crysna 0.0.4

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Files changed (138) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/CHANGES +24 -0
  4. data/Gemfile +26 -0
  5. data/Gemfile.lock +91 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.rdoc +19 -0
  8. data/Rakefile +53 -0
  9. data/VERSION +1 -0
  10. data/bin/checkmodel +66 -0
  11. data/bin/collectcell +92 -0
  12. data/bin/fitframe +68 -0
  13. data/bin/occupiedpolyhedralsite +96 -0
  14. data/bin/occupiedscattersite +77 -0
  15. data/bin/site2poscar +66 -0
  16. data/bin/site2pov +30 -0
  17. data/bin/sitecombination +69 -0
  18. data/bin/sitemigration +80 -0
  19. data/bin/sitemigrationdistance +87 -0
  20. data/bin/siteoperation +109 -0
  21. data/bin/sitesingle +36 -0
  22. data/bin/siteuniq +32 -0
  23. data/bin/symidsite +65 -0
  24. data/bin/transitcell +46 -0
  25. data/crysna.gemspec +219 -0
  26. data/lib/crysna.rb +26 -0
  27. data/lib/crysna/atom.rb +97 -0
  28. data/lib/crysna/cell.rb +314 -0
  29. data/lib/crysna/frameatom.rb +13 -0
  30. data/lib/crysna/frameinterstitialcell.rb +309 -0
  31. data/lib/crysna/interstitialatom.rb +13 -0
  32. data/lib/crysna/modelstructure.rb +333 -0
  33. data/lib/crysna/optionmanager.rb +177 -0
  34. data/lib/crysna/site.rb +35 -0
  35. data/lib/crysna/siteconfiguration.rb +26 -0
  36. data/lib/crysna/sitenamelabeledcell.rb +220 -0
  37. data/lib/crysna/siteoperation.rb +56 -0
  38. data/lib/crysna/sitewithposition.rb +24 -0
  39. data/lib/crysna/transitionfinder.rb +448 -0
  40. data/lib/crysna/transitionfinder/cell.rb +144 -0
  41. data/lib/crysna/transitionfinder/cellmanager.rb +129 -0
  42. data/lib/crysna/transitionfinder/edge.rb +54 -0
  43. data/test/.gitignore +1 -0
  44. data/test/cell_orig/POSCAR +17 -0
  45. data/test/cell_orig/model.yaml +122 -0
  46. data/test/collectcells/.gitignore +2 -0
  47. data/test/collectcells/model.yaml +154 -0
  48. data/test/collectcells/nooutcar/minexpconfiguration.yaml +22 -0
  49. data/test/collectcells/normal-higher/OUTCAR +2406 -0
  50. data/test/collectcells/normal-higher/minexpconfiguration.yaml +22 -0
  51. data/test/collectcells/normal-lower/OUTCAR +2406 -0
  52. data/test/collectcells/normal-lower/minexpconfiguration.yaml +22 -0
  53. data/test/collectcells/normal/OUTCAR +2406 -0
  54. data/test/collectcells/normal/minexpconfiguration.yaml +22 -0
  55. data/test/collectcells/normalB/OUTCAR +2406 -0
  56. data/test/collectcells/normalB/minexpconfiguration.yaml +22 -0
  57. data/test/collectcells/unfinished/OUTCAR +40702 -0
  58. data/test/collectcells/unfinished/minexpconfiguration.yaml +22 -0
  59. data/test/collectcells/unidentified/OUTCAR +3541 -0
  60. data/test/collectcells/unidentified/minexpconfiguration.yaml +2 -0
  61. data/test/fitmodelstructure/.gitignore +1 -0
  62. data/test/fitmodelstructure/AgI/CONTCAR +17 -0
  63. data/test/fitmodelstructure/AgI/fitmodelstructure.log +1161 -0
  64. data/test/fitmodelstructure/AgI/model.yaml +45 -0
  65. data/test/fitmodelstructure/normal/CONTCAR +17 -0
  66. data/test/fitmodelstructure/normal/fitmodelstructure.log +5063 -0
  67. data/test/fitmodelstructure/normal/model.yaml +122 -0
  68. data/test/fitmodelstructure/unidentified/CONTCAR +44 -0
  69. data/test/fitmodelstructure/unidentified/fitmodelstructure.log +8833 -0
  70. data/test/fitmodelstructure/unidentified/model.yaml +154 -0
