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/transitcell/.gitignore ADDED
@@ -0,0 +1,2 @@
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+ transitcell.dot
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+ transitcell.png
data/test/transitcell/collectcells.yaml ADDED
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+ ---
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+ "0":
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+ sites:
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+ 0: ["A", "B"]
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+ 1: ["E"]
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+ toten: 0.0
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+ "1":
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+ sites:
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+ 0: ["A", "C"]
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+ 1: ["E"]
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+ toten: 1.0
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+ "2":
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+ sites:
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+ 0: ["A", "D"]
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+ 1: ["E"]
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+ toten: 2.0
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+ "3":
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+ sites:
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+ 0: ["B", "C"]
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+ 1: ["E"]
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+ toten: 3.0
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+ "4":
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+ sites:
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+ 0: ["B", "D"]
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+ 1: ["E"]
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+ toten: 4.0
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+ "5":
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+ sites:
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+ 0: ["C", "D"]
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+ 1: ["E"]
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+ toten: 5.0
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+ "6":
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+ sites:
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+ 0: ["A", "B"]
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+ 1: ["F"]
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+ toten: 6.0
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+ "7":
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+ sites:
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+ 0: ["A", "C"]
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+ 1: ["F"]
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+ toten: 7.0
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+ "8":
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+ sites:
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+ 0: ["A", "D"]
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+ 1: ["F"]
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+ toten: 8.0
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+ "9":
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+ sites:
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+ 0: ["B", "C"]
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+ 1: ["F"]
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+ toten: 9.0
data/test/transitcell/sitemigrations.yaml ADDED
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+ ---
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+ "A": [["D", [-1, 0, 0]], ["B", [0, 0, 0]]]
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+ "B": [["A", [0, 0, 0]], ["C", [0, 0, 0]]]
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+ "C": [["B", [0, 0, 0]], ["D", [0, 0, 0]]]
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+ "D": [["C", [0, 0, 0]], ["A", [1, 0, 0]]]
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+ "E": [["F", [0, 0, 0]]]
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+ "F": [["E", [0, 0, 0]], ["F", [0, 0, 0]]]
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+ "G": [["F", [0, 0, 0]]]
data/test/transitcell/siteoperations.yaml ADDED
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+ ---
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+ -
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+ "A": ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "B": ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "C": ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "D": ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "E": ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "F": ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "G": ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ -
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+ "A": ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "B": ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "C": ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "D": ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "E": ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "F": ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ "G": ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
data/test/transitcell/transitcell.log ADDED
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+ Crysna::TransitionFinder.find_path
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+ Starting point:
3
+ ABE(A555-B555-E555) is added as cur_index of 0
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+ ------------------------------
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+ Crysna::TransitionFinder.expand_edges with cell_id of 0
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+ [0] A555-B555-E555, energy=0.0, reach_flag=true, name="0"
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+ --------------------
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+ Migrating atom: index=0, element=0, site=A
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+ ----------
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+ To site=D, global_vector=[-1, 0, 0]
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+ Generated cell: BDE(B555-D455-E555)
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+ minimum_operation id: 1
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+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ Min-expressed cell: ACG(A655-C555-G555)
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+ This cell is not in @cell_manager.
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+ This cell is contained in @cell_candidates.
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+ The cell is added into @cell_manager as index of 1
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+ New edge: cell_ids of (0 -- 1), energy=4.0
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+ ----------
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+ To site=B, global_vector=[0, 0, 0]
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+ Generated cell: BBE(B555-B555-E555)
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+ minimum_operation id: 0
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+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ Min-expressed cell: BBE(B555-B555-E555)
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+ This cell is not in @cell_manager.
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+ This cell is not in @cell_candidates.
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+ Truncated.
40
+ --------------------
41
+ Migrating atom: index=1, element=0, site=B
42
+ ----------
43
+ To site=A, global_vector=[0, 0, 0]
44
+ Generated cell: AAE(A555-A555-E555)
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+ minimum_operation id: 0
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+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
48
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ Min-expressed cell: AAE(A555-A555-E555)
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+ This cell is not in @cell_manager.
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+ This cell is not in @cell_candidates.
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+ Truncated.
57
+ ----------
58
+ To site=C, global_vector=[0, 0, 0]
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+ Generated cell: ACE(A555-C555-E555)
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+ minimum_operation id: 0
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+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
62
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
64
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
66
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
67
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
68
+ Min-expressed cell: ACE(A555-C555-E555)
69
+ This cell is not in @cell_manager.
70
+ This cell is contained in @cell_candidates.
71
+ The cell is added into @cell_manager as index of 2
72
+ New edge: cell_ids of (0 -- 2), energy=1.0
73
+ --------------------
74
+ Migrating atom: index=2, element=1, site=E
75
+ ----------
76
+ To site=F, global_vector=[0, 0, 0]
77
+ Generated cell: ABF(A555-B555-F555)
78
+ minimum_operation id: 0
79
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
80
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
81
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
83
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
85
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
86
+ Min-expressed cell: ABF(A555-B555-F555)
87
+ This cell is not in @cell_manager.
88
+ This cell is contained in @cell_candidates.
