@mat3ra/made 2026.8.13-0 → 2026.8.26-0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (493) hide show
  1. package/package.json +9 -5
  2. package/.babelrc +0 -10
  3. package/.eslintrc.json +0 -11
  4. package/.gitattributes +0 -1
  5. package/.husky/post-checkout +0 -3
  6. package/.husky/post-commit +0 -3
  7. package/.husky/post-merge +0 -3
  8. package/.husky/pre-commit +0 -6
  9. package/.husky/pre-push +0 -3
  10. package/.mocharc.json +0 -5
  11. package/.pre-commit-config.yaml +0 -26
  12. package/.prettierignore +0 -2
  13. package/.prettierrc +0 -6
  14. package/AGENTS.md +0 -133
  15. package/MANIFEST.in +0 -1
  16. package/data/constants.json +0 -13
  17. package/data/reciprocal_paths.json +0 -111
  18. package/images/made/tools/tools_diagram_general.png +0 -3
  19. package/images/made/tools/tools_diagram_interface.png +0 -3
  20. package/pyproject.toml +0 -123
  21. package/scripts/generate-mixins.ts +0 -28
  22. package/src/__init__.py +0 -0
  23. package/src/js/Material.ts +0 -618
  24. package/src/js/basis/basis.ts +0 -634
  25. package/src/js/basis/constrained_basis.ts +0 -115
  26. package/src/js/basis/coordinates.ts +0 -92
  27. package/src/js/basis/elements.ts +0 -24
  28. package/src/js/basis/helpers.ts +0 -20
  29. package/src/js/basis/labels.ts +0 -6
  30. package/src/js/cell/cell.ts +0 -149
  31. package/src/js/cell/conventional_cell.ts +0 -86
  32. package/src/js/cell/primitive_cell.ts +0 -166
  33. package/src/js/constants/molecule.ts +0 -18
  34. package/src/js/constants.ts +0 -4
  35. package/src/js/constraints/constraints.ts +0 -45
  36. package/src/js/generated/MaterialSchemaMixin.ts +0 -79
  37. package/src/js/lattice/lattice.ts +0 -308
  38. package/src/js/lattice/lattice_types.ts +0 -134
  39. package/src/js/lattice/reciprocal/lattice_reciprocal.ts +0 -206
  40. package/src/js/lattice/reciprocal/paths.ts +0 -39
  41. package/src/js/lattice/reciprocal/symmetry_points.ts +0 -886
  42. package/src/js/lattice/unit_cell.ts +0 -66
  43. package/src/js/made.ts +0 -62
  44. package/src/js/parsers/cif.ts +0 -25
  45. package/src/js/parsers/errors.ts +0 -6
  46. package/src/js/parsers/espresso.ts +0 -29
  47. package/src/js/parsers/native_format_parsers.ts +0 -52
  48. package/src/js/parsers/parsers.ts +0 -13
  49. package/src/js/parsers/poscar.ts +0 -218
  50. package/src/js/parsers/xyz.ts +0 -190
  51. package/src/js/parsers/xyz_combinatorial_basis.ts +0 -268
  52. package/src/js/tools/basis.ts +0 -131
  53. package/src/js/tools/cell.ts +0 -40
  54. package/src/js/tools/index.ts +0 -11
  55. package/src/js/tools/material.ts +0 -64
  56. package/src/js/tools/supercell.ts +0 -89
  57. package/src/js/tools/surface.ts +0 -213
  58. package/src/py/__init__.py +0 -0
  59. package/src/py/mat3ra/__init__.py +0 -1
  60. package/src/py/mat3ra/made/__init__.py +0 -7
  61. package/src/py/mat3ra/made/basis/__init__.py +0 -255
  62. package/src/py/mat3ra/made/basis/coordinates.py +0 -43
  63. package/src/py/mat3ra/made/cell/__init__.py +0 -55
  64. package/src/py/mat3ra/made/cell/primitive_cell.py +0 -156
  65. package/src/py/mat3ra/made/data_helper.py +0 -5
  66. package/src/py/mat3ra/made/lattice.py +0 -195
  67. package/src/py/mat3ra/made/material.py +0 -135
  68. package/src/py/mat3ra/made/metadata.py +0 -45
  69. package/src/py/mat3ra/made/reciprocal/__init__.py +0 -5
  70. package/src/py/mat3ra/made/reciprocal/lattice_reciprocal.py +0 -147
  71. package/src/py/mat3ra/made/reciprocal/paths.py +0 -30
  72. package/src/py/mat3ra/made/reciprocal/symmetry_points.py +0 -385
  73. package/src/py/mat3ra/made/tools/README.md +0 -173
  74. package/src/py/mat3ra/made/tools/__init__.py +0 -0
  75. package/src/py/mat3ra/made/tools/analyze/__init__.py +0 -31
  76. package/src/py/mat3ra/made/tools/analyze/basis/__init__.py +0 -3
  77. package/src/py/mat3ra/made/tools/analyze/basis/analyzer.py +0 -50
  78. package/src/py/mat3ra/made/tools/analyze/build_metadata_analyzer.py +0 -32
  79. package/src/py/mat3ra/made/tools/analyze/build_metadata_analyzer_factory.py +0 -31
  80. package/src/py/mat3ra/made/tools/analyze/coordination.py +0 -56
  81. package/src/py/mat3ra/made/tools/analyze/crystal_site/__init__.py +0 -0
  82. package/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_crystal_site_material_analyzer.py +0 -35
  83. package/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_material_analyzer.py +0 -49
  84. package/src/py/mat3ra/made/tools/analyze/crystal_site/crystal_site_analyzer.py +0 -65
  85. package/src/py/mat3ra/made/tools/analyze/crystal_site/voronoi_crystal_site_analyzer.py +0 -47
  86. package/src/py/mat3ra/made/tools/analyze/enums.py +0 -33
  87. package/src/py/mat3ra/made/tools/analyze/fingerprint/__init__.py +0 -4
  88. package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/__init__.py +0 -0
  89. package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/layered_fingerprint_along_axis.py +0 -83
  90. package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/unique_element_string_per_layer.py +0 -9
  91. package/src/py/mat3ra/made/tools/analyze/interface/__init__.py +0 -20
  92. package/src/py/mat3ra/made/tools/analyze/interface/commensurate.py +0 -156
  93. package/src/py/mat3ra/made/tools/analyze/interface/enums.py +0 -60
  94. package/src/py/mat3ra/made/tools/analyze/interface/grain_boundary.py +0 -80
  95. package/src/py/mat3ra/made/tools/analyze/interface/simple.py +0 -251
  96. package/src/py/mat3ra/made/tools/analyze/interface/twisted_nanoribbons.py +0 -91
  97. package/src/py/mat3ra/made/tools/analyze/interface/utils/__init__.py +0 -77
  98. package/src/py/mat3ra/made/tools/analyze/interface/utils/holders.py +0 -14
  99. package/src/py/mat3ra/made/tools/analyze/interface/utils/vector.py +0 -56
  100. package/src/py/mat3ra/made/tools/analyze/interface/zsl.py +0 -259
  101. package/src/py/mat3ra/made/tools/analyze/interface_material.py +0 -45
  102. package/src/py/mat3ra/made/tools/analyze/lattice/__init__.py +0 -2
  103. package/src/py/mat3ra/made/tools/analyze/lattice/analyzer.py +0 -126
  104. package/src/py/mat3ra/made/tools/analyze/lattice/helpers.py +0 -31