  71. data/test/helper.rb +17 -0
  72. data/test/identifypolyhedralsites/.gitignore +1 -0
  73. data/test/identifypolyhedralsites/identifyatomsites.log +333 -0
  74. data/test/identifypolyhedralsites/normal/fitmodelstructure.yaml +60 -0
  75. data/test/identifypolyhedralsites/normal/model.yaml +122 -0
  76. data/test/identifypolyhedralsites/unidentified/fitmodelstructure.yaml +2 -0
  77. data/test/identifypolyhedralsites/unidentified/model.yaml +154 -0
  78. data/test/identifypolyhedralsites/volumemismatch/fitmodelstructure.yaml +101 -0
  79. data/test/identifypolyhedralsites/volumemismatch/model.yaml +154 -0
  80. data/test/identifyscattersites/CONTCAR +17 -0
  81. data/test/identifyscattersites/POSCAR +12 -0
  82. data/test/identifyscattersites/fitmodelstructure.log +1 -0
  83. data/test/identifyscattersites/fitmodelstructure.yaml +0 -0
  84. data/test/identifyscattersites/identifyscattersites.yaml +5 -0
  85. data/test/identifyscattersites/model.yaml +45 -0
  86. data/test/minexpconfiguration/.gitignore +1 -0
  87. data/test/minexpconfiguration/collective/AgI/.gitignore +2 -0
  88. data/test/minexpconfiguration/collective/AgI/siteoperations.yaml +51265 -0
  89. data/test/minexpconfiguration/collective/AgI/sitesingle.yaml +15 -0
  90. data/test/minexpconfiguration/collective/AgI/test.sh +2 -0
  91. data/test/minexpconfiguration/normal/identifysites.yaml +22 -0
  92. data/test/minexpconfiguration/normal/minexpconfiguration.log +0 -0
  93. data/test/minexpconfiguration/normal/siteoperations.yaml +1793 -0
  94. data/test/minexpconfiguration/unidentified/identifysites.yaml +2 -0
  95. data/test/minexpconfiguration/unidentified/siteoperations.yaml +1793 -0
  96. data/test/sitecombination/initsites.yaml +7 -0
  97. data/test/sitecombination/initsites_test2.yaml +8 -0
  98. data/test/sitecombination/sitecombination.yaml +29 -0
  99. data/test/siteconfiguration/elements-sitenames.yaml +2 -0
  100. data/test/siteconfiguration/latticeaxes.yaml +3 -0
  101. data/test/siteconfiguration/sitenames-coordinates.yaml +4 -0
  102. data/test/sitemigrationsdistance/model.yaml +45 -0
  103. data/test/siteoperations/.gitignore +2 -0
  104. data/test/siteoperations/model.yaml +43 -0
  105. data/test/siteoperations/symmetryoperations.yaml +1441 -0
  106. data/test/sitesingle/.gitignore +1 -0
  107. data/test/sitesingle/sitecombination.yaml +29 -0
  108. data/test/siteuniq/minexpconfiguration.yaml +15 -0
  109. data/test/siteuniq/siteuniq.yaml +8 -0
  110. data/test/test_atom.rb +206 -0
  111. data/test/test_cell.rb +604 -0
  112. data/test/test_commands.rb +340 -0
  113. data/test/test_crystana.rb +7 -0
  114. data/test/test_frameatom.rb +22 -0
  115. data/test/test_frameinterstitialcell.rb +939 -0
  116. data/test/test_interstitialatom.rb +22 -0
  117. data/test/test_modelstructure.rb +807 -0
  118. data/test/test_optionmanager.rb +172 -0
  119. data/test/test_site.rb +40 -0
  120. data/test/test_siteconfiguration.rb +29 -0
  121. data/test/test_sitenamelabeledcell.rb +528 -0
  122. data/test/test_siteoperation.rb +79 -0
  123. data/test/test_sitewithposition.rb +20 -0
  124. data/test/test_transitionfinder.rb +432 -0
  125. data/test/transitcell/.gitignore +2 -0
  126. data/test/transitcell/collectcells.yaml +51 -0
  127. data/test/transitcell/sitemigrations.yaml +8 -0
  128. data/test/transitcell/siteoperations.yaml +17 -0