89
+ The cell is added into @cell_manager as index of 3
90
+ New edge: cell_ids of (0 -- 3), energy=6.0
91
+ ----------Iteration 1----------------------------------------
92
+ ------------------------------------------------------------
93
+ cur_index:0
94
+ [0] A555-B555-E555, energy=0.0, reach_flag=true, name="0"
95
+ ------------------------------
96
+ reach_unreach_edges
97
+ ----------
98
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
99
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
100
+ Index of operation to minimize: 1
101
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
107
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
108
+ energy=4.0
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+ ----------
110
+ From atom(elem:0, site:B, site_global_vector:[0, 0, 0])
111
+ To atom(elem:0, site:C, site_global_vector:[0, 0, 0])
112
+ Index of operation to minimize: 0
113
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
116
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
119
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ energy=1.0
121
+ ----------
122
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
123
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
124
+ Index of operation to minimize: 0
125
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
126
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
127
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
128
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
129
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
132
+ energy=6.0
133
+ --------------------
134
+ Chosen edge: From atom(elem:0, site:B, site_global_vector:[0, 0, 0])
135
+ To atom(elem:0, site:C, site_global_vector:[0, 0, 0])
136
+ Index of operation to minimize: 0
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+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
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+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
139
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
140
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
141
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
142
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
143
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
144
+ energy=1.0
145
+ ------------------------------
146
+ Cells state
147
+ --------------------
148
+ [0] A555-B555-E555, energy=0.0, reach_flag=true, name="0"
149
+ Number of from_edges: 1
150
+ ----------
151
+ Nil edge(Starting point)
152
+ --------------------
153
+ [1] A655-C555-G555, energy=4.0, reach_flag=false, name="4"
154
+ Number of from_edges: 0
155
+ --------------------
156
+ [2] A555-C555-E555, energy=1.0, reach_flag=true, name="1"
157
+ Number of from_edges: 1
158
+ ----------
159
+ Nodes: [0, 2]
160
+ From atom(elem:0, site:B, site_global_vector:[0, 0, 0])
161
+ To atom(elem:0, site:C, site_global_vector:[0, 0, 0])
162
+ Index of operation to minimize: 0
163
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
164
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
165
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
166
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
167
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
168
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
169
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
170
+ --------------------
171
+ [3] A555-B555-F555, energy=6.0, reach_flag=false, name="6"
172
+ Number of from_edges: 0
173
+ ------------------------------
174
+ cur_index is set to be 2
175
+ ------------------------------
176
+ Crysna::TransitionFinder.expand_edges with cell_id of 2
177
+ [2] A555-C555-E555, energy=1.0, reach_flag=true, name="1"
178
+ --------------------
179
+ Migrating atom: index=0, element=0, site=A
180
+ ----------
181
+ To site=D, global_vector=[-1, 0, 0]
182
+ Generated cell: CDE(C555-D455-E555)
183
+ minimum_operation id: 1
184
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
185
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
186
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
187
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
188
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
189
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
190
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
191
+ Min-expressed cell: ABG(A655-B555-G555)
192
+ This cell is not in @cell_manager.
193
+ This cell is contained in @cell_candidates.
194
+ The cell is added into @cell_manager as index of 4
195
+ New edge: cell_ids of (2 -- 4), energy=5.0
196
+ ----------
197
+ To site=B, global_vector=[0, 0, 0]
198
+ Generated cell: BCE(B555-C555-E555)
199
+ minimum_operation id: 0
200
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
201
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
202
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
203
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
204
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
205
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
206
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
207
+ Min-expressed cell: BCE(B555-C555-E555)
208
+ This cell is not in @cell_manager.
209
+ This cell is contained in @cell_candidates.
210
+ The cell is added into @cell_manager as index of 5
211
+ New edge: cell_ids of (2 -- 5), energy=3.0
212
+ --------------------
213
+ Migrating atom: index=1, element=0, site=C
214
+ ----------
215
+ To site=B, global_vector=[0, 0, 0]
216
+ Generated cell: ABE(A555-B555-E555)
217
+ minimum_operation id: 0
218
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
219
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
220
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
221
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
222
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
223
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
224
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
225
+ Min-expressed cell: ABE(A555-B555-E555)
226
+ This cell is contained in @cell_manager.
227
+ Truncated.
228
+ ----------
229
+ To site=D, global_vector=[0, 0, 0]
230
+ Generated cell: ADE(A555-D555-E555)
231
+ minimum_operation id: 0
232
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
233
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
234
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
235
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
236
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
237
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
238
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
239
+ Min-expressed cell: ADE(A555-D555-E555)
240
+ This cell is not in @cell_manager.
241
+ This cell is contained in @cell_candidates.
242
+ The cell is added into @cell_manager as index of 6
243
+ New edge: cell_ids of (2 -- 6), energy=2.0
244
+ --------------------
245
+ Migrating atom: index=2, element=1, site=E
246
+ ----------
247
+ To site=F, global_vector=[0, 0, 0]
248
+ Generated cell: ACF(A555-C555-F555)
249
+ minimum_operation id: 0
250
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
251
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
252
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
253
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
254
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
255
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
256
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
257
+ Min-expressed cell: ACF(A555-C555-F555)
258
+ This cell is not in @cell_manager.