  105. package/src/py/mat3ra/made/tools/analyze/lattice_lines.py +0 -30
  106. package/src/py/mat3ra/made/tools/analyze/lattice_planes.py +0 -192
  107. package/src/py/mat3ra/made/tools/analyze/lattice_swap_analyzer.py +0 -105
  108. package/src/py/mat3ra/made/tools/analyze/material.py +0 -276
  109. package/src/py/mat3ra/made/tools/analyze/other.py +0 -434
  110. package/src/py/mat3ra/made/tools/analyze/rdf.py +0 -74
  111. package/src/py/mat3ra/made/tools/analyze/slab.py +0 -76
  112. package/src/py/mat3ra/made/tools/analyze/solid_solution_analyzer.py +0 -171
  113. package/src/py/mat3ra/made/tools/analyze/terrace.py +0 -105
  114. package/src/py/mat3ra/made/tools/analyze/utils.py +0 -162
  115. package/src/py/mat3ra/made/tools/bond_directions/__init__.py +0 -0
  116. package/src/py/mat3ra/made/tools/bond_directions/bond_directions.py +0 -150
  117. package/src/py/mat3ra/made/tools/bond_directions/bond_directions_for_element_list.py +0 -7
  118. package/src/py/mat3ra/made/tools/bond_directions/bond_directions_templates_enum.py +0 -8
  119. package/src/py/mat3ra/made/tools/bond_directions/bond_directions_templates_for_element.py +0 -16
  120. package/src/py/mat3ra/made/tools/build/__init__.py +0 -25
  121. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/__init__.py +0 -7
  122. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/helpers.py +0 -59
  123. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/types.py +0 -26
  124. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/utils.py +0 -139
  125. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/__init__.py +0 -47
  126. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/__init__.py +0 -11
  127. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/build_parameters.py +0 -5
  128. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/builder.py +0 -164
  129. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/configuration.py +0 -48
  130. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/helpers.py +0 -134
  131. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/__init__.py +0 -6
  132. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/helpers.py +0 -157
  133. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/enums.py +0 -7
  134. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/__init__.py +0 -7
  135. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/configuration.py +0 -13
  136. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/helpers.py +0 -70
  137. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/utils.py +0 -87
  138. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/zsl/__init__.py +0 -6
  139. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/zsl/helpers.py +0 -129
  140. package/src/py/mat3ra/made/tools/build/defective_structures/__init__.py +0 -0
  141. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/__init__.py +0 -0
  142. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/__init__.py +0 -0
  143. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/build_parameters.py +0 -12
  144. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/builder.py +0 -17
  145. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/configuration.py +0 -40
  146. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/helpers.py +0 -82
  147. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/__init__.py +0 -1
  148. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/__init__.py +0 -9
  149. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/builder.py +0 -37
  150. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/configuration.py +0 -30
  151. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/enums.py +0 -8
  152. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/helpers.py +0 -76
  153. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/__init__.py +0 -0
  154. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/__init__.py +0 -0
  155. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/builder.py +0 -11
  156. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/configuration.py +0 -18
  157. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/helpers.py +0 -137
  158. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/types.py +0 -22
  159. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/__init__.py +0 -0
  160. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/builder.py +0 -28
  161. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/configuration.py +0 -55
  162. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/helpers.py +0 -75
  163. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/builder.py +0 -15
  164. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/configuration.py +0 -16
  165. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/helpers.py +0 -116
  166. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/build_parameters.py +0 -10
  167. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/builder.py +0 -30
  168. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/configuration.py +0 -11
  169. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/helpers.py +0 -78
  170. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/__init__.py +0 -0
  171. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/__init__.py +0 -0
  172. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/builder.py +0 -31
  173. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/configuration.py +0 -45
  174. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/helpers.py +0 -80
  175. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/__init__.py +0 -40
  176. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/atom_placement_method_enum.py +0 -14
  177. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/__init__.py +0 -7
  178. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/builder.py +0 -42
  179. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/configuration.py +0 -27
  180. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/complex_defect_type_enum.py +0 -5
  181. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/factories.py +0 -69
