vasputils 0.0.1 → 0.0.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (42) hide show
  1. data/Gemfile +1 -1
  2. data/VERSION +1 -1
  3. data/bin/qsubvasp +30 -0
  4. data/lib/vasputils/vaspdir.rb +176 -218
  5. data/test/test_vaspdir.rb +59 -189
  6. data/test/vaspdir/finished/CONTCAR +17 -0
  7. data/test/vaspdir/finished/INCAR +27 -0
  8. data/test/vaspdir/finished/KPOINTS +6 -0
  9. data/test/vaspdir/finished/OUTCAR +1436 -0
  10. data/test/vaspdir/finished/POSCAR +12 -0
  11. data/test/vaspdir/finished/POTCAR +16 -0
  12. data/test/vaspdir/finished/lock +0 -0
  13. data/test/vaspdir/lack-INCAR/KPOINTS +5 -4
  14. data/test/vaspdir/lack-INCAR/POSCAR +11 -56
  15. data/test/vaspdir/lack-INCAR/POTCAR +13 -695
  16. data/test/vaspdir/lack-KPOINTS/INCAR +2 -3
  17. data/test/vaspdir/lack-KPOINTS/POSCAR +11 -56
  18. data/test/vaspdir/lack-KPOINTS/POTCAR +13 -695
  19. data/test/vaspdir/lack-POSCAR/INCAR +2 -3
  20. data/test/vaspdir/lack-POSCAR/KPOINTS +5 -4
  21. data/test/vaspdir/lack-POSCAR/POTCAR +13 -695
  22. data/test/vaspdir/lack-POTCAR/INCAR +2 -3
  23. data/test/vaspdir/lack-POTCAR/KPOINTS +5 -4
  24. data/test/vaspdir/lack-POTCAR/POSCAR +11 -56
  25. data/test/vaspdir/locked/INCAR +28 -0
  26. data/test/vaspdir/locked/KPOINTS +6 -0
  27. data/test/vaspdir/locked/POSCAR +12 -0
  28. data/test/vaspdir/locked/POTCAR +16 -0
  29. data/test/vaspdir/locked/lock +0 -0
  30. data/test/vaspdir/not-yet/INCAR +28 -0
  31. data/test/vaspdir/not-yet/KPOINTS +6 -0
  32. data/test/vaspdir/not-yet/POSCAR +12 -0
  33. data/test/vaspdir/not-yet/POTCAR +16 -0
  34. data/test/vaspdir/started/CONTCAR +17 -0
  35. data/test/vaspdir/started/INCAR +27 -0
  36. data/test/vaspdir/started/KPOINTS +6 -0
  37. data/test/vaspdir/started/OUTCAR +1028 -0
  38. data/test/vaspdir/started/POSCAR +12 -0
  39. data/test/vaspdir/started/POTCAR +16 -0
  40. data/test/vaspdir/started/lock +0 -0
  41. data/vasputils.gemspec +27 -3
  42. metadata +48 -23
data/test/vaspdir/lack-POTCAR/INCAR CHANGED
@@ -2,9 +2,8 @@
2
2
 
3
3
  SYSTEM = Untitled (VASP)
4
4
  PREC = High
5
- IBRION = 2 #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient
6
- NSW = 100 #maximum number of ionic steps
7
- ISIF = 2
5
+ IBRION = -1 #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient
6
+ NSW = 0 #maximum number of ionic steps
8
7
  ENCUT = 400
9
8
  NELM = 60 #maximum number of electronic steps
10
9
  NELMIN = 2 #minimum number of electronic steps
data/test/vaspdir/lack-POTCAR/KPOINTS CHANGED
@@ -1,5 +1,6 @@
1
- K dimer
2
- 1
3
- Cartesian
4
- 0.0 0.0 0.0 1.0
1
+ Automatic mesh
2
+ 0
3
+ Monkhorst Pack
4
+ 5 5 5
5
+ 0. 0. 0.