259
+ This cell is contained in @cell_candidates.
260
+ The cell is added into @cell_manager as index of 7
261
+ New edge: cell_ids of (2 -- 7), energy=7.0
262
+ ----------Iteration 2----------------------------------------
263
+ ------------------------------------------------------------
264
+ cur_index:2
265
+ [2] A555-C555-E555, energy=1.0, reach_flag=true, name="1"
266
+ ------------------------------
267
+ reach_unreach_edges
268
+ ----------
269
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
270
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
271
+ Index of operation to minimize: 1
272
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
273
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
274
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
275
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
276
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
277
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
278
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
279
+ energy=4.0
280
+ ----------
281
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
282
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
283
+ Index of operation to minimize: 0
284
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
285
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
286
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
287
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
288
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
289
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
290
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
291
+ energy=6.0
292
+ ----------
293
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
294
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
295
+ Index of operation to minimize: 1
296
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
297
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
298
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
299
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
300
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
301
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
302
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
303
+ energy=5.0
304
+ ----------
305
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
306
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
307
+ Index of operation to minimize: 0
308
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
309
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
310
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
311
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
312
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
313
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
314
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
315
+ energy=3.0
316
+ ----------
317
+ From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
318
+ To atom(elem:0, site:D, site_global_vector:[0, 0, 0])
319
+ Index of operation to minimize: 0
320
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
321
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
322
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
323
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
324
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
325
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
326
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
327
+ energy=2.0
328
+ ----------
329
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
330
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
331
+ Index of operation to minimize: 0
332
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
333
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
334
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
335
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
336
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
337
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
338
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
339
+ energy=7.0
340
+ --------------------
341
+ Chosen edge: From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
342
+ To atom(elem:0, site:D, site_global_vector:[0, 0, 0])
343
+ Index of operation to minimize: 0
344
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
345
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
346
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
347
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
348
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
349
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
350
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
351
+ energy=2.0
352
+ ------------------------------
353
+ Cells state
354
+ --------------------
355
+ [0] A555-B555-E555, energy=0.0, reach_flag=true, name="0"
356
+ Number of from_edges: 1
357
+ ----------
358
+ Nil edge(Starting point)
359
+ --------------------
360
+ [1] A655-C555-G555, energy=4.0, reach_flag=false, name="4"
361
+ Number of from_edges: 0
362
+ --------------------
363
+ [2] A555-C555-E555, energy=1.0, reach_flag=true, name="1"
364
+ Number of from_edges: 1
365
+ ----------
366
+ Nodes: [0, 2]
367
+ From atom(elem:0, site:B, site_global_vector:[0, 0, 0])
368
+ To atom(elem:0, site:C, site_global_vector:[0, 0, 0])
369
+ Index of operation to minimize: 0
370
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
371
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
372
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
373
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
374
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
375
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
376
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
377
+ --------------------
378
+ [3] A555-B555-F555, energy=6.0, reach_flag=false, name="6"
379
+ Number of from_edges: 0
380
+ --------------------
381
+ [4] A655-B555-G555, energy=5.0, reach_flag=false, name="5"
382
+ Number of from_edges: 0
383
+ --------------------
384
+ [5] B555-C555-E555, energy=3.0, reach_flag=false, name="3"
385
+ Number of from_edges: 0
386
+ --------------------
387
+ [6] A555-D555-E555, energy=2.0, reach_flag=true, name="2"
388
+ Number of from_edges: 1
389
+ ----------
390
+ Nodes: [2, 6]
391
+ From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
392
+ To atom(elem:0, site:D, site_global_vector:[0, 0, 0])
393
+ Index of operation to minimize: 0
394
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
395
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
396
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
397
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
398
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
399
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
400
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
401
+ --------------------
402
+ [7] A555-C555-F555, energy=7.0, reach_flag=false, name="7"
403
+ Number of from_edges: 0
404
+ ------------------------------
405
+ cur_index is set to be 6
406
+ ------------------------------
407
+ Crysna::TransitionFinder.expand_edges with cell_id of 6
408
+ [6] A555-D555-E555, energy=2.0, reach_flag=true, name="2"
409
+ --------------------
410
+ Migrating atom: index=0, element=0, site=A
411
+ ----------
412
+ To site=D, global_vector=[-1, 0, 0]
413
+ Generated cell: DDE(D455-D555-E555)
414
+ minimum_operation id: 1
415
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
416
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
417
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
418
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
419
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
420
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
421
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
422
+ Min-expressed cell: AAG(A555-A655-G555)
423
+ This cell is not in @cell_manager.
424
+ This cell is not in @cell_candidates.
425
+ Truncated.
426
+ ----------
427
+ To site=B, global_vector=[0, 0, 0]
428
+ Generated cell: BDE(B555-D555-E555)
429
+ minimum_operation id: 1
430
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
431
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
432
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
433
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
434
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
435
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
436
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
437
+ Min-expressed cell: ACG(A555-C555-G555)
438
+ This cell is not in @cell_manager.
439
+ This cell is contained in @cell_candidates.