  129. data/test/transitcell/transitcell.log +1342 -0
  130. data/test/transitionfinder/collectcells.yaml +81 -0
  131. data/test/transitionfinder/sitemigrations.yaml +33 -0
  132. data/test/transitionfinder/siteoperations.yaml +16 -0
  133. data/test/transitionfinder/test_cell.rb +287 -0
  134. data/test/transitionfinder/test_cellmanager.rb +185 -0
  135. data/test/transitionfinder/test_edge.rb +49 -0
  136. data/test/uniquesitesgenerator/elements-sitenames.yaml +1 -0
  137. data/test/uniquesitesgenerator/siteoperations.yaml +9 -0
  138. metadata +406 -0
data/test/identifypolyhedralsites/normal/fitmodelstructure.yaml ADDED
@@ -0,0 +1,60 @@
1
+ ---
2
+ frame_atoms:
3
+ FS_000:
4
+ element: 0
5
+ coordinates:
6
+ - 0.0
7
+ - 1.734723475976807e-18
8
+ - 8.673617379884035e-19
9
+ FS_001:
10
+ element: 0
11
+ coordinates:
12
+ - 0.0
13
+ - 1.734723475976807e-18
14
+ - 0.009999999999999995
15
+ FS_003:
16
+ element: 0
17
+ coordinates:
18
+ - 0.0
19
+ - 1.734723475976807e-18
20
+ - 0.03
21
+ FS_020:
22
+ element: 0
23
+ coordinates:
24
+ - 0.0
25
+ - 0.01999999999999999
26
+ - 8.673617379884035e-19
27
+ FS_060:
28
+ element: 0
29
+ coordinates:
30
+ - 0.0
31
+ - 0.06
32
+ - 8.673617379884035e-19
33
+ FS_300:
34
+ element: 0
35
+ coordinates:
36
+ - 0.03
37
+ - 1.734723475976807e-18
38
+ - 8.673617379884035e-19
39
+ FS_900:
40
+ element: 0
41
+ coordinates:
42
+ - 0.09
43
+ - 1.734723475976807e-18
44
+ - 8.673617379884035e-19
45
+ interstitials:
46
+ - element: 1
47
+ coordinates:
48
+ - 0.009999999999999995
49
+ - 0.009999999999999997
50
+ - 0.009999999999999995
51
+ - element: 2
52
+ coordinates:
53
+ - 0.9
54
+ - 0.9
55
+ - 0.9
56
+ - element: 2
57
+ coordinates:
58
+ - 0.1
59
+ - 0.1
60
+ - 0.1
data/test/identifypolyhedralsites/normal/model.yaml ADDED
@@ -0,0 +1,122 @@
1
+ ---
2
+ frame_elements:
3
+ - 0
4
+ frame_sites:
5
+ FS_000:
6
+ - 0.0
7
+ - 0.0
8
+ - 0.0
9
+ FS_001:
10
+ - 0.0
11
+ - 0.0
12
+ - 0.01
13
+ FS_003:
14
+ - 0.0
15
+ - 0.0
16
+ - 0.03
17
+ FS_020:
18
+ - 0.0
19
+ - 0.02
20
+ - 0.0
21
+ FS_060:
22
+ - 0.0
23
+ - 0.06
24
+ - 0.0
25
+ FS_300:
26
+ - 0.03
27
+ - 0.0
28
+ - 0.0
29
+ FS_900:
30
+ - 0.09
31
+ - 0.0
32
+ - 0.0
33
+ symmetry_operations:
34
+ - rotation:
35
+ - - 1
36
+ - 0
37
+ - 0
38
+ - - 0
39
+ - 1
40
+ - 0
41
+ - - 0
42
+ - 0
43
+ - 1
44
+ translation:
45
+ - 0.0
46
+ - 0.0
47
+ - 0.0
48
+ - rotation:
49
+ - - -1
50
+ - 0
51
+ - 0
52
+ - - 0
53
+ - -1
54
+ - 0
55
+ - - 0
56
+ - 0
57
+ - -1
58
+ translation:
59
+ - 0.0
60
+ - 0.0
61
+ - 0.0
62
+ octahedral_sites:
63
+ Oc_000:
64
+ - - - FS_000
65
+ - - 0
66
+ - 0
67
+ - 1
68
+ - - FS_000
69
+ - - 1
70
+ - 1
71
+ - 0
72
+ - - - FS_000
73
+ - - 0
74
+ - 1
75
+ - 0
76
+ - - FS_000
77
+ - - 1
78
+ - 0
79
+ - 1
80
+ - - - FS_000
81
+ - - 1
82
+ - 0
83
+ - 0
84
+ - - FS_000
85
+ - - 0
86
+ - 1
87
+ - 1
88
+ tetrahedral_sites:
89
+ Te_000:
90
+ - - FS_000
91
+ - - 0
92
+ - 0
93
+ - 0
94
+ - - FS_000
95
+ - - 0
96
+ - 0
97
+ - 1
98
+ - - FS_000
99
+ - - 0
100
+ - 1
101
+ - 0
102
+ - - FS_000
103
+ - - 1
104
+ - 0
105
+ - 0
106
+ Te_001:
107
+ - - FS_000
108
+ - - 1
109
+ - 1
110
+ - 1
111
+ - - FS_000
112
+ - - 1
113
+ - 1
114
+ - 0
115
+ - - FS_000
116
+ - - 1
117
+ - 0
118
+ - 1
119
+ - - FS_000
120
+ - - 0
121
+ - 1
122
+ - 1
data/test/identifypolyhedralsites/unidentified/fitmodelstructure.yaml ADDED
@@ -0,0 +1,2 @@
1
+ --- Structure cannot be identified.