5
6
 
data/test/vaspdir/lack-POTCAR/POSCAR CHANGED
@@ -1,57 +1,12 @@
1
- Hg: 50 Atome emty-core PP
2
- 10.797
3
- 1.000000 0.000000 0.000000
4
- 0.000000 1.000000 0.000000
5
- 0.000000 0.000000 1.000000
6
- 50
1
+ Untitled (VASP)
2
+ 1.00000000000000
3
+ 3.6509999999999998 0.0000000000000000 0.0000000000000000
4
+ -1.8254999999999919 3.1618587492169889 0.0000000000000000
5
+ 0.0000000000000000 0.0000000000000000 3.8879999999999999
6
+ 3 1
7
+ Selective dynamics
7
8
  Direct
8
- 0.300387 0.972562 0.679901
9
- 0.100399 0.866618 0.886586
10
- 0.423249 0.857844 0.900790
11
- 0.613554 0.944543 0.680853
12
- 0.970627 0.656315 0.884095
13
- 0.351857 0.342419 0.112772
14
- 0.322561 0.435330 0.683309
15
- 0.801257 0.977938 0.924631
16
- 0.355613 0.279208 0.451754
17
- 0.610843 0.151156 0.009135
18
- 0.664978 0.522227 0.668415
19
- 0.895048 0.463963 0.971092
20
- 0.143442 0.605562 0.116262
21
- 0.158326 0.370853 0.885693
22
- 0.529145 0.457905 0.887851
23
- 0.623846 0.898892 0.135456
24
- 0.828795 0.231410 0.139571
25
- 0.387649 0.992483 0.194004
26
- 0.290196 0.108184 0.933770
27
- 0.778191 0.980289 0.401008
28
- 0.978383 0.437601 0.269070
29
- 0.086086 0.515543 0.571579
30
- 0.644305 0.468538 0.145630
31
- 0.966275 0.219162 0.433028
32
- 0.797059 0.662811 0.149471
33
- 0.288510 0.799938 0.385229
34
- 0.288030 0.501670 0.364813
35
- 0.665728 0.713615 0.835633
36
- 0.956106 0.927573 0.104753
37
- 0.249434 0.863491 0.128942
38
- 0.431306 0.634852 0.124986
39
- 0.596244 0.739948 0.374908
40
- 0.117453 0.029291 0.402524
41
- 0.610587 0.185561 0.273152
42
- 0.460139 0.008115 0.471084
43
- 0.764721 0.260565 0.835285
44
- 0.027998 0.134521 0.918215
45
- 0.122932 0.171092 0.656118
46
- 0.697215 0.235320 0.554313
47
- 0.792514 0.499263 0.399819
48
- 0.908128 0.395570 0.648346
49
- 0.145878 0.240224 0.206085
50
- 0.541993 0.482572 0.401045
51
- 0.450011 0.684620 0.606616
52
- 0.806597 0.736448 0.597417
53
- 0.998756 0.742263 0.334617
54
- 0.261399 0.640158 0.824182
55
- 0.901735 0.975298 0.656187
56
- 0.075248 0.785818 0.587437
57
- 0.469267 0.192855 0.692567
9
+ 0.0000000000000000 0.0000000000000000 0.5000000000000000 T T T
10
+ 0.3333333333333333 0.6666666666666666 0.0000000000000000 T T T
11
+ 0.6666666666666666 0.3333333333333333 0.0000000000000000 T T T
12
+ 0.0000000000000000 0.0000000000000000 0.0000000000000000 F F F
data/test/vaspdir/locked/INCAR ADDED
@@ -0,0 +1,28 @@
1
+ # SCF input for VASP
2
+
3
+ SYSTEM = Untitled (VASP)
4
+ PREC = High
5
+ IBRION = 2 #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient
6
+ NSW = 100 #maximum number of ionic steps
7
+ ISIF = 2
8
+ ENCUT = 400
9
+ NELM = 60 #maximum number of electronic steps
10
+ NELMIN = 2 #minimum number of electronic steps
11
+ EDIFF = 1.0e-05
12
+ EDIFFG = -0.02
13
+ VOSKOWN = 1
14
+ NBLOCK = 1
15
+ ISPIN = 1 #1:non spin polarized, 2:spin polarized
16
+ INIWAV = 1
17
+ ISTART = 1
18
+ ICHARG = 1
19
+ LWAVE = .TRUE.
