vasputils 0.0.11 → 0.0.12
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- data/CHANGES +49 -28
- data/Gemfile +10 -9
- data/VERSION +1 -1
- data/{test/vaspgeometryoptimizer/ended-Iter1/try00/CONTCAR → bin/changeincar} +0 -0
- data/bin/checkvasp +106 -75
- data/bin/genincar +4 -4
- data/bin/genkpoints +13 -13
- data/bin/genpotcar +2 -2
- data/bin/latticeconstants +10 -12
- data/bin/qsubvasp +63 -80
- data/bin/resetvaspdir +51 -0
- data/bin/resetvaspgeomopt +73 -0
- data/bin/runvasp +42 -49
- data/bin/runvaspdir +19 -0
- data/bin/runvaspgeomopt +19 -0
- data/bin/showvaspdir +171 -0
- data/bin/showvaspgeomopt +83 -0
- data/bin/symposcar +89 -113
- data/bin/varycondition +28 -0
- data/example/dot.vasputils +26 -232
- data/lib/vasputils/conditionvarier.rb +157 -0
- data/lib/vasputils/incar.rb +40 -43
- data/lib/vasputils/kpoints.rb +31 -33
- data/lib/vasputils/outcar.rb +53 -53
- data/lib/vasputils/poscar.rb +148 -150
- data/lib/vasputils/potcar/concatenater.rb +22 -22
- data/lib/vasputils/potcar.rb +12 -12
- data/lib/vasputils/setting.rb +22 -22
- data/lib/vasputils/vaspdir.rb +199 -86
- data/lib/vasputils/vaspgeometryoptimizer.rb +233 -100
- data/lib/vasputils.rb +7 -65
- data/test/conditionanalyzer/00/POSCAR +8 -0
- data/test/conditionanalyzer/00/encut400_k444/CONTCAR +8 -0
- data/test/conditionanalyzer/00/encut400_k444/INCAR +28 -0
- data/test/conditionanalyzer/00/encut400_k444/KPOINTS +6 -0
- data/test/conditionanalyzer/00/encut400_k444/OUTCAR +1436 -0
- data/test/conditionanalyzer/00/encut400_k444/POSCAR +8 -0
- data/test/conditionanalyzer/00/encut400_k444/POTCAR +16 -0
- data/test/conditionanalyzer/00/encut400_k555/CONTCAR +8 -0
- data/test/conditionanalyzer/00/encut400_k555/INCAR +28 -0
- data/test/conditionanalyzer/00/encut400_k555/KPOINTS +6 -0
- data/test/conditionanalyzer/00/encut400_k555/OUTCAR +1436 -0
- data/test/conditionanalyzer/00/encut400_k555/POSCAR +8 -0
- data/test/conditionanalyzer/00/encut400_k555/POTCAR +16 -0
- data/test/conditionanalyzer/00/encut500_k444/CONTCAR +8 -0
- data/test/conditionanalyzer/00/encut500_k444/INCAR +28 -0
- data/test/conditionanalyzer/00/encut500_k444/KPOINTS +6 -0
- data/test/conditionanalyzer/00/encut500_k444/OUTCAR +1436 -0
- data/test/conditionanalyzer/00/encut500_k444/POSCAR +8 -0
- data/test/conditionanalyzer/00/encut500_k444/POTCAR +16 -0
- data/test/conditionanalyzer/00/encut500_k555/CONTCAR +8 -0
- data/test/conditionanalyzer/00/encut500_k555/INCAR +28 -0
- data/test/conditionanalyzer/00/encut500_k555/KPOINTS +6 -0
- data/test/conditionanalyzer/00/encut500_k555/OUTCAR +1436 -0
- data/test/conditionanalyzer/00/encut500_k555/POSCAR +8 -0
- data/test/conditionanalyzer/00/encut500_k555/POTCAR +16 -0
- data/test/{vaspkpointsfinder/01-01-01/try00 → conditionanalyzer/01/00-original}/INCAR +3 -3
- data/test/conditionanalyzer/01/00-original/KPOINTS +6 -0
- data/test/conditionanalyzer/01/00-original/POSCAR +10 -0
- data/test/conditionanalyzer/01/01-ENCUT/1000/try02/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/1000/try02/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/1000/try02/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/1000/try02/OUTCAR +1692 -0
- data/test/conditionanalyzer/01/01-ENCUT/1000/try02/POSCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/1200/try02/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/1200/try02/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/1200/try02/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/1200/try02/OUTCAR +1692 -0
- data/test/conditionanalyzer/01/01-ENCUT/1200/try02/POSCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/1500/try02/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/1500/try02/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/1500/try02/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/1500/try02/OUTCAR +1742 -0
- data/test/conditionanalyzer/01/01-ENCUT/1500/try02/POSCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/500/try05/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/500/try05/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/500/try05/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/500/try05/OUTCAR +1644 -0
- data/test/conditionanalyzer/01/01-ENCUT/500/try05/POSCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/600/try01/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/600/try01/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/600/try01/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/600/try01/OUTCAR +1644 -0
- data/test/conditionanalyzer/01/01-ENCUT/600/try01/POSCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/700/try01/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/700/try01/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/700/try01/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/700/try01/OUTCAR +1644 -0
- data/test/conditionanalyzer/01/01-ENCUT/700/try01/POSCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/800/try01/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/800/try01/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/800/try01/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/800/try01/OUTCAR +3610 -0
- data/test/conditionanalyzer/01/01-ENCUT/800/try01/POSCAR +10 -0
- data/test/conditionanalyzer/01/01-ENCUT/900/try01/CONTCAR +13 -0
- data/test/conditionanalyzer/01/01-ENCUT/900/try01/INCAR +17 -0
- data/test/conditionanalyzer/01/01-ENCUT/900/try01/KPOINTS +6 -0
- data/test/conditionanalyzer/01/01-ENCUT/900/try01/OUTCAR +1692 -0
- data/test/conditionanalyzer/01/01-ENCUT/900/try01/POSCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/16x16x16/try07/CONTCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/16x16x16/try07/INCAR +17 -0
- data/test/conditionanalyzer/01/02-KPOINTS/16x16x16/try07/KPOINTS +6 -0
- data/test/conditionanalyzer/01/02-KPOINTS/16x16x16/try07/OUTCAR +12318 -0
- data/test/conditionanalyzer/01/02-KPOINTS/16x16x16/try07/POSCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/1x1x1/try07/CONTCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/1x1x1/try07/INCAR +17 -0
- data/test/{vaspkpointsfinder/01-01-01/try00 → conditionanalyzer/01/02-KPOINTS/1x1x1/try07}/KPOINTS +1 -1
- data/test/conditionanalyzer/01/02-KPOINTS/1x1x1/try07/OUTCAR +1337 -0
- data/test/conditionanalyzer/01/02-KPOINTS/1x1x1/try07/POSCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/2x2x2/try10/CONTCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/2x2x2/try10/INCAR +17 -0
- data/test/conditionanalyzer/01/02-KPOINTS/2x2x2/try10/KPOINTS +6 -0
- data/test/conditionanalyzer/01/02-KPOINTS/2x2x2/try10/OUTCAR +9885 -0