2
+ ...
data/test/identifypolyhedralsites/unidentified/model.yaml ADDED
@@ -0,0 +1,154 @@
1
+ # Made from Li3PO4 structure.
2
+ frame_elements: [ 2 ]
3
+
4
+ frame_sites:
5
+ FS_00: [ 0.29230, 0.31330, 0.39610]
6
+ FS_01: [ 0.70770, 0.31330, 0.39610]
7
+ FS_02: [ 0.00000, 0.81860, 0.31720]
8
+ FS_03: [ 0.50000, 0.89480, 0.40040]
9
+ FS_04: [ 0.00000, 0.10520, 0.90040]
10
+ FS_05: [ 0.50000, 0.18140, 0.81720]
11
+ FS_06: [ 0.20770, 0.68670, 0.89610]
12
+ FS_07: [ 0.79230, 0.68670, 0.89610]
13
+
14
+ symmetry_operations:
15
+ -
16
+ rotation:
17
+ - [ 1, 0, 0]
18
+ - [ 0, 1, 0]
19
+ - [ 0, 0, 1]
20
+ translation: [0.000000, 0.000000, 0.000000]
21
+ -
22
+ rotation:
23
+ - [-1, 0, 0]
24
+ - [ 0, 1, 0]
25
+ - [ 0, 0, 1]
26
+ translation: [0.000000, 0.000000, 0.000000]
27
+ -
28
+ rotation:
29
+ - [ 1, 0, 0]
30
+ - [ 0, -1, 0]
31
+ - [ 0, 0, 1]
32
+ translation: [0.500000, 1.000000, 0.500000]
33
+ -
34
+ rotation:
35
+ - [-1, 0, 0]
36
+ - [ 0, -1, 0]
37
+ - [ 0, 0, 1]
38
+ translation: [0.500000, 1.000000, 0.500000]
39
+
40
+ octahedral_sites:
41
+ A:
42
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ -1, 0, 0]]]
43
+ - [["FS_01", [ -1, 0, 0]], ["FS_06", [ 0, 0, 0]]]
44
+ - [["FS_02", [ 0, 0, 0]], ["FS_04", [ 0, 0, 0]]]
45
+ B:
46
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ 0, 0, 0]]]
47
+ - [["FS_01", [ 0, 0, 0]], ["FS_06", [ 0, 0, 0]]]
48
+ - [["FS_03", [ 0, 0, 0]], ["FS_05", [ 0, 0, 0]]]
49
+ C:
50
+ - [["FS_00", [ 0, 0, 0]], ["FS_06", [ 0,-1, 0]]]
51
+ - [["FS_02", [ 0,-1, 0]], ["FS_05", [ 0, 0, 0]]]
52
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 0, 0, 0]]]
53
+ D:
54
+ - [["FS_01", [ 0, 0, 0]], ["FS_07", [ 0,-1, 0]]]
55
+ - [["FS_02", [ 1,-1, 0]], ["FS_05", [ 0, 0, 0]]]
56
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 1, 0, 0]]]
57
+ E:
58
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ -1, 0, -1]]]
59
+ - [["FS_01", [ -1, 0, 0]], ["FS_06", [ 0, 0, -1]]]
60
+ - [["FS_02", [ 0, 0, 0]], ["FS_04", [ 0, 0, -1]]]
61
+ F:
62
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ 0, 0, -1]]]
63
+ - [["FS_01", [ 0, 0, 0]], ["FS_06", [ 0, 0, -1]]]
64
+ - [["FS_03", [ 0, 0, 0]], ["FS_05", [ 0, 0, -1]]]
65
+ G:
66
+ - [["FS_00", [ 0, 0, 0]], ["FS_06", [ 0,-1, -1]]]
67
+ - [["FS_02", [ 0,-1, 0]], ["FS_05", [ 0, 0, -1]]]
68
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 0, 0, -1]]]
69
+ H:
70
+ - [["FS_01", [ 0, 0, 0]], ["FS_07", [ 0,-1, -1]]]
71
+ - [["FS_02", [ 1,-1, 0]], ["FS_05", [ 0, 0, -1]]]
72
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 1, 0, -1]]]
73
+
74
+ tetrahedral_sites:
75
+ I:
76
+ - ["FS_00", [ 0, 0, 0]]
77
+ - ["FS_01", [ -1, 0, 0]]
78
+ - ["FS_02", [ 0, -1, 0]]
79