20
+ LCHARG = .TRUE.
21
+ ISMEAR = 0
22
+ SIGMA = 0.1
23
+ IALGO = 38 #38:KosugiAlgorithm, 48:RMM-DIIS
24
+ #LREAL = .FALSE.
25
+ LREAL = Auto #fast & not accurate
26
+ NGX = 36
27
+ NGY = 36
28
+ NGZ = 42
data/test/vaspdir/locked/KPOINTS ADDED
@@ -0,0 +1,6 @@
1
+ Automatic mesh
2
+ 0
3
+ Monkhorst Pack
4
+ 5 5 5
5
+ 0. 0. 0.
6
+
data/test/vaspdir/locked/POSCAR ADDED
@@ -0,0 +1,12 @@
1
+ Untitled (VASP)
2
+ 1.00000000000000
3
+ 3.6509999999999998 0.0000000000000000 0.0000000000000000
4
+ -1.8254999999999919 3.1618587492169889 0.0000000000000000
5
+ 0.0000000000000000 0.0000000000000000 3.8879999999999999
6
+ 3 1
7
+ Selective dynamics
8
+ Direct
9
+ 0.0000000000000000 0.0000000000000000 0.5000000000000000 T T T
10
+ 0.3333333333333333 0.6666666666666666 0.0000000000000000 T T T
11
+ 0.6666666666666666 0.3333333333333333 0.0000000000000000 T T T
12
+ 0.0000000000000000 0.0000000000000000 0.0000000000000000 F F F
data/test/vaspdir/locked/POTCAR ADDED
@@ -0,0 +1,16 @@
1
+ PAW_GGA Li_sv 23Jan2001
2
+ 3.00000000000000000
3
+ parameters from PSCTR are:
4
+ VRHFIN =Li: 1s2s2p
5
+ LEXCH = 91
6
+ EATOM = 203.0979 eV, 14.9273 Ry
7
+
8
+ TITEL = PAW_GGA Li_sv 23Jan2001
9
+ PAW_GGA N 31May2000
10
+ 5.00000000000000000
11
+ parameters from PSCTR are:
12
+ VRHFIN =N: s2p3
13
+ LEXCH = 91
14
+ EATOM = 265.0126 eV, 19.4779 Ry
15
+
16
+ TITEL = PAW_GGA N 31May2000
data/test/vaspdir/locked/lock ADDED
File without changes
data/test/vaspdir/not-yet/INCAR ADDED
@@ -0,0 +1,28 @@
1
+ # SCF input for VASP
2
+
3
+ SYSTEM = Untitled (VASP)
4
+ PREC = High
5
+ IBRION = 2 #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient
6
+ NSW = 100 #maximum number of ionic steps
7
+ ISIF = 2
8
+ ENCUT = 400
9
+ NELM = 60 #maximum number of electronic steps
10
+ NELMIN = 2 #minimum number of electronic steps
11
+ EDIFF = 1.0e-05
12
+ EDIFFG = -0.02
13
+ VOSKOWN = 1
14
+ NBLOCK = 1
15
+ ISPIN = 1 #1:non spin polarized, 2:spin polarized
16
+ INIWAV = 1
17
+ ISTART = 1
18
+ ICHARG = 1
19
+ LWAVE = .TRUE.
20
+ LCHARG = .TRUE.
21
+ ISMEAR = 0
22
+ SIGMA = 0.1
23
+ IALGO = 38 #38:KosugiAlgorithm, 48:RMM-DIIS
24
+ #LREAL = .FALSE.
25
+ LREAL = Auto #fast & not accurate
26
+ NGX = 36
27
+ NGY = 36
28
+ NGZ = 42
data/test/vaspdir/not-yet/KPOINTS ADDED
@@ -0,0 +1,6 @@
1
+ Automatic mesh
2
+ 0
3
+ Monkhorst Pack
4
+ 5 5 5
5
+ 0. 0. 0.