- data/test/conditionanalyzer/01/02-KPOINTS/2x2x2/try10/POSCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x32/try06/CONTCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x32/try06/INCAR +17 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x32/try06/KPOINTS +6 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x32/try06/OUTCAR +72342 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x32/try06/POSCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x64/try04/CONTCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x64/try04/INCAR +17 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x64/try04/KPOINTS +6 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x64/try04/OUTCAR +139254 -0
- data/test/conditionanalyzer/01/02-KPOINTS/32x32x64/try04/POSCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/4x4x4/try05/CONTCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/4x4x4/try05/INCAR +17 -0
- data/test/conditionanalyzer/01/02-KPOINTS/4x4x4/try05/KPOINTS +6 -0
- data/test/conditionanalyzer/01/02-KPOINTS/4x4x4/try05/OUTCAR +1644 -0
- data/test/conditionanalyzer/01/02-KPOINTS/4x4x4/try05/POSCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/64x64x64/INCAR +17 -0
- data/test/conditionanalyzer/01/02-KPOINTS/64x64x64/KPOINTS +6 -0
- data/test/conditionanalyzer/01/02-KPOINTS/64x64x64/OUTCAR +507061 -0
- data/test/conditionanalyzer/01/02-KPOINTS/64x64x64/POSCAR +10 -0
- data/test/conditionanalyzer/01/02-KPOINTS/8x8x8/try05/CONTCAR +13 -0
- data/test/conditionanalyzer/01/02-KPOINTS/8x8x8/try05/INCAR +17 -0
- data/test/conditionanalyzer/01/02-KPOINTS/8x8x8/try05/KPOINTS +6 -0
- data/test/conditionanalyzer/01/02-KPOINTS/8x8x8/try05/OUTCAR +3298 -0
- data/test/conditionanalyzer/01/02-KPOINTS/8x8x8/try05/POSCAR +13 -0
- data/test/conditionanalyzer/mixed_conditions/orthorhombic/CONTCAR +17 -0
- data/test/conditionanalyzer/mixed_conditions/orthorhombic/INCAR +28 -0
- data/test/conditionanalyzer/mixed_conditions/orthorhombic/KPOINTS +6 -0
- data/test/conditionanalyzer/mixed_conditions/orthorhombic/OUTCAR +1436 -0
- data/test/conditionanalyzer/mixed_conditions/orthorhombic/POSCAR +12 -0
- data/test/conditionanalyzer/mixed_conditions/orthorhombic/POTCAR +16 -0
- data/test/conditionanalyzer/mixed_conditions/tetragonal/CONTCAR +17 -0
- data/test/conditionanalyzer/mixed_conditions/tetragonal/INCAR +28 -0
- data/test/conditionanalyzer/mixed_conditions/tetragonal/KPOINTS +6 -0
- data/test/conditionanalyzer/mixed_conditions/tetragonal/OUTCAR +1436 -0
- data/test/conditionanalyzer/mixed_conditions/tetragonal/POSCAR +12 -0
- data/test/conditionanalyzer/mixed_conditions/tetragonal/POTCAR +16 -0
- data/test/conditionanalyzer/picker/encut400_k444-cubic/INCAR +28 -0
- data/test/conditionanalyzer/picker/encut400_k444-cubic/KPOINTS +6 -0
- data/test/conditionanalyzer/picker/encut400_k444-cubic/OUTCAR +1436 -0
- data/test/conditionanalyzer/picker/encut400_k444-cubic/POSCAR +9 -0
- data/test/conditionanalyzer/picker/encut400_k444-cubic/POTCAR +16 -0
- data/test/conditionanalyzer/picker/encut400_k444-tetragonal-b/INCAR +28 -0
- data/test/conditionanalyzer/picker/encut400_k444-tetragonal-b/KPOINTS +6 -0
- data/test/conditionanalyzer/picker/encut400_k444-tetragonal-b/OUTCAR +1436 -0
- data/test/conditionanalyzer/picker/encut400_k444-tetragonal-b/POSCAR +9 -0
- data/test/conditionanalyzer/picker/encut400_k444-tetragonal-b/POTCAR +16 -0
- data/test/conditionanalyzer/picker/encut400_k444-unfinished/INCAR +28 -0
- data/test/conditionanalyzer/picker/encut400_k444-unfinished/KPOINTS +6 -0
- data/test/conditionanalyzer/picker/encut400_k444-unfinished/OUTCAR +1381 -0
- data/test/conditionanalyzer/picker/encut400_k444-unfinished/POSCAR +12 -0
- data/test/conditionanalyzer/picker/encut400_k444-unfinished/POTCAR +16 -0
- data/test/conditionanalyzer/picker/hexiagonal/CONTCAR +13 -0
- data/test/conditionanalyzer/picker/hexiagonal/INCAR +17 -0
- data/test/conditionanalyzer/picker/hexiagonal/KPOINTS +6 -0
- data/test/conditionanalyzer/picker/hexiagonal/OUTCAR +1644 -0
- data/test/conditionanalyzer/picker/hexiagonal/POSCAR +13 -0
- data/test/conditionvarier/standard/INCAR +28 -0
- data/test/conditionvarier/standard/KPOINTS +6 -0
- data/test/conditionvarier/standard/POSCAR +12 -0
- data/test/conditionvarier/standard/POTCAR +16 -0
- data/test/helper.rb +4 -4
- data/test/poscar/symmetry/cubic/POSCAR +8 -0
- data/test/poscar/symmetry/hexagonal/POSCAR +8 -0
- data/test/poscar/symmetry/monoclinic/POSCAR +8 -0
- data/test/poscar/symmetry/orthorhombic/POSCAR +8 -0
- data/test/poscar/symmetry/tetragonal/POSCAR +8 -0
- data/test/poscar/symmetry/tetragonal-b/POSCAR +8 -0
- data/test/poscar/symmetry/triclinic/POSCAR +10 -0
- data/test/poscar/symmetry/trigonal/POSCAR +9 -0
- data/test/test_conditionvarier.rb +201 -0
- data/test/test_incar.rb +144 -144
- data/test/test_kpoints.rb +91 -91
- data/test/test_outcar.rb +154 -154
- data/test/test_poscar.rb +263 -262
- data/test/test_potcar.rb +31 -31
- data/test/test_potcar_concatenater.rb +39 -39
- data/test/test_setting.rb +15 -14
- data/test/test_vaspdir.rb +193 -126
- data/test/test_vaspgeometryoptimizer.rb +177 -78
- data/test/test_vasputils.rb +48 -48
- data/test/vaspdir/reset_init/finished/orig/CONTCAR +17 -0
- data/test/vaspdir/reset_init/finished/orig/INCAR +27 -0
- data/test/vaspdir/reset_init/finished/orig/KPOINTS +6 -0
- data/test/vaspdir/reset_init/finished/orig/OUTCAR +1436 -0
- data/test/vaspdir/reset_init/finished/orig/POSCAR +12 -0
- data/test/vaspdir/reset_init/finished/orig/POTCAR +16 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir0/CONTCAR +17 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir0/INCAR +27 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir0/KPOINTS +6 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir0/OUTCAR +1436 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir0/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir0/POTCAR +16 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir1/CONTCAR +17 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir1/INCAR +27 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir1/KPOINTS +6 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir1/OUTCAR +1436 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir1/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/multiple_vaspdir/vaspdir1/POTCAR +16 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/DOSCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/EIGENVAL +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/OSZICAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/PCDAT +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/POSCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/WAVECAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/XDATCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt00/vasprun.xml +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/no-contcar/geomopt01/.gitignore +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/CHG +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/CHGCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/CONTCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/DOSCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/EIGENVAL +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/OSZICAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/PCDAT +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/POSCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/WAVECAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/XDATCAR +0 -0