440
+ The cell is added into @cell_manager as index of 8
441
+ New edge: cell_ids of (6 -- 8), energy=4.0
442
+ --------------------
443
+ Migrating atom: index=1, element=0, site=D
444
+ ----------
445
+ To site=C, global_vector=[0, 0, 0]
446
+ Generated cell: ACE(A555-C555-E555)
447
+ minimum_operation id: 0
448
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
449
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
450
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
451
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
452
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
453
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
454
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
455
+ Min-expressed cell: ACE(A555-C555-E555)
456
+ This cell is contained in @cell_manager.
457
+ Truncated.
458
+ ----------
459
+ To site=A, global_vector=[1, 0, 0]
460
+ Generated cell: AAE(A555-A655-E555)
461
+ minimum_operation id: 0
462
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
463
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
464
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
465
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
466
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
467
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
468
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
469
+ Min-expressed cell: AAE(A555-A555-E555)
470
+ This cell is not in @cell_manager.
471
+ This cell is not in @cell_candidates.
472
+ Truncated.
473
+ --------------------
474
+ Migrating atom: index=2, element=1, site=E
475
+ ----------
476
+ To site=F, global_vector=[0, 0, 0]
477
+ Generated cell: ADF(A555-D555-F555)
478
+ minimum_operation id: 0
479
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
480
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
481
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
482
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
483
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
484
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
485
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
486
+ Min-expressed cell: ADF(A555-D555-F555)
487
+ This cell is not in @cell_manager.
488
+ This cell is contained in @cell_candidates.
489
+ The cell is added into @cell_manager as index of 9
490
+ New edge: cell_ids of (6 -- 9), energy=8.0
491
+ ----------Iteration 3----------------------------------------
492
+ ------------------------------------------------------------
493
+ cur_index:6
494
+ [6] A555-D555-E555, energy=2.0, reach_flag=true, name="2"
495
+ ------------------------------
496
+ reach_unreach_edges
497
+ ----------
498
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
499
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
500
+ Index of operation to minimize: 1
501
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
502
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
503
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
504
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
505
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
506
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
507
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
508
+ energy=4.0
509
+ ----------
510
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
511
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
512
+ Index of operation to minimize: 0
513
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
514
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
515
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
516
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
517
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
518
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
519
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
520
+ energy=6.0
521
+ ----------
522
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
523
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
524
+ Index of operation to minimize: 1
525
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
526
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
527
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
528
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
529
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
530
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
531
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
532
+ energy=5.0
533
+ ----------
534
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
535
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
536
+ Index of operation to minimize: 0
537
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
538
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
539
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
540
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
541
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
542
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
543
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
544
+ energy=3.0
545
+ ----------
546
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
547
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
548
+ Index of operation to minimize: 0
549
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
550
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
551
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
552
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
553
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
554
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
555
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
556
+ energy=7.0
557
+ ----------
558
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
559
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
560
+ Index of operation to minimize: 1
561
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
562
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
563
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
564
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
565
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
566
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
567
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
568
+ energy=4.0
569
+ ----------
570
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
571
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
572
+ Index of operation to minimize: 0
573
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
574
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
575
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
576
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
577
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
578
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
579
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
580
+ energy=8.0
581
+ --------------------
582
+ Chosen edge: From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
583
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
584
+ Index of operation to minimize: 0
585
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
586
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
587
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
588
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
589
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
590
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
591
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
592
+ energy=3.0
593
+ ------------------------------
594
+ Cells state
595
+ --------------------
596
+ [0] A555-B555-E555, energy=0.0, reach_flag=true, name="0"
597
+ Number of from_edges: 1
598
+ ----------
599
+ Nil edge(Starting point)
600
+ --------------------
601
+ [1] A655-C555-G555, energy=4.0, reach_flag=false, name="4"
602
+ Number of from_edges: 0
603
+ --------------------
604
+ [2] A555-C555-E555, energy=1.0, reach_flag=true, name="1"
605
+ Number of from_edges: 1
606
+ ----------
607
+ Nodes: [0, 2]
608
+ From atom(elem:0, site:B, site_global_vector:[0, 0, 0])
609
+ To atom(elem:0, site:C, site_global_vector:[0, 0, 0])
610
+ Index of operation to minimize: 0
611
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
612
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
613
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
614
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
615
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
616
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
617
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
618
+ --------------------
619
+ [3] A555-B555-F555, energy=6.0, reach_flag=false, name="6"
620
+ Number of from_edges: 0
621
+ --------------------
622
+ [4] A655-B555-G555, energy=5.0, reach_flag=false, name="5"
623
+ Number of from_edges: 0
624
+ --------------------
625
+ [5] B555-C555-E555, energy=3.0, reach_flag=true, name="3"
626
+ Number of from_edges: 1
627
+ ----------
628
+ Nodes: [2, 5]
629
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
630
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
631
+ Index of operation to minimize: 0
632
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
633
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
634
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
635
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
636
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
637
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
638
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
639
+ --------------------
640
+ [6] A555-D555-E555, energy=2.0, reach_flag=true, name="2"
641
+ Number of from_edges: 1
642
+ ----------
643
+ Nodes: [2, 6]
644
+ From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
645
+ To atom(elem:0, site:D, site_global_vector:[0, 0, 0])
646
+ Index of operation to minimize: 0
647
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
648
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
649
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
650
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
651
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
652
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
653
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
654
+ --------------------
655
+ [7] A555-C555-F555, energy=7.0, reach_flag=false, name="7"
656
+ Number of from_edges: 0
657
+ --------------------
658
+ [8] A555-C555-G555, energy=4.0, reach_flag=false, name="4"
659
+ Number of from_edges: 0
660
+ --------------------
661
+ [9] A555-D555-F555, energy=8.0, reach_flag=false, name="8"
662
+ Number of from_edges: 0
663
+ ------------------------------
664
+ cur_index is set to be 5
665
+ ------------------------------
666
+ Crysna::TransitionFinder.expand_edges with cell_id of 5
667
+ [5] B555-C555-E555, energy=3.0, reach_flag=true, name="3"
668
+ --------------------
669
+ Migrating atom: index=0, element=0, site=B
670
+ ----------
671
+ To site=A, global_vector=[0, 0, 0]
672
+ Generated cell: ACE(A555-C555-E555)
673
+ minimum_operation id: 0
674
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
675
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
676
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
677
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
678
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
679
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
680
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
681
+ Min-expressed cell: ACE(A555-C555-E555)
682
+ This cell is contained in @cell_manager.