+ - ["FS_04", [ 0, 0, 0]]
80
+ J:
81
+ - ["FS_00", [ 0, 0, 0]]
82
+ - ["FS_01", [ 0, 0, 0]]
83
+ - ["FS_03", [ 0, -1, 0]]
84
+ - ["FS_05", [ 0, 0, 0]]
85
+ K:
86
+ - ["FS_00", [ 0, 0, 0]]
87
+ - ["FS_02", [ 0, 0, 0]]
88
+ - ["FS_03", [ 0, 0, 0]]
89
+ - ["FS_06", [ 0, 0, 0]]
90
+ L:
91
+ - ["FS_01", [ 0, 0, 0]]
92
+ - ["FS_02", [ 1, 0, 0]]
93
+ - ["FS_03", [ 0, 0, 0]]
94
+ - ["FS_07", [ 0, 0, 0]]
95
+ M:
96
+ - ["FS_04", [ 0, 0, -1]]
97
+ - ["FS_06", [ 0, 0, -1]]
98
+ - ["FS_05", [ 0, 0, -1]]
99
+ - ["FS_00", [ 0, 0, 0]]
100
+ N:
101
+ - ["FS_04", [ 1, 0, -1]]
102
+ - ["FS_05", [ 0, 0, -1]]
103
+ - ["FS_07", [ 0, 0, -1]]
104
+ - ["FS_01", [ 0, 0, 0]]
105
+ O:
106
+ - ["FS_04", [ 0, 1, -1]]
107
+ - ["FS_06", [ 0, 0, -1]]
108
+ - ["FS_07", [ -1, 0, -1]]
109
+ - ["FS_02", [ 0, 0, 0]]
110
+ P:
111
+ - ["FS_05", [ 0, 1, -1]]
112
+ - ["FS_06", [ 0, 0, -1]]
113
+ - ["FS_07", [ 0, 0, -1]]
114
+ - ["FS_03", [ 0, 0, 0]]
115
+ Q:
116
+ - ["FS_00", [ 0, 0, 0]]
117
+ - ["FS_01", [ -1, 0, 0]]
118
+ - ["FS_02", [ 0, -1, 0]]
119
+ - ["FS_04", [ 0, 0, -1]]
120
+ R:
121
+ - ["FS_00", [ 0, 0, 0]]
122
+ - ["FS_01", [ 0, 0, 0]]
123
+ - ["FS_03", [ 0, -1, 0]]
124
+ - ["FS_05", [ 0, 0, -1]]
125
+ S:
126
+ - ["FS_00", [ 0, 0, 0]]
127
+ - ["FS_02", [ 0, 0, 0]]
128
+ - ["FS_03", [ 0, 0, 0]]
129
+ - ["FS_06", [ 0, 0, -1]]
130
+ T:
131
+ - ["FS_01", [ 0, 0, 0]]
132
+ - ["FS_02", [ 1, 0, 0]]
133
+ - ["FS_03", [ 0, 0, 0]]
134
+ - ["FS_07", [ 0, 0, -1]]
135
+ U:
136
+ - ["FS_04", [ 0, 0, 0]]
137
+ - ["FS_06", [ 0, 0, 0]]
138
+ - ["FS_05", [ 0, 0, 0]]
139
+ - ["FS_00", [ 0, 0, 0]]
140
+ V:
141
+ - ["FS_04", [ 1, 0, 0]]
142
+ - ["FS_05", [ 0, 0, 0]]
143
+ - ["FS_07", [ 0, 0, 0]]
144
+ - ["FS_01", [ 0, 0, 0]]
145
+ W:
146
+ - ["FS_04", [ 0, 1, 0]]
147
+ - ["FS_06", [ 0, 0, 0]]
148
+ - ["FS_07", [ -1, 0, 0]]
149
+ - ["FS_02", [ 0, 0, 0]]
150
+ X:
151
+ - ["FS_05", [ 0, 1, 0]]
152
+ - ["FS_06", [ 0, 0, 0]]
153
+ - ["FS_07", [ 0, 0, 0]]
154
+ - ["FS_03", [ 0, 0, 0]]
data/test/identifypolyhedralsites/volumemismatch/fitmodelstructure.yaml ADDED
@@ -0,0 +1,101 @@
1
+ ---
2
+ frame_atoms:
3
+ FS_02:
4
+ element: 2
5
+ coordinates:
6
+ - 0.0245801991241974
7
+ - 0.7628061515333462
8
+ - 0.2606905312906442
9
+ FS_07:
10
+ element: 2
11
+ coordinates:
12
+ - 0.9150687917149467
13
+ - 0.549243883856426
14
+ - 0.8169426849208484
15
+ FS_04:
16
+ element: 2
17
+ coordinates:
18
+ - -0.16322716207537713
19
+ - 0.06931104845074199
20
+ - 0.6017633220596417
21
+ FS_00:
22
+ element: 2
23
+ coordinates:
24
+ - 0.5197129699889187
25
+ - 0.5286162316553549
26
+ - 0.29374421669506245
27
+ FS_01:
28
+ element: 2
29
+ coordinates:
30
+ - 0.5582265079463964
31
+ - 0.4606321506991682
32