- data/test/vaspgeometryoptimizer/prepare_next/normal/geomopt00/vasprun.xml +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt00/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt00/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt01/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt01/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt01/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt01/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt01/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt01/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt02/CONTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt02/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt02/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt02/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/geomopt02/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_init/orig/lock_vaspgeomopt/dummy +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt00/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt00/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt01/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt01/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt01/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt01/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt01/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt01/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt02/CONTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt02/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt02/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt02/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt02/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/geomopt02/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/empty-contcar/orig/lock_vaspgeomopt/dummy +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt00/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt00/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt01/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt01/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt01/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt01/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt01/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt01/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt02/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt02/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt02/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/geomopt02/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/no-contcar/orig/lock_vaspgeomopt/dummy +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt00/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt00/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt01/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt01/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt01/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt01/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt01/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt01/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt02/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt02/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt02/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt02/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/geomopt02/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_next/poscar-contcar/orig/lock_vaspgeomopt/dummy +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt00/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt00/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt01/CONTCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt01/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt01/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt01/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt01/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt01/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt02/CONTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt02/INCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt02/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt02/POSCAR +12 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/geomopt02/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/reset_reincarnation/orig/lock_vaspgeomopt/dummy +0 -0
- data/test/vaspgeometryoptimizer/started/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/started/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/started/geomopt00/POSCAR +0 -0
- data/test/vaspgeometryoptimizer/started/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt00/CONTCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt00/INCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt00/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt00/OUTCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt00/POSCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt00/POTCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt01/INCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt01/KPOINTS +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt01/POSCAR +0 -0
- data/test/vaspgeometryoptimizer/till01/geomopt01/POTCAR +0 -0
- metadata +464 -106
- data/bin/genvaspdir +0 -17
- data/bin/rmvaspout +0 -40
- data/lib/vasputils/vaspkpointsfinder.rb +0 -72
- data/test/test_vaspkpointsfinder.rb +0 -25
- data/test/vaspkpointsfinder/01-01-01/try00/POSCAR +0 -8
- data/vasputils.gemspec +0 -567