683
+ Truncated.
684
+ ----------
685
+ To site=C, global_vector=[0, 0, 0]
686
+ Generated cell: CCE(C555-C555-E555)
687
+ minimum_operation id: 1
688
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
689
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
690
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
691
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
692
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
693
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
694
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
695
+ Min-expressed cell: BBG(B555-B555-G555)
696
+ This cell is not in @cell_manager.
697
+ This cell is not in @cell_candidates.
698
+ Truncated.
699
+ --------------------
700
+ Migrating atom: index=1, element=0, site=C
701
+ ----------
702
+ To site=B, global_vector=[0, 0, 0]
703
+ Generated cell: BBE(B555-B555-E555)
704
+ minimum_operation id: 0
705
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
706
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
707
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
708
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
709
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
710
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
711
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
712
+ Min-expressed cell: BBE(B555-B555-E555)
713
+ This cell is not in @cell_manager.
714
+ This cell is not in @cell_candidates.
715
+ Truncated.
716
+ ----------
717
+ To site=D, global_vector=[0, 0, 0]
718
+ Generated cell: BDE(B555-D555-E555)
719
+ minimum_operation id: 1
720
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
721
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
722
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
723
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
724
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
725
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
726
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
727
+ Min-expressed cell: ACG(A555-C555-G555)
728
+ This cell is contained in @cell_manager.
729
+ Truncated.
730
+ --------------------
731
+ Migrating atom: index=2, element=1, site=E
732
+ ----------
733
+ To site=F, global_vector=[0, 0, 0]
734
+ Generated cell: BCF(B555-C555-F555)
735
+ minimum_operation id: 0
736
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
737
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
738
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
739
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
740
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
741
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
742
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
743
+ Min-expressed cell: BCF(B555-C555-F555)
744
+ This cell is not in @cell_manager.
745
+ This cell is contained in @cell_candidates.
746
+ The cell is added into @cell_manager as index of 10
747
+ New edge: cell_ids of (5 -- 10), energy=9.0
748
+ ----------Iteration 4----------------------------------------
749
+ ------------------------------------------------------------
750
+ cur_index:5
751
+ [5] B555-C555-E555, energy=3.0, reach_flag=true, name="3"
752
+ ------------------------------
753
+ reach_unreach_edges
754
+ ----------
755
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
756
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
757
+ Index of operation to minimize: 1
758
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
759
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
760
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
761
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
762
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
763
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
764
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
765
+ energy=4.0
766
+ ----------
767
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
768
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
769
+ Index of operation to minimize: 0
770
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
771
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
772
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
773
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
774
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
775
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
776
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
777
+ energy=6.0
778
+ ----------
779
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
780
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
781
+ Index of operation to minimize: 1
782
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
783
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
784
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
785
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
786
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
787
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
788
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
789
+ energy=5.0
790
+ ----------
791
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
792
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
793
+ Index of operation to minimize: 0
794
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
795
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
796
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
797
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
798
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
799
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
800
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
801
+ energy=7.0
802
+ ----------
803
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
804
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
805
+ Index of operation to minimize: 1
806
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
807
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
808
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
809
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
810
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
811
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
812
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
813
+ energy=4.0
814
+ ----------
815
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
816
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
817
+ Index of operation to minimize: 0
818
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
819
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
820
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
821
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
822
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
823
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
824
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
825
+ energy=8.0
826
+ ----------
827
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
828
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
829
+ Index of operation to minimize: 0
830
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
831
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
832
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
833
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
834
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
835
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
836
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
837
+ energy=9.0
838
+ --------------------
839
+ Chosen edge: From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
840
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
