Using·errtol_s:·7775242.648804290 Vnewton:·Using·errtol_s:·7775242.648804
291 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.777567e+01291 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.819566e+01
292 Vprtstp:·iteration·=·0292 Vprtstp:·iteration·=·0
293 Vprtstp:·relative·residual·=·1.000000e+00293 Vprtstp:·relative·residual·=·1.000000e+00
294 Vprtstp:·contraction·number·=·1.000000e+00294 Vprtstp:·contraction·number·=·1.000000e+00
295 Vprtstp:·iteration·=·1295 Vprtstp:·iteration·=·1
296 Vprtstp:·relative·residual·=·5.252805e+05296 Vprtstp:·relative·residual·=·5.252805e+05
297 Vprtstp:·contraction·number·=·5.252805e+05297 Vprtstp:·contraction·number·=·5.252805e+05
298 Vnewton:·Attempting·damping,·relres·=·0.062556298 Vnewton:·Attempting·damping,·relres·=·0.062556
299 Vnewton:·Attempting·damping,·relres·=·0.525334299 Vnewton:·Attempting·damping,·relres·=·0.525334
300 Vnewton:·Damping·accepted,·relres·=·0.062556300 Vnewton:·Damping·accepted,·relres·=·0.062556
301 Vnewton:·Damping·disabled301 Vnewton:·Damping·disabled
302 Vprtstp:·iteration·=·1302 Vprtstp:·iteration·=·1
303 Vprtstp:·relative·residual·=·6.255619e-02303 Vprtstp:·relative·residual·=·6.255619e-02
304 Vprtstp:·contraction·number·=·6.255619e-02304 Vprtstp:·contraction·number·=·6.255619e-02
305 Vnewton:·Using·errtol_s:·486389.547875305 Vnewton:·Using·errtol_s:·486389.547875
306 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.776460e+01306 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.768827e+01
307 Vprtstp:·iteration·=·0307 Vprtstp:·iteration·=·0
308 Vprtstp:·relative·residual·=·1.000000e+00308 Vprtstp:·relative·residual·=·1.000000e+00
309 Vprtstp:·contraction·number·=·1.000000e+00309 Vprtstp:·contraction·number·=·1.000000e+00
310 Vprtstp:·iteration·=·1310 Vprtstp:·iteration·=·1
311 Vprtstp:·relative·residual·=·1.109788e+05311 Vprtstp:·relative·residual·=·1.109788e+05
312 Vprtstp:·contraction·number·=·1.109788e+05312 Vprtstp:·contraction·number·=·1.109788e+05
313 Vprtstp:·iteration·=·2313 Vprtstp:·iteration·=·2
314 Vprtstp:·relative·residual·=·1.292368e-02314 Vprtstp:·relative·residual·=·1.292368e-02
315 Vprtstp:·contraction·number·=·2.065932e-01315 Vprtstp:·contraction·number·=·2.065932e-01
316 Vnewton:·Using·errtol_s:·100484.762247316 Vnewton:·Using·errtol_s:·100484.762247
317 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.580447e+01317 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.546396e+01
318 Vprtstp:·iteration·=·0318 Vprtstp:·iteration·=·0
319 Vprtstp:·relative·residual·=·1.000000e+00319 Vprtstp:·relative·residual·=·1.000000e+00
320 Vprtstp:·contraction·number·=·1.000000e+00320 Vprtstp:·contraction·number·=·1.000000e+00
321 Vprtstp:·iteration·=·1321 Vprtstp:·iteration·=·1
322 Vprtstp:·relative·residual·=·3.281526e+04322 Vprtstp:·relative·residual·=·3.281526e+04
323 Vprtstp:·contraction·number·=·3.281526e+04323 Vprtstp:·contraction·number·=·3.281526e+04
324 Vprtstp:·iteration·=·3324 Vprtstp:·iteration·=·3
325 Vprtstp:·relative·residual·=·3.798952e-03325 Vprtstp:·relative·residual·=·3.798952e-03
326 Vprtstp:·contraction·number·=·2.939527e-01326 Vprtstp:·contraction·number·=·2.939527e-01
327 Vnewton:·Using·errtol_s:·29537.770540327 Vnewton:·Using·errtol_s:·29537.770540
328 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·4.393495e+01328 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·4.340487e+01
329 Vprtstp:·iteration·=·0329 Vprtstp:·iteration·=·0
330 Vprtstp:·relative·residual·=·1.000000e+00330 Vprtstp:·relative·residual·=·1.000000e+00
331 Vprtstp:·contraction·number·=·1.000000e+00331 Vprtstp:·contraction·number·=·1.000000e+00
332 Vprtstp:·iteration·=·1332 Vprtstp:·iteration·=·1
333 Vprtstp:·relative·residual·=·1.139405e+04333 Vprtstp:·relative·residual·=·1.139405e+04
334 Vprtstp:·contraction·number·=·1.139405e+04334 Vprtstp:·contraction·number·=·1.139405e+04
335 Vprtstp:·iteration·=·4335 Vprtstp:·iteration·=·4
336 Vprtstp:·relative·residual·=·1.318894e-03336 Vprtstp:·relative·residual·=·1.318894e-03
337 Vprtstp:·contraction·number·=·3.471731e-01337 Vprtstp:·contraction·number·=·3.471731e-01
338 Vnewton:·Using·errtol_s:·10254.719067338 Vnewton:·Using·errtol_s:·10254.719067
339 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·5.208506e+01339 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·5.135077e+01
340 Vprtstp:·iteration·=·0340 Vprtstp:·iteration·=·0
341 Vprtstp:·relative·residual·=·1.000000e+00341 Vprtstp:·relative·residual·=·1.000000e+00
342 Vprtstp:·contraction·number·=·1.000000e+00342 Vprtstp:·contraction·number·=·1.000000e+00
343 Vprtstp:·iteration·=·1343 Vprtstp:·iteration·=·1
344 Vprtstp:·relative·residual·=·4.292845e+03344 Vprtstp:·relative·residual·=·4.292845e+03
345 Vprtstp:·contraction·number·=·4.292845e+03345 Vprtstp:·contraction·number·=·4.292845e+03
346 Vprtstp:·iteration·=·5346 Vprtstp:·iteration·=·5
347 Vprtstp:·relative·residual·=·4.969084e-04347 Vprtstp:·relative·residual·=·4.969084e-04
348 Vprtstp:·contraction·number·=·3.767615e-01348 Vprtstp:·contraction·number·=·3.767615e-01
349 Vnewton:·Using·errtol_s:·3863.583447349 Vnewton:·Using·errtol_s:·3863.583447
350 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·6.020158e+01350 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·5.936796e+01
351 Vprtstp:·iteration·=·0351 Vprtstp:·iteration·=·0
352 Vprtstp:·relative·residual·=·1.000000e+00352 Vprtstp:·relative·residual·=·1.000000e+00
353 Vprtstp:·contraction·number·=·1.000000e+00353 Vprtstp:·contraction·number·=·1.000000e+00
354 Vprtstp:·iteration·=·1354 Vprtstp:·iteration·=·1
355 Vprtstp:·relative·residual·=·1.746643e+03355 Vprtstp:·relative·residual·=·1.746643e+03
356 Vprtstp:·contraction·number·=·1.746643e+03356 Vprtstp:·contraction·number·=·1.746643e+03
357 Vprtstp:·iteration·=·6357 Vprtstp:·iteration·=·6
358 Vprtstp:·relative·residual·=·2.021786e-04358 Vprtstp:·relative·residual·=·2.021786e-04
359 Vprtstp:·contraction·number·=·4.068730e-01359 Vprtstp:·contraction·number·=·4.068730e-01
360 Vnewton:·Using·errtol_s:·1571.987642360 Vnewton:·Using·errtol_s:·1571.987642
361 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·6.844522e+01361 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·6.745562e+01
362 Vprtstp:·iteration·=·0362 Vprtstp:·iteration·=·0
363 Vprtstp:·relative·residual·=·1.000000e+00363 Vprtstp:·relative·residual·=·1.000000e+00
364 Vprtstp:·contraction·number·=·1.000000e+00364 Vprtstp:·contraction·number·=·1.000000e+00
365 Vprtstp:·iteration·=·1365 Vprtstp:·iteration·=·1
366 Vprtstp:·relative·residual·=·7.833563e+02366 Vprtstp:·relative·residual·=·7.833563e+02
367 Vprtstp:·contraction·number·=·7.833563e+02367 Vprtstp:·contraction·number·=·7.833563e+02
368 Vprtstp:·iteration·=·7368 Vprtstp:·iteration·=·7
369 Vprtstp:·relative·residual·=·9.067555e-05369 Vprtstp:·relative·residual·=·9.067555e-05
370 Vprtstp:·contraction·number·=·4.484923e-01370 Vprtstp:·contraction·number·=·4.484923e-01
371 Vnewton:·Using·errtol_s:·705.024393371 Vnewton:·Using·errtol_s:·705.024393
372 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·7.646641e+01372 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·7.540617e+01
373 Vprtstp:·iteration·=·0373 Vprtstp:·iteration·=·0
374 Vprtstp:·relative·residual·=·1.000000e+00374 Vprtstp:·relative·residual·=·1.000000e+00
375 Vprtstp:·contraction·number·=·1.000000e+00375 Vprtstp:·contraction·number·=·1.000000e+00
376 Vprtstp:·iteration·=·1376 Vprtstp:·iteration·=·1
377 Vprtstp:·relative·residual·=·3.880760e+02377 Vprtstp:·relative·residual·=·3.880760e+02
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⊟
7.34 KB
./usr/share/apbs/examples/alkanes/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:30:35·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:05:01·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·2-methylbutane.pdb9 NOsh:·Storing·molecule·0·path·2-methylbutane.pdb
Offset 302, 130 lines modifiedOffset 302, 130 lines modified
302 Vclist_ctor2:··Using·1.05·max·radius302 Vclist_ctor2:··Using·1.05·max·radius
303 Vclist_setupGrid:··Grid·lengths·=·(13.5347,·12.2207,·11.3787)303 Vclist_setupGrid:··Grid·lengths·=·(13.5347,·12.2207,·11.3787)
304 Vclist_setupGrid:··Grid·lower·corner·=·(-6.76736,·-6.11036,·-5.68936)304 Vclist_setupGrid:··Grid·lower·corner·=·(-6.76736,·-6.11036,·-5.68936)
305 Vclist_assignAtoms:··Have·6745·atom·entries305 Vclist_assignAtoms:··Have·6745·atom·entries
306 Vacc_storeParms:··Surf.·density·=·100306 Vacc_storeParms:··Surf.·density·=·100
307 Vacc_storeParms:··Max·area·=·109.953307 Vacc_storeParms:··Max·area·=·109.953
308 Vacc_storeParms:··Using·11012-point·reference·sphere308 Vacc_storeParms:··Using·11012-point·reference·sphere
309 Vacc_SASA:·Time·elapsed:·0.035335309 Vacc_SASA:·Time·elapsed:·0.036061
310 initAPOL:·Time·elapsed:·7.107459310 initAPOL:·Time·elapsed:·7.281695
311 APOL:·Setting·up·hash·table·and·accessibility·object...311 APOL:·Setting·up·hash·table·and·accessibility·object...
312 Vclist_ctor2:··Using·15·x·12·x·11·hash·table312 Vclist_ctor2:··Using·15·x·12·x·11·hash·table
313 Vclist_ctor2:··automatic·domain·setup.313 Vclist_ctor2:··automatic·domain·setup.
314 Vclist_ctor2:··Using·1.05·max·radius314 Vclist_ctor2:··Using·1.05·max·radius
315 Vclist_setupGrid:··Grid·lengths·=·(13.0267,·11.7717,·11.1107)315 Vclist_setupGrid:··Grid·lengths·=·(13.0267,·11.7717,·11.1107)
316 Vclist_setupGrid:··Grid·lower·corner·=·(-2.59636,·-5.18336,·-14.1304)316 Vclist_setupGrid:··Grid·lower·corner·=·(-2.59636,·-5.18336,·-14.1304)
317 Vclist_assignAtoms:··Have·4888·atom·entries317 Vclist_assignAtoms:··Have·4888·atom·entries
318 Vacc_storeParms:··Surf.·density·=·100318 Vacc_storeParms:··Surf.·density·=·100
319 Vacc_storeParms:··Max·area·=·109.953319 Vacc_storeParms:··Max·area·=·109.953
320 Vacc_storeParms:··Using·11012-point·reference·sphere320 Vacc_storeParms:··Using·11012-point·reference·sphere
321 Vacc_SASA:·Time·elapsed:·0.028590321 Vacc_SASA:·Time·elapsed:·0.028246
322 initAPOL:·Time·elapsed:·5.824950322 initAPOL:·Time·elapsed:·5.997025
323 APOL:·Setting·up·hash·table·and·accessibility·object...323 APOL:·Setting·up·hash·table·and·accessibility·object...
324 Vclist_ctor2:··Using·14·x·12·x·15·hash·table324 Vclist_ctor2:··Using·14·x·12·x·15·hash·table
325 Vclist_ctor2:··automatic·domain·setup.325 Vclist_ctor2:··automatic·domain·setup.
326 Vclist_ctor2:··Using·1.05·max·radius326 Vclist_ctor2:··Using·1.05·max·radius
327 Vclist_setupGrid:··Grid·lengths·=·(12.7417,·11.4947,·13.2787)327 Vclist_setupGrid:··Grid·lengths·=·(12.7417,·11.4947,·13.2787)
328 Vclist_setupGrid:··Grid·lower·corner·=·(-5.24736,·-5.15936,·-5.87136)328 Vclist_setupGrid:··Grid·lower·corner·=·(-5.24736,·-5.15936,·-5.87136)
329 Vclist_assignAtoms:··Have·6902·atom·entries329 Vclist_assignAtoms:··Have·6902·atom·entries
330 Vacc_storeParms:··Surf.·density·=·100330 Vacc_storeParms:··Surf.·density·=·100
331 Vacc_storeParms:··Max·area·=·109.953331 Vacc_storeParms:··Max·area·=·109.953
332 Vacc_storeParms:··Using·11012-point·reference·sphere332 Vacc_storeParms:··Using·11012-point·reference·sphere
333 Vacc_SASA:·Time·elapsed:·0.037917333 Vacc_SASA:·Time·elapsed:·0.037287
334 initAPOL:·Time·elapsed:·7.538482334 initAPOL:·Time·elapsed:·7.747837
335 APOL:·Setting·up·hash·table·and·accessibility·object...335 APOL:·Setting·up·hash·table·and·accessibility·object...
336 Vclist_ctor2:··Using·14·x·12·x·13·hash·table336 Vclist_ctor2:··Using·14·x·12·x·13·hash·table
337 Vclist_ctor2:··automatic·domain·setup.337 Vclist_ctor2:··automatic·domain·setup.
338 Vclist_ctor2:··Using·1.05·max·radius338 Vclist_ctor2:··Using·1.05·max·radius
339 Vclist_setupGrid:··Grid·lengths·=·(12.4767,·11.4917,·12.3367)339 Vclist_setupGrid:··Grid·lengths·=·(12.4767,·11.4917,·12.3367)
340 Vclist_setupGrid:··Grid·lower·corner·=·(-4.91836,·-5.22036,·-4.87936)340 Vclist_setupGrid:··Grid·lower·corner·=·(-4.91836,·-5.22036,·-4.87936)