6
+
data/test/vaspdir/not-yet/POSCAR ADDED
@@ -0,0 +1,12 @@
1
+ Untitled (VASP)
2
+ 1.00000000000000
3
+ 3.6509999999999998 0.0000000000000000 0.0000000000000000
4
+ -1.8254999999999919 3.1618587492169889 0.0000000000000000
5
+ 0.0000000000000000 0.0000000000000000 3.8879999999999999
6
+ 3 1
7
+ Selective dynamics
8
+ Direct
9
+ 0.0000000000000000 0.0000000000000000 0.5000000000000000 T T T
10
+ 0.3333333333333333 0.6666666666666666 0.0000000000000000 T T T
11
+ 0.6666666666666666 0.3333333333333333 0.0000000000000000 T T T
12
+ 0.0000000000000000 0.0000000000000000 0.0000000000000000 F F F
data/test/vaspdir/not-yet/POTCAR ADDED
@@ -0,0 +1,16 @@
1
+ PAW_GGA Li_sv 23Jan2001
2
+ 3.00000000000000000
3
+ parameters from PSCTR are:
4
+ VRHFIN =Li: 1s2s2p
5
+ LEXCH = 91
6
+ EATOM = 203.0979 eV, 14.9273 Ry
7
+
8
+ TITEL = PAW_GGA Li_sv 23Jan2001
9
+ PAW_GGA N 31May2000
10
+ 5.00000000000000000
11
+ parameters from PSCTR are:
12
+ VRHFIN =N: s2p3
13
+ LEXCH = 91
14
+ EATOM = 265.0126 eV, 19.4779 Ry
15
+
16
+ TITEL = PAW_GGA N 31May2000
data/test/vaspdir/started/CONTCAR ADDED
@@ -0,0 +1,17 @@
1
+ Untitled (VASP)
2
+ 1.00000000000000
3
+ 3.6509999999999998 0.0000000000000000 0.0000000000000000
4
+ -1.8254999999999919 3.1618587492169889 0.0000000000000000
5
+ 0.0000000000000000 0.0000000000000000 3.8879999999999999
6
+ 3 1
7
+ Selective dynamics
8
+ Direct
9
+ 0.0000000000000000 0.0000000000000000 0.5000000000000000 T T T
10
+ 0.3333333333333357 0.6666666666666642 0.0000000000000000 T T T
11
+ 0.6666666666666642 0.3333333333333357 0.0000000000000000 T T T
12
+ 0.0000000000000000 0.0000000000000000 0.0000000000000000 F F F
13
+
14
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00
15
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00
16
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00
17
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00
data/test/vaspdir/started/INCAR ADDED
@@ -0,0 +1,27 @@
1
+ # SCF input for VASP
2
+
3
+ SYSTEM = Untitled (VASP)
4
+ PREC = High
5
+ IBRION = -1 #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient
6
+ NSW = 0 #maximum number of ionic steps
7
+ ENCUT = 400
8
+ NELM = 60 #maximum number of electronic steps
9
+ NELMIN = 2 #minimum number of electronic steps
10
+ EDIFF = 1.0e-05
11
+ EDIFFG = -0.02
12
+ VOSKOWN = 1
13
+ NBLOCK = 1
14
+ ISPIN = 1 #1:non spin polarized, 2:spin polarized
15
+ INIWAV = 1
16
+ ISTART = 1
17
+ ICHARG = 1
18
+ LWAVE = .TRUE.
19
+ LCHARG = .TRUE.
20
+ ISMEAR = 0
21
+ SIGMA = 0.1
22
+ IALGO = 38 #38:KosugiAlgorithm, 48:RMM-DIIS
23
+ #LREAL = .FALSE.
24
+ LREAL = Auto #fast & not accurate
25
+ NGX = 36
26
+ NGY = 36
27
+ NGZ = 42
data/test/vaspdir/started/KPOINTS ADDED
@@ -0,0 +1,6 @@
1
+ Automatic mesh
2
+ 0
3
+ Monkhorst Pack
4
+ 5 5 5
5
+ 0. 0. 0.
6
+