+ - 0.5322594842766315
33
+ FS_06:
34
+ element: 2
35
+ coordinates:
36
+ - 0.3695329684085804
37
+ - 0.5896840973893296
38
+ - 0.9451728739969046
39
+ FS_05:
40
+ element: 2
41
+ coordinates:
42
+ - 0.49414405512833354
43
+ - 0.11698288590431272
44
+ - 0.9993437049828294
45
+ FS_03:
46
+ element: 2
47
+ coordinates:
48
+ - 0.2819616697640042
49
+ - 0.9227235505113206
50
+ - 0.5696831817774374
51
+ interstitials:
52
+ - element: 0
53
+ coordinates:
54
+ - 0.671589041492811
55
+ - 0.6997162096756488
56
+ - 0.7410688271693666
57
+ - element: 0
58
+ coordinates:
59
+ - 0.517911159139028
60
+ - 0.12054138985063556
61
+ - 0.6500765125929414
62
+ - element: 0
63
+ coordinates:
64
+ - 0.1440441911304787
65
+ - 0.7818618874606633
66
+ - 0.9034628966732846
67
+ - element: 0
68
+ coordinates:
69
+ - 0.8824397505035888
70
+ - 0.46813189712200565
71
+ - 0.5191380756830264
72
+ - element: 0
73
+ coordinates:
74
+ - 0.3873037398333166
75
+ - 0.8051960215774434
76
+ - 0.18853791989451668
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+ - element: 0
78
+ coordinates:
79
+ - 0.8011178056982855
80
+ - 0.2190527155122971
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+ - 0.8820328631450373
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+ - element: 0
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+ coordinates:
84
+ - 0.2783850359654947
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+ - 0.5659226902059151
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+ - 0.6549283349733009
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+ - element: 0
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+ coordinates:
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+ - 0.8117078147562422
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+ - 0.5980664917295178
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+ - 0.11959913259026889
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+ - element: 1
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+ coordinates:
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+ - 0.07240931018393851
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+ - -0.002167413807968366
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+ - 0.430921534185972
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+ - element: 1
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+ coordinates:
99
+ - 0.3437821779478965
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+ - 0.31849110582275764
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+ - 0.13540121926137727
data/test/identifypolyhedralsites/volumemismatch/model.yaml ADDED
@@ -0,0 +1,154 @@
1
+ # Made from Li3PO4 structure.