841
+ Index of operation to minimize: 1
842
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
843
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
844
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
845
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
846
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
847
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
848
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
849
+ energy=4.0
850
+ ------------------------------
851
+ Cells state
852
+ --------------------
853
+ [0] A555-B555-E555, energy=0.0, reach_flag=true, name="0"
854
+ Number of from_edges: 1
855
+ ----------
856
+ Nil edge(Starting point)
857
+ --------------------
858
+ [1] A655-C555-G555, energy=4.0, reach_flag=true, name="4"
859
+ Number of from_edges: 1
860
+ ----------
861
+ Nodes: [0, 1]
862
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
863
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
864
+ Index of operation to minimize: 1
865
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
866
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
867
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
868
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
869
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
870
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
871
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
872
+ --------------------
873
+ [2] A555-C555-E555, energy=1.0, reach_flag=true, name="1"
874
+ Number of from_edges: 1
875
+ ----------
876
+ Nodes: [0, 2]
877
+ From atom(elem:0, site:B, site_global_vector:[0, 0, 0])
878
+ To atom(elem:0, site:C, site_global_vector:[0, 0, 0])
879
+ Index of operation to minimize: 0
880
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
881
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
882
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
883
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
884
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
885
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
886
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
887
+ --------------------
888
+ [3] A555-B555-F555, energy=6.0, reach_flag=false, name="6"
889
+ Number of from_edges: 0
890
+ --------------------
891
+ [4] A655-B555-G555, energy=5.0, reach_flag=false, name="5"
892
+ Number of from_edges: 0
893
+ --------------------
894
+ [5] B555-C555-E555, energy=3.0, reach_flag=true, name="3"
895
+ Number of from_edges: 1
896
+ ----------
897
+ Nodes: [2, 5]
898
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
899
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
900
+ Index of operation to minimize: 0
901
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
902
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
903
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
904
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
905
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
906
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
907
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
908
+ --------------------
909
+ [6] A555-D555-E555, energy=2.0, reach_flag=true, name="2"
910
+ Number of from_edges: 1
911
+ ----------
912
+ Nodes: [2, 6]
913
+ From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
914
+ To atom(elem:0, site:D, site_global_vector:[0, 0, 0])
915
+ Index of operation to minimize: 0
916
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
917
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
918
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
919
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
920
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
921
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
922
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
923
+ --------------------
924
+ [7] A555-C555-F555, energy=7.0, reach_flag=false, name="7"
925
+ Number of from_edges: 0
926
+ --------------------
927
+ [8] A555-C555-G555, energy=4.0, reach_flag=false, name="4"
928
+ Number of from_edges: 0
929
+ --------------------
930
+ [9] A555-D555-F555, energy=8.0, reach_flag=false, name="8"
931
+ Number of from_edges: 0
932
+ --------------------
933
+ [10] B555-C555-F555, energy=9.0, reach_flag=false, name="9"
934
+ Number of from_edges: 0
935
+ ------------------------------
936
+ cur_index is set to be 1
937
+ ------------------------------
938
+ Crysna::TransitionFinder.expand_edges with cell_id of 1
939
+ [1] A655-C555-G555, energy=4.0, reach_flag=true, name="4"
940
+ --------------------
941
+ Migrating atom: index=0, element=0, site=A
942
+ ----------
943
+ To site=D, global_vector=[-1, 0, 0]
944
+ Generated cell: CDG(C555-D555-G555)
945
+ minimum_operation id: 1
946
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
947
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
948
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
949
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
950
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
951
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
952
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
953
+ Min-expressed cell: ABE(A555-B555-E555)
954
+ This cell is contained in @cell_manager.
955
+ Truncated.
956
+ ----------
957
+ To site=B, global_vector=[0, 0, 0]
958
+ Generated cell: BCG(B655-C555-G555)
959
+ minimum_operation id: 1
960
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
961
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
962
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
963
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
964
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
965
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
966
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
967
+ Min-expressed cell: BCE(B555-C455-E555)
968
+ This cell is not in @cell_manager.
969
+ This cell is contained in @cell_candidates.
970
+ The cell is added into @cell_manager as index of 11
971
+ New edge: cell_ids of (1 -- 11), energy=4.0
972
+ --------------------
973
+ Migrating atom: index=1, element=0, site=C
974
+ ----------
975
+ To site=B, global_vector=[0, 0, 0]
976
+ Generated cell: ABG(A655-B555-G555)
977
+ minimum_operation id: 0
978
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
979
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
980
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
981
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
982
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
983
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
984
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
985
+ Min-expressed cell: ABG(A555-B555-G555)
986
+ This cell is not in @cell_manager.
987
+ This cell is contained in @cell_candidates.
988
+ The cell is added into @cell_manager as index of 12
989
+ New edge: cell_ids of (1 -- 12), energy=5.0
990
+ ----------
991
+ To site=D, global_vector=[0, 0, 0]
992
+ Generated cell: ADG(A655-D555-G555)
993
+ minimum_operation id: 1
994
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
995
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
996
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
997
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
998
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
999
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1000
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1001
+ Min-expressed cell: ADE(A555-D455-E555)
1002
+ This cell is not in @cell_manager.
1003
+ This cell is contained in @cell_candidates.