  182. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/helpers.py +0 -92
  183. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/__init__.py +0 -7
  184. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/builder.py +0 -8
  185. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/configuration.py +0 -29
  186. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/helpers.py +0 -48
  187. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/interstitial_placement_method_enum.py +0 -8
  188. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/point_defect_type_enum.py +0 -8
  189. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/__init__.py +0 -7
  190. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/builder.py +0 -6
  191. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/configuration.py +0 -41
  192. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/helpers.py +0 -43
  193. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/substitution_placement_method_enum.py +0 -7
  194. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/types.py +0 -24
  195. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/__init__.py +0 -7
  196. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/builder.py +0 -19
  197. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/configuration.py +0 -27
  198. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/helpers.py +0 -42
  199. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/vacancy_placement_method_enum.py +0 -7
  200. package/src/py/mat3ra/made/tools/build/pristine_structures/__init__.py +0 -0
  201. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/__init__.py +0 -0
  202. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/builder.py +0 -80
  203. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/configurations.py +0 -22
  204. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/helpers.py +0 -40
  205. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/__init__.py +0 -0
  206. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/__init__.py +0 -29
  207. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/build_parameters.py +0 -5
  208. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/builders.py +0 -56
  209. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/configuration.py +0 -33
  210. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/helpers.py +0 -76
  211. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/__init__.py +0 -11
  212. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/build_parameters.py +0 -9
  213. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/builders.py +0 -83
  214. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/configuration.py +0 -35
  215. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/helpers.py +0 -62
  216. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/__init__.py +0 -9
  217. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/build_parameters.py +0 -8
  218. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/builder.py +0 -42
  219. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/configuration.py +0 -99
  220. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/helpers.py +0 -95
  221. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/termination_utils.py +0 -14
  222. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/utils.py +0 -61
  223. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab_strained_supercell/builder.py +0 -22
  224. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab_strained_supercell/configuration.py +0 -17
  225. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/__init__.py +0 -0
  226. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/__init__.py +0 -19
  227. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/analyzer.py +0 -86
  228. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/ase_based/__init__.py +0 -7
  229. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/ase_based/builder.py +0 -54
  230. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/ase_based/configuration.py +0 -19
  231. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/enums.py +0 -42
  232. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/helpers.py +0 -127
  233. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/merge_based/__init__.py +0 -7
  234. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/merge_based/builder.py +0 -33
  235. package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/merge_based/configuration.py +0 -16
  236. package/src/py/mat3ra/made/tools/build/processed_structures/__init__.py +0 -0
  237. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/__init__.py +0 -0
  238. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/__init__.py +0 -0
  239. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/__init__.py +0 -9
  240. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/coordination_based_passivation_material_analyzer.py +0 -112
  241. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/passivation_material_analyzer.py +0 -16
  242. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/surface_passivation_material_analyzer.py +0 -32
  243. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/builder.py +0 -23
  244. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/configuration.py +0 -31
  245. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/enums.py +0 -7
  246. package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/helpers.py +0 -151
  247. package/src/py/mat3ra/made/tools/build_components/__init__.py +0 -10
  248. package/src/py/mat3ra/made/tools/build_components/entities/__init__.py +0 -0
  249. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/__init__.py +0 -0
  250. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/one_dimensional/miller_indices_2d.py +0 -0
  251. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/two_dimensional/miller_indices.py +0 -18
  252. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/two_dimensional/termination.py +0 -33
  253. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/__init__.py +0 -0