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try00 → conditionanalyzer/01/00-original}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try01 → conditionanalyzer/01/01-ENCUT/1000/try02}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter2/try00 → conditionanalyzer/01/01-ENCUT/1200/try02}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter2/try01 → conditionanalyzer/01/01-ENCUT/1500/try02}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/not-yet/try00 → conditionanalyzer/01/01-ENCUT/500/try05}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/prepare_next/try00 → conditionanalyzer/01/01-ENCUT/600/try01}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/started/try00 → conditionanalyzer/01/01-ENCUT/700/try01}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/till01/try00 → conditionanalyzer/01/01-ENCUT/800/try01}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/till01 → conditionanalyzer/01/01-ENCUT/900}/try01/POTCAR +0 -0
- /data/test/{vaspkpointsfinder/01-01-01/try00 → conditionanalyzer/01/02-KPOINTS/16x16x16/try07}/POTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try00/INCAR → conditionanalyzer/01/02-KPOINTS/1x1x1/try07/POTCAR} +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try00/KPOINTS → conditionanalyzer/01/02-KPOINTS/2x2x2/try10/POTCAR} +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try00/OUTCAR → conditionanalyzer/01/02-KPOINTS/32x32x32/try06/POTCAR} +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try00/POSCAR → conditionanalyzer/01/02-KPOINTS/32x32x64/try04/POTCAR} +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try01/INCAR → conditionanalyzer/01/02-KPOINTS/4x4x4/try05/POTCAR} +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter2/try00 → conditionanalyzer/01/02-KPOINTS/64x64x64}/CONTCAR +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try01/KPOINTS → conditionanalyzer/01/02-KPOINTS/64x64x64/POTCAR} +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter1/try01/POSCAR → conditionanalyzer/01/02-KPOINTS/8x8x8/try05/POTCAR} +0 -0
- /data/test/{vaspgeometryoptimizer/ended-Iter2/try00/INCAR → conditionanalyzer/picker/hexiagonal/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00 → ended-Iter1/geomopt00}/CONTCAR +0 -0
- /data/test/vaspgeometryoptimizer/{ended-Iter2/try01 → ended-Iter1/geomopt00}/INCAR +0 -0
- /data/test/vaspgeometryoptimizer/{ended-Iter2/try00 → ended-Iter1/geomopt00}/KPOINTS +0 -0
- /data/test/vaspgeometryoptimizer/{ended-Iter2/try00 → ended-Iter1/geomopt00}/OUTCAR +0 -0
- /data/test/vaspgeometryoptimizer/{ended-Iter2/try00 → ended-Iter1/geomopt00}/POSCAR +0 -0
- /data/test/vaspgeometryoptimizer/{ended-Iter2/try01/KPOINTS → ended-Iter1/geomopt00/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{not-yet/try00 → ended-Iter1/geomopt01}/INCAR +0 -0
- /data/test/vaspgeometryoptimizer/{not-yet/try00 → ended-Iter1/geomopt01}/KPOINTS +0 -0
- /data/test/vaspgeometryoptimizer/ended-Iter1/{try01 → geomopt01}/OUTCAR +0 -0
- /data/test/vaspgeometryoptimizer/{ended-Iter2/try01 → ended-Iter1/geomopt01}/POSCAR +0 -0
- /data/test/vaspgeometryoptimizer/{not-yet/try00/POSCAR → ended-Iter1/geomopt01/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try00 → ended-Iter2/geomopt00}/CONTCAR +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00 → ended-Iter2/geomopt00}/INCAR +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00 → ended-Iter2/geomopt00}/KPOINTS +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00 → ended-Iter2/geomopt00}/OUTCAR +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00 → ended-Iter2/geomopt00}/POSCAR +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/CHG → ended-Iter2/geomopt00/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{started/try00 → ended-Iter2/geomopt01}/INCAR +0 -0
- /data/test/vaspgeometryoptimizer/{started/try00 → ended-Iter2/geomopt01}/KPOINTS +0 -0
- /data/test/vaspgeometryoptimizer/ended-Iter2/{try01 → geomopt01}/OUTCAR +0 -0
- /data/test/vaspgeometryoptimizer/{started/try00 → ended-Iter2/geomopt01}/POSCAR +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/CHGCAR → ended-Iter2/geomopt01/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try00 → not-geomopt/not-geomopt-subdir/calcA}/INCAR +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try00 → not-geomopt/not-geomopt-subdir/calcA}/KPOINTS +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try00 → not-geomopt/not-geomopt-subdir/calcA}/POSCAR +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/DOSCAR → not-geomopt/not-geomopt-subdir/calcA/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try01 → not-geomopt/not-geomopt-subdir/calcB}/INCAR +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try01 → not-geomopt/not-geomopt-subdir/calcB}/KPOINTS +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try01 → not-geomopt/not-geomopt-subdir/calcB}/POSCAR +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/EIGENVAL → not-geomopt/not-geomopt-subdir/calcB/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/OSZICAR → not-yet/geomopt00/INCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/PCDAT → not-yet/geomopt00/KPOINTS} +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/WAVECAR → not-yet/geomopt00/POSCAR} +0 -0
- /data/test/vaspgeometryoptimizer/{prepare_next/try00/XDATCAR → not-yet/geomopt00/POTCAR} +0 -0
- /data/test/vaspgeometryoptimizer/prepare_next/{try00/vasprun.xml → no-contcar/geomopt00/CHG} +0 -0
- /data/test/vaspgeometryoptimizer/{till01/try00/OUTCAR → prepare_next/no-contcar/geomopt00/CHGCAR} +0 -0
data/CHANGES
CHANGED
@@ -1,48 +1,69 @@
|
|
1
1
|
= vasputils changelog
|
2
2
|
|
3
|
-
== Master (for 0.0.
|
3
|
+
== Master (for 0.0.13)
|
4
|
+
|
5
|
+
== Version 0.0.12 [2014-08-30] released
|
6
|
+
- Update bin/symposcar .
|
7
|
+
- Add options to bin/checkvasp and modified output format.
|
8
|
+
- Rename VaspGeomOpt to VaspGeometryOptimizer
|
9
|
+
- Add VaspGeometryOptimizer::reset_init
|
10
|
+
- Add VaspGeometryOptimizer::reset_next
|
11
|
+
- Add VaspGeometryOptimizer::reset_reincarnation
|
12
|
+
- Add bin/resetvaspgeompot
|
13
|
+
- Remove bin/nextvasp. Use bin/resetvaspgeomopt -n.
|
14
|
+
- Rename bin/setvaspdir to bin/resetvaspdir
|
15
|
+
- Remove optiions from bin/resetvaspdir
|
16
|
+
- Change prefix for subdir of VaspGeomOpt from "try" to "geomopt"
|
17
|
+
- Change indent width from 2 to 4.
|
18
|
+
- Add bin/varycondition and related libraries.
|
19
|
+
- Raise InitializeError when VaspGeometryOptimizer.new is failed.
|
20
|
+
- Divide bin/checkvasp to bin/showvaspdir and bin/showvaspgeomopt.
|
21
|
+
- Divide bin/runvasp to bin/runvaspdir and bin/runvaspgeomopt.
|
22
|
+
- Add some options to bin/showvaspdir
|
23
|
+
- Update dependency on other gems.