341 Vclist_assignAtoms:··Have·4977·atom·entries341 Vclist_assignAtoms:··Have·4977·atom·entries
342 Vacc_storeParms:··Surf.·density·=·100342 Vacc_storeParms:··Surf.·density·=·100
343 Vacc_storeParms:··Max·area·=·109.953343 Vacc_storeParms:··Max·area·=·109.953
344 Vacc_storeParms:··Using·11012-point·reference·sphere344 Vacc_storeParms:··Using·11012-point·reference·sphere
345 Vacc_SASA:·Time·elapsed:·0.026374345 Vacc_SASA:·Time·elapsed:·0.026068
346 initAPOL:·Time·elapsed:·5.413352346 initAPOL:·Time·elapsed:·5.590699
347 APOL:·Setting·up·hash·table·and·accessibility·object...347 APOL:·Setting·up·hash·table·and·accessibility·object...
348 Vclist_ctor2:··Using·9·x·9·x·10·hash·table348 Vclist_ctor2:··Using·9·x·9·x·10·hash·table
349 Vclist_ctor2:··automatic·domain·setup.349 Vclist_ctor2:··automatic·domain·setup.
350 Vclist_ctor2:··Using·1.05·max·radius350 Vclist_ctor2:··Using·1.05·max·radius
351 Vclist_setupGrid:··Grid·lengths·=·(10.0327,·10.2387,·10.6647)351 Vclist_setupGrid:··Grid·lengths·=·(10.0327,·10.2387,·10.6647)
352 Vclist_setupGrid:··Grid·lower·corner·=·(-4.79536,·-5.14036,·-4.56736)352 Vclist_setupGrid:··Grid·lower·corner·=·(-4.79536,·-5.14036,·-4.56736)
353 Vclist_assignAtoms:··Have·1946·atom·entries353 Vclist_assignAtoms:··Have·1946·atom·entries
354 Vacc_storeParms:··Surf.·density·=·100354 Vacc_storeParms:··Surf.·density·=·100
355 Vacc_storeParms:··Max·area·=·109.953355 Vacc_storeParms:··Max·area·=·109.953
356 Vacc_storeParms:··Using·11012-point·reference·sphere356 Vacc_storeParms:··Using·11012-point·reference·sphere
357 Vacc_SASA:·Time·elapsed:·0.015251357 Vacc_SASA:·Time·elapsed:·0.014840
358 initAPOL:·Time·elapsed:·3.326363358 initAPOL:·Time·elapsed:·3.493075
359 APOL:·Setting·up·hash·table·and·accessibility·object...359 APOL:·Setting·up·hash·table·and·accessibility·object...
360 Vclist_ctor2:··Using·19·x·15·x·12·hash·table360 Vclist_ctor2:··Using·19·x·15·x·12·hash·table
361 Vclist_ctor2:··automatic·domain·setup.361 Vclist_ctor2:··automatic·domain·setup.
362 Vclist_ctor2:··Using·1.05·max·radius362 Vclist_ctor2:··Using·1.05·max·radius
363 Vclist_setupGrid:··Grid·lengths·=·(15.0957,·13.1957,·11.4487)363 Vclist_setupGrid:··Grid·lengths·=·(15.0957,·13.1957,·11.4487)
364 Vclist_setupGrid:··Grid·lower·corner·=·(-2.59636,·-6.60736,·-14.1304)364 Vclist_setupGrid:··Grid·lower·corner·=·(-2.59636,·-6.60736,·-14.1304)
365 Vclist_assignAtoms:··Have·9434·atom·entries365 Vclist_assignAtoms:··Have·9434·atom·entries
366 Vacc_storeParms:··Surf.·density·=·100366 Vacc_storeParms:··Surf.·density·=·100
367 Vacc_storeParms:··Max·area·=·109.953367 Vacc_storeParms:··Max·area·=·109.953
368 Vacc_storeParms:··Using·11012-point·reference·sphere368 Vacc_storeParms:··Using·11012-point·reference·sphere
369 Vacc_SASA:·Time·elapsed:·0.041819369 Vacc_SASA:·Time·elapsed:·0.043570
370 initAPOL:·Time·elapsed:·8.552576370 initAPOL:·Time·elapsed:·8.763385
371 APOL:·Setting·up·hash·table·and·accessibility·object...371 APOL:·Setting·up·hash·table·and·accessibility·object...
372 Vclist_ctor2:··Using·13·x·12·x·14·hash·table372 Vclist_ctor2:··Using·13·x·12·x·14·hash·table
373 Vclist_ctor2:··automatic·domain·setup.373 Vclist_ctor2:··automatic·domain·setup.
374 Vclist_ctor2:··Using·1.05·max·radius374 Vclist_ctor2:··Using·1.05·max·radius
375 Vclist_setupGrid:··Grid·lengths·=·(12.0577,·11.5517,·12.5037)375 Vclist_setupGrid:··Grid·lengths·=·(12.0577,·11.5517,·12.5037)
376 Vclist_setupGrid:··Grid·lower·corner·=·(12.5656,·12.8626,·12.9606)376 Vclist_setupGrid:··Grid·lower·corner·=·(12.5656,·12.8626,·12.9606)
377 Vclist_assignAtoms:··Have·5377·atom·entries377 Vclist_assignAtoms:··Have·5377·atom·entries
378 Vacc_storeParms:··Surf.·density·=·100378 Vacc_storeParms:··Surf.·density·=·100
379 Vacc_storeParms:··Max·area·=·109.953379 Vacc_storeParms:··Max·area·=·109.953
380 Vacc_storeParms:··Using·11012-point·reference·sphere380 Vacc_storeParms:··Using·11012-point·reference·sphere
381 Vacc_SASA:·Time·elapsed:·0.032635381 Vacc_SASA:·Time·elapsed:·0.031445
382 initAPOL:·Time·elapsed:·6.376478382 initAPOL:·Time·elapsed:·6.262404
383 APOL:·Setting·up·hash·table·and·accessibility·object...383 APOL:·Setting·up·hash·table·and·accessibility·object...
384 Vclist_ctor2:··Using·9·x·9·x·8·hash·table384 Vclist_ctor2:··Using·9·x·9·x·8·hash·table
385 Vclist_ctor2:··automatic·domain·setup.385 Vclist_ctor2:··automatic·domain·setup.
386 Vclist_ctor2:··Using·1.05·max·radius386 Vclist_ctor2:··Using·1.05·max·radius
387 Vclist_setupGrid:··Grid·lengths·=·(10.1767,·10.1117,·9.66772)387 Vclist_setupGrid:··Grid·lengths·=·(10.1767,·10.1117,·9.66772)
388 Vclist_setupGrid:··Grid·lower·corner·=·(12.9396,·12.7376,·12.9816)388 Vclist_setupGrid:··Grid·lower·corner·=·(12.9396,·12.7376,·12.9816)
389 Vclist_assignAtoms:··Have·1014·atom·entries389 Vclist_assignAtoms:··Have·1014·atom·entries
390 Vacc_storeParms:··Surf.·density·=·100390 Vacc_storeParms:··Surf.·density·=·100
391 Vacc_storeParms:··Max·area·=·109.953391 Vacc_storeParms:··Max·area·=·109.953
392 Vacc_storeParms:··Using·11012-point·reference·sphere392 Vacc_storeParms:··Using·11012-point·reference·sphere
393 Vacc_SASA:·Time·elapsed:·0.008930393 Vacc_SASA:·Time·elapsed:·0.009133
394 initAPOL:·Time·elapsed:·2.182165394 initAPOL:·Time·elapsed:·2.248791
395 APOL:·Setting·up·hash·table·and·accessibility·object...395 APOL:·Setting·up·hash·table·and·accessibility·object...
396 Vclist_ctor2:··Using·13·x·13·x·14·hash·table396 Vclist_ctor2:··Using·13·x·13·x·14·hash·table
397 Vclist_ctor2:··automatic·domain·setup.397 Vclist_ctor2:··automatic·domain·setup.
398 Vclist_ctor2:··Using·1.05·max·radius398 Vclist_ctor2:··Using·1.05·max·radius
399 Vclist_setupGrid:··Grid·lengths·=·(12.2347,·12.1667,·12.6837)399 Vclist_setupGrid:··Grid·lengths·=·(12.2347,·12.1667,·12.6837)
400 Vclist_setupGrid:··Grid·lower·corner·=·(12.5496,·12.8526,·12.8586)400 Vclist_setupGrid:··Grid·lower·corner·=·(12.5496,·12.8526,·12.8586)
401 Vclist_assignAtoms:··Have·6725·atom·entries401 Vclist_assignAtoms:··Have·6725·atom·entries
402 Vacc_storeParms:··Surf.·density·=·100402 Vacc_storeParms:··Surf.·density·=·100
403 Vacc_storeParms:··Max·area·=·109.953403 Vacc_storeParms:··Max·area·=·109.953
404 Vacc_storeParms:··Using·11012-point·reference·sphere404 Vacc_storeParms:··Using·11012-point·reference·sphere
405 Vacc_SASA:·Time·elapsed:·0.037017405 Vacc_SASA:·Time·elapsed:·0.038255
406 initAPOL:·Time·elapsed:·7.519642406 initAPOL:·Time·elapsed:·7.795208
407 APOL:·Setting·up·hash·table·and·accessibility·object...407 APOL:·Setting·up·hash·table·and·accessibility·object...
408 Vclist_ctor2:··Using·17·x·14·x·11·hash·table408 Vclist_ctor2:··Using·17·x·14·x·11·hash·table
409 Vclist_ctor2:··automatic·domain·setup.409 Vclist_ctor2:··automatic·domain·setup.
410 Vclist_ctor2:··Using·1.05·max·radius410 Vclist_ctor2:··Using·1.05·max·radius
411 Vclist_setupGrid:··Grid·lengths·=·(14.1127,·12.8537,·11.1297)411 Vclist_setupGrid:··Grid·lengths·=·(14.1127,·12.8537,·11.1297)
412 Vclist_setupGrid:··Grid·lower·corner·=·(-2.59636,·-6.26536,·-14.1304)412 Vclist_setupGrid:··Grid·lower·corner·=·(-2.59636,·-6.26536,·-14.1304)
413 Vclist_assignAtoms:··Have·6650·atom·entries413 Vclist_assignAtoms:··Have·6650·atom·entries
414 Vacc_storeParms:··Surf.·density·=·100414 Vacc_storeParms:··Surf.·density·=·100
415 Vacc_storeParms:··Max·area·=·109.953415 Vacc_storeParms:··Max·area·=·109.953
416 Vacc_storeParms:··Using·11012-point·reference·sphere416 Vacc_storeParms:··Using·11012-point·reference·sphere
417 Vacc_SASA:·Time·elapsed:·0.034051417 Vacc_SASA:·Time·elapsed:·0.033595
Max diff block lines reached; 717/7443 bytes (9.63%) of diff not shown.
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204 KB
./usr/share/apbs/examples/born/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·15:30:09·20243 #·Creation·Date·and·Time:··Mon·Jan··8·19:30:25·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·ion.xml9 NOsh:·Storing·molecule·0·path·ion.xml
Offset 194, 32 lines modifiedOffset 194, 32 lines modified
194 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1194 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
195 Setting·PDE·center·to·local·center...195 Setting·PDE·center·to·local·center...
196 Vpmg_fillco:··filling·in·source·term.196 Vpmg_fillco:··filling·in·source·term.
197 fillcoCharge:··Calling·fillcoChargeSpline2...197 fillcoCharge:··Calling·fillcoChargeSpline2...
198 Vpmg_fillco:··filling·in·source·term.198 Vpmg_fillco:··filling·in·source·term.
199 Vpmg_fillco:··marking·ion·and·solvent·accessibility.199 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
200 fillcoCoef:··Calling·fillcoCoefMol...200 fillcoCoef:··Calling·fillcoCoefMol...
201 Vacc_SASA:·Time·elapsed:·0.002997201 Vacc_SASA:·Time·elapsed:·0.000622
202 Vpmg_fillco:··done·filling·coefficient·arrays202 Vpmg_fillco:··done·filling·coefficient·arrays
203 Vpmg_fillco:··filling·boundary·arrays203 Vpmg_fillco:··filling·boundary·arrays
204 Vpmg_fillco:··done·filling·boundary·arrays204 Vpmg_fillco:··done·filling·boundary·arrays
205 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·4.942700e-02205 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·4.039500e-02
206 Vnm_tstart:·starting·timer·28·(Solver·timer)..206 Vnm_tstart:·starting·timer·28·(Solver·timer)..
207 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..207 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
208 Vbuildops:·Fine:·(065,·065,·065)208 Vbuildops:·Fine:·(065,·065,·065)
209 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)209 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
210 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.942600e-02210 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.084300e-02
211 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..211 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
212 Vbuildops:·Galer:·(033,·033,·033)212 Vbuildops:·Galer:·(033,·033,·033)
213 Vbuildops:·Galer:·(017,·017,·017)213 Vbuildops:·Galer:·(017,·017,·017)
214 Vbuildops:·Galer:·(009,·009,·009)214 Vbuildops:·Galer:·(009,·009,·009)
215 Vbuildops:·Galer:·(005,·005,·005)215 Vbuildops:·Galer:·(005,·005,·005)
216 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.423200e-01216 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.810610e-01
217 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..217 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
218 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.078300e-01218 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.292080e-01
219 Vprtstp:·iteration·=·0219 Vprtstp:·iteration·=·0
220 Vprtstp:·relative·residual·=·1.000000e+00220 Vprtstp:·relative·residual·=·1.000000e+00
221 Vprtstp:·contraction·number·=·1.000000e+00221 Vprtstp:·contraction·number·=·1.000000e+00
222 Vprtstp:·iteration·=·1222 Vprtstp:·iteration·=·1
223 Vprtstp:·relative·residual·=·1.252488e-01223 Vprtstp:·relative·residual·=·1.252488e-01
224 Vprtstp:·contraction·number·=·1.252488e-01224 Vprtstp:·contraction·number·=·1.252488e-01
225 Vprtstp:·iteration·=·2225 Vprtstp:·iteration·=·2
Offset 242, 33 lines modifiedOffset 242, 33 lines modified
242 Vprtstp:·contraction·number·=·2.345457e-01242 Vprtstp:·contraction·number·=·2.345457e-01
243 Vprtstp:·iteration·=·8243 Vprtstp:·iteration·=·8
244 Vprtstp:·relative·residual·=·1.154547e-06244 Vprtstp:·relative·residual·=·1.154547e-06
245 Vprtstp:·contraction·number·=·2.398447e-01245 Vprtstp:·contraction·number·=·2.398447e-01
246 Vprtstp:·iteration·=·9246 Vprtstp:·iteration·=·9
247 Vprtstp:·relative·residual·=·2.798201e-07247 Vprtstp:·relative·residual·=·2.798201e-07
248 Vprtstp:·contraction·number·=·2.423636e-01248 Vprtstp:·contraction·number·=·2.423636e-01
249 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.668195e+00249 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.855067e+00
250 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.905504e+00250 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.121505e+00
251 Vpmg_setPart:··lower·corner·=·(-25,·-25,·-25)251 Vpmg_setPart:··lower·corner·=·(-25,·-25,·-25)
252 Vpmg_setPart:··upper·corner·=·(25,·25,·25)252 Vpmg_setPart:··upper·corner·=·(25,·25,·25)
253 Vpmg_setPart:··actual·minima·=·(-25,·-25,·-25)253 Vpmg_setPart:··actual·minima·=·(-25,·-25,·-25)
254 Vpmg_setPart:··actual·maxima·=·(25,·25,·25)254 Vpmg_setPart:··actual·maxima·=·(25,·25,·25)
255 Vpmg_setPart:··bflag[FRONT]·=·0255 Vpmg_setPart:··bflag[FRONT]·=·0
256 Vpmg_setPart:··bflag[BACK]·=·0256 Vpmg_setPart:··bflag[BACK]·=·0
257 Vpmg_setPart:··bflag[LEFT]·=·0257 Vpmg_setPart:··bflag[LEFT]·=·0
258 Vpmg_setPart:··bflag[RIGHT]·=·0258 Vpmg_setPart:··bflag[RIGHT]·=·0
259 Vpmg_setPart:··bflag[UP]·=·0259 Vpmg_setPart:··bflag[UP]·=·0
260 Vpmg_setPart:··bflag[DOWN]·=·0260 Vpmg_setPart:··bflag[DOWN]·=·0
261 Vnm_tstart:·starting·timer·29·(Energy·timer)..261 Vnm_tstart:·starting·timer·29·(Energy·timer)..
262 Vpmg_energy:··calculating·only·q-phi·energy262 Vpmg_energy:··calculating·only·q-phi·energy
263 Vpmg_qfEnergyVolume:··Calculating·energy263 Vpmg_qfEnergyVolume:··Calculating·energy
264 Vpmg_energy:··qfEnergy·=·7.750853990251E+02·kT264 Vpmg_energy:··qfEnergy·=·7.750853990251E+02·kT
265 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.715000e-03265 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·2.354000e-03
266 Vnm_tstart:·starting·timer·30·(Force·timer)..266 Vnm_tstart:·starting·timer·30·(Force·timer)..
267 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·3.000000e-06267 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·4.000000e-06
268 Vnm_tstart:·starting·timer·27·(Setup·timer)..268 Vnm_tstart:·starting·timer·27·(Setup·timer)..
269 Setting·up·PBE·object...269 Setting·up·PBE·object...
270 Vpbe_ctor2:··solute·radius·=·3270 Vpbe_ctor2:··solute·radius·=·3
271 Vpbe_ctor2:··solute·dimensions·=·6·x·6·x·6271 Vpbe_ctor2:··solute·dimensions·=·6·x·6·x·6
272 Vpbe_ctor2:··solute·charge·=·1272 Vpbe_ctor2:··solute·charge·=·1
273 Vpbe_ctor2:··bulk·ionic·strength·=·0273 Vpbe_ctor2:··bulk·ionic·strength·=·0
274 Vpbe_ctor2:··xkappa·=·0274 Vpbe_ctor2:··xkappa·=·0
Offset 315, 30 lines modifiedOffset 315, 30 lines modified
315 VPMG::extEnergy:·extQfEnergy·=·0·kT315 VPMG::extEnergy:·extQfEnergy·=·0·kT
316 VPMG::extEnergy:·extDiEnergy·=·0.111569·kT316 VPMG::extEnergy:·extDiEnergy·=·0.111569·kT
317 Vpmg_fillco:··filling·in·source·term.317 Vpmg_fillco:··filling·in·source·term.
318 fillcoCharge:··Calling·fillcoChargeSpline2...318 fillcoCharge:··Calling·fillcoChargeSpline2...