  254. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/crystal_site/__init__.py +0 -2
  255. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/crystal_site/crystal_site.py +0 -24
  256. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/crystal_site/crystal_site_list.py +0 -9
  257. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/point_defect_site/builder.py +0 -32
  258. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/point_defect_site/configuration.py +0 -14
  259. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/void_region/__init__.py +0 -0
  260. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/void_region/builder.py +0 -29
  261. package/src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/void_region/configuration.py +0 -19
  262. package/src/py/mat3ra/made/tools/build_components/entities/core/two_dimensional/vacuum/builder.py +0 -48
  263. package/src/py/mat3ra/made/tools/build_components/entities/core/two_dimensional/vacuum/configuration.py +0 -17
  264. package/src/py/mat3ra/made/tools/build_components/entities/core/zero_dimensional/atom/builder.py +0 -25
  265. package/src/py/mat3ra/made/tools/build_components/entities/core/zero_dimensional/atom/configuration.py +0 -8
  266. package/src/py/mat3ra/made/tools/build_components/entities/reusable/__init__.py +0 -0
  267. package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/__init__.py +0 -16
  268. package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/base_configuration_pydantic.py +0 -5
  269. package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/base_single_builder.py +0 -87
  270. package/src/py/mat3ra/made/tools/build_components/entities/reusable/base_builder/build_parameters.py +0 -5
  271. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/__init__.py +0 -0
  272. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/__init__.py +0 -4
  273. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/builder.py +0 -46
  274. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/configuration.py +0 -19
  275. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/edge_types.py +0 -51
  276. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/helpers.py +0 -58
  277. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated/__init__.py +0 -4
  278. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated/builder.py +0 -42
  279. package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated/configuration.py +0 -21
  280. package/src/py/mat3ra/made/tools/build_components/entities/reusable/three_dimensional/supercell/__init__.py +0 -0
  281. package/src/py/mat3ra/made/tools/build_components/entities/reusable/three_dimensional/supercell/configuration.py +0 -11
  282. package/src/py/mat3ra/made/tools/build_components/entities/reusable/three_dimensional/supercell/helpers.py +0 -38
  283. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/__init__.py +0 -24
  284. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/__init__.py +0 -7
  285. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/builder.py +0 -62
  286. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/configuration.py +0 -14
  287. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/helpers.py +0 -42
  288. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/crystal_lattice_planes/__init__.py +0 -7
  289. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/crystal_lattice_planes/builder.py +0 -39
  290. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/crystal_lattice_planes/configuration.py +0 -24
  291. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/__init__.py +0 -10
  292. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/builder.py +0 -36
  293. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/configuration.py +0 -31
  294. package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/helpers.py +0 -80
  295. package/src/py/mat3ra/made/tools/build_components/entities/reusable/zero_dimensional/__init__.py +0 -0
  296. package/src/py/mat3ra/made/tools/build_components/entities/reusable/zero_dimensional/coordinates_shape_enum.py +0 -8
  297. package/src/py/mat3ra/made/tools/build_components/metadata/__init__.py +0 -2
  298. package/src/py/mat3ra/made/tools/build_components/metadata/build_metadata.py +0 -7
  299. package/src/py/mat3ra/made/tools/build_components/metadata/material_build_metadata.py +0 -35
  300. package/src/py/mat3ra/made/tools/build_components/metadata/material_with_build_metadata.py +0 -8
  301. package/src/py/mat3ra/made/tools/build_components/mixins/__init__.py +0 -2
  302. package/src/py/mat3ra/made/tools/build_components/mixins/convert_generated_items_ase_atoms_mixin.py +0 -8
  303. package/src/py/mat3ra/made/tools/build_components/mixins/convert_generated_items_pymatgen_structure_mixin.py +0 -8
  304. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/__init__.py +0 -0
  305. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/enums.py +0 -11
  306. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/__init__.py +0 -6
  307. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/build_parameters.py +0 -18
  308. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/builder.py +0 -93
  309. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/configuration.py +0 -20
  310. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/stack/builder.py +0 -83
  311. package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/stack/configuration.py +0 -24
  312. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/__init__.py +0 -15
  313. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/build_parameters.py +0 -5
  314. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/builders/base.py +0 -33
  315. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/builders/isometric.py +0 -25
  316. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/configuration.py +0 -24
  317. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/__init__.py +0 -13
  318. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/atomic_mass_dependent_function_holder.py +0 -32
  319. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/function_holder.py +0 -80
