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/sitecombination/initsites.yaml ADDED
@@ -0,0 +1,7 @@
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+ Ag:
2
+ - ['2A', '2B']
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+ - ['2A', '2B']
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+
5
+ I:
6
+ - ['IA']
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+ - ['IB']
data/test/sitecombination/initsites_test2.yaml ADDED
@@ -0,0 +1,8 @@
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+ Ag:
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+ - ['1A', '2A']
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+ - ['1B', '2B']
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+ - ['1C', '2C']
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+
6
+ I:
7
+ - ['IA']
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+ - ['IB', '2X']
data/test/sitecombination/sitecombination.yaml ADDED
@@ -0,0 +1,29 @@
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+ ---
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+ '0':
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+ Ag:
4
+ - 2A
5
+ - 2A
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+ I:
7
+ - IA
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+ - IB
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+ '1':
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+ Ag:
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+ - 2A
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+ - 2B
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+ I:
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+ - IA
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+ - IB
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+ '2':
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+ Ag:
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+ - 2B
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+ - 2A
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+ I:
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+ - IA
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+ - IB
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+ '3':
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+ Ag:
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+ - 2B
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+ - 2B
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+ I:
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+ - IA
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+ - IB
data/test/siteconfiguration/elements-sitenames.yaml ADDED
@@ -0,0 +1,2 @@
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+ 0: ["S00", "S01"]
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+ 1: ["S02", "S03"]
data/test/siteconfiguration/latticeaxes.yaml ADDED
@@ -0,0 +1,3 @@
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+ - [ 2.0, 0.0, 0.0 ]
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+ - [ 0.0, 2.0, 0.0 ]
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+ - [ 0.0, 0.0, 2.0 ]
data/test/siteconfiguration/sitenames-coordinates.yaml ADDED
@@ -0,0 +1,4 @@
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+ S00: [0.00, 0.00, 0.00]
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+ S01: [0.00, 0.00, 0.25]
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+ S02: [0.00, 0.00, 0.50]
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+ S03: [0.00, 0.00, 0.75]
data/test/sitemigrationsdistance/model.yaml ADDED
@@ -0,0 +1,45 @@
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+ frame_elements: ['1']
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+
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+ frame_sites:
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+ IB: [0.500000000, 0.500000000, 0.500000000]
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+ IA: [0.000000000, 0.000000000, 0.000000000]
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+
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+ scatter_sites:
8
+ 2X: [ 0.885, 0.500, 0.885]
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+ 2W: [ 0.500, 0.885, 0.885]
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+ 2V: [ 0.500, 0.115, 0.885]
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+ 2U: [ 0.115, 0.500, 0.885]
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+ 2T: [ 0.615, 0.000, 0.615]
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+ 2S: [ 0.385, 0.000, 0.615]
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+ 2R: [ 0.000, 0.615, 0.615]
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+ 2Q: [ 0.000, 0.385, 0.615]
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+ 2P: [ 0.885, 0.885, 0.500]
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+ 2O: [ 0.885, 0.115, 0.500]
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+ 2N: [ 0.115, 0.885, 0.500]
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+ 2M: [ 0.115, 0.115, 0.500]
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+ 2L: [ 0.615, 0.000, 0.385]
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+ 2K: [ 0.385, 0.000, 0.385]
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+ 2J: [ 0.000, 0.615, 0.385]
23
+ 2I: [ 0.000, 0.385, 0.385]
24
+ 2H: [ 0.885, 0.500, 0.115]
25
+ 2G: [ 0.500, 0.885, 0.115]
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+ 2F: [ 0.500, 0.115, 0.115]