319 Vpmg_fillco:··filling·in·source·term.319 Vpmg_fillco:··filling·in·source·term.
320 Vpmg_fillco:··marking·ion·and·solvent·accessibility.320 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
321 fillcoCoef:··Calling·fillcoCoefMol...321 fillcoCoef:··Calling·fillcoCoefMol...
322 Vacc_SASA:·Time·elapsed:·0.000499322 Vacc_SASA:·Time·elapsed:·0.000519
323 Vpmg_fillco:··done·filling·coefficient·arrays323 Vpmg_fillco:··done·filling·coefficient·arrays
324 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.213540e-01324 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.270410e-01
325 Vnm_tstart:·starting·timer·28·(Solver·timer)..325 Vnm_tstart:·starting·timer·28·(Solver·timer)..
326 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..326 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
327 Vbuildops:·Fine:·(065,·065,·065)327 Vbuildops:·Fine:·(065,·065,·065)
328 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)328 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
329 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.590100e-02329 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.076600e-02
330 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..330 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
331 Vbuildops:·Galer:·(033,·033,·033)331 Vbuildops:·Galer:·(033,·033,·033)
332 Vbuildops:·Galer:·(017,·017,·017)332 Vbuildops:·Galer:·(017,·017,·017)
333 Vbuildops:·Galer:·(009,·009,·009)333 Vbuildops:·Galer:·(009,·009,·009)
334 Vbuildops:·Galer:·(005,·005,·005)334 Vbuildops:·Galer:·(005,·005,·005)
335 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.396380e-01335 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.838330e-01
336 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..336 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
337 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.336648e+00337 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.593760e+00
338 Vprtstp:·iteration·=·0338 Vprtstp:·iteration·=·0
339 Vprtstp:·relative·residual·=·1.000000e+00339 Vprtstp:·relative·residual·=·1.000000e+00
340 Vprtstp:·contraction·number·=·1.000000e+00340 Vprtstp:·contraction·number·=·1.000000e+00
341 Vprtstp:·iteration·=·1341 Vprtstp:·iteration·=·1
342 Vprtstp:·relative·residual·=·1.284366e-01342 Vprtstp:·relative·residual·=·1.284366e-01
343 Vprtstp:·contraction·number·=·1.284366e-01343 Vprtstp:·contraction·number·=·1.284366e-01
344 Vprtstp:·iteration·=·2344 Vprtstp:·iteration·=·2
Offset 370, 33 lines modifiedOffset 370, 33 lines modified
370 Vprtstp:·contraction·number·=·3.689006e-01370 Vprtstp:·contraction·number·=·3.689006e-01
371 Vprtstp:·iteration·=·11371 Vprtstp:·iteration·=·11
372 Vprtstp:·relative·residual·=·1.340984e-06372 Vprtstp:·relative·residual·=·1.340984e-06
373 Vprtstp:·contraction·number·=·3.689051e-01373 Vprtstp:·contraction·number·=·3.689051e-01
374 Vprtstp:·iteration·=·12374 Vprtstp:·iteration·=·12
375 Vprtstp:·relative·residual·=·4.946966e-07375 Vprtstp:·relative·residual·=·4.946966e-07
376 Vprtstp:·contraction·number·=·3.689058e-01376 Vprtstp:·contraction·number·=·3.689058e-01
377 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·3.503409e+00377 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·3.817024e+00
378 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.732714e+00378 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·4.087775e+00
379 Vpmg_setPart:··lower·corner·=·(-12.2474,·-12.2474,·-12.2474)379 Vpmg_setPart:··lower·corner·=·(-12.2474,·-12.2474,·-12.2474)
380 Vpmg_setPart:··upper·corner·=·(12.2474,·12.2474,·12.2474)380 Vpmg_setPart:··upper·corner·=·(12.2474,·12.2474,·12.2474)
381 Vpmg_setPart:··actual·minima·=·(-12.2474,·-12.2474,·-12.2474)381 Vpmg_setPart:··actual·minima·=·(-12.2474,·-12.2474,·-12.2474)
382 Vpmg_setPart:··actual·maxima·=·(12.2474,·12.2474,·12.2474)382 Vpmg_setPart:··actual·maxima·=·(12.2474,·12.2474,·12.2474)
383 Vpmg_setPart:··bflag[FRONT]·=·0383 Vpmg_setPart:··bflag[FRONT]·=·0
384 Vpmg_setPart:··bflag[BACK]·=·0384 Vpmg_setPart:··bflag[BACK]·=·0
385 Vpmg_setPart:··bflag[LEFT]·=·0385 Vpmg_setPart:··bflag[LEFT]·=·0
386 Vpmg_setPart:··bflag[RIGHT]·=·0386 Vpmg_setPart:··bflag[RIGHT]·=·0
387 Vpmg_setPart:··bflag[UP]·=·0387 Vpmg_setPart:··bflag[UP]·=·0
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⊟
62.7 KB
./usr/share/apbs/examples/hca-bind/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:34:26·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:11:51·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·acet.pqr9 NOsh:·Storing·molecule·0·path·acet.pqr
Offset 289, 32 lines modifiedOffset 289, 32 lines modified
289 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1289 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
290 Setting·PDE·center·to·local·center...290 Setting·PDE·center·to·local·center...
291 Vpmg_fillco:··filling·in·source·term.291 Vpmg_fillco:··filling·in·source·term.
292 fillcoCharge:··Calling·fillcoChargeSpline1...292 fillcoCharge:··Calling·fillcoChargeSpline1...
293 Vpmg_fillco:··filling·in·source·term.293 Vpmg_fillco:··filling·in·source·term.
294 Vpmg_fillco:··marking·ion·and·solvent·accessibility.294 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
295 fillcoCoef:··Calling·fillcoCoefMol...295 fillcoCoef:··Calling·fillcoCoefMol...
296 Vacc_SASA:·Time·elapsed:·0.016624296 Vacc_SASA:·Time·elapsed:·0.013031
297 Vpmg_fillco:··done·filling·coefficient·arrays297 Vpmg_fillco:··done·filling·coefficient·arrays
298 Vpmg_fillco:··filling·boundary·arrays298 Vpmg_fillco:··filling·boundary·arrays
299 Vpmg_fillco:··done·filling·boundary·arrays299 Vpmg_fillco:··done·filling·boundary·arrays
300 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·5.361500e-02300 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.575300e-02
301 Vnm_tstart:·starting·timer·28·(Solver·timer)..301 Vnm_tstart:·starting·timer·28·(Solver·timer)..
302 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..302 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
303 Vbuildops:·Fine:·(065,·065,·065)303 Vbuildops:·Fine:·(065,·065,·065)
304 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)304 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
305 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.343900e-02305 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.770500e-02
306 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..306 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
307 Vbuildops:·Galer:·(033,·033,·033)307 Vbuildops:·Galer:·(033,·033,·033)
308 Vbuildops:·Galer:·(017,·017,·017)308 Vbuildops:·Galer:·(017,·017,·017)
309 Vbuildops:·Galer:·(009,·009,·009)309 Vbuildops:·Galer:·(009,·009,·009)
310 Vbuildops:·Galer:·(005,·005,·005)310 Vbuildops:·Galer:·(005,·005,·005)
311 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.492840e-01311 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.722570e-01
312 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..312 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
313 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·4.867570e-01313 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·4.575410e-01
314 Vprtstp:·iteration·=·0314 Vprtstp:·iteration·=·0
315 Vprtstp:·relative·residual·=·1.000000e+00315 Vprtstp:·relative·residual·=·1.000000e+00
316 Vprtstp:·contraction·number·=·1.000000e+00316 Vprtstp:·contraction·number·=·1.000000e+00
317 Vprtstp:·iteration·=·1317 Vprtstp:·iteration·=·1
318 Vprtstp:·relative·residual·=·1.087255e-01318 Vprtstp:·relative·residual·=·1.087255e-01
319 Vprtstp:·contraction·number·=·1.087255e-01319 Vprtstp:·contraction·number·=·1.087255e-01
320 Vprtstp:·iteration·=·2320 Vprtstp:·iteration·=·2
Offset 331, 32 lines modifiedOffset 331, 32 lines modified
331 Vprtstp:·contraction·number·=·1.074047e-01331 Vprtstp:·contraction·number·=·1.074047e-01
332 Vprtstp:·iteration·=·6332 Vprtstp:·iteration·=·6
333 Vprtstp:·relative·residual·=·1.481057e-06333 Vprtstp:·relative·residual·=·1.481057e-06
334 Vprtstp:·contraction·number·=·1.080656e-01334 Vprtstp:·contraction·number·=·1.080656e-01
335 Vprtstp:·iteration·=·7335 Vprtstp:·iteration·=·7
336 Vprtstp:·relative·residual·=·1.608051e-07336 Vprtstp:·relative·residual·=·1.608051e-07
337 Vprtstp:·contraction·number·=·1.085746e-01337 Vprtstp:·contraction·number·=·1.085746e-01
338 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.717546e+00338 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.068047e+00
339 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·1.978412e+00339 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.320167e+00
340 Vpmg_setPart:··lower·corner·=·(-54.0285,·-44.1015,·-32.821)340 Vpmg_setPart:··lower·corner·=·(-54.0285,·-44.1015,·-32.821)
341 Vpmg_setPart:··upper·corner·=·(41.9715,·51.8985,·63.179)341 Vpmg_setPart:··upper·corner·=·(41.9715,·51.8985,·63.179)
342 Vpmg_setPart:··actual·minima·=·(-54.0285,·-44.1015,·-32.821)342 Vpmg_setPart:··actual·minima·=·(-54.0285,·-44.1015,·-32.821)
343 Vpmg_setPart:··actual·maxima·=·(41.9715,·51.8985,·63.179)343 Vpmg_setPart:··actual·maxima·=·(41.9715,·51.8985,·63.179)
344 Vpmg_setPart:··bflag[FRONT]·=·0344 Vpmg_setPart:··bflag[FRONT]·=·0
345 Vpmg_setPart:··bflag[BACK]·=·0345 Vpmg_setPart:··bflag[BACK]·=·0
346 Vpmg_setPart:··bflag[LEFT]·=·0346 Vpmg_setPart:··bflag[LEFT]·=·0
347 Vpmg_setPart:··bflag[RIGHT]·=·0347 Vpmg_setPart:··bflag[RIGHT]·=·0
348 Vpmg_setPart:··bflag[UP]·=·0348 Vpmg_setPart:··bflag[UP]·=·0
349 Vpmg_setPart:··bflag[DOWN]·=·0349 Vpmg_setPart:··bflag[DOWN]·=·0
350 Vnm_tstart:·starting·timer·29·(Energy·timer)..350 Vnm_tstart:·starting·timer·29·(Energy·timer)..
351 Vpmg_energy:··calculating·only·q-phi·energy351 Vpmg_energy:··calculating·only·q-phi·energy
352 Vpmg_energy:··qfEnergy·=·1.785902379684E+02·kT352 Vpmg_energy:··qfEnergy·=·1.785902379684E+02·kT
353 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.500000e-04353 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.580000e-04
354 Vnm_tstart:·starting·timer·30·(Force·timer)..354 Vnm_tstart:·starting·timer·30·(Force·timer)..
355 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·4.000000e-06355 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·5.000000e-06
356 Vnm_tstart:·starting·timer·27·(Setup·timer)..356 Vnm_tstart:·starting·timer·27·(Setup·timer)..
357 Setting·up·PBE·object...357 Setting·up·PBE·object...
358 Vpbe_ctor2:··solute·radius·=·6.35359358 Vpbe_ctor2:··solute·radius·=·6.35359
359 Vpbe_ctor2:··solute·dimensions·=·7.389·x·11.027·x·9.931359 Vpbe_ctor2:··solute·dimensions·=·7.389·x·11.027·x·9.931
360 Vpbe_ctor2:··solute·charge·=·-1360 Vpbe_ctor2:··solute·charge·=·-1
361 Vpbe_ctor2:··bulk·ionic·strength·=·0361 Vpbe_ctor2:··bulk·ionic·strength·=·0
362 Vpbe_ctor2:··xkappa·=·0362 Vpbe_ctor2:··xkappa·=·0
Offset 402, 30 lines modifiedOffset 402, 30 lines modified
402 VPMG::extEnergy:·extQfEnergy·=·0·kT402 VPMG::extEnergy:·extQfEnergy·=·0·kT
403 VPMG::extEnergy:·extDiEnergy·=·0.104294·kT403 VPMG::extEnergy:·extDiEnergy·=·0.104294·kT
404 Vpmg_fillco:··filling·in·source·term.404 Vpmg_fillco:··filling·in·source·term.
405 fillcoCharge:··Calling·fillcoChargeSpline1...405 fillcoCharge:··Calling·fillcoChargeSpline1...
406 Vpmg_fillco:··filling·in·source·term.406 Vpmg_fillco:··filling·in·source·term.
407 Vpmg_fillco:··marking·ion·and·solvent·accessibility.407 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
408 fillcoCoef:··Calling·fillcoCoefMol...408 fillcoCoef:··Calling·fillcoCoefMol...