1004
+ The cell is added into @cell_manager as index of 13
1005
+ New edge: cell_ids of (1 -- 13), energy=4.0
1006
+ --------------------
1007
+ Migrating atom: index=2, element=1, site=G
1008
+ ----------
1009
+ To site=F, global_vector=[0, 0, 0]
1010
+ Generated cell: ACF(A655-C555-F555)
1011
+ minimum_operation id: 0
1012
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1013
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1014
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1015
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1016
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1017
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1018
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1019
+ Min-expressed cell: ACF(A555-C555-F555)
1020
+ This cell is contained in @cell_manager.
1021
+ Truncated.
1022
+ ----------Iteration 5----------------------------------------
1023
+ ------------------------------------------------------------
1024
+ cur_index:1
1025
+ [1] A655-C555-G555, energy=4.0, reach_flag=true, name="4"
1026
+ ------------------------------
1027
+ reach_unreach_edges
1028
+ ----------
1029
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
1030
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
1031
+ Index of operation to minimize: 0
1032
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1033
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1034
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1035
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1036
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1037
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1038
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1039
+ energy=6.0
1040
+ ----------
1041
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
1042
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
1043
+ Index of operation to minimize: 1
1044
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1045
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1046
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1047
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1048
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1049
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1050
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1051
+ energy=5.0
1052
+ ----------
1053
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
1054
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
1055
+ Index of operation to minimize: 0
1056
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1057
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1058
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1059
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1060
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1061
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1062
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1063
+ energy=7.0
1064
+ ----------
1065
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
1066
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
1067
+ Index of operation to minimize: 1
1068
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1069
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1070
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1071
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1072
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1073
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1074
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1075
+ energy=4.0
1076
+ ----------
1077
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
1078
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
1079
+ Index of operation to minimize: 0
1080
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1081
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1082
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1083
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1084
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1085
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1086
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1087
+ energy=8.0
1088
+ ----------
1089
+ From atom(elem:1, site:E, site_global_vector:[0, 0, 0])
1090
+ To atom(elem:1, site:F, site_global_vector:[0, 0, 0])
1091
+ Index of operation to minimize: 0
1092
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1093
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1094
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1095
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1096
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1097
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1098
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1099
+ energy=9.0
1100
+ ----------
1101
+ From atom(elem:0, site:A, site_global_vector:[1, 0, 0])
1102
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
1103
+ Index of operation to minimize: 1
1104
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1105
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1106
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1107
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1108
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1109
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1110
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1111
+ energy=4.0
1112
+ ----------
1113
+ From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
1114
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
1115
+ Index of operation to minimize: 0
1116
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1117
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1118
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1119
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1120
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1121
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1122
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1123
+ energy=5.0
1124
+ ----------
1125
+ From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
1126
+ To atom(elem:0, site:D, site_global_vector:[0, 0, 0])
1127
+ Index of operation to minimize: 1
1128
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1129
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1130
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1131
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1132
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1133
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1134
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1135
+ energy=4.0
1136
+ --------------------
1137
+ Chosen edge: From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
1138
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
1139
+ Index of operation to minimize: 1
1140
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1141
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1142
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1143
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1144
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1145
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1146
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1147
+ energy=4.0
1148
+ ------------------------------
1149
+ Cells state
1150
+ --------------------
1151
+ [0] A555-B555-E555, energy=0.0, reach_flag=true, name="0"
1152
+ Number of from_edges: 1
1153
+ ----------
1154
+ Nil edge(Starting point)
1155
+ --------------------
1156
+ [1] A655-C555-G555, energy=4.0, reach_flag=true, name="4"
1157
+ Number of from_edges: 1
1158
+ ----------
1159
+ Nodes: [0, 1]
1160
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
1161
+ To atom(elem:0, site:D, site_global_vector:[-1, 0, 0])
1162
+ Index of operation to minimize: 1
1163
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1164
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1165
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1166
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1167
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1168
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1169
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1170
+ --------------------
1171
+ [2] A555-C555-E555, energy=1.0, reach_flag=true, name="1"