|
4
24
|
|
5
25
|
== Version 0.0.11
|
6
|
-
Modify bin/qsubvasp
|
7
|
-
Add VaspUtils::generate_kmeshes
|
8
|
-
Add example/dot.vasputils
|
9
|
-
Add Setting class
|
10
|
-
Add Potcar::Concatenater
|
11
|
-
Add Incar.dump
|
12
|
-
Modify vasputils/poscar.rb to adjust vasp 5.2 style
|
26
|
+
- Modify bin/qsubvasp
|
27
|
+
- Add VaspUtils::generate_kmeshes
|
28
|
+
- Add example/dot.vasputils
|
29
|
+
- Add Setting class
|
30
|
+
- Add Potcar::Concatenater
|
31
|
+
- Add Incar.dump
|
32
|
+
- Modify vasputils/poscar.rb to adjust vasp 5.2 style
|
33
|
+
- Renamed and modified bin/rmvaspout to bin/redovasp
|
34
|
+
- Add bin/nextvasp
|
13
35
|
|
14
36
|
== Version 0.0.10
|
15
|
-
Delete Outcar.volume
|
16
|
-
Delete Outcar.irreducible_kpoints
|
17
|
-
Accelerate Outcar, using UNIX commands: grep, tail, and head
|
18
|
-
Modify bin/symposcar
|
19
|
-
Add bin/rmvaspout
|
20
|
-
Change name space for classes
|
37
|
+
- Delete Outcar.volume
|
38
|
+
- Delete Outcar.irreducible_kpoints
|
39
|
+
- Accelerate Outcar, using UNIX commands: grep, tail, and head
|
40
|
+
- Modify bin/symposcar
|
41
|
+
- Add bin/rmvaspout
|
42
|
+
- Change name space for classes
|
21
43
|
|
22
44
|
== Version 0.0.9
|
23
|
-
Add VaspDir.poscar
|
24
|
-
Add bin/checkvasp
|
25
|
-
Delete bin/lsvasp, bin/lsvaspdir, bin/lsvaspseries
|
45
|
+
- Add VaspDir.poscar
|
46
|
+
- Add bin/checkvasp
|
47
|
+
- Delete bin/lsvasp, bin/lsvaspdir, bin/lsvaspseries
|
26
48
|
|
27
49
|
== Version 0.0.8
|
28
|
-
Modified bin/qsubvasp, add -g option
|
50
|
+
- Modified bin/qsubvasp, add -g option
|
29
51
|
|
30
52
|
== Version 0.0.7
|
31
|
-
Modified bin/qsubvasp
|
53
|
+
- Modified bin/qsubvasp
|
32
54
|
|
33
55
|
== Version 0.0.6
|
34
|
-
bin/qsubvasp is added
|
35
|
-
lib/vaspdir is modified to raise ExecuteError when vasp failed
|
56
|
+
- bin/qsubvasp is added
|
57
|
+
- lib/vaspdir is modified to raise ExecuteError when vasp failed
|
36
58
|
|
37
59
|
== Version 0.0.5
|
38
|
-
Modifiy error process in VaspDir.calculate
|
39
|
-
Add
|
40
|
-
Add qsubvasp
|
60
|
+
- Modifiy error process in VaspDir.calculate
|
61
|
+
- Add qsubvasp
|
41
62
|
|
42
63
|
== Version 0.0.4
|
43
|
-
Modified to use Comana
|
44
|
-
bin/runvasp is added
|
45
|
-
VaspDir is modified
|
46
|
-
VaspGeomOpt is added
|
64
|
+
- Modified to use Comana
|
65
|
+
- bin/runvasp is added
|
66
|
+
- VaspDir is modified
|
67
|
+
- VaspGeomOpt is added
|
47
68
|
|
48
69
|
== Version 0.0.3
|
data/Gemfile
CHANGED
@@ -6,14 +6,15 @@ source "http://rubygems.org"
|
|
6
6
|
# Add dependencies to develop your gem here.
|
7
7
|
# Include everything needed to run rake, tests, features, etc.
|
8
8
|
group :development do
|
9
|
-
gem "rdoc", "
|
10
|
-
gem "bundler", "
|
11
|
-
gem "jeweler", "
|
12
|
-
gem "simplecov", ">= 0"
|
13
|
-
gem "
|
14
|
-
gem "
|
15
|
-
gem "malge", ">= 0.0.1"
|
9
|
+
gem "rdoc", "~> 4.1.1"
|
10
|
+
gem "bundler", "~> 1.7.2"
|
11
|
+
gem "jeweler", "~> 2.0.1"
|
12
|
+
gem "simplecov", ">= 0.9.0"
|
13
|
+
gem "mageo", ">= 0.0.3"
|
14
|
+
gem "malge", ">= 0.0.8"
|
16
15
|
gem "maset", ">= 0.0.0"
|
17
|
-
gem "comana", ">= 0.0.
|
18
|
-
gem "builtinextension", ">= 0.
|
16
|
+
gem "comana", ">= 0.0.10"
|
17
|
+
gem "builtinextension", ">= 0.1.2"
|
18
|
+
gem "crystalcell", ">= 0.0.2"
|
19
|
+
#gem "psych", ">= 0"
|
19
20
|
end
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.0.
|
1
|
+
0.0.12
|
File without changes
|
data/bin/checkvasp
CHANGED
@@ -1,80 +1,111 @@
|
|
1
1
|
#! /usr/bin/env ruby
|
2
2
|
# coding: utf-8
|
3
3
|
|
4
|
-
|
4
|
+
puts "'checkvasp' is obsoleted. Use showvaspdir and showvaspgeomopt."
|
5
|
+
exit
|
5
6
|
|
6
|
-
|
7
|
-
|
8
|
-
|
9
|
-
require "
|
10
|
-
|
11
|
-
#require "vasputils
|
12
|
-
#
|
13
|
-
require "pp"
|
7
|
+
## Show state of vasp geometry optimization calculations.
|
8
|
+
#
|
9
|
+
##require "vasputils/calcseries.rb"
|
10
|
+
#require "rubygems"
|
11
|
+
#gem "vasputils"
|
12
|
+
#require "vasputils.rb"
|
13
|
+
#
|
14
|
+
#require "pp"
|
14
15
|
#require "optparse"
|
15
|
-
|
16
|
-
|
17
|
-
|
18
|
-
|
19
|
-
|
20
|
-
|
21
|
-
|
22
|
-
|
23
|
-
|
24
|
-
|
25
|
-
|
26
|
-
|
27
|
-
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
32
|
-
|
33
|
-
|
34
|
-
|
35
|
-
|
36
|
-
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
68
|
-
|
69
|
-
rescue
|
70
|
-
|
71
|
-
end
|
72
|
-
|
73
|
-
|
74
|
-
|
75
|
-
|
76
|
-
|
77
|
-
|
78
|
-
|
79
|
-
|
80
|
-
|
16
|
+
#
|
17
|
+
### option analysis
|
18
|
+
#OPTIONS = {}
|
19
|
+
#op = OptionParser.new
|
20
|
+
#OPTIONS[:show_state] = []
|
21
|
+
#op.on("-f", "--finished" , "Show finished. -a is ignored."){OPTIONS[:show_state] << :finished}
|
22
|
+
#op.on("-y", "--yet" , "Show yet." ){OPTIONS[:show_state] << :yet}
|
23
|
+
#op.on("-t", "--terminated", "Show terminated." ){OPTIONS[:show_state] << :terminated}
|
24
|
+
#op.on("-s", "--started" , "Show sarted." ){OPTIONS[:show_state] << :started}
|
25
|
+
#op.on("-l", "--files-with-matches", "Show filename only." ){OPTIONS[:filename ] = true}
|
26
|
+
#op.parse!(ARGV)