409 Vacc_SASA:·Time·elapsed:·0.014525409 Vacc_SASA:·Time·elapsed:·0.012203
410 Vpmg_fillco:··done·filling·coefficient·arrays410 Vpmg_fillco:··done·filling·coefficient·arrays
411 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·9.552800e-02411 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·8.850400e-02
412 Vnm_tstart:·starting·timer·28·(Solver·timer)..412 Vnm_tstart:·starting·timer·28·(Solver·timer)..
413 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..413 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
414 Vbuildops:·Fine:·(065,·065,·065)414 Vbuildops:·Fine:·(065,·065,·065)
415 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)415 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
416 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.035900e-02416 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.646200e-02
417 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..417 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
418 Vbuildops:·Galer:·(033,·033,·033)418 Vbuildops:·Galer:·(033,·033,·033)
419 Vbuildops:·Galer:·(017,·017,·017)419 Vbuildops:·Galer:·(017,·017,·017)
420 Vbuildops:·Galer:·(009,·009,·009)420 Vbuildops:·Galer:·(009,·009,·009)
421 Vbuildops:·Galer:·(005,·005,·005)421 Vbuildops:·Galer:·(005,·005,·005)
422 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.232950e-01422 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.726680e-01
423 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..423 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
424 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.509364e+00424 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.874334e+00
425 Vprtstp:·iteration·=·0425 Vprtstp:·iteration·=·0
426 Vprtstp:·relative·residual·=·1.000000e+00426 Vprtstp:·relative·residual·=·1.000000e+00
427 Vprtstp:·contraction·number·=·1.000000e+00427 Vprtstp:·contraction·number·=·1.000000e+00
428 Vprtstp:·iteration·=·1428 Vprtstp:·iteration·=·1
429 Vprtstp:·relative·residual·=·1.287269e-01429 Vprtstp:·relative·residual·=·1.287269e-01
430 Vprtstp:·contraction·number·=·1.287269e-01430 Vprtstp:·contraction·number·=·1.287269e-01
431 Vprtstp:·iteration·=·2431 Vprtstp:·iteration·=·2
Offset 451, 32 lines modifiedOffset 451, 32 lines modified
451 Vprtstp:·contraction·number·=·3.073619e-01451 Vprtstp:·contraction·number·=·3.073619e-01
452 Vprtstp:·iteration·=·9452 Vprtstp:·iteration·=·9
453 Vprtstp:·relative·residual·=·1.517211e-06453 Vprtstp:·relative·residual·=·1.517211e-06
454 Vprtstp:·contraction·number·=·3.092055e-01454 Vprtstp:·contraction·number·=·3.092055e-01
455 Vprtstp:·iteration·=·10455 Vprtstp:·iteration·=·10
456 Vprtstp:·relative·residual·=·4.703221e-07456 Vprtstp:·relative·residual·=·4.703221e-07
457 Vprtstp:·contraction·number·=·3.099912e-01457 Vprtstp:·contraction·number·=·3.099912e-01
458 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.493711e+00458 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.919060e+00
459 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.694443e+00459 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.170445e+00
460 Vpmg_setPart:··lower·corner·=·(-24.6188,·-14.6918,·-3.41132)460 Vpmg_setPart:··lower·corner·=·(-24.6188,·-14.6918,·-3.41132)
461 Vpmg_setPart:··upper·corner·=·(12.5618,·22.4888,·33.7693)461 Vpmg_setPart:··upper·corner·=·(12.5618,·22.4888,·33.7693)
462 Vpmg_setPart:··actual·minima·=·(-24.6188,·-14.6918,·-3.41132)462 Vpmg_setPart:··actual·minima·=·(-24.6188,·-14.6918,·-3.41132)
463 Vpmg_setPart:··actual·maxima·=·(12.5618,·22.4888,·33.7693)463 Vpmg_setPart:··actual·maxima·=·(12.5618,·22.4888,·33.7693)
464 Vpmg_setPart:··bflag[FRONT]·=·0464 Vpmg_setPart:··bflag[FRONT]·=·0
465 Vpmg_setPart:··bflag[BACK]·=·0465 Vpmg_setPart:··bflag[BACK]·=·0
466 Vpmg_setPart:··bflag[LEFT]·=·0466 Vpmg_setPart:··bflag[LEFT]·=·0
467 Vpmg_setPart:··bflag[RIGHT]·=·0467 Vpmg_setPart:··bflag[RIGHT]·=·0
468 Vpmg_setPart:··bflag[UP]·=·0468 Vpmg_setPart:··bflag[UP]·=·0
469 Vpmg_setPart:··bflag[DOWN]·=·0469 Vpmg_setPart:··bflag[DOWN]·=·0
Max diff block lines reached; 57170/64089 bytes (89.20%) of diff not shown.
⊟
8.74 KB
./usr/share/apbs/examples/ion-pmf/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:36:09·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:15:35·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·ion-pmf.pdb9 NOsh:·Storing·molecule·0·path·ion-pmf.pdb
Offset 161, 28 lines modifiedOffset 161, 28 lines modified
161 Vpmg_fillco:··filling·in·source·term.161 Vpmg_fillco:··filling·in·source·term.
162 Vpmg_fillco:··marking·ion·and·solvent·accessibility.162 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
163 fillcoCoef:··Calling·fillcoCoefSpline...163 fillcoCoef:··Calling·fillcoCoefSpline...
164 Vpmg_fillco:··filling·coefficient·arrays164 Vpmg_fillco:··filling·coefficient·arrays
165 Vpmg_fillco:··done·filling·coefficient·arrays165 Vpmg_fillco:··done·filling·coefficient·arrays
166 Vpmg_fillco:··filling·boundary·arrays166 Vpmg_fillco:··filling·boundary·arrays
167 Vpmg_fillco:··done·filling·boundary·arrays167 Vpmg_fillco:··done·filling·boundary·arrays
168 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·4.088900e-02168 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.580000e-02
169 Vnm_tstart:·starting·timer·28·(Solver·timer)..169 Vnm_tstart:·starting·timer·28·(Solver·timer)..
170 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..170 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
171 Vbuildops:·Fine:·(065,·065,·065)171 Vbuildops:·Fine:·(065,·065,·065)
172 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)172 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
173 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.945000e-02173 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.325300e-02
174 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..174 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
175 Vbuildops:·Galer:·(033,·033,·033)175 Vbuildops:·Galer:·(033,·033,·033)
176 Vbuildops:·Galer:·(017,·017,·017)176 Vbuildops:·Galer:·(017,·017,·017)
177 Vbuildops:·Galer:·(009,·009,·009)177 Vbuildops:·Galer:·(009,·009,·009)
178 Vbuildops:·Galer:·(005,·005,·005)178 Vbuildops:·Galer:·(005,·005,·005)
179 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.240230e-01179 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.930340e-01
180 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..180 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
181 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.615970e-01181 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.429830e-01
182 Vprtstp:·iteration·=·0182 Vprtstp:·iteration·=·0
183 Vprtstp:·relative·residual·=·1.000000e+00183 Vprtstp:·relative·residual·=·1.000000e+00
184 Vprtstp:·contraction·number·=·1.000000e+00184 Vprtstp:·contraction·number·=·1.000000e+00
185 Vprtstp:·iteration·=·1185 Vprtstp:·iteration·=·1
186 Vprtstp:·relative·residual·=·1.194542e-01186 Vprtstp:·relative·residual·=·1.194542e-01
187 Vprtstp:·contraction·number·=·1.194542e-01187 Vprtstp:·contraction·number·=·1.194542e-01
188 Vprtstp:·iteration·=·2188 Vprtstp:·iteration·=·2
Offset 202, 33 lines modifiedOffset 202, 33 lines modified
202 Vprtstp:·contraction·number·=·1.749569e-01202 Vprtstp:·contraction·number·=·1.749569e-01
203 Vprtstp:·iteration·=·7203 Vprtstp:·iteration·=·7
204 Vprtstp:·relative·residual·=·1.117484e-06204 Vprtstp:·relative·residual·=·1.117484e-06
205 Vprtstp:·contraction·number·=·1.874072e-01205 Vprtstp:·contraction·number·=·1.874072e-01
206 Vprtstp:·iteration·=·8206 Vprtstp:·iteration·=·8
207 Vprtstp:·relative·residual·=·2.180018e-07207 Vprtstp:·relative·residual·=·2.180018e-07
208 Vprtstp:·contraction·number·=·1.950826e-01208 Vprtstp:·contraction·number·=·1.950826e-01
209 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.955718e+00209 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.598426e+00
210 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.154469e+00210 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.882163e+00
211 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)211 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)
212 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)212 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)
213 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)213 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)
214 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)214 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)
215 Vpmg_setPart:··bflag[FRONT]·=·0215 Vpmg_setPart:··bflag[FRONT]·=·0
216 Vpmg_setPart:··bflag[BACK]·=·0216 Vpmg_setPart:··bflag[BACK]·=·0
217 Vpmg_setPart:··bflag[LEFT]·=·0217 Vpmg_setPart:··bflag[LEFT]·=·0
218 Vpmg_setPart:··bflag[RIGHT]·=·0218 Vpmg_setPart:··bflag[RIGHT]·=·0
219 Vpmg_setPart:··bflag[UP]·=·0219 Vpmg_setPart:··bflag[UP]·=·0
220 Vpmg_setPart:··bflag[DOWN]·=·0220 Vpmg_setPart:··bflag[DOWN]·=·0
221 Vnm_tstart:·starting·timer·29·(Energy·timer)..221 Vnm_tstart:·starting·timer·29·(Energy·timer)..
222 Vpmg_energy:··calculating·only·q-phi·energy222 Vpmg_energy:··calculating·only·q-phi·energy
223 Vpmg_qfEnergyVolume:··Calculating·energy223 Vpmg_qfEnergyVolume:··Calculating·energy
224 Vpmg_energy:··qfEnergy·=·6.324828953427E+03·kT224 Vpmg_energy:··qfEnergy·=·6.324828953427E+03·kT
225 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·2.010000e-03225 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·2.280000e-03
226 Vnm_tstart:·starting·timer·30·(Force·timer)..226 Vnm_tstart:·starting·timer·30·(Force·timer)..
227 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·2.682600e-02227 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·2.812700e-02
228 Vnm_tstart:·starting·timer·27·(Setup·timer)..228 Vnm_tstart:·starting·timer·27·(Setup·timer)..
229 Setting·up·PBE·object...229 Setting·up·PBE·object...
230 Vpbe_ctor2:··solute·radius·=·4230 Vpbe_ctor2:··solute·radius·=·4
231 Vpbe_ctor2:··solute·dimensions·=·8·x·4·x·4231 Vpbe_ctor2:··solute·dimensions·=·8·x·4·x·4
232 Vpbe_ctor2:··solute·charge·=·2232 Vpbe_ctor2:··solute·charge·=·2
233 Vpbe_ctor2:··bulk·ionic·strength·=·0233 Vpbe_ctor2:··bulk·ionic·strength·=·0
234 Vpbe_ctor2:··xkappa·=·0234 Vpbe_ctor2:··xkappa·=·0
Offset 249, 28 lines modifiedOffset 249, 28 lines modified
249 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1249 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
250 Setting·PDE·center·to·local·center...250 Setting·PDE·center·to·local·center...
251 Vpmg_fillco:··filling·in·source·term.251 Vpmg_fillco:··filling·in·source·term.
252 fillcoCharge:··Calling·fillcoChargeSpline2...252 fillcoCharge:··Calling·fillcoChargeSpline2...
253 Vpmg_fillco:··filling·in·source·term.253 Vpmg_fillco:··filling·in·source·term.
254 Vpmg_fillco:··filling·boundary·arrays254 Vpmg_fillco:··filling·boundary·arrays
255 Vpmg_fillco:··done·filling·boundary·arrays255 Vpmg_fillco:··done·filling·boundary·arrays
256 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.739600e-02256 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.471500e-02
257 Vnm_tstart:·starting·timer·28·(Solver·timer)..257 Vnm_tstart:·starting·timer·28·(Solver·timer)..
258 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..258 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
259 Vbuildops:·Fine:·(065,·065,·065)259 Vbuildops:·Fine:·(065,·065,·065)
260 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)260 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
261 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.946000e-02261 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.043200e-02
262 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..262 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
263 Vbuildops:·Galer:·(033,·033,·033)263 Vbuildops:·Galer:·(033,·033,·033)
264 Vbuildops:·Galer:·(017,·017,·017)264 Vbuildops:·Galer:·(017,·017,·017)
265 Vbuildops:·Galer:·(009,·009,·009)265 Vbuildops:·Galer:·(009,·009,·009)
266 Vbuildops:·Galer:·(005,·005,·005)266 Vbuildops:·Galer:·(005,·005,·005)
267 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.240540e-01267 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.865240e-01
268 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..268 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
269 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.489124e+00269 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.289743e+00
270 Vprtstp:·iteration·=·0270 Vprtstp:·iteration·=·0
271 Vprtstp:·relative·residual·=·1.000000e+00271 Vprtstp:·relative·residual·=·1.000000e+00
272 Vprtstp:·contraction·number·=·1.000000e+00272 Vprtstp:·contraction·number·=·1.000000e+00
273 Vprtstp:·iteration·=·1273 Vprtstp:·iteration·=·1
274 Vprtstp:·relative·residual·=·1.110640e-01274 Vprtstp:·relative·residual·=·1.110640e-01
275 Vprtstp:·contraction·number·=·1.110640e-01275 Vprtstp:·contraction·number·=·1.110640e-01
276 Vprtstp:·iteration·=·2276 Vprtstp:·iteration·=·2
Offset 287, 50 lines modifiedOffset 287, 50 lines modified
287 Vprtstp:·contraction·number·=·1.067494e-01287 Vprtstp:·contraction·number·=·1.067494e-01
288 Vprtstp:·iteration·=·6288 Vprtstp:·iteration·=·6
289 Vprtstp:·relative·residual·=·1.466502e-06289 Vprtstp:·relative·residual·=·1.466502e-06
290 Vprtstp:·contraction·number·=·1.074548e-01290 Vprtstp:·contraction·number·=·1.074548e-01
291 Vprtstp:·iteration·=·7291 Vprtstp:·iteration·=·7
292 Vprtstp:·relative·residual·=·1.584103e-07292 Vprtstp:·relative·residual·=·1.584103e-07
293 Vprtstp:·contraction·number·=·1.080191e-01293 Vprtstp:·contraction·number·=·1.080191e-01
294 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.710915e+00294 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.267616e+00
295 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·1.907710e+00295 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.540554e+00
296 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)296 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)
297 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)297 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)
298 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)298 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)
299 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)299 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)
300 Vpmg_setPart:··bflag[FRONT]·=·0300 Vpmg_setPart:··bflag[FRONT]·=·0
301 Vpmg_setPart:··bflag[BACK]·=·0301 Vpmg_setPart:··bflag[BACK]·=·0
302 Vpmg_setPart:··bflag[LEFT]·=·0302 Vpmg_setPart:··bflag[LEFT]·=·0
303 Vpmg_setPart:··bflag[RIGHT]·=·0303 Vpmg_setPart:··bflag[RIGHT]·=·0
304 Vpmg_setPart:··bflag[UP]·=·0304 Vpmg_setPart:··bflag[UP]·=·0
305 Vpmg_setPart:··bflag[DOWN]·=·0305 Vpmg_setPart:··bflag[DOWN]·=·0
306 Vnm_tstart:·starting·timer·29·(Energy·timer)..306 Vnm_tstart:·starting·timer·29·(Energy·timer)..
307 Vpmg_energy:··calculating·only·q-phi·energy307 Vpmg_energy:··calculating·only·q-phi·energy
308 Vpmg_qfEnergyVolume:··Calculating·energy308 Vpmg_qfEnergyVolume:··Calculating·energy
309 Vpmg_energy:··qfEnergy·=·7.232617942545E+03·kT309 Vpmg_energy:··qfEnergy·=·7.232617942545E+03·kT
310 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.931000e-03310 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·2.442000e-03
Max diff block lines reached; 1991/8871 bytes (22.44%) of diff not shown.
⊟
81.6 KB
./usr/share/apbs/examples/ionize/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:35:42·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:14:08·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·acetic-acid.xml9 NOsh:·Storing·molecule·0·path·acetic-acid.xml
Offset 481, 32 lines modifiedOffset 481, 32 lines modified
481 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1481 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
482 Setting·PDE·center·to·local·center...482 Setting·PDE·center·to·local·center...
483 Vpmg_fillco:··filling·in·source·term.483 Vpmg_fillco:··filling·in·source·term.
484 fillcoCharge:··Calling·fillcoChargeSpline1...484 fillcoCharge:··Calling·fillcoChargeSpline1...
485 Vpmg_fillco:··filling·in·source·term.485 Vpmg_fillco:··filling·in·source·term.
486 Vpmg_fillco:··marking·ion·and·solvent·accessibility.486 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
487 fillcoCoef:··Calling·fillcoCoefMol...487 fillcoCoef:··Calling·fillcoCoefMol...