2
+ frame_elements: [ 2 ]
3
+
4
+ frame_sites:
5
+ FS_00: [ 0.29230, 0.31330, 0.39610]
6
+ FS_01: [ 0.70770, 0.31330, 0.39610]
7
+ FS_02: [ 0.00000, 0.81860, 0.31720]
8
+ FS_03: [ 0.50000, 0.89480, 0.40040]
9
+ FS_04: [ 0.00000, 0.10520, 0.90040]
10
+ FS_05: [ 0.50000, 0.18140, 0.81720]
11
+ FS_06: [ 0.20770, 0.68670, 0.89610]
12
+ FS_07: [ 0.79230, 0.68670, 0.89610]
13
+
14
+ symmetry_operations:
15
+ -
16
+ rotation:
17
+ - [ 1, 0, 0]
18
+ - [ 0, 1, 0]
19
+ - [ 0, 0, 1]
20
+ translation: [0.000000, 0.000000, 0.000000]
21
+ -
22
+ rotation:
23
+ - [-1, 0, 0]
24
+ - [ 0, 1, 0]
25
+ - [ 0, 0, 1]
26
+ translation: [0.000000, 0.000000, 0.000000]
27
+ -
28
+ rotation:
29
+ - [ 1, 0, 0]
30
+ - [ 0, -1, 0]
31
+ - [ 0, 0, 1]
32
+ translation: [0.500000, 1.000000, 0.500000]
33
+ -
34
+ rotation:
35
+ - [-1, 0, 0]
36
+ - [ 0, -1, 0]
37
+ - [ 0, 0, 1]
38
+ translation: [0.500000, 1.000000, 0.500000]
39
+
40
+ octahedral_sites:
41
+ A:
42
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ -1, 0, 0]]]
43
+ - [["FS_01", [ -1, 0, 0]], ["FS_06", [ 0, 0, 0]]]
44
+ - [["FS_02", [ 0, 0, 0]], ["FS_04", [ 0, 0, 0]]]
45
+ B:
46
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ 0, 0, 0]]]
47
+ - [["FS_01", [ 0, 0, 0]], ["FS_06", [ 0, 0, 0]]]
48
+ - [["FS_03", [ 0, 0, 0]], ["FS_05", [ 0, 0, 0]]]
49
+ C:
50
+ - [["FS_00", [ 0, 0, 0]], ["FS_06", [ 0,-1, 0]]]
51
+ - [["FS_02", [ 0,-1, 0]], ["FS_05", [ 0, 0, 0]]]
52
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 0, 0, 0]]]
53
+ D:
54
+ - [["FS_01", [ 0, 0, 0]], ["FS_07", [ 0,-1, 0]]]
55
+ - [["FS_02", [ 1,-1, 0]], ["FS_05", [ 0, 0, 0]]]
56
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 1, 0, 0]]]
57
+ E:
58
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ -1, 0, -1]]]
59
+ - [["FS_01", [ -1, 0, 0]], ["FS_06", [ 0, 0, -1]]]
60
+ - [["FS_02", [ 0, 0, 0]], ["FS_04", [ 0, 0, -1]]]
61
+ F:
62
+ - [["FS_00", [ 0, 0, 0]], ["FS_07", [ 0, 0, -1]]]
63
+ - [["FS_01", [ 0, 0, 0]], ["FS_06", [ 0, 0, -1]]]
64
+ - [["FS_03", [ 0, 0, 0]], ["FS_05", [ 0, 0, -1]]]
65
+ G:
66
+ - [["FS_00", [ 0, 0, 0]], ["FS_06", [ 0,-1, -1]]]
67
+ - [["FS_02", [ 0,-1, 0]], ["FS_05", [ 0, 0, -1]]]
68
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 0, 0, -1]]]
69
+ H:
70