  320. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/maxwell_boltzmann.py +0 -39
  321. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/perturbation_function_holder.py +0 -45
  322. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/sine_wave_perturbation_function_holder.py +0 -29
  323. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/helpers.py +0 -83
  324. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/strain/__init__.py +0 -5
  325. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/strain/builder.py +0 -25
  326. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/strain/configuration.py +0 -23
  327. package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/strain/helpers.py +0 -49
  328. package/src/py/mat3ra/made/tools/build_components/utils.py +0 -44
  329. package/src/py/mat3ra/made/tools/calculate/__init__.py +0 -149
  330. package/src/py/mat3ra/made/tools/calculate/ase/__init__.py +0 -133
  331. package/src/py/mat3ra/made/tools/calculate/ase/constraints.py +0 -91
  332. package/src/py/mat3ra/made/tools/calculate/calculators/__init__.py +0 -4
  333. package/src/py/mat3ra/made/tools/calculate/calculators/interface_material_calculator.py +0 -70
  334. package/src/py/mat3ra/made/tools/calculate/calculators/interface_material_calculator_parameters.py +0 -14
  335. package/src/py/mat3ra/made/tools/calculate/calculators/material_calculator.py +0 -32
  336. package/src/py/mat3ra/made/tools/calculate/calculators/material_calculator_parameters.py +0 -17
  337. package/src/py/mat3ra/made/tools/calculate/interaction_functions.py +0 -23
  338. package/src/py/mat3ra/made/tools/convert/__init__.py +0 -286
  339. package/src/py/mat3ra/made/tools/convert/interface_parts_enum.py +0 -9
  340. package/src/py/mat3ra/made/tools/convert/utils.py +0 -96
  341. package/src/py/mat3ra/made/tools/entities/__init__.py +0 -5
  342. package/src/py/mat3ra/made/tools/entities/coordinate/__init__.py +0 -14
  343. package/src/py/mat3ra/made/tools/entities/coordinate/box_coordinate_condition.py +0 -15
  344. package/src/py/mat3ra/made/tools/entities/coordinate/coordinate_condition.py +0 -16
  345. package/src/py/mat3ra/made/tools/entities/coordinate/coordinate_functions.py +0 -158
  346. package/src/py/mat3ra/made/tools/entities/coordinate/cylinder_coordinate_condition.py +0 -17
  347. package/src/py/mat3ra/made/tools/entities/coordinate/plane_coordinate_condition.py +0 -14
  348. package/src/py/mat3ra/made/tools/entities/coordinate/sphere_coordinate_condition.py +0 -15
  349. package/src/py/mat3ra/made/tools/entities/coordinate/triangular_prism_coordinate_condition.py +0 -26
  350. package/src/py/mat3ra/made/tools/entities/termination_holder.py +0 -12
  351. package/src/py/mat3ra/made/tools/helpers.py +0 -168
  352. package/src/py/mat3ra/made/tools/modify.py +0 -627
  353. package/src/py/mat3ra/made/tools/operations/core/binary.py +0 -106
  354. package/src/py/mat3ra/made/tools/operations/core/unary.py +0 -170
  355. package/src/py/mat3ra/made/tools/operations/core/utils.py +0 -138
  356. package/src/py/mat3ra/made/tools/operations/reusable/unary.py +0 -53
  357. package/src/py/mat3ra/made/tools/optimize.py +0 -55
  358. package/src/py/mat3ra/made/tools/third_party.py +0 -69
  359. package/src/py/mat3ra/made/tools/utils.py +0 -182
  360. package/src/py/mat3ra/made/utils.py +0 -144
  361. package/tests/.gitattributes +0 -1
  362. package/tests/fixtures/AsGe-basis.json +0 -3
  363. package/tests/fixtures/C2H4-translated.json +0 -3
  364. package/tests/fixtures/C2H4.json +0 -3
  365. package/tests/fixtures/FeLiSi-basis.json +0 -3
  366. package/tests/fixtures/FeO.json +0 -3
  367. package/tests/fixtures/Ge2-basis.json +0 -3
  368. package/tests/fixtures/Graphene.json +0 -3
  369. package/tests/fixtures/Graphene.poscar +0 -3
  370. package/tests/fixtures/H2+H-final.json +0 -3
  371. package/tests/fixtures/H2+H-image.json +0 -3
  372. package/tests/fixtures/H2+H-initial.json +0 -3
  373. package/tests/fixtures/H2O.poscar +0 -3
  374. package/tests/fixtures/LiFeSi-basis-labels.json +0 -3
  375. package/tests/fixtures/LiFeSi-basis.json +0 -3
  376. package/tests/fixtures/Na.json +0 -3
  377. package/tests/fixtures/Na4Cl4-cartesian.json +0 -3
  378. package/tests/fixtures/Na4Cl4.json +0 -3
  379. package/tests/fixtures/Na4Cl4.poscar +0 -3
  380. package/tests/fixtures/Ni-hex.json +0 -3
  381. package/tests/fixtures/Ni-hex.poscar +0 -3
  382. package/tests/fixtures/OSi-basis.json +0 -3
  383. package/tests/fixtures/Si-hex.poscar +0 -3
  384. package/tests/fixtures/Si-pwscf.in +0 -3
  385. package/tests/fixtures/Si-slab.json +0 -3
  386. package/tests/fixtures/Si-supercell.json +0 -3
  387. package/tests/fixtures/Si2-basis-repeated.json +0 -3
  388. package/tests/fixtures/Si2-basis.json +0 -3
  389. package/tests/fixtures/Zr1H23Zr1H1.json +0 -3
  390. package/tests/fixtures/Zr1H23Zr1H1.poscar +0 -3
  391. package/tests/fixtures/atomic-constraints.json +0 -3
  392. package/tests/fixtures/hashes.json +0 -3
  393. package/tests/fixtures/si-slab-100.json +0 -3
  394. package/tests/fixtures/si-slab-111-0-vacuum.json +0 -3
  395. package/tests/fixtures/si-slab-111-0.5-vacuum-gamma-120.json +0 -3
  396. package/tests/fixtures/si-slab-111-0.5-vacuum-ratio.json +0 -3
  397. package/tests/fixtures/si-standata.json +0 -3
  398. package/tests/js/basis/basis.ts +0 -247
  399. package/tests/js/cell/cell.ts +0 -182
  400. package/tests/js/cell/primitive_cell.ts +0 -21
  401. package/tests/js/constraints/constraints.ts +0 -11
  402. package/tests/js/fixtures.ts +0 -123
  403. package/tests/js/lattice/lattice.ts +0 -43
  404. package/tests/js/lattice/lattice_reciprocal.ts +0 -104
  405. package/tests/js/material/material.ts +0 -161
  406. package/tests/js/parsers/espresso.ts +0 -12
  407. package/tests/js/parsers/native_formats.ts +0 -35
  408. package/tests/js/parsers/poscar.ts +0 -89
  409. package/tests/js/parsers/xyz.ts +0 -33
  410. package/tests/js/parsers/xyz_combinatorial_basis.ts +0 -156
  411. package/tests/js/register-esse-schemas.cjs +0 -10
  412. package/tests/js/setup.ts +0 -6