488 Vacc_SASA:·Time·elapsed:·0.007433488 Vacc_SASA:·Time·elapsed:·0.004390
489 Vpmg_fillco:··done·filling·coefficient·arrays489 Vpmg_fillco:··done·filling·coefficient·arrays
490 Vpmg_fillco:··filling·boundary·arrays490 Vpmg_fillco:··filling·boundary·arrays
491 Vpmg_fillco:··done·filling·boundary·arrays491 Vpmg_fillco:··done·filling·boundary·arrays
492 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·6.223500e-02492 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·5.114500e-02
493 Vnm_tstart:·starting·timer·28·(Solver·timer)..493 Vnm_tstart:·starting·timer·28·(Solver·timer)..
494 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..494 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
495 Vbuildops:·Fine:·(065,·065,·065)495 Vbuildops:·Fine:·(065,·065,·065)
496 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)496 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
497 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.799100e-02497 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.173600e-02
498 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..498 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
499 Vbuildops:·Galer:·(033,·033,·033)499 Vbuildops:·Galer:·(033,·033,·033)
500 Vbuildops:·Galer:·(017,·017,·017)500 Vbuildops:·Galer:·(017,·017,·017)
501 Vbuildops:·Galer:·(009,·009,·009)501 Vbuildops:·Galer:·(009,·009,·009)
502 Vbuildops:·Galer:·(005,·005,·005)502 Vbuildops:·Galer:·(005,·005,·005)
503 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.526800e-01503 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.837510e-01
504 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..504 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
505 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.598510e-01505 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.538720e-01
506 Vprtstp:·iteration·=·0506 Vprtstp:·iteration·=·0
507 Vprtstp:·relative·residual·=·1.000000e+00507 Vprtstp:·relative·residual·=·1.000000e+00
508 Vprtstp:·contraction·number·=·1.000000e+00508 Vprtstp:·contraction·number·=·1.000000e+00
509 Vprtstp:·iteration·=·1509 Vprtstp:·iteration·=·1
510 Vprtstp:·relative·residual·=·3.188999e-01510 Vprtstp:·relative·residual·=·3.188999e-01
511 Vprtstp:·contraction·number·=·3.188999e-01511 Vprtstp:·contraction·number·=·3.188999e-01
512 Vprtstp:·iteration·=·2512 Vprtstp:·iteration·=·2
Offset 535, 30 lines modifiedOffset 535, 30 lines modified
535 Vprtstp:·contraction·number·=·2.912126e-01535 Vprtstp:·contraction·number·=·2.912126e-01
536 Vprtstp:·iteration·=·10536 Vprtstp:·iteration·=·10
537 Vprtstp:·relative·residual·=·2.816386e-06537 Vprtstp:·relative·residual·=·2.816386e-06
538 Vprtstp:·contraction·number·=·2.924708e-01538 Vprtstp:·contraction·number·=·2.924708e-01
539 Vprtstp:·iteration·=·11539 Vprtstp:·iteration·=·11
540 Vprtstp:·relative·residual·=·8.271441e-07540 Vprtstp:·relative·residual·=·8.271441e-07
541 Vprtstp:·contraction·number·=·2.936899e-01541 Vprtstp:·contraction·number·=·2.936899e-01
542 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.653586e+00542 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·3.403729e+00
543 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.915379e+00543 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.674656e+00
544 Vpmg_setPart:··lower·corner·=·(-6,·-6.1535,·-4.713)544 Vpmg_setPart:··lower·corner·=·(-6,·-6.1535,·-4.713)
545 Vpmg_setPart:··upper·corner·=·(6,·5.8465,·7.287)545 Vpmg_setPart:··upper·corner·=·(6,·5.8465,·7.287)
546 Vpmg_setPart:··actual·minima·=·(-6,·-6.1535,·-4.713)546 Vpmg_setPart:··actual·minima·=·(-6,·-6.1535,·-4.713)
547 Vpmg_setPart:··actual·maxima·=·(6,·5.8465,·7.287)547 Vpmg_setPart:··actual·maxima·=·(6,·5.8465,·7.287)
548 Vpmg_setPart:··bflag[FRONT]·=·0548 Vpmg_setPart:··bflag[FRONT]·=·0
549 Vpmg_setPart:··bflag[BACK]·=·0549 Vpmg_setPart:··bflag[BACK]·=·0
550 Vpmg_setPart:··bflag[LEFT]·=·0550 Vpmg_setPart:··bflag[LEFT]·=·0
551 Vpmg_setPart:··bflag[RIGHT]·=·0551 Vpmg_setPart:··bflag[RIGHT]·=·0
552 Vpmg_setPart:··bflag[UP]·=·0552 Vpmg_setPart:··bflag[UP]·=·0
553 Vpmg_setPart:··bflag[DOWN]·=·0553 Vpmg_setPart:··bflag[DOWN]·=·0
554 Vnm_tstart:·starting·timer·29·(Energy·timer)..554 Vnm_tstart:·starting·timer·29·(Energy·timer)..
555 Vpmg_energy:··calculating·only·q-phi·energy555 Vpmg_energy:··calculating·only·q-phi·energy
556 Vpmg_energy:··qfEnergy·=·4.781227236323E+03·kT556 Vpmg_energy:··qfEnergy·=·4.781227236323E+03·kT
557 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.320000e-04557 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·8.500000e-05
558 Vnm_tstart:·starting·timer·30·(Force·timer)..558 Vnm_tstart:·starting·timer·30·(Force·timer)..
559 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·5.000000e-06559 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·5.000000e-06
560 Vnm_tstart:·starting·timer·27·(Setup·timer)..560 Vnm_tstart:·starting·timer·27·(Setup·timer)..
561 Setting·up·PBE·object...561 Setting·up·PBE·object...
562 Vpbe_ctor2:··solute·radius·=·3.17612562 Vpbe_ctor2:··solute·radius·=·3.17612
563 Vpbe_ctor2:··solute·dimensions·=·4.116·x·5.186·x·5.967563 Vpbe_ctor2:··solute·dimensions·=·4.116·x·5.186·x·5.967
564 Vpbe_ctor2:··solute·charge·=·-1.66533e-16564 Vpbe_ctor2:··solute·charge·=·-1.66533e-16
Offset 606, 30 lines modifiedOffset 606, 30 lines modified
606 VPMG::extEnergy:·extQfEnergy·=·0·kT606 VPMG::extEnergy:·extQfEnergy·=·0·kT
607 VPMG::extEnergy:·extDiEnergy·=·0.0505207·kT607 VPMG::extEnergy:·extDiEnergy·=·0.0505207·kT
608 Vpmg_fillco:··filling·in·source·term.608 Vpmg_fillco:··filling·in·source·term.
609 fillcoCharge:··Calling·fillcoChargeSpline1...609 fillcoCharge:··Calling·fillcoChargeSpline1...
610 Vpmg_fillco:··filling·in·source·term.610 Vpmg_fillco:··filling·in·source·term.
611 Vpmg_fillco:··marking·ion·and·solvent·accessibility.611 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
612 fillcoCoef:··Calling·fillcoCoefMol...612 fillcoCoef:··Calling·fillcoCoefMol...
613 Vacc_SASA:·Time·elapsed:·0.005124613 Vacc_SASA:·Time·elapsed:·0.003822
614 Vpmg_fillco:··done·filling·coefficient·arrays614 Vpmg_fillco:··done·filling·coefficient·arrays
615 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.054100e-01615 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.011260e-01
616 Vnm_tstart:·starting·timer·28·(Solver·timer)..616 Vnm_tstart:·starting·timer·28·(Solver·timer)..
617 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..617 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
618 Vbuildops:·Fine:·(065,·065,·065)618 Vbuildops:·Fine:·(065,·065,·065)
619 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)619 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
620 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.859400e-02620 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.222700e-02
621 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..621 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
622 Vbuildops:·Galer:·(033,·033,·033)622 Vbuildops:·Galer:·(033,·033,·033)
623 Vbuildops:·Galer:·(017,·017,·017)623 Vbuildops:·Galer:·(017,·017,·017)
624 Vbuildops:·Galer:·(009,·009,·009)624 Vbuildops:·Galer:·(009,·009,·009)
625 Vbuildops:·Galer:·(005,·005,·005)625 Vbuildops:·Galer:·(005,·005,·005)
626 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.237600e-01626 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.807040e-01
627 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..627 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
628 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.326618e+00628 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·4.139248e+00
629 Vprtstp:·iteration·=·0629 Vprtstp:·iteration·=·0
630 Vprtstp:·relative·residual·=·1.000000e+00630 Vprtstp:·relative·residual·=·1.000000e+00
631 Vprtstp:·contraction·number·=·1.000000e+00631 Vprtstp:·contraction·number·=·1.000000e+00
632 Vprtstp:·iteration·=·1632 Vprtstp:·iteration·=·1
633 Vprtstp:·relative·residual·=·2.598074e-01633 Vprtstp:·relative·residual·=·2.598074e-01
634 Vprtstp:·contraction·number·=·2.598074e-01634 Vprtstp:·contraction·number·=·2.598074e-01
635 Vprtstp:·iteration·=·2635 Vprtstp:·iteration·=·2
Offset 661, 32 lines modifiedOffset 661, 32 lines modified
661 Vprtstp:·contraction·number·=·3.326351e-01661 Vprtstp:·contraction·number·=·3.326351e-01
662 Vprtstp:·iteration·=·11662 Vprtstp:·iteration·=·11
663 Vprtstp:·relative·residual·=·2.087103e-06663 Vprtstp:·relative·residual·=·2.087103e-06
664 Vprtstp:·contraction·number·=·3.343120e-01664 Vprtstp:·contraction·number·=·3.343120e-01
665 Vprtstp:·iteration·=·12665 Vprtstp:·iteration·=·12
666 Vprtstp:·relative·residual·=·7.014192e-07666 Vprtstp:·relative·residual·=·7.014192e-07
667 Vprtstp:·contraction·number·=·3.360731e-01667 Vprtstp:·contraction·number·=·3.360731e-01
668 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.899303e+00668 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·3.762945e+00
669 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.098562e+00669 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·4.033274e+00
670 Vpmg_setPart:··lower·corner·=·(-3,·-3.1535,·-1.713)670 Vpmg_setPart:··lower·corner·=·(-3,·-3.1535,·-1.713)
671 Vpmg_setPart:··upper·corner·=·(3,·2.8465,·4.287)671 Vpmg_setPart:··upper·corner·=·(3,·2.8465,·4.287)
672 Vpmg_setPart:··actual·minima·=·(-3,·-3.1535,·-1.713)672 Vpmg_setPart:··actual·minima·=·(-3,·-3.1535,·-1.713)
673 Vpmg_setPart:··actual·maxima·=·(3,·2.8465,·4.287)673 Vpmg_setPart:··actual·maxima·=·(3,·2.8465,·4.287)
674 Vpmg_setPart:··bflag[FRONT]·=·0674 Vpmg_setPart:··bflag[FRONT]·=·0
675 Vpmg_setPart:··bflag[BACK]·=·0675 Vpmg_setPart:··bflag[BACK]·=·0
676 Vpmg_setPart:··bflag[LEFT]·=·0676 Vpmg_setPart:··bflag[LEFT]·=·0
677 Vpmg_setPart:··bflag[RIGHT]·=·0677 Vpmg_setPart:··bflag[RIGHT]·=·0
678 Vpmg_setPart:··bflag[UP]·=·0678 Vpmg_setPart:··bflag[UP]·=·0
679 Vpmg_setPart:··bflag[DOWN]·=·0679 Vpmg_setPart:··bflag[DOWN]·=·0
680 Vnm_tstart:·starting·timer·29·(Energy·timer)..680 Vnm_tstart:·starting·timer·29·(Energy·timer)..
681 Vpmg_energy:··calculating·only·q-phi·energy681 Vpmg_energy:··calculating·only·q-phi·energy
Max diff block lines reached; 76665/83496 bytes (91.82%) of diff not shown.
⊟
83.1 KB
./usr/share/apbs/examples/pka-lig/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:36:47·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:16:45·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·bx6_7_lig_apbs.pqr9 NOsh:·Storing·molecule·0·path·bx6_7_lig_apbs.pqr
Offset 340, 31 lines modifiedOffset 340, 31 lines modified
340 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1340 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
341 Setting·PDE·center·to·local·center...341 Setting·PDE·center·to·local·center...
342 Vpmg_fillco:··filling·in·source·term.342 Vpmg_fillco:··filling·in·source·term.
343 fillcoCharge:··Calling·fillcoChargeSpline1...343 fillcoCharge:··Calling·fillcoChargeSpline1...
344 Vpmg_fillco:··filling·in·source·term.344 Vpmg_fillco:··filling·in·source·term.
345 Vpmg_fillco:··marking·ion·and·solvent·accessibility.345 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
346 fillcoCoef:··Calling·fillcoCoefMol...346 fillcoCoef:··Calling·fillcoCoefMol...
347 Vacc_SASA:·Time·elapsed:·0.041508347 Vacc_SASA:·Time·elapsed:·0.039790
348 Vpmg_fillco:··done·filling·coefficient·arrays348 Vpmg_fillco:··done·filling·coefficient·arrays
349 Vpmg_fillco:··filling·boundary·arrays349 Vpmg_fillco:··filling·boundary·arrays
350 Vpmg_fillco:··done·filling·boundary·arrays350 Vpmg_fillco:··done·filling·boundary·arrays
351 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.038970e-01351 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·9.719500e-02
352 Vnm_tstart:·starting·timer·28·(Solver·timer)..352 Vnm_tstart:·starting·timer·28·(Solver·timer)..
353 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..353 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
354 Vbuildops:·Fine:·(097,·097,·097)354 Vbuildops:·Fine:·(097,·097,·097)
355 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)355 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
356 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·1.614520e-01356 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·1.686350e-01
357 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..357 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
358 Vbuildops:·Galer:·(049,·049,·049)358 Vbuildops:·Galer:·(049,·049,·049)
359 Vbuildops:·Galer:·(025,·025,·025)359 Vbuildops:·Galer:·(025,·025,·025)
360 Vbuildops:·Galer:·(013,·013,·013)360 Vbuildops:·Galer:·(013,·013,·013)
361 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·5.474610e-01361 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·6.225350e-01
362 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..362 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
363 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.111041e+00363 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.191868e+00
364 Vprtstp:·iteration·=·0364 Vprtstp:·iteration·=·0
365 Vprtstp:·relative·residual·=·1.000000e+00365 Vprtstp:·relative·residual·=·1.000000e+00
366 Vprtstp:·contraction·number·=·1.000000e+00366 Vprtstp:·contraction·number·=·1.000000e+00
367 Vprtstp:·iteration·=·1367 Vprtstp:·iteration·=·1
368 Vprtstp:·relative·residual·=·1.561608e-01368 Vprtstp:·relative·residual·=·1.561608e-01
369 Vprtstp:·contraction·number·=·1.561608e-01369 Vprtstp:·contraction·number·=·1.561608e-01
370 Vprtstp:·iteration·=·2370 Vprtstp:·iteration·=·2
Offset 390, 32 lines modifiedOffset 390, 32 lines modified
390 Vprtstp:·contraction·number·=·2.750705e-01390 Vprtstp:·contraction·number·=·2.750705e-01
391 Vprtstp:·iteration·=·9391 Vprtstp:·iteration·=·9
392 Vprtstp:·relative·residual·=·1.932473e-06392 Vprtstp:·relative·residual·=·1.932473e-06
393 Vprtstp:·contraction·number·=·2.767817e-01393 Vprtstp:·contraction·number·=·2.767817e-01
394 Vprtstp:·iteration·=·10394 Vprtstp:·iteration·=·10
395 Vprtstp:·relative·residual·=·5.373027e-07395 Vprtstp:·relative·residual·=·5.373027e-07
396 Vprtstp:·contraction·number·=·2.780389e-01396 Vprtstp:·contraction·number·=·2.780389e-01
397 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·8.821031e+00397 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·8.629908e+00
398 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·9.595711e+00398 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·9.487422e+00