|
27
|
+
#
|
28
|
+
### if all select are not set, all are set.
|
29
|
+
#if OPTIONS[:show_state].size == 0
|
30
|
+
# OPTIONS[:all] = true
|
31
|
+
#end
|
32
|
+
##pp OPTIONS; exit
|
33
|
+
#
|
34
|
+
#LONGEST_STATE = :terminated.size
|
35
|
+
#KLASSES = [VaspUtils::VaspDir, VaspUtils::VaspGeometryOptimizer]
|
36
|
+
#
|
37
|
+
#dirs = ARGV
|
38
|
+
#dirs = Dir.glob("*").sort if ARGV.empty?
|
39
|
+
#
|
40
|
+
#def guess(dir)
|
41
|
+
# KLASSES.each do |klass|
|
42
|
+
# begin
|
43
|
+
# vd = klass.new(dir)
|
44
|
+
# return klass
|
45
|
+
# rescue klass::InitializeError
|
46
|
+
# end
|
47
|
+
# end
|
48
|
+
# raise "Cannot identify class for directory #{dir}."
|
49
|
+
#end
|
50
|
+
#
|
51
|
+
#def show(klass_name, state, try, toten, i_step, e_step, dir)
|
52
|
+
# if (OPTIONS[:all]) || (OPTIONS[:show_state].include? state)
|
53
|
+
# unless OPTIONS[:filename]
|
54
|
+
# printf "%-11s ", klass_name
|
55
|
+
# printf "%-10s ", state
|
56
|
+
# printf "%5s ", try
|
57
|
+
# printf "%17s %3s (%3s) ", toten, i_step, e_step
|
58
|
+
# end
|
59
|
+
# print dir
|
60
|
+
# puts
|
61
|
+
# end
|
62
|
+
#end
|
63
|
+
#
|
64
|
+
#dirs.each do |dir|
|
65
|
+
# next unless File.directory? dir
|
66
|
+
#
|
67
|
+
# begin
|
68
|
+
# klass = guess(dir)
|
69
|
+
# klass_name = klass.to_s
|
70
|
+
# rescue
|
71
|
+
# klass_name = "UnknownDir"
|
72
|
+
# end
|
73
|
+
#
|
74
|
+
# case klass_name
|
75
|
+
# when "VaspUtils::VaspDir"
|
76
|
+
# klass_name = "VaspDir"
|
77
|
+
# calc = klass.new(dir)
|
78
|
+
# state = calc.state
|
79
|
+
# try = ""
|
80
|
+
# begin
|
81
|
+
# outcar = calc.outcar
|
82
|
+
# toten = sprintf("%17.6f", outcar[:totens][-1].to_f)
|
83
|
+
# i_step = outcar[:ionic_steps]
|
84
|
+
# e_step = outcar[:electronic_steps]
|
85
|
+
# rescue
|
86
|
+
# toten = i_step = e_step = ""
|
87
|
+
# end
|
88
|
+
#
|
89
|
+
# when "VaspUtils::VaspGeometryOptimizer"
|
90
|
+
# klass_name = "VaspGeomOpt"
|
91
|
+
# calc = klass.new(dir)
|
92
|
+
# state = calc.state
|
93
|
+
#
|
94
|
+
# ld = calc.latest_dir
|
95
|
+
# try = sprintf "%5s", ld.dir.sub(/.*try/, "try")
|
96
|
+
# begin
|
97
|
+
# outcar = ld.outcar
|
98
|
+
# toten = sprintf("%15.6f ", outcar[:totens][-1].to_f)
|
99
|
+
# i_step = outcar[:ionic_steps]
|
100
|
+
# e_step = outcar[:electronic_steps]
|
101
|
+
# rescue
|
102
|
+
# toten = i_step = e_step = ""
|
103
|
+
# end
|
104
|
+
#
|
105
|
+
# when "UnknownDir"
|
106
|
+
# klass_name = "UnknownDir"
|
107
|
+
# state = try = toten = i_step = e_step = ""
|
108
|
+
# end
|
109
|
+
# show(klass_name, state, try, toten, i_step, e_step, dir)
|
110
|
+
#
|
111
|
+
#end
|
data/bin/genincar
CHANGED
@@ -21,8 +21,8 @@ op.parse!(ARGV)
|
|
21
21
|
|
22
22
|
encut = ARGV[0].to_i
|
23
23
|
if encut == 0
|
24
|
-
|
25
|
-
|
24
|
+
puts "ENCUT must be indicated as an argument."
|
25
|
+
exit
|
26
26
|
end
|
27
27
|
|
28
28
|
setting = VaspUtils::Setting.new
|
@@ -32,8 +32,8 @@ items = setting["incar_default"]
|
|
32
32
|
items["ENCUT"] = encut
|
33
33
|
|
34
34
|
VaspUtils::Incar.dump(items, STDOUT)
|
35
|
-
#
|
36
|
-
#
|
35
|
+
# setting['potcar_dir'],
|
36
|
+
# setting['element_potcar']
|
37
37
|
#)
|
38
38
|
#vpc.dump(elements, STDOUT)
|
39
39
|
|
data/bin/genkpoints
CHANGED
@@ -15,28 +15,28 @@ require "vasputils.rb"
|
|
15
15
|
#op.parse!(ARGV)
|
16
16
|
|
17
17
|
unless ARGV.size == 4
|
18
|
-
|
19
|
-
|
20
|
-
|
21
|
-
|
18
|
+
puts "USAGE: genkpoints style kx ky kz"
|
19
|
+
puts " where style is m or g, indicating Monkhorst or GammaCenter, respectively."