  413. package/tests/js/tools/basis.ts +0 -22
  414. package/tests/js/tools/supercell.ts +0 -58
  415. package/tests/js/tools/surface.ts +0 -111
  416. package/tests/py/conftest.py +0 -34
  417. package/tests/py/mat3ra/debug_utils.py +0 -75
  418. package/tests/py/unit/__init__.py +0 -0
  419. package/tests/py/unit/fixtures/__init__.py +0 -0
  420. package/tests/py/unit/fixtures/adatom.py +0 -60
  421. package/tests/py/unit/fixtures/bulk.py +0 -162
  422. package/tests/py/unit/fixtures/cuts.py +0 -118
  423. package/tests/py/unit/fixtures/grain_boundary.py +0 -875
  424. package/tests/py/unit/fixtures/interface/commensurate.py +0 -498
  425. package/tests/py/unit/fixtures/interface/gaas_dia.py +0 -837
  426. package/tests/py/unit/fixtures/interface/gr_ni_111_top_hcp.py +0 -123
  427. package/tests/py/unit/fixtures/interface/simple.py +0 -84
  428. package/tests/py/unit/fixtures/interface/twisted_nanoribbons.py +0 -131
  429. package/tests/py/unit/fixtures/interface/zsl.py +0 -756
  430. package/tests/py/unit/fixtures/island.py +0 -336
  431. package/tests/py/unit/fixtures/merge.py +0 -147
  432. package/tests/py/unit/fixtures/monolayer.py +0 -46
  433. package/tests/py/unit/fixtures/nanoparticle.py +0 -116
  434. package/tests/py/unit/fixtures/nanoribbon/__init__.py +0 -0
  435. package/tests/py/unit/fixtures/nanoribbon/armchair.py +0 -102
  436. package/tests/py/unit/fixtures/nanoribbon/nanoribbon.py +0 -145
  437. package/tests/py/unit/fixtures/nanoribbon/zigzag.py +0 -54
  438. package/tests/py/unit/fixtures/pair_defects.py +0 -41
  439. package/tests/py/unit/fixtures/passivated/nanoribbon.py +0 -69
  440. package/tests/py/unit/fixtures/passivated/slab.py +0 -58
  441. package/tests/py/unit/fixtures/point_defects.py +0 -158
  442. package/tests/py/unit/fixtures/slab.py +0 -606
  443. package/tests/py/unit/fixtures/strain.py +0 -42
  444. package/tests/py/unit/fixtures/supercell.py +0 -64
  445. package/tests/py/unit/fixtures/terrace.py +0 -70
  446. package/tests/py/unit/fixtures/thrid_party/ase_atoms.py +0 -13
  447. package/tests/py/unit/test_analyze_lattice_planes.py +0 -131
  448. package/tests/py/unit/test_cell.py +0 -104
  449. package/tests/py/unit/test_data_files.py +0 -68
  450. package/tests/py/unit/test_lattice.py +0 -103
  451. package/tests/py/unit/test_lattice_type_extended.py +0 -53
  452. package/tests/py/unit/test_material.py +0 -158
  453. package/tests/py/unit/test_operations.py +0 -126
  454. package/tests/py/unit/test_primitive_cell.py +0 -118
  455. package/tests/py/unit/test_reciprocal_lattice.py +0 -86
  456. package/tests/py/unit/test_reciprocal_paths.py +0 -64
  457. package/tests/py/unit/test_symmetry_points.py +0 -151
  458. package/tests/py/unit/test_tools_analyze.py +0 -219
  459. package/tests/py/unit/test_tools_analyze_basis.py +0 -105
  460. package/tests/py/unit/test_tools_analyze_interface.py +0 -223
  461. package/tests/py/unit/test_tools_analyze_interface_material.py +0 -63
  462. package/tests/py/unit/test_tools_analyze_interface_zsl.py +0 -187
  463. package/tests/py/unit/test_tools_analyze_lattice.py +0 -74
  464. package/tests/py/unit/test_tools_analyze_swap.py +0 -80
  465. package/tests/py/unit/test_tools_build.py +0 -158
  466. package/tests/py/unit/test_tools_build_defect/__init__.py +0 -0
  467. package/tests/py/unit/test_tools_build_defect/test_adatom.py +0 -84
  468. package/tests/py/unit/test_tools_build_defect/test_island.py +0 -45
  469. package/tests/py/unit/test_tools_build_defect/test_pair_defect.py +0 -84
  470. package/tests/py/unit/test_tools_build_defect/test_point_defect.py +0 -196
  471. package/tests/py/unit/test_tools_build_defect/test_slab_stack.py +0 -30
  472. package/tests/py/unit/test_tools_build_defect/test_solid_solution.py +0 -90
  473. package/tests/py/unit/test_tools_build_defect/test_terrace.py +0 -44
  474. package/tests/py/unit/test_tools_build_grain_boundary.py +0 -133
  475. package/tests/py/unit/test_tools_build_heterostructure.py +0 -46
  476. package/tests/py/unit/test_tools_build_interface.py +0 -292
  477. package/tests/py/unit/test_tools_build_interface_zsl.py +0 -263
  478. package/tests/py/unit/test_tools_build_maxwell_disorder.py +0 -123
  479. package/tests/py/unit/test_tools_build_metadata.py +0 -79
  480. package/tests/py/unit/test_tools_build_monolayer.py +0 -33
  481. package/tests/py/unit/test_tools_build_nanoparticle.py +0 -42
  482. package/tests/py/unit/test_tools_build_nanoribbon.py +0 -45
  483. package/tests/py/unit/test_tools_build_passivation.py +0 -85
  484. package/tests/py/unit/test_tools_build_perturbation.py +0 -103
  485. package/tests/py/unit/test_tools_build_slab.py +0 -382
  486. package/tests/py/unit/test_tools_build_strain.py +0 -36
  487. package/tests/py/unit/test_tools_build_supercell.py +0 -47
  488. package/tests/py/unit/test_tools_calculate.py +0 -67
  489. package/tests/py/unit/test_tools_convert.py +0 -174
  490. package/tests/py/unit/test_tools_modify.py +0 -248
  491. package/tests/py/unit/utils.py +0 -142
  492. package/tsconfig-transpile.json +0 -3
  493. package/tsconfig.json +0 -3
@@ -1,58 +0,0 @@
1
- import { Matrix3X3Schema } from "@mat3ra/esse/dist/js/types";
2
- import { Utils } from "@mat3ra/utils";
3
- import { expect } from "chai";
4
-
5
- import { Basis } from "../../../src/js/basis/basis";
6
- import { Made } from "../../../src/js/made";
7
- import Material from "../../../src/js/Material";
8
- import { Silicon, SiSupercell } from "../fixtures";
9
-
10
- const { assertDeepAlmostEqual } = Utils.assertion;
11
-
12
- describe("Tools:Supercell", () => {
13
- it("should generate supercell", () => {
14
- const material = new Material(Silicon);
15
- const supercell = Made.tools.supercell.generateConfig(material, [
16
- [2, 0, 0],
17
- [0, 2, 0],
18
- [0, 0, 2],
19
- ] as Matrix3X3Schema);
20
- // expect(supercell.lattice).deep.equal(SiSupercell.lattice, "lattices are not equal");
21
- assertDeepAlmostEqual(supercell.lattice, SiSupercell.lattice, ["vectors"]);
22
-
23
- const basis1 = new Basis(SiSupercell.basis);
24
- const basis2 = new Basis(supercell.basis);
25
-
26