399 Vpmg_setPart:··lower·corner·=·(-6.031,·-67.507,·-7.978)399 Vpmg_setPart:··lower·corner·=·(-6.031,·-67.507,·-7.978)
400 Vpmg_setPart:··upper·corner·=·(63.969,·2.493,·62.022)400 Vpmg_setPart:··upper·corner·=·(63.969,·2.493,·62.022)
401 Vpmg_setPart:··actual·minima·=·(-6.031,·-67.507,·-7.978)401 Vpmg_setPart:··actual·minima·=·(-6.031,·-67.507,·-7.978)
402 Vpmg_setPart:··actual·maxima·=·(63.969,·2.493,·62.022)402 Vpmg_setPart:··actual·maxima·=·(63.969,·2.493,·62.022)
403 Vpmg_setPart:··bflag[FRONT]·=·0403 Vpmg_setPart:··bflag[FRONT]·=·0
404 Vpmg_setPart:··bflag[BACK]·=·0404 Vpmg_setPart:··bflag[BACK]·=·0
405 Vpmg_setPart:··bflag[LEFT]·=·0405 Vpmg_setPart:··bflag[LEFT]·=·0
406 Vpmg_setPart:··bflag[RIGHT]·=·0406 Vpmg_setPart:··bflag[RIGHT]·=·0
407 Vpmg_setPart:··bflag[UP]·=·0407 Vpmg_setPart:··bflag[UP]·=·0
408 Vpmg_setPart:··bflag[DOWN]·=·0408 Vpmg_setPart:··bflag[DOWN]·=·0
409 Vnm_tstart:·starting·timer·29·(Energy·timer)..409 Vnm_tstart:·starting·timer·29·(Energy·timer)..
410 Vpmg_energy:··calculating·only·q-phi·energy410 Vpmg_energy:··calculating·only·q-phi·energy
411 Vpmg_energy:··qfEnergy·=·1.795090079491E+03·kT411 Vpmg_energy:··qfEnergy·=·1.795090079491E+03·kT
412 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.390000e-04412 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.430000e-04
413 Vnm_tstart:·starting·timer·30·(Force·timer)..413 Vnm_tstart:·starting·timer·30·(Force·timer)..
414 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·5.000000e-06414 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·4.000000e-06
415 Vnm_tstart:·starting·timer·27·(Setup·timer)..415 Vnm_tstart:·starting·timer·27·(Setup·timer)..
416 Setting·up·PBE·object...416 Setting·up·PBE·object...
417 Vpbe_ctor2:··solute·radius·=·10.66417 Vpbe_ctor2:··solute·radius·=·10.66
418 Vpbe_ctor2:··solute·dimensions·=·17.188·x·12.75·x·15.33418 Vpbe_ctor2:··solute·dimensions·=·17.188·x·12.75·x·15.33
419 Vpbe_ctor2:··solute·charge·=·1.11022e-16419 Vpbe_ctor2:··solute·charge·=·1.11022e-16
420 Vpbe_ctor2:··bulk·ionic·strength·=·0420 Vpbe_ctor2:··bulk·ionic·strength·=·0
421 Vpbe_ctor2:··xkappa·=·0421 Vpbe_ctor2:··xkappa·=·0
Offset 461, 29 lines modifiedOffset 461, 29 lines modified
461 VPMG::extEnergy:·extQfEnergy·=·0·kT461 VPMG::extEnergy:·extQfEnergy·=·0·kT
462 VPMG::extEnergy:·extDiEnergy·=·0.123733·kT462 VPMG::extEnergy:·extDiEnergy·=·0.123733·kT
463 Vpmg_fillco:··filling·in·source·term.463 Vpmg_fillco:··filling·in·source·term.
464 fillcoCharge:··Calling·fillcoChargeSpline1...464 fillcoCharge:··Calling·fillcoChargeSpline1...
465 Vpmg_fillco:··filling·in·source·term.465 Vpmg_fillco:··filling·in·source·term.
466 Vpmg_fillco:··marking·ion·and·solvent·accessibility.466 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
467 fillcoCoef:··Calling·fillcoCoefMol...467 fillcoCoef:··Calling·fillcoCoefMol...
468 Vacc_SASA:·Time·elapsed:·0.042025468 Vacc_SASA:·Time·elapsed:·0.037595
469 Vpmg_fillco:··done·filling·coefficient·arrays469 Vpmg_fillco:··done·filling·coefficient·arrays
470 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·2.646520e-01470 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·2.861110e-01
471 Vnm_tstart:·starting·timer·28·(Solver·timer)..471 Vnm_tstart:·starting·timer·28·(Solver·timer)..
472 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..472 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
473 Vbuildops:·Fine:·(097,·097,·097)473 Vbuildops:·Fine:·(097,·097,·097)
474 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)474 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
475 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·1.618140e-01475 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·1.689160e-01
476 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..476 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
477 Vbuildops:·Galer:·(049,·049,·049)477 Vbuildops:·Galer:·(049,·049,·049)
478 Vbuildops:·Galer:·(025,·025,·025)478 Vbuildops:·Galer:·(025,·025,·025)
479 Vbuildops:·Galer:·(013,·013,·013)479 Vbuildops:·Galer:·(013,·013,·013)
480 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·5.501780e-01480 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·6.044190e-01
481 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..481 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
482 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.099811e+01482 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.097681e+01
483 Vprtstp:·iteration·=·0483 Vprtstp:·iteration·=·0
484 Vprtstp:·relative·residual·=·1.000000e+00484 Vprtstp:·relative·residual·=·1.000000e+00
485 Vprtstp:·contraction·number·=·1.000000e+00485 Vprtstp:·contraction·number·=·1.000000e+00
486 Vprtstp:·iteration·=·1486 Vprtstp:·iteration·=·1
487 Vprtstp:·relative·residual·=·2.152775e-01487 Vprtstp:·relative·residual·=·2.152775e-01
488 Vprtstp:·contraction·number·=·2.152775e-01488 Vprtstp:·contraction·number·=·2.152775e-01
489 Vprtstp:·iteration·=·2489 Vprtstp:·iteration·=·2
Offset 515, 30 lines modifiedOffset 515, 30 lines modified
515 Vprtstp:·contraction·number·=·3.353090e-01515 Vprtstp:·contraction·number·=·3.353090e-01
516 Vprtstp:·iteration·=·11516 Vprtstp:·iteration·=·11
517 Vprtstp:·relative·residual·=·1.328976e-06517 Vprtstp:·relative·residual·=·1.328976e-06
518 Vprtstp:·contraction·number·=·3.371305e-01518 Vprtstp:·contraction·number·=·3.371305e-01
519 Vprtstp:·iteration·=·12519 Vprtstp:·iteration·=·12
520 Vprtstp:·relative·residual·=·4.496116e-07520 Vprtstp:·relative·residual·=·4.496116e-07
521 Vprtstp:·contraction·number·=·3.383143e-01521 Vprtstp:·contraction·number·=·3.383143e-01
522 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.039387e+01522 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.032714e+01
523 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·1.116875e+01523 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·1.116649e+01
524 Vpmg_setPart:··lower·corner·=·(12.822,·-45.153,·9.545)524 Vpmg_setPart:··lower·corner·=·(12.822,·-45.153,·9.545)
525 Vpmg_setPart:··upper·corner·=·(36.822,·-21.153,·33.545)525 Vpmg_setPart:··upper·corner·=·(36.822,·-21.153,·33.545)
526 Vpmg_setPart:··actual·minima·=·(12.822,·-45.153,·9.545)526 Vpmg_setPart:··actual·minima·=·(12.822,·-45.153,·9.545)
527 Vpmg_setPart:··actual·maxima·=·(36.822,·-21.153,·33.545)527 Vpmg_setPart:··actual·maxima·=·(36.822,·-21.153,·33.545)
528 Vpmg_setPart:··bflag[FRONT]·=·0528 Vpmg_setPart:··bflag[FRONT]·=·0
529 Vpmg_setPart:··bflag[BACK]·=·0529 Vpmg_setPart:··bflag[BACK]·=·0
530 Vpmg_setPart:··bflag[LEFT]·=·0530 Vpmg_setPart:··bflag[LEFT]·=·0
531 Vpmg_setPart:··bflag[RIGHT]·=·0531 Vpmg_setPart:··bflag[RIGHT]·=·0
532 Vpmg_setPart:··bflag[UP]·=·0532 Vpmg_setPart:··bflag[UP]·=·0
533 Vpmg_setPart:··bflag[DOWN]·=·0533 Vpmg_setPart:··bflag[DOWN]·=·0
534 Vnm_tstart:·starting·timer·29·(Energy·timer)..534 Vnm_tstart:·starting·timer·29·(Energy·timer)..
535 Vpmg_energy:··calculating·only·q-phi·energy535 Vpmg_energy:··calculating·only·q-phi·energy
Max diff block lines reached; 78043/84974 bytes (91.84%) of diff not shown.
⊟
41.4 KB
./usr/share/apbs/examples/point-pmf/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:40:07·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:23:59·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·mol0.pqr9 NOsh:·Storing·molecule·0·path·mol0.pqr
Offset 184, 28 lines modifiedOffset 184, 28 lines modified
184 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1184 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
185 Setting·PDE·center·to·local·center...185 Setting·PDE·center·to·local·center...
186 Vpmg_fillco:··filling·in·source·term.186 Vpmg_fillco:··filling·in·source·term.
187 fillcoCharge:··Calling·fillcoChargeSpline1...187 fillcoCharge:··Calling·fillcoChargeSpline1...
188 Vpmg_fillco:··filling·in·source·term.188 Vpmg_fillco:··filling·in·source·term.
189 Vpmg_fillco:··filling·boundary·arrays189 Vpmg_fillco:··filling·boundary·arrays
190 Vpmg_fillco:··done·filling·boundary·arrays190 Vpmg_fillco:··done·filling·boundary·arrays
191 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·2.982100e-02191 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.932500e-02
192 Vnm_tstart:·starting·timer·28·(Solver·timer)..192 Vnm_tstart:·starting·timer·28·(Solver·timer)..
193 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..193 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
194 Vbuildops:·Fine:·(065,·065,·065)194 Vbuildops:·Fine:·(065,·065,·065)
195 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)195 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
196 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.087200e-02196 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.769600e-02
197 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..197 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
198 Vbuildops:·Galer:·(033,·033,·033)198 Vbuildops:·Galer:·(033,·033,·033)
199 Vbuildops:·Galer:·(017,·017,·017)199 Vbuildops:·Galer:·(017,·017,·017)
200 Vbuildops:·Galer:·(009,·009,·009)200 Vbuildops:·Galer:·(009,·009,·009)
201 Vbuildops:·Galer:·(005,·005,·005)201 Vbuildops:·Galer:·(005,·005,·005)
202 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.229660e-01202 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.726230e-01
203 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..203 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
204 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.492990e-01204 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.958360e-01
205 Vprtstp:·iteration·=·0205 Vprtstp:·iteration·=·0
206 Vprtstp:·relative·residual·=·1.000000e+00206 Vprtstp:·relative·residual·=·1.000000e+00
207 Vprtstp:·contraction·number·=·1.000000e+00207 Vprtstp:·contraction·number·=·1.000000e+00
208 Vprtstp:·iteration·=·1208 Vprtstp:·iteration·=·1
209 Vprtstp:·relative·residual·=·1.117158e-01209 Vprtstp:·relative·residual·=·1.117158e-01
210 Vprtstp:·contraction·number·=·1.117158e-01210 Vprtstp:·contraction·number·=·1.117158e-01
211 Vprtstp:·iteration·=·2211 Vprtstp:·iteration·=·2
Offset 222, 33 lines modifiedOffset 222, 33 lines modified
222 Vprtstp:·contraction·number·=·1.067217e-01222 Vprtstp:·contraction·number·=·1.067217e-01
223 Vprtstp:·iteration·=·6223 Vprtstp:·iteration·=·6
224 Vprtstp:·relative·residual·=·1.472908e-06224 Vprtstp:·relative·residual·=·1.472908e-06
225 Vprtstp:·contraction·number·=·1.074130e-01225 Vprtstp:·contraction·number·=·1.074130e-01
226 Vprtstp:·iteration·=·7226 Vprtstp:·iteration·=·7
227 Vprtstp:·relative·residual·=·1.590269e-07227 Vprtstp:·relative·residual·=·1.590269e-07
228 Vprtstp:·contraction·number·=·1.079680e-01228 Vprtstp:·contraction·number·=·1.079680e-01
229 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.708286e+00229 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.201098e+00
230 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·1.903418e+00230 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.453404e+00
231 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)231 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)
232 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)232 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)
233 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)233 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)
234 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)234 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)
235 Vpmg_setPart:··bflag[FRONT]·=·0235 Vpmg_setPart:··bflag[FRONT]·=·0
236 Vpmg_setPart:··bflag[BACK]·=·0236 Vpmg_setPart:··bflag[BACK]·=·0
237 Vpmg_setPart:··bflag[LEFT]·=·0237 Vpmg_setPart:··bflag[LEFT]·=·0
238 Vpmg_setPart:··bflag[RIGHT]·=·0238 Vpmg_setPart:··bflag[RIGHT]·=·0
239 Vpmg_setPart:··bflag[UP]·=·0239 Vpmg_setPart:··bflag[UP]·=·0
240 Vpmg_setPart:··bflag[DOWN]·=·0240 Vpmg_setPart:··bflag[DOWN]·=·0
241 Vnm_tstart:·starting·timer·29·(Energy·timer)..241 Vnm_tstart:·starting·timer·29·(Energy·timer)..
242 Vpmg_energy:··calculating·only·q-phi·energy242 Vpmg_energy:··calculating·only·q-phi·energy
243 Vpmg_energy:··qfEnergy·=·7.887170085535E+01·kT243 Vpmg_energy:··qfEnergy·=·7.887170085535E+01·kT
244 Vpmg_qmEnergy:··Zero·energy·for·zero·ionic·strength!244 Vpmg_qmEnergy:··Zero·energy·for·zero·ionic·strength!
245 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.691000e-02245 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.750100e-02
246 Vnm_tstart:·starting·timer·30·(Force·timer)..246 Vnm_tstart:·starting·timer·30·(Force·timer)..
247 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·3.000000e-06247 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·5.000000e-06
248 Vnm_tstart:·starting·timer·27·(Setup·timer)..248 Vnm_tstart:·starting·timer·27·(Setup·timer)..
249 Setting·up·PBE·object...249 Setting·up·PBE·object...
250 Vpbe_ctor2:··solute·radius·=·0250 Vpbe_ctor2:··solute·radius·=·0
251 Vpbe_ctor2:··solute·dimensions·=·0·x·0·x·0251 Vpbe_ctor2:··solute·dimensions·=·0·x·0·x·0
252 Vpbe_ctor2:··solute·charge·=·1252 Vpbe_ctor2:··solute·charge·=·1
253 Vpbe_ctor2:··bulk·ionic·strength·=·0253 Vpbe_ctor2:··bulk·ionic·strength·=·0
254 Vpbe_ctor2:··xkappa·=·0254 Vpbe_ctor2:··xkappa·=·0
Offset 269, 28 lines modifiedOffset 269, 28 lines modified
269 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1269 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
270 Setting·PDE·center·to·local·center...270 Setting·PDE·center·to·local·center...
271 Vpmg_fillco:··filling·in·source·term.271 Vpmg_fillco:··filling·in·source·term.
272 fillcoCharge:··Calling·fillcoChargeSpline1...272 fillcoCharge:··Calling·fillcoChargeSpline1...