1172
+ Number of from_edges: 1
1173
+ ----------
1174
+ Nodes: [0, 2]
1175
+ From atom(elem:0, site:B, site_global_vector:[0, 0, 0])
1176
+ To atom(elem:0, site:C, site_global_vector:[0, 0, 0])
1177
+ Index of operation to minimize: 0
1178
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1179
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1180
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1181
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1182
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1183
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1184
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1185
+ --------------------
1186
+ [3] A555-B555-F555, energy=6.0, reach_flag=false, name="6"
1187
+ Number of from_edges: 0
1188
+ --------------------
1189
+ [4] A655-B555-G555, energy=5.0, reach_flag=false, name="5"
1190
+ Number of from_edges: 0
1191
+ --------------------
1192
+ [5] B555-C555-E555, energy=3.0, reach_flag=true, name="3"
1193
+ Number of from_edges: 1
1194
+ ----------
1195
+ Nodes: [2, 5]
1196
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
1197
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
1198
+ Index of operation to minimize: 0
1199
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1200
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1201
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1202
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1203
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1204
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1205
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1206
+ --------------------
1207
+ [6] A555-D555-E555, energy=2.0, reach_flag=true, name="2"
1208
+ Number of from_edges: 1
1209
+ ----------
1210
+ Nodes: [2, 6]
1211
+ From atom(elem:0, site:C, site_global_vector:[0, 0, 0])
1212
+ To atom(elem:0, site:D, site_global_vector:[0, 0, 0])
1213
+ Index of operation to minimize: 0
1214
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1215
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1216
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1217
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1218
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1219
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1220
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1221
+ --------------------
1222
+ [7] A555-C555-F555, energy=7.0, reach_flag=false, name="7"
1223
+ Number of from_edges: 0
1224
+ --------------------
1225
+ [8] A555-C555-G555, energy=4.0, reach_flag=true, name="4"
1226
+ Number of from_edges: 1
1227
+ ----------
1228
+ Nodes: [6, 8]
1229
+ From atom(elem:0, site:A, site_global_vector:[0, 0, 0])
1230
+ To atom(elem:0, site:B, site_global_vector:[0, 0, 0])
1231
+ Index of operation to minimize: 1
1232
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1233
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1234
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1235
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1236
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1237
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1238
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1239
+ --------------------
1240
+ [9] A555-D555-F555, energy=8.0, reach_flag=false, name="8"
1241
+ Number of from_edges: 0
1242
+ --------------------
1243
+ [10] B555-C555-F555, energy=9.0, reach_flag=false, name="9"
1244
+ Number of from_edges: 0
1245
+ --------------------
1246
+ [11] B555-C455-E555, energy=3.0, reach_flag=false, name="3"
1247
+ Number of from_edges: 0
1248
+ --------------------
1249
+ [12] A555-B555-G555, energy=5.0, reach_flag=false, name="5"
1250
+ Number of from_edges: 0
1251
+ --------------------
1252
+ [13] A555-D455-E555, energy=2.0, reach_flag=false, name="2"
1253
+ Number of from_edges: 0
1254
+ ------------------------------
1255
+ cur_index is set to be 8
1256
+ ------------------------------
1257
+ Crysna::TransitionFinder.expand_edges with cell_id of 8
1258
+ [8] A555-C555-G555, energy=4.0, reach_flag=true, name="4"
1259
+ --------------------
1260
+ Migrating atom: index=0, element=0, site=A
1261
+ ----------
1262
+ To site=D, global_vector=[-1, 0, 0]
1263
+ Generated cell: CDG(C555-D455-G555)
1264
+ minimum_operation id: 1
1265
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1266
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1267
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1268
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1269
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1270
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1271
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1272
+ Min-expressed cell: ABE(A655-B555-E555)
1273
+ This cell is not in @cell_manager.
1274
+ This cell is contained in @cell_candidates.
1275
+ The cell is added into @cell_manager as index of 14
1276
+ New edge: cell_ids of (8 -- 14), energy=4.0
1277
+ ----------
1278
+ To site=B, global_vector=[0, 0, 0]
1279
+ Generated cell: BCG(B555-C555-G555)
1280
+ minimum_operation id: 1
1281
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1282
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1283
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1284
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1285
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1286
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1287
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1288
+ Min-expressed cell: BCE(B555-C555-E555)
1289
+ This cell is contained in @cell_manager.
1290
+ Truncated.
1291
+ --------------------
1292
+ Migrating atom: index=1, element=0, site=C
1293
+ ----------
1294
+ To site=B, global_vector=[0, 0, 0]
1295
+ Generated cell: ABG(A555-B555-G555)
1296
+ minimum_operation id: 0
1297
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1298
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1299
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1300
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1301
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1302
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1303
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1304
+ Min-expressed cell: ABG(A555-B555-G555)
1305
+ This cell is contained in @cell_manager.
1306
+ Truncated.
1307
+ ----------
1308
+ To site=D, global_vector=[0, 0, 0]
1309
+ Generated cell: ADG(A555-D555-G555)
1310
+ minimum_operation id: 1
1311
+ A => ["D", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1312
+ B => ["C", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1313
+ C => ["B", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1314
+ D => ["A", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1315
+ E => ["G", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1316
+ F => ["F", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1317
+ G => ["E", [0, 0, 0], [[-1, 0, 0], [0, 0, 0], [0, 0, 0]]]
1318
+ Min-expressed cell: ADE(A555-D555-E555)
1319
+ This cell is contained in @cell_manager.
1320
+ Truncated.
1321
+ --------------------
1322
+ Migrating atom: index=2, element=1, site=G
1323
+ ----------
1324
+ To site=F, global_vector=[0, 0, 0]
1325
+ Generated cell: ACF(A555-C555-F555)
1326
+ minimum_operation id: 0
1327
+ A => ["A", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1328
+ B => ["B", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1329
+ C => ["C", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1330
+ D => ["D", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1331
+ E => ["E", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1332
+ F => ["F", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1333
+ G => ["G", [0, 0, 0], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]]
1334
+ Min-expressed cell: ACF(A555-C555-F555)
1335
+ This cell is contained in @cell_manager.
1336
+ Truncated.
1337
+ ----------Iteration 6----------------------------------------
1338
+ ------------------------------------------------------------
1339
+ cur_index:8
1340
+ [8] A555-C555-G555, energy=4.0, reach_flag=true, name="4"
1341
+ truncate condition reached by contain_periodically_shift_cells.
1342
+ [[0], [1, 8], [2], [5], [6]]