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+ 2E: [ 0.115, 0.500, 0.115]
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+ 2D: [ 0.615, 0.615, 0.000]
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+ 2C: [ 0.615, 0.385, 0.000]
30
+ 2B: [ 0.385, 0.615, 0.000]
31
+ 2A: [ 0.385, 0.385, 0.000]
32
+ 1L: [ 0.500, 0.000, 0.750]
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+ 1K: [ 0.000, 0.500, 0.750]
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+ 1J: [ 0.750, 0.000, 0.500]
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+ 1I: [ 0.250, 0.000, 0.500]
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+ 1H: [ 0.000, 0.750, 0.500]
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+ 1G: [ 0.000, 0.250, 0.500]
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+ 1F: [ 0.500, 0.000, 0.250]
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+ 1E: [ 0.000, 0.500, 0.250]
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+ 1D: [ 0.750, 0.500, 0.000]
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+ 1C: [ 0.500, 0.750, 0.000]
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+ 1B: [ 0.500, 0.250, 0.000]
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+ 1A: [ 0.250, 0.500, 0.000]
44
+ IB: [ 0.500, 0.500, 0.500]
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+ IA: [ 0.000, 0.000, 0.000]
data/test/siteoperations/.gitignore ADDED
@@ -0,0 +1,2 @@
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+ siteoperations.log
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+ siteoperations.yaml
data/test/siteoperations/model.yaml ADDED
@@ -0,0 +1,43 @@
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+ frame_sites:
2
+ IB: [0.500000000, 0.500000000, 0.500000000]
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+ IA: [0.000000000, 0.000000000, 0.000000000]
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+
5
+ scatter_sites:
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+ 2X: [ 0.885, 0.500, 0.885]
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+ 2W: [ 0.500, 0.885, 0.885]
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+ 2V: [ 0.500, 0.115, 0.885]
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+ 2U: [ 0.115, 0.500, 0.885]
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+ 2T: [ 0.615, 0.000, 0.615]
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+ 2S: [ 0.385, 0.000, 0.615]
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+ 2R: [ 0.000, 0.615, 0.615]
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+ 2Q: [ 0.000, 0.385, 0.615]
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+ 2P: [ 0.885, 0.885, 0.500]
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+ 2O: [ 0.885, 0.115, 0.500]
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+ 2N: [ 0.115, 0.885, 0.500]
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+ 2M: [ 0.115, 0.115, 0.500]
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+ 2L: [ 0.615, 0.000, 0.385]
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+ 2K: [ 0.385, 0.000, 0.385]
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+ 2J: [ 0.000, 0.615, 0.385]
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+ 2I: [ 0.000, 0.385, 0.385]
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+ 2H: [ 0.885, 0.500, 0.115]
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+ 2G: [ 0.500, 0.885, 0.115]
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+ 2F: [ 0.500, 0.115, 0.115]
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+ 2E: [ 0.115, 0.500, 0.115]
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+ 2D: [ 0.615, 0.615, 0.000]
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+ 2C: [ 0.615, 0.385, 0.000]
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+ 2B: [ 0.385, 0.615, 0.000]
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+ 2A: [ 0.385, 0.385, 0.000]
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+ 1L: [ 0.500, 0.000, 0.750]
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+ 1K: [ 0.000, 0.500, 0.750]
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+ 1J: [ 0.750, 0.000, 0.500]
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+ 1I: [ 0.250, 0.000, 0.500]
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+ 1H: [ 0.000, 0.750, 0.500]
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+ 1G: [ 0.000, 0.250, 0.500]
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+ 1F: [ 0.500, 0.000, 0.250]
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+ 1E: [ 0.000, 0.500, 0.250]
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+ 1D: [ 0.750, 0.500, 0.000]
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+ 1C: [ 0.500, 0.750, 0.000]
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+ 1B: [ 0.500, 0.250, 0.000]
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+ 1A: [ 0.250, 0.500, 0.000]
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+ IB: [ 0.500, 0.500, 0.500]
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+ IA: [ 0.000, 0.000, 0.000]
data/test/siteoperations/symmetryoperations.yaml ADDED
@@ -0,0 +1,1441 @@
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+ ---
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+ - operation_id: 0
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+ rotation:
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+ - - 1.0
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