273 Vpmg_fillco:··filling·in·source·term.273 Vpmg_fillco:··filling·in·source·term.
274 Vpmg_fillco:··filling·boundary·arrays274 Vpmg_fillco:··filling·boundary·arrays
275 Vpmg_fillco:··done·filling·boundary·arrays275 Vpmg_fillco:··done·filling·boundary·arrays
276 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.975500e-02276 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.041000e-02
277 Vnm_tstart:·starting·timer·28·(Solver·timer)..277 Vnm_tstart:·starting·timer·28·(Solver·timer)..
278 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..278 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
279 Vbuildops:·Fine:·(065,·065,·065)279 Vbuildops:·Fine:·(065,·065,·065)
280 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)280 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
281 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.921400e-02281 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·5.233500e-02
282 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..282 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
283 Vbuildops:·Galer:·(033,·033,·033)283 Vbuildops:·Galer:·(033,·033,·033)
284 Vbuildops:·Galer:·(017,·017,·017)284 Vbuildops:·Galer:·(017,·017,·017)
285 Vbuildops:·Galer:·(009,·009,·009)285 Vbuildops:·Galer:·(009,·009,·009)
286 Vbuildops:·Galer:·(005,·005,·005)286 Vbuildops:·Galer:·(005,·005,·005)
287 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.261070e-01287 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.894470e-01
288 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..288 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
289 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.227632e+00289 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.833041e+00
290 Vprtstp:·iteration·=·0290 Vprtstp:·iteration·=·0
291 Vprtstp:·relative·residual·=·1.000000e+00291 Vprtstp:·relative·residual·=·1.000000e+00
292 Vprtstp:·contraction·number·=·1.000000e+00292 Vprtstp:·contraction·number·=·1.000000e+00
293 Vprtstp:·iteration·=·1293 Vprtstp:·iteration·=·1
294 Vprtstp:·relative·residual·=·1.116487e-01294 Vprtstp:·relative·residual·=·1.116487e-01
295 Vprtstp:·contraction·number·=·1.116487e-01295 Vprtstp:·contraction·number·=·1.116487e-01
296 Vprtstp:·iteration·=·2296 Vprtstp:·iteration·=·2
Offset 307, 33 lines modifiedOffset 307, 33 lines modified
307 Vprtstp:·contraction·number·=·1.068390e-01307 Vprtstp:·contraction·number·=·1.068390e-01
308 Vprtstp:·iteration·=·6308 Vprtstp:·iteration·=·6
309 Vprtstp:·relative·residual·=·1.476968e-06309 Vprtstp:·relative·residual·=·1.476968e-06
310 Vprtstp:·contraction·number·=·1.075610e-01310 Vprtstp:·contraction·number·=·1.075610e-01
311 Vprtstp:·iteration·=·7311 Vprtstp:·iteration·=·7
312 Vprtstp:·relative·residual·=·1.596976e-07312 Vprtstp:·relative·residual·=·1.596976e-07
313 Vprtstp:·contraction·number·=·1.081253e-01313 Vprtstp:·contraction·number·=·1.081253e-01
314 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.680020e+00314 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.283497e+00
315 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·1.884697e+00315 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.561129e+00
316 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)316 Vpmg_setPart:··lower·corner·=·(-6.72,·-6.72,·-6.72)
317 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)317 Vpmg_setPart:··upper·corner·=·(6.72,·6.72,·6.72)
318 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)318 Vpmg_setPart:··actual·minima·=·(-6.72,·-6.72,·-6.72)
319 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)319 Vpmg_setPart:··actual·maxima·=·(6.72,·6.72,·6.72)
320 Vpmg_setPart:··bflag[FRONT]·=·0320 Vpmg_setPart:··bflag[FRONT]·=·0
321 Vpmg_setPart:··bflag[BACK]·=·0321 Vpmg_setPart:··bflag[BACK]·=·0
322 Vpmg_setPart:··bflag[LEFT]·=·0322 Vpmg_setPart:··bflag[LEFT]·=·0
323 Vpmg_setPart:··bflag[RIGHT]·=·0323 Vpmg_setPart:··bflag[RIGHT]·=·0
324 Vpmg_setPart:··bflag[UP]·=·0324 Vpmg_setPart:··bflag[UP]·=·0
325 Vpmg_setPart:··bflag[DOWN]·=·0325 Vpmg_setPart:··bflag[DOWN]·=·0
326 Vnm_tstart:·starting·timer·29·(Energy·timer)..326 Vnm_tstart:·starting·timer·29·(Energy·timer)..
327 Vpmg_energy:··calculating·only·q-phi·energy327 Vpmg_energy:··calculating·only·q-phi·energy
328 Vpmg_energy:··qfEnergy·=·7.241648379021E+01·kT328 Vpmg_energy:··qfEnergy·=·7.241648379021E+01·kT
329 Vpmg_qmEnergy:··Zero·energy·for·zero·ionic·strength!329 Vpmg_qmEnergy:··Zero·energy·for·zero·ionic·strength!
330 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.674400e-02330 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.782300e-02
Max diff block lines reached; 35388/42270 bytes (83.72%) of diff not shown.
⊟
948 KB
./usr/share/apbs/examples/protein-rna/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:40:28·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:24:48·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·model_outNB.pqr9 NOsh:·Storing·molecule·0·path·model_outNB.pqr
Offset 274, 151 lines modifiedOffset 274, 151 lines modified
274 Vpmp_ctor2:··Using·meth·=·1,·mgsolv·=·0274 Vpmp_ctor2:··Using·meth·=·1,·mgsolv·=·0
275 Setting·PDE·center·to·local·center...275 Setting·PDE·center·to·local·center...
276 Vpmg_fillco:··filling·in·source·term.276 Vpmg_fillco:··filling·in·source·term.
277 fillcoCharge:··Calling·fillcoChargeSpline2...277 fillcoCharge:··Calling·fillcoChargeSpline2...
278 Vpmg_fillco:··filling·in·source·term.278 Vpmg_fillco:··filling·in·source·term.
279 Vpmg_fillco:··marking·ion·and·solvent·accessibility.279 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
280 fillcoCoef:··Calling·fillcoCoefMol...280 fillcoCoef:··Calling·fillcoCoefMol...
281 Vacc_SASA:·Time·elapsed:·0.902195281 Vacc_SASA:·Time·elapsed:·0.914771
282 Vpmg_fillco:··done·filling·coefficient·arrays282 Vpmg_fillco:··done·filling·coefficient·arrays
283 Vpmg_fillco:··filling·boundary·arrays283 Vpmg_fillco:··filling·boundary·arrays
284 Vpmg_fillco:··done·filling·boundary·arrays284 Vpmg_fillco:··done·filling·boundary·arrays
285 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.640195e+00285 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·1.633093e+00
286 Vnm_tstart:·starting·timer·28·(Solver·timer)..286 Vnm_tstart:·starting·timer·28·(Solver·timer)..
287 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·fine·problem·setup)..287 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·fine·problem·setup)..
288 Vbuildops:·Fine:·(065,·097,·129)288 Vbuildops:·Fine:·(065,·097,·129)
289 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)289 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
290 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·fine·problem·setup).··CPU·TIME·=·1.380650e-01290 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·fine·problem·setup).··CPU·TIME·=·1.435950e-01
291 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·coarse·problem·setup)..291 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·coarse·problem·setup)..
292 Vbuildops:·Galer:·(033,·049,·065)292 Vbuildops:·Galer:·(033,·049,·065)
293 Vbuildops:·Galer:·(017,·025,·033)293 Vbuildops:·Galer:·(017,·025,·033)
294 Vbuildops:·Galer:·(009,·013,·017)294 Vbuildops:·Galer:·(009,·013,·017)
295 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·coarse·problem·setup).··CPU·TIME·=·4.302650e-01295 Vnm_tstop:·stopping·timer·30·(Vnewdrv2:·coarse·problem·setup).··CPU·TIME·=·5.084310e-01
296 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·solve)..296 Vnm_tstart:·starting·timer·30·(Vnewdrv2:·solve)..
297 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.352123e+00297 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.416095e+00
298 Vprtstp:·iteration·=·0298 Vprtstp:·iteration·=·0
299 Vprtstp:·relative·residual·=·1.000000e+00299 Vprtstp:·relative·residual·=·1.000000e+00
300 Vprtstp:·contraction·number·=·1.000000e+00300 Vprtstp:·contraction·number·=·1.000000e+00
301 Vnewton:·Damping·enabled301 Vnewton:·Damping·enabled
302 Vnewton:·Using·errtol_s:·3489953.107213302 Vnewton:·Using·errtol_s:·3489953.107213
303 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.147534e+00303 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.253931e+00
304 Vprtstp:·iteration·=·0304 Vprtstp:·iteration·=·0
305 Vprtstp:·relative·residual·=·1.000000e+00305 Vprtstp:·relative·residual·=·1.000000e+00
306 Vprtstp:·contraction·number·=·1.000000e+00306 Vprtstp:·contraction·number·=·1.000000e+00
307 Vprtstp:·iteration·=·1307 Vprtstp:·iteration·=·1
308 Vprtstp:·relative·residual·=·4.541420e+05308 Vprtstp:·relative·residual·=·4.541420e+05
309 Vprtstp:·contraction·number·=·4.541420e+05309 Vprtstp:·contraction·number·=·4.541420e+05
310 Vnewton:·Attempting·damping,·relres·=·0.152961310 Vnewton:·Attempting·damping,·relres·=·0.152961
311 Vnewton:·Attempting·damping,·relres·=·0.557868311 Vnewton:·Attempting·damping,·relres·=·0.557868
312 Vnewton:·Damping·accepted,·relres·=·0.152961312 Vnewton:·Damping·accepted,·relres·=·0.152961
313 Vnewton:·Damping·disabled313 Vnewton:·Damping·disabled
314 Vprtstp:·iteration·=·1314 Vprtstp:·iteration·=·1
315 Vprtstp:·relative·residual·=·1.529613e-01315 Vprtstp:·relative·residual·=·1.529613e-01
316 Vprtstp:·contraction·number·=·1.529613e-01316 Vprtstp:·contraction·number·=·1.529613e-01
317 Vnewton:·Using·errtol_s:·533827.862441317 Vnewton:·Using·errtol_s:·533827.862441
318 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·4.906533e+00318 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·5.347204e+00
319 Vprtstp:·iteration·=·0319 Vprtstp:·iteration·=·0
320 Vprtstp:·relative·residual·=·1.000000e+00320 Vprtstp:·relative·residual·=·1.000000e+00
321 Vprtstp:·contraction·number·=·1.000000e+00321 Vprtstp:·contraction·number·=·1.000000e+00
322 Vprtstp:·iteration·=·1322 Vprtstp:·iteration·=·1
323 Vprtstp:·relative·residual·=·7.616204e+04323 Vprtstp:·relative·residual·=·7.616204e+04
324 Vprtstp:·contraction·number·=·7.616204e+04324 Vprtstp:·contraction·number·=·7.616204e+04
325 Vprtstp:·iteration·=·2325 Vprtstp:·iteration·=·2
326 Vprtstp:·relative·residual·=·2.889845e-02326 Vprtstp:·relative·residual·=·2.889845e-02
327 Vprtstp:·contraction·number·=·1.889265e-01327 Vprtstp:·contraction·number·=·1.889265e-01
328 Vnewton:·Using·errtol_s:·100854.249053328 Vnewton:·Using·errtol_s:·100854.249053
329 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·6.331627e+00329 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·7.141940e+00
330 Vprtstp:·iteration·=·0330 Vprtstp:·iteration·=·0
331 Vprtstp:·relative·residual·=·1.000000e+00331 Vprtstp:·relative·residual·=·1.000000e+00
332 Vprtstp:·contraction·number·=·1.000000e+00332 Vprtstp:·contraction·number·=·1.000000e+00
333 Vprtstp:·iteration·=·1333 Vprtstp:·iteration·=·1
334 Vprtstp:·relative·residual·=·1.621156e+04334 Vprtstp:·relative·residual·=·1.621156e+04
335 Vprtstp:·contraction·number·=·1.621156e+04335 Vprtstp:·contraction·number·=·1.621156e+04
336 Vprtstp:·iteration·=·3336 Vprtstp:·iteration·=·3
337 Vprtstp:·relative·residual·=·6.485254e-03337 Vprtstp:·relative·residual·=·6.485254e-03
338 Vprtstp:·contraction·number·=·2.244153e-01338 Vprtstp:·contraction·number·=·2.244153e-01
339 Vnewton:·Using·errtol_s:·22633.233232339 Vnewton:·Using·errtol_s:·22633.233232
340 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·7.760812e+00340 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·8.909277e+00
341 Vprtstp:·iteration·=·0341 Vprtstp:·iteration·=·0
342 Vprtstp:·relative·residual·=·1.000000e+00342 Vprtstp:·relative·residual·=·1.000000e+00
343 Vprtstp:·contraction·number·=·1.000000e+00343 Vprtstp:·contraction·number·=·1.000000e+00
344 Vprtstp:·iteration·=·1344 Vprtstp:·iteration·=·1
345 Vprtstp:·relative·residual·=·4.163481e+03345 Vprtstp:·relative·residual·=·4.163481e+03
346 Vprtstp:·contraction·number·=·4.163481e+03346 Vprtstp:·contraction·number·=·4.163481e+03
347 Vprtstp:·iteration·=·4347 Vprtstp:·iteration·=·4
348 Vprtstp:·relative·residual·=·1.448984e-03348 Vprtstp:·relative·residual·=·1.448984e-03
349 Vprtstp:·contraction·number·=·2.234275e-01349 Vprtstp:·contraction·number·=·2.234275e-01
350 Vnewton:·Using·errtol_s:·5056.886378350 Vnewton:·Using·errtol_s:·5056.886378
351 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·9.187275e+00351 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.064684e+01
352 Vprtstp:·iteration·=·0352 Vprtstp:·iteration·=·0
353 Vprtstp:·relative·residual·=·1.000000e+00353 Vprtstp:·relative·residual·=·1.000000e+00
354 Vprtstp:·contraction·number·=·1.000000e+00354 Vprtstp:·contraction·number·=·1.000000e+00
355 Vprtstp:·iteration·=·1355 Vprtstp:·iteration·=·1
356 Vprtstp:·relative·residual·=·1.135331e+03356 Vprtstp:·relative·residual·=·1.135331e+03
357 Vprtstp:·contraction·number·=·1.135331e+03357 Vprtstp:·contraction·number·=·1.135331e+03
358 Vprtstp:·iteration·=·5358 Vprtstp:·iteration·=·5
359 Vprtstp:·relative·residual·=·3.105204e-04359 Vprtstp:·relative·residual·=·3.105204e-04
360 Vprtstp:·contraction·number·=·2.143021e-01360 Vprtstp:·contraction·number·=·2.143021e-01
361 Vnewton:·Using·errtol_s:·1083.701574361 Vnewton:·Using·errtol_s:·1083.701574
362 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.060207e+01362 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.228533e+01
363 Vprtstp:·iteration·=·0363 Vprtstp:·iteration·=·0
364 Vprtstp:·relative·residual·=·1.000000e+00364 Vprtstp:·relative·residual·=·1.000000e+00
365 Vprtstp:·contraction·number·=·1.000000e+00365 Vprtstp:·contraction·number·=·1.000000e+00
366 Vprtstp:·iteration·=·1366 Vprtstp:·iteration·=·1
367 Vprtstp:·relative·residual·=·3.001303e+02367 Vprtstp:·relative·residual·=·3.001303e+02
368 Vprtstp:·contraction·number·=·3.001303e+02368 Vprtstp:·contraction·number·=·3.001303e+02
369 Vprtstp:·iteration·=·6369 Vprtstp:·iteration·=·6
370 Vprtstp:·relative·residual·=·7.746175e-05370 Vprtstp:·relative·residual·=·7.746175e-05
371 Vprtstp:·contraction·number·=·2.494579e-01371 Vprtstp:·contraction·number·=·2.494579e-01
372 Vnewton:·Using·errtol_s:·270.337872372 Vnewton:·Using·errtol_s:·270.337872
373 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.202412e+01373 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.403876e+01
374 Vprtstp:·iteration·=·0374 Vprtstp:·iteration·=·0
375 Vprtstp:·relative·residual·=·1.000000e+00375 Vprtstp:·relative·residual·=·1.000000e+00
376 Vprtstp:·contraction·number·=·1.000000e+00376 Vprtstp:·contraction·number·=·1.000000e+00
377 Vprtstp:·iteration·=·1377 Vprtstp:·iteration·=·1
378 Vprtstp:·relative·residual·=·8.503484e+01378 Vprtstp:·relative·residual·=·8.503484e+01
379 Vprtstp:·contraction·number·=·8.503484e+01379 Vprtstp:·contraction·number·=·8.503484e+01
380 Vprtstp:·iteration·=·7380 Vprtstp:·iteration·=·7
381 Vprtstp:·relative·residual·=·2.192913e-05381 Vprtstp:·relative·residual·=·2.192913e-05
382 Vprtstp:·contraction·number·=·2.830962e-01382 Vprtstp:·contraction·number·=·2.830962e-01
383 Vnewton:·Using·errtol_s:·76.531632383 Vnewton:·Using·errtol_s:·76.531632
384 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.344302e+01384 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·1.574011e+01
385 Vprtstp:·iteration·=·0385 Vprtstp:·iteration·=·0
386 Vprtstp:·relative·residual·=·1.000000e+00386 Vprtstp:·relative·residual·=·1.000000e+00
387 Vprtstp:·contraction·number·=·1.000000e+00387 Vprtstp:·contraction·number·=·1.000000e+00
388 Vprtstp:·iteration·=·1388 Vprtstp:·iteration·=·1
389 Vprtstp:·relative·residual·=·2.526272e+01389 Vprtstp:·relative·residual·=·2.526272e+01
Max diff block lines reached; 964601/970990 bytes (99.34%) of diff not shown.