|
20
|
+
puts " kx, ky, kz indicate mesh points for each direction."
|
21
|
+
exit
|
22
22
|
end
|
23
23
|
|
24
24
|
data = {}
|
25
25
|
if ARGV[0] =~ /^m/i
|
26
|
-
|
26
|
+
data[:type] = :monkhorst
|
27
27
|
elsif ARGV[0] =~ /^g/i
|
28
|
-
|
28
|
+
data[:type] = :gamma_center
|
29
29
|
else
|
30
|
-
|
31
|
-
|
30
|
+
puts "Unknown type. Exit."
|
31
|
+
exit
|
32
32
|
end
|
33
33
|
|
34
34
|
data[:mesh] = ARGV[1..3].map do |i|
|
35
|
-
|
36
|
-
|
37
|
-
|
38
|
-
|
39
|
-
|
35
|
+
unless i.to_i
|
36
|
+
puts "Mesh divisions must be larger than 0. Exit"
|
37
|
+
exit
|
38
|
+
end
|
39
|
+
i.to_i
|
40
40
|
end
|
41
41
|
|
42
42
|
data[:shift] = [0.0, 0.0, 0.0]
|
data/bin/genpotcar
CHANGED
data/bin/latticeconstants
CHANGED
@@ -1,19 +1,17 @@
|
|
1
1
|
#! /usr/bin/env ruby
|
2
2
|
|
3
3
|
require "rubygems"
|
4
|
+
require "vasputils"
|
4
5
|
|
5
|
-
gem "
|
6
|
-
require "
|
6
|
+
#gem "crystalcell"
|
7
|
+
#require "crystalcell/latticeaxes.rb"
|
8
|
+
#require "crystalcell/cell.rb"
|
7
9
|
|
8
|
-
|
9
|
-
require "crystalcell/latticeaxes.rb"
|
10
|
-
require "crystalcell/cell.rb"
|
11
|
-
|
12
|
-
puts " a, b, c, alpha, beta, gamma, volume, file"
|
10
|
+
puts " a, b, c, alpha, beta, gamma, volume, file"
|
13
11
|
ARGV.each do |file|
|
14
|
-
|
15
|
-
|
16
|
-
|
17
|
-
|
18
|
-
|
12
|
+
axes = VaspUtils::Poscar.load_file(file).axes
|
13
|
+
printf("%8.5f, %8.5f, %8.5f, %6.2f, %6.2f, %6.2f, ",
|
14
|
+
*(axes.get_lattice_constants))
|
15
|
+
printf("%10.5f, ", CrystalCell::Cell.new(axes).calc_volume) # show volume
|
16
|
+
puts file
|
19
17
|
end
|
data/bin/qsubvasp
CHANGED
@@ -1,19 +1,20 @@
|
|
1
1
|
#! /usr/bin/env ruby
|
2
2
|
# coding: utf-8
|
3
|
-
|
4
|
-
|
5
|
-
|
6
|
-
|
7
|
-
|
8
|
-
|
9
|
-
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
-
|
14
|
-
|
15
|
-
|
16
|
-
|
3
|
+
|
4
|
+
USAGE = <<HERE
|
5
|
+
USAGE: qsubvasp [-c CLUSTER_NAME] [-n num] calc_dir
|
6
|
+
|
7
|
+
[-n INDICATOR]
|
8
|
+
Integer can be uused as INDICATOR.
|
9
|
+
If INDICATOR cannot be evaluated as positive integer,
|
10
|
+
try to find tue hostname of localhost and
|
11
|
+
key of
|
12
|
+
the INDICATOR in ~/.clustersetting
|
13
|
+
Default value is 1.
|
14
|
+
|
15
|
+
calc_dir is a vasp directory as usual,
|
16
|
+
when with -g option, VaspGeometryOptimizer directory.
|
17
|
+
HERE
|
17
18
|
|
18
19
|
#require "optparse"
|
19
20
|
require "pp"
|
@@ -21,88 +22,70 @@ require "yaml"
|
|
21
22
|
require "optparse"
|
22
23
|
|
23
24
|
require "rubygems"
|
24
|
-
|
25
|
-
require "comana/queuesubmitter.rb"
|
26
|
-
require "comana/machineinfo.rb"
|
25
|
+
require "comana"
|
27
26
|
|
28
27
|
gem "vasputils"
|
29
28
|
require "vasputils.rb"
|
30
29
|
|
31
|
-
|
30
|
+
OPTIONS = {}
|
32
31
|
|
33
32
|
op = OptionParser.new
|
34
|
-
op.on("-c cluster", "--cluster" , "Cluster name."){|v|
|
35
|
-
op.on("-n number", "--
|
36
|
-
|
33
|
+
op.on("-c cluster", "--cluster=name" , "Cluster name."){|v| OPTIONS[:cluster] = v }
|
34
|
+
op.on("-n number", "--nodes=num", "Indicate node number, or key in ~/.clustersetting."){|v|
|
35
|
+
OPTIONS[:num_nodes] = v
|
37
36
|
}
|
38
|
-
op.on("-g", "--geom-opt", "Geometry optimization."){
|
37
|
+
op.on("-g", "--geom-opt", "Geometry optimization."){ OPTIONS[:geomopt] = true}
|
38
|
+
op.on("-p num", "--priority=num", "Set priority of job."){|v| OPTIONS[:priority] = v }
|
39
39
|
op.parse!(ARGV)
|
40
40
|
|
41
41
|
def condition_check(opts)
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
# cluster
|
46
|
-
name = opts["cluster"]
|
47
|
-
#pp mi.get_info(name)
|
48
|
-
if name
|
49
|
-
conds["cluster"] = name
|
50
|
-
else
|
51
|
-
puts "-c CLUSTER_NAME is necessary."