- expect(basis1.isEqualTo(basis2)).to.be.equal(true);
27
- });
28
-
29
- it("should generate supercell with removed constraints", () => {
30
- const newBasisXYZ = `Si 0.000000 0.000000 0.000000
31
- Ge 0.250000 0.250000 0.250000
32
- `;
33
- const poscarNoConstraints = `Silicon FCC - supercell [[2,0,0],[0,1,0],[0,0,1]]
34
- 1.0
35
- 6.697840000\t 0.000000000\t 3.867000000
36
- 1.116307000\t 3.157392000\t 1.933500000
37
- 0.000000000\t 0.000000000\t 3.867000000
38
- Si Ge
39
- 2 2
40
- direct
41
- 0.000000000 0.000000000 0.000000000 Si
42
- 0.500000000 0.000000000 0.000000000 Si
43
- 0.125000000 0.250000000 0.250000000 Ge
44
- 0.625000000 0.250000000 0.250000000 Ge`;
45
- const material = new Material(Silicon);
46
- const clonedMaterial = material.clone();
47
- clonedMaterial.setBasis(newBasisXYZ, "xyz", clonedMaterial.getBasis().units);
48
- const supercellConfig = Made.tools.supercell.generateConfig(clonedMaterial, [
49
- [2, 0, 0],
50
- [0, 1, 0],
51
- [0, 0, 1],
52
- ] as Matrix3X3Schema);
53
-
54
- const newMaterial = new Material(supercellConfig);
55
- const poscar = newMaterial.getAsPOSCAR(true);
56
- expect(poscar).to.be.equal(poscarNoConstraints);
57
- });
58
- });
@@ -1,111 +0,0 @@
1
- import type { MaterialSchema } from "@mat3ra/esse/dist/js/types";
2
- import { Utils } from "@mat3ra/utils";
3
-
4
- import Material from "../../../src/js/Material";
5
- import tools from "../../../src/js/tools";
6
- import { SlabConfigSchema } from "../../../src/js/tools/surface";
7
- import { Silicon, SiSlab100, SiSlab111, SiSlab111NoVacuum } from "../fixtures";
8
-
9
- const { assertDeepAlmostEqual } = Utils.assertion;
10
-
11
- const generateSlabWithVacuum = (slabConfig: SlabConfigSchema, vacuumRatio: number) => {
12
- const slabMaterial = new Material(slabConfig);
13
- const { outOfPlaneAxisIndex } = slabConfig;
14
- const AXES = ["a", "b", "c"] as const;
15
-
16
- tools.material.scaleOneLatticeVector(
17
- slabMaterial,
18
- AXES[outOfPlaneAxisIndex],
19
- 1 / (1 - vacuumRatio),
20
- );
21
-
22
- return slabMaterial;
23
- };
24
-
25
- describe("Tools:Surface", () => {
26
- it("should return slab (100)", () => {
27
- const material = new Material(Silicon);
28
- const slabConfig = tools.surface.generateConfig(material, [1, 0, 0], 3, 1, 1);
29
- assertDeepAlmostEqual(SiSlab100, slabConfig);
30
- });
31
-
32
- it("should return slab (111)", () => {
33
- const material = new Material(Silicon);
34
- const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
35
- assertDeepAlmostEqual(SiSlab111NoVacuum, slabConfig);
36
- });
37
-
38
- it("should return slab (111) even if ids shifted", () => {
39
- const adjustedSilicon: MaterialSchema = {
40
- ...Silicon,
41
- basis: {
42
- ...Silicon.basis,
43
- elements: [
44
- {
45
- id: 10,
46
- value: "Si",
47
- },
48
- {
49
- id: 14,
50
- value: "Si",
51
- },
52
- ],
53
- coordinates: [
54
- {
55
- id: 10,
56
- value: [0.0, 0.0, 0.0],
57
- },
58
- {
59
- id: 14,
60
- value: [0.25, 0.25, 0.25],
61
- },
62
- ],
63
- },
64
- };
65
- const material = new Material(adjustedSilicon);
66
- const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
67
- assertDeepAlmostEqual(SiSlab111NoVacuum, slabConfig);
68
- });
69
-
70
- it("should return slab (111) with vacuum", () => {
71
- const material = new Material(Silicon);
72
- const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
73
- const vacuumRatio = 0.5;
74
- const slabMaterial = generateSlabWithVacuum(slabConfig, vacuumRatio);
75
- const expectedSlabMaterial = new Material(SiSlab111);
76
- // Structural comparison: omit hash (now included in Material.toJSON).
77
- assertDeepAlmostEqual(expectedSlabMaterial.toJSONEnhanced(), slabMaterial.toJSONEnhanced());
78
- });
79
-
80
- it("should return slab (111) with vacuum for gamma = 59.999", () => {
81
- const adjustedSilicon = {
82
- ...Silicon,
83
- lattice: {
84
- ...Silicon.lattice,
85
- gamma: 59.999,
86
- },
87
- };
88
- const material = new Material(adjustedSilicon);
89
- const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
90
- const vacuumRatio = 0.5;
91
- const slabMaterial = generateSlabWithVacuum(slabConfig, vacuumRatio);
92
- const expectedSlabMaterial = new Material(SiSlab111);
93
- assertDeepAlmostEqual(expectedSlabMaterial.toJSONEnhanced(), slabMaterial.toJSONEnhanced());
94
- });
95
-
96
- it("should return slab (111) with vacuum for gamma = 60.001", () => {
97
- const adjustedSilicon = {
98
- ...Silicon,
99
- lattice: {
100
- ...Silicon.lattice,
101
- gamma: 60.001,
102
- },
103
- };
104
- const material = new Material(adjustedSilicon);
105
- const slabConfig = tools.surface.generateConfig(material, [1, 1, 1], 3, 1, 1);
106
- const vacuumRatio = 0.5;
107
- const slabMaterial = generateSlabWithVacuum(slabConfig, vacuumRatio);
108
- const expectedSlabMaterial = new Material(SiSlab111);
109
- assertDeepAlmostEqual(expectedSlabMaterial.toJSONEnhanced(), slabMaterial.toJSONEnhanced());
110
- });
111
- });
@@ -1,34 +0,0 @@
1
- ## To avoid the following problem with spglib
2
- # .venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115
3
- # tests/py/unit/test_tools_build_defect.py::test_create_island
4
- # tests/py/unit/test_tools_build_slab.py::test_build_slab
5
- # /Users/mat3ra/code/GREEN/stack/lib/made/.venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115:
6
- # DeprecationWarning: dict interface (SpglibDataset['rotations']) is deprecated.
7
- # Use attribute interface ({self.__class__.__name__}.{key}) instead
8
- # warnings.warn(
9
- #
10
- # -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
11
- ##
12
-
13
- import warnings
14
-
15
-
16
- def pytest_configure(config):
17
- warnings.filterwarnings("ignore", category=DeprecationWarning, module="spglib.*")
18
-
19
-
20
- _orig_warn = warnings.warn
21
-
22
-
23
- def custom_warn(message, category=None, *args, **kwargs):
24
- # spglib emits DeprecationWarnings without using `stacklevel`,
25
- # so pytest and warning filters can't suppress them properly.
26
- # These warnings always appear to come from inside spglib itself.
27
- # This patch intercepts `warnings.warn` to ignore only those specific messages.