⊟
29.0 KB
./usr/share/apbs/examples/solv/io.mc
    
Offset 1, 10 lines modifiedOffset 1, 10 lines modified
1 ##############################################################################1 ##############################################################################
2 #·MC-shell·I/O·capture·file.2 #·MC-shell·I/O·capture·file.
3 #·Creation·Date·and·Time:··Sun·Jan··7·16:40:19·20243 #·Creation·Date·and·Time:··Mon·Jan··8·21:24:32·2024
  
4 ##############################################################################4 ##############################################################################
5 Hello·world·from·PE·05 Hello·world·from·PE·0
6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..6 Vnm_tstart:·starting·timer·26·(APBS·WALL·CLOCK)..
7 NOsh_parseInput:··Starting·file·parsing...7 NOsh_parseInput:··Starting·file·parsing...
8 NOsh:·Parsing·READ·section8 NOsh:·Parsing·READ·section
9 NOsh:·Storing·molecule·0·path·methanol.pqr9 NOsh:·Storing·molecule·0·path·methanol.pqr
Offset 245, 32 lines modifiedOffset 245, 32 lines modified
245 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1245 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
246 Setting·PDE·center·to·local·center...246 Setting·PDE·center·to·local·center...
247 Vpmg_fillco:··filling·in·source·term.247 Vpmg_fillco:··filling·in·source·term.
248 fillcoCharge:··Calling·fillcoChargeSpline1...248 fillcoCharge:··Calling·fillcoChargeSpline1...
249 Vpmg_fillco:··filling·in·source·term.249 Vpmg_fillco:··filling·in·source·term.
250 Vpmg_fillco:··marking·ion·and·solvent·accessibility.250 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
251 fillcoCoef:··Calling·fillcoCoefMol...251 fillcoCoef:··Calling·fillcoCoefMol...
252 Vacc_SASA:·Time·elapsed:·0.002947252 Vacc_SASA:·Time·elapsed:·0.002318
253 Vpmg_fillco:··done·filling·coefficient·arrays253 Vpmg_fillco:··done·filling·coefficient·arrays
254 Vpmg_fillco:··filling·boundary·arrays254 Vpmg_fillco:··filling·boundary·arrays
255 Vpmg_fillco:··done·filling·boundary·arrays255 Vpmg_fillco:··done·filling·boundary·arrays
256 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·4.247100e-02256 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·2.774500e-02
257 Vnm_tstart:·starting·timer·28·(Solver·timer)..257 Vnm_tstart:·starting·timer·28·(Solver·timer)..
258 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..258 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
259 Vbuildops:·Fine:·(065,·065,·065)259 Vbuildops:·Fine:·(065,·065,·065)
260 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)260 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
261 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.762500e-02261 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.765800e-02
262 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..262 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
263 Vbuildops:·Galer:·(033,·033,·033)263 Vbuildops:·Galer:·(033,·033,·033)
264 Vbuildops:·Galer:·(017,·017,·017)264 Vbuildops:·Galer:·(017,·017,·017)
265 Vbuildops:·Galer:·(009,·009,·009)265 Vbuildops:·Galer:·(009,·009,·009)
266 Vbuildops:·Galer:·(005,·005,·005)266 Vbuildops:·Galer:·(005,·005,·005)
267 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.280180e-01267 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.857960e-01
268 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..268 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
269 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·2.656170e-01269 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.193980e-01
270 Vprtstp:·iteration·=·0270 Vprtstp:·iteration·=·0
271 Vprtstp:·relative·residual·=·1.000000e+00271 Vprtstp:·relative·residual·=·1.000000e+00
272 Vprtstp:·contraction·number·=·1.000000e+00272 Vprtstp:·contraction·number·=·1.000000e+00
273 Vprtstp:·iteration·=·1273 Vprtstp:·iteration·=·1
274 Vprtstp:·relative·residual·=·2.930795e-01274 Vprtstp:·relative·residual·=·2.930795e-01
275 Vprtstp:·contraction·number·=·2.930795e-01275 Vprtstp:·contraction·number·=·2.930795e-01
276 Vprtstp:·iteration·=·2276 Vprtstp:·iteration·=·2
Offset 299, 32 lines modifiedOffset 299, 32 lines modified
299 Vprtstp:·contraction·number·=·3.064107e-01299 Vprtstp:·contraction·number·=·3.064107e-01
300 Vprtstp:·iteration·=·10300 Vprtstp:·iteration·=·10
301 Vprtstp:·relative·residual·=·2.158998e-06301 Vprtstp:·relative·residual·=·2.158998e-06
302 Vprtstp:·contraction·number·=·3.114698e-01302 Vprtstp:·contraction·number·=·3.114698e-01
303 Vprtstp:·iteration·=·11303 Vprtstp:·iteration·=·11
304 Vprtstp:·relative·residual·=·6.836605e-07304 Vprtstp:·relative·residual·=·6.836605e-07
305 Vprtstp:·contraction·number·=·3.166565e-01305 Vprtstp:·contraction·number·=·3.166565e-01
306 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.896289e+00306 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·3.357879e+00
307 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.095100e+00307 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·3.625319e+00
308 Vpmg_setPart:··lower·corner·=·(-7.69135,·-8,·-8.2417)308 Vpmg_setPart:··lower·corner·=·(-7.69135,·-8,·-8.2417)
309 Vpmg_setPart:··upper·corner·=·(8.30865,·8,·7.7583)309 Vpmg_setPart:··upper·corner·=·(8.30865,·8,·7.7583)
310 Vpmg_setPart:··actual·minima·=·(-7.69135,·-8,·-8.2417)310 Vpmg_setPart:··actual·minima·=·(-7.69135,·-8,·-8.2417)
311 Vpmg_setPart:··actual·maxima·=·(8.30865,·8,·7.7583)311 Vpmg_setPart:··actual·maxima·=·(8.30865,·8,·7.7583)
312 Vpmg_setPart:··bflag[FRONT]·=·0312 Vpmg_setPart:··bflag[FRONT]·=·0
313 Vpmg_setPart:··bflag[BACK]·=·0313 Vpmg_setPart:··bflag[BACK]·=·0
314 Vpmg_setPart:··bflag[LEFT]·=·0314 Vpmg_setPart:··bflag[LEFT]·=·0
315 Vpmg_setPart:··bflag[RIGHT]·=·0315 Vpmg_setPart:··bflag[RIGHT]·=·0
316 Vpmg_setPart:··bflag[UP]·=·0316 Vpmg_setPart:··bflag[UP]·=·0
317 Vpmg_setPart:··bflag[DOWN]·=·0317 Vpmg_setPart:··bflag[DOWN]·=·0
318 Vnm_tstart:·starting·timer·29·(Energy·timer)..318 Vnm_tstart:·starting·timer·29·(Energy·timer)..
319 Vpmg_energy:··calculating·only·q-phi·energy319 Vpmg_energy:··calculating·only·q-phi·energy
320 Vpmg_energy:··qfEnergy·=·1.481476875907E+03·kT320 Vpmg_energy:··qfEnergy·=·1.481476875907E+03·kT
321 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.120000e-04321 Vnm_tstop:·stopping·timer·29·(Energy·timer).··CPU·TIME·=·1.060000e-04
322 Vnm_tstart:·starting·timer·30·(Force·timer)..322 Vnm_tstart:·starting·timer·30·(Force·timer)..
323 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·5.000000e-06323 Vnm_tstop:·stopping·timer·30·(Force·timer).··CPU·TIME·=·4.000000e-06
324 Vnm_tstart:·starting·timer·27·(Setup·timer)..324 Vnm_tstart:·starting·timer·27·(Setup·timer)..
325 Setting·up·PBE·object...325 Setting·up·PBE·object...
326 Vpbe_ctor2:··solute·radius·=·2.83039326 Vpbe_ctor2:··solute·radius·=·2.83039
327 Vpbe_ctor2:··solute·dimensions·=·3.775·x·3.775·x·4.8153327 Vpbe_ctor2:··solute·dimensions·=·3.775·x·3.775·x·4.8153
328 Vpbe_ctor2:··solute·charge·=·5.55112e-17328 Vpbe_ctor2:··solute·charge·=·5.55112e-17
329 Vpbe_ctor2:··bulk·ionic·strength·=·0329 Vpbe_ctor2:··bulk·ionic·strength·=·0
330 Vpbe_ctor2:··xkappa·=·0330 Vpbe_ctor2:··xkappa·=·0
Offset 345, 32 lines modifiedOffset 345, 32 lines modified
345 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1345 Vpmp_ctor2:··Using·meth·=·2,·mgsolv·=·1
346 Setting·PDE·center·to·local·center...346 Setting·PDE·center·to·local·center...
347 Vpmg_fillco:··filling·in·source·term.347 Vpmg_fillco:··filling·in·source·term.
348 fillcoCharge:··Calling·fillcoChargeSpline1...348 fillcoCharge:··Calling·fillcoChargeSpline1...
349 Vpmg_fillco:··filling·in·source·term.349 Vpmg_fillco:··filling·in·source·term.
350 Vpmg_fillco:··marking·ion·and·solvent·accessibility.350 Vpmg_fillco:··marking·ion·and·solvent·accessibility.
351 fillcoCoef:··Calling·fillcoCoefMol...351 fillcoCoef:··Calling·fillcoCoefMol...
352 Vacc_SASA:·Time·elapsed:·0.001173352 Vacc_SASA:·Time·elapsed:·0.002262
353 Vpmg_fillco:··done·filling·coefficient·arrays353 Vpmg_fillco:··done·filling·coefficient·arrays
354 Vpmg_fillco:··filling·boundary·arrays354 Vpmg_fillco:··filling·boundary·arrays
355 Vpmg_fillco:··done·filling·boundary·arrays355 Vpmg_fillco:··done·filling·boundary·arrays
356 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·4.648200e-02356 Vnm_tstop:·stopping·timer·27·(Setup·timer).··CPU·TIME·=·3.936200e-02
357 Vnm_tstart:·starting·timer·28·(Solver·timer)..357 Vnm_tstart:·starting·timer·28·(Solver·timer)..
358 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..358 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·fine·problem·setup)..
359 Vbuildops:·Fine:·(065,·065,·065)359 Vbuildops:·Fine:·(065,·065,·065)
360 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)360 Vbuildops:·Operator·stencil·(lev,·numdia)·=·(1,·4)
361 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.978000e-02361 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·fine·problem·setup).··CPU·TIME·=·4.871700e-02
362 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..362 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·coarse·problem·setup)..
363 Vbuildops:·Galer:·(033,·033,·033)363 Vbuildops:·Galer:·(033,·033,·033)
364 Vbuildops:·Galer:·(017,·017,·017)364 Vbuildops:·Galer:·(017,·017,·017)
365 Vbuildops:·Galer:·(009,·009,·009)365 Vbuildops:·Galer:·(009,·009,·009)
366 Vbuildops:·Galer:·(005,·005,·005)366 Vbuildops:·Galer:·(005,·005,·005)
367 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.447430e-01367 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·coarse·problem·setup).··CPU·TIME·=·1.868870e-01
368 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..368 Vnm_tstart:·starting·timer·30·(Vmgdrv2:·solve)..
369 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.455371e+00369 Vnm_tstop:·stopping·timer·40·(MG·iteration).··CPU·TIME·=·3.992766e+00
370 Vprtstp:·iteration·=·0370 Vprtstp:·iteration·=·0
371 Vprtstp:·relative·residual·=·1.000000e+00371 Vprtstp:·relative·residual·=·1.000000e+00
372 Vprtstp:·contraction·number·=·1.000000e+00372 Vprtstp:·contraction·number·=·1.000000e+00
373 Vprtstp:·iteration·=·1373 Vprtstp:·iteration·=·1
374 Vprtstp:·relative·residual·=·1.518468e-01374 Vprtstp:·relative·residual·=·1.518468e-01
375 Vprtstp:·contraction·number·=·1.518468e-01375 Vprtstp:·contraction·number·=·1.518468e-01
376 Vprtstp:·iteration·=·2376 Vprtstp:·iteration·=·2
Offset 387, 30 lines modifiedOffset 387, 30 lines modified
387 Vprtstp:·contraction·number·=·1.057725e-01387 Vprtstp:·contraction·number·=·1.057725e-01
388 Vprtstp:·iteration·=·6388 Vprtstp:·iteration·=·6
389 Vprtstp:·relative·residual·=·1.782567e-06389 Vprtstp:·relative·residual·=·1.782567e-06
390 Vprtstp:·contraction·number·=·1.074900e-01390 Vprtstp:·contraction·number·=·1.074900e-01
391 Vprtstp:·iteration·=·7391 Vprtstp:·iteration·=·7
392 Vprtstp:·relative·residual·=·1.936135e-07392 Vprtstp:·relative·residual·=·1.936135e-07
393 Vprtstp:·contraction·number·=·1.086150e-01393 Vprtstp:·contraction·number·=·1.086150e-01
394 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·1.918833e+00394 Vnm_tstop:·stopping·timer·30·(Vmgdrv2:·solve).··CPU·TIME·=·2.098594e+00
395 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.156505e+00395 Vnm_tstop:·stopping·timer·28·(Solver·timer).··CPU·TIME·=·2.365878e+00
396 Vpmg_setPart:··lower·corner·=·(-7.69135,·-8,·-8.2417)396 Vpmg_setPart:··lower·corner·=·(-7.69135,·-8,·-8.2417)
397 Vpmg_setPart:··upper·corner·=·(8.30865,·8,·7.7583)397 Vpmg_setPart:··upper·corner·=·(8.30865,·8,·7.7583)
398 Vpmg_setPart:··actual·minima·=·(-7.69135,·-8,·-8.2417)398 Vpmg_setPart:··actual·minima·=·(-7.69135,·-8,·-8.2417)
399 Vpmg_setPart:··actual·maxima·=·(8.30865,·8,·7.7583)399 Vpmg_setPart:··actual·maxima·=·(8.30865,·8,·7.7583)
400 Vpmg_setPart:··bflag[FRONT]·=·0400 Vpmg_setPart:··bflag[FRONT]·=·0
401 Vpmg_setPart:··bflag[BACK]·=·0401 Vpmg_setPart:··bflag[BACK]·=·0
402 Vpmg_setPart:··bflag[LEFT]·=·0402 Vpmg_setPart:··bflag[LEFT]·=·0
403 Vpmg_setPart:··bflag[RIGHT]·=·0403 Vpmg_setPart:··bflag[RIGHT]·=·0
Max diff block lines reached; 22722/29605 bytes (76.75%) of diff not shown.
Generated by diffoscope 240