|
52
|
-
exit
|
53
|
-
end
|
42
|
+
# Condition Check
|
43
|
+
mi = Comana::ClusterSetting.load_file("#{ENV["HOME"]}/.clustersetting")
|
44
|
+
conds = {}
|
54
45
|
|
55
|
-
|
56
|
-
|
57
|
-
puts "Indicate only one directory for vasp. Argument: #{ARGV}"
|
58
|
-
exit
|
59
|
-
end
|
60
|
-
if opts["geomopt"]
|
61
|
-
begin
|
62
|
-
conds["target"] = VaspUtils::VaspGeometryOptimizer.new(File.expand_path(ARGV[0]))
|
63
|
-
conds["command"] = "runvasp -g"
|
64
|
-
rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
|
65
|
-
puts "Seem not to be a directory for VaspGeometryOptimizer #{ARGV}"
|
66
|
-
exit
|
67
|
-
end
|
68
|
-
else
|
69
|
-
begin
|
70
|
-
conds["target"] = VaspUtils::VaspDir.new(File.expand_path(ARGV[0]))
|
71
|
-
conds["command"] = "runvasp"
|
72
|
-
rescue VaspUtils::VaspDir::InitializeError
|
73
|
-
puts "Seem not to be a directory for VaspDir #{ARGV}"
|
74
|
-
exit
|
75
|
-
end
|
76
|
-
end
|
46
|
+
conds[:cluster] = opts[:cluster]
|
47
|
+
conds[:num_nodes] = opts[:num_nodes].to_i if opts[:num_nodes]
|
77
48
|
|
78
|
-
|
79
|
-
|
80
|
-
|
81
|
-
|
82
|
-
|
83
|
-
|
84
|
-
|
85
|
-
|
49
|
+
# target and command
|
50
|
+
unless ARGV.size == 1
|
51
|
+
puts "Indicate only one directory for vasp. Argument: #{ARGV}"
|
52
|
+
exit
|
53
|
+
end
|
54
|
+
if opts[:geomopt]
|
55
|
+
begin
|
56
|
+
conds[:target] = VaspUtils::VaspGeometryOptimizer.new(File.expand_path(ARGV[0]))
|
57
|
+
conds[:command] = "runvasp -g"
|
58
|
+
rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
|
59
|
+
puts "Seem not to be a directory for VaspGeometryOptimizer #{ARGV}"
|
60
|
+
exit
|
61
|
+
end
|
86
62
|
else
|
87
|
-
|
88
|
-
|
63
|
+
begin
|
64
|
+
conds[:target] = VaspUtils::VaspDir.new(File.expand_path(ARGV[0]))
|
65
|
+
conds[:command] = "runvasp"
|
66
|
+
rescue VaspUtils::VaspDir::InitializeError
|
67
|
+
puts "Seem not to be a directory for VaspDir #{ARGV}"
|
68
|
+
exit
|
69
|
+
end
|
89
70
|
end
|
90
|
-
|
91
|
-
|
71
|
+
|
72
|
+
conds[:priority] = opts[:priority].to_i
|
73
|
+
conds
|
92
74
|
end
|
93
|
-
opts = condition_check(
|
75
|
+
opts = condition_check(OPTIONS)
|
76
|
+
#pp opts; exit
|
94
77
|
|
95
|
-
|
96
|
-
|
78
|
+
print ARGV[0] + ", "
|
79
|
+
qs = Comana::QueueSubmitter.new(opts)
|
97
80
|
|
98
81
|
begin
|
99
|
-
|
100
|
-
|
101
|
-
|
102
|
-
rescue QueueSubmitter::AlreadyStartedError
|
103
|
-
|
104
|
-
|
105
|
-
rescue QueueSubmitter::PrepareNextError
|
106
|
-
|
107
|
-
|
82
|
+
qs.start
|
83
|
+
puts "Submitted. Exit."
|
84
|
+
exit
|
85
|
+
rescue Comana::QueueSubmitter::AlreadyStartedError
|
86
|
+
puts "Already started. Exit."
|
87
|
+
exit
|
88
|
+
#rescue Comana::QueueSubmitter::PrepareNextError
|
89
|
+
# puts "Must not happen."
|
90
|
+
# exit
|
108
91
|
end
|
data/bin/resetvaspdir
ADDED
@@ -0,0 +1,51 @@
|
|
1
|
+
#! /usr/bin/env ruby
|
2
|
+
# coding: utf-8
|
3
|
+
|
4
|
+
require "optparse"
|
5
|
+
require "fileutils"
|
6
|
+
require "rubygems"
|
7
|
+
require "comana"
|
8
|
+
require "vasputils"
|
9
|
+
|
10
|
+
## option analysis
|
11
|
+
#OPTIONS = {}
|
12
|
+
#op = OptionParser.new
|
13
|
+
#op.on("-r", "--reset", "Reset to initial state, remove except for 4 files."){OPTIONS[:reset] = true}
|
14
|
+
#op.on("-y", "--yes" , "Answer yes to all questions." ){OPTIONS[:yes] = true}
|
15
|
+
#op.on("-n", "--no" , "Answer no to all questions." ){OPTIONS[:no ] = true}
|
16
|
+
#op.parse!(ARGV)
|
17
|
+
|
18
|
+
tgts = ARGV
|
19
|
+
tgts = [ENV['PWD']] if tgts.size == 0
|
20
|
+
|
21
|
+
#pp tgts; exit
|
22
|
+
|
23
|
+
#def ask
|
24
|
+
# print " Execute? [y/n]: "
|
25
|
+
# if OPTIONS[:yes]
|
26
|
+
# puts "-y option is indicated."
|
27
|
+
# return true
|
28
|
+
# end
|
29
|
+
#
|
30
|
+
# if OPTIONS[:no]
|
31
|
+
# puts "-n option is indicated."
|
32
|
+
# return false
|
33
|
+
# end
|
34
|
+
#
|
35
|
+
# /^y/i =~ $stdin.readline
|
36
|
+
#end
|
37
|
+
|
38
|
+
tgts.each do |tgt_dir|
|
39
|
+
puts "Directory: #{tgt_dir}"
|
40
|
+
|
41
|
+
# Check tgt_dir is VaspDir?
|
42
|
+
begin
|
43
|
+
vd = VaspUtils::VaspDir.new(tgt_dir)
|
44
|
+
rescue VaspUtils::VaspDir::InitializeError
|
45
|
+
puts " Not VaspDir: #{tgt_dir}"
|
46
|
+
next
|
47
|
+
end
|
48
|
+
|
49
|
+
vd.reset_init
|
50
|
+
|
51
|
+
end
|