+ - [["FS_01", [ 0, 0, 0]], ["FS_07", [ 0,-1, -1]]]
71
+ - [["FS_02", [ 1,-1, 0]], ["FS_05", [ 0, 0, -1]]]
72
+ - [["FS_03", [ 0,-1, 0]], ["FS_04", [ 1, 0, -1]]]
73
+
74
+ tetrahedral_sites:
75
+ I:
76
+ - ["FS_00", [ 0, 0, 0]]
77
+ - ["FS_01", [ -1, 0, 0]]
78
+ - ["FS_02", [ 0, -1, 0]]
79
+ - ["FS_04", [ 0, 0, 0]]
80
+ J:
81
+ - ["FS_00", [ 0, 0, 0]]
82
+ - ["FS_01", [ 0, 0, 0]]
83
+ - ["FS_03", [ 0, -1, 0]]
84
+ - ["FS_05", [ 0, 0, 0]]
85
+ K:
86
+ - ["FS_00", [ 0, 0, 0]]
87
+ - ["FS_02", [ 0, 0, 0]]
88
+ - ["FS_03", [ 0, 0, 0]]
89
+ - ["FS_06", [ 0, 0, 0]]
90
+ L:
91
+ - ["FS_01", [ 0, 0, 0]]
92
+ - ["FS_02", [ 1, 0, 0]]
93
+ - ["FS_03", [ 0, 0, 0]]
94
+ - ["FS_07", [ 0, 0, 0]]
95
+ M:
96
+ - ["FS_04", [ 0, 0, -1]]
97
+ - ["FS_06", [ 0, 0, -1]]
98
+ - ["FS_05", [ 0, 0, -1]]
99
+ - ["FS_00", [ 0, 0, 0]]
100
+ N:
101
+ - ["FS_04", [ 1, 0, -1]]
102
+ - ["FS_05", [ 0, 0, -1]]
103
+ - ["FS_07", [ 0, 0, -1]]
104
+ - ["FS_01", [ 0, 0, 0]]
105
+ O:
106
+ - ["FS_04", [ 0, 1, -1]]
107
+ - ["FS_06", [ 0, 0, -1]]
108
+ - ["FS_07", [ -1, 0, -1]]
109
+ - ["FS_02", [ 0, 0, 0]]
110
+ P:
111
+ - ["FS_05", [ 0, 1, -1]]
112
+ - ["FS_06", [ 0, 0, -1]]
113
+ - ["FS_07", [ 0, 0, -1]]
114
+ - ["FS_03", [ 0, 0, 0]]
115
+ Q:
116
+ - ["FS_00", [ 0, 0, 0]]
117
+ - ["FS_01", [ -1, 0, 0]]
118
+ - ["FS_02", [ 0, -1, 0]]
119
+ - ["FS_04", [ 0, 0, -1]]
120
+ R:
121
+ - ["FS_00", [ 0, 0, 0]]
122
+ - ["FS_01", [ 0, 0, 0]]
123
+ - ["FS_03", [ 0, -1, 0]]
124
+ - ["FS_05", [ 0, 0, -1]]
125
+ S:
126
+ - ["FS_00", [ 0, 0, 0]]
127
+ - ["FS_02", [ 0, 0, 0]]
128
+ - ["FS_03", [ 0, 0, 0]]
129
+ - ["FS_06", [ 0, 0, -1]]
130
+ T:
131
+ - ["FS_01", [ 0, 0, 0]]
132
+ - ["FS_02", [ 1, 0, 0]]
133
+ - ["FS_03", [ 0, 0, 0]]
134
+ - ["FS_07", [ 0, 0, -1]]
135
+ U:
136
+ - ["FS_04", [ 0, 0, 0]]
137
+ - ["FS_06", [ 0, 0, 0]]
138
+ - ["FS_05", [ 0, 0, 0]]
139
+ - ["FS_00", [ 0, 0, 0]]
140
+ V:
141
+ - ["FS_04", [ 1, 0, 0]]
142
+ - ["FS_05", [ 0, 0, 0]]
143
+ - ["FS_07", [ 0, 0, 0]]
144
+ - ["FS_01", [ 0, 0, 0]]
145
+ W:
146
+ - ["FS_04", [ 0, 1, 0]]
147
+ - ["FS_06", [ 0, 0, 0]]
148
+ - ["FS_07", [ -1, 0, 0]]
149
+ - ["FS_02", [ 0, 0, 0]]
150
+ X:
151
+ - ["FS_05", [ 0, 1, 0]]
152
+ - ["FS_06", [ 0, 0, 0]]
153
+ - ["FS_07", [ 0, 0, 0]]
154
+ - ["FS_03", [ 0, 0, 0]]