28
-
29
- if isinstance(message, str) and "SpglibDataset" in message and category is DeprecationWarning:
30
- return # suppress
31
- return _orig_warn(message, category, *args, **kwargs)
32
-
33
-
34
- warnings.warn = custom_warn
@@ -1,75 +0,0 @@
1
- import os
2
- import tempfile
3
- import time
4
- import webbrowser
5
-
6
- # Use a default div id
7
- default_div_id = "wave-div"
8
- default_width = 1200
9
- default_height = 1200
10
-
11
-
12
- def get_wave_html(div_id=default_div_id, width=default_width, height=default_height, title="Material"):
13
- size = min(width, height) # Make it square using the smaller dimension
14
- return f"""
15
- <h2>{title}</h2>
16
- <div id="{div_id}" style="width:{size}px; height:{size}px; border:1px solid #333;"></div>
17
- """
18
-
19
-
20
- def get_wave_js(material_json, div_id=default_div_id):
21
- return (
22
- f"""
23
- const materialConfig = {material_json};
24
- const container = document.getElementById('{div_id}');
25
- """
26
- + """
27
- (async function() {
28
- const module = await import('https://exabyte-io.github.io/wave.js/main.js');
29
- window.renderThreeDEditor(materialConfig, container);
30
- })();
31
- document.head.insertAdjacentHTML(
32
- 'beforeend',
33
- '<link rel="stylesheet" href="https://exabyte-io.github.io/wave.js/main.css"/>'
34
- );
35
- """
36
- )
37
-
38
-
39
- def debug_visualize_material(material, width=default_width, height=default_height, title="Material"):
40
- """
41
- Generates a temporary HTML file that uses Wave.js to visualize the material,
42
- and opens it in the default browser.
43
-
44
- Call this function from the PyCharm debugger (e.g., via Evaluate Expression).
45
- """
46
- # Convert your material to JSON.
47
- # (Assuming material.to_json() returns a JSON-serializable object)
48
- material_json = material.to_json()
49
- title = material.name if hasattr(material, "name") else title
50
- # Generate a unique div id so multiple calls don't conflict
51
- div_id = f"wave-{int(time.time())}"
52
-
53
- # Create HTML content that includes our working code
54
- html_content = f"""
55
- <!DOCTYPE html>
56
- <html>
57
- <head>
58
- <meta charset="UTF-8">
59
- <title>Wave.js Debug Viewer</title>
60
- </head>
61
- <body>
62
- {get_wave_html(div_id, width, height, title)}
63
- <script type="module">
64
- {get_wave_js(material_json, div_id)}
65
- </script>
66
- </body>
67
- </html>
68
- """
69
-
70
- # Write the HTML to a temporary file and open it in the default browser
71
- fd, file_path = tempfile.mkstemp(suffix=".html", prefix="wave_debug_")
72
- with os.fdopen(fd, "w", encoding="utf-8") as f:
73
- f.write(html_content)
74
-
75
- webbrowser.open("file://" + file_path)
File without changes
File without changes
@@ -1,60 +0,0 @@
1
- SLAB_Si_3_ADATOMS = {
2
- "name": "Si(001), termination Si_P4/mmm_2, Slab, C, N, Si Adatom",
3
- "basis": {
4
- "elements": [
5
- {"id": 0, "value": "Si"},
6
- {"id": 1, "value": "Si"},
7
- {"id": 2, "value": "Si"},
8
- {"id": 3, "value": "Si"},
9
- {"id": 4, "value": "Si"},
10
- {"id": 5, "value": "Si"},
11
- {"id": 6, "value": "Si"},
12
- {"id": 7, "value": "Si"},
13
- {"id": 8, "value": "Si"},
14
- {"id": 9, "value": "Si"},
15
- {"id": 10, "value": "Si"},
16
- {"id": 11, "value": "Si"},
17
- {"id": 12, "value": "Si"},
18
- {"id": 13, "value": "Si"},
19
- {"id": 14, "value": "Si"},
20
- {"id": 15, "value": "Si"},
21
- {"id": 16, "value": "Si"},
22
- {"id": 17, "value": "C"},
23
- {"id": 18, "value": "N"},
24
- ],
25
- "coordinates": [
26
- {"id": 0, "value": [0.5, 0, 0.204677904]},
27
- {"id": 1, "value": [0.25, 0.25, 0.136452118]},
28
- {"id": 2, "value": [0.5, 0.5, 0.068226332]},
29
- {"id": 3, "value": [0.25, 0.75, 5.46e-7]},
30
- {"id": 4, "value": [0, 0, 0.068226332]},
31
- {"id": 5, "value": [0.75, 0.25, 5.46e-7]},
32
- {"id": 6, "value": [0, 0.5, 0.204677904]},
33
- {"id": 7, "value": [0.75, 0.75, 0.136452118]},
34
- {"id": 8, "value": [0.5, 0, 0.477581049]},
35
- {"id": 9, "value": [0.25, 0.25, 0.409355263]},
36
- {"id": 10, "value": [0.5, 0.5, 0.341129477]},
37
- {"id": 11, "value": [0.25, 0.75, 0.272903691]},
38
- {"id": 12, "value": [0, 0, 0.341129477]},
39
- {"id": 13, "value": [0.75, 0.25, 0.272903691]},
40
- {"id": 14, "value": [0, 0.5, 0.477581049]},
41
- {"id": 15, "value": [0.75, 0.75, 0.409355263]},
42
- {"id": 16, "value": [0.5, 0.5, 0.577390366]},
43
- {"id": 17, "value": [0.25, 0.25, 0.552439285]},
44
- {"id": 18, "value": [0.75, 0.75, 0.527488203]},
45
- ],
46
- "units": "crystal",
47
- "labels": [],
48
- "constraints": [],
49
- },
50
- "lattice": {
51
- "a": 5.468763846,
52
- "b": 5.468763846,
53
- "c": 20.03921150886921,
54
- "alpha": 90,
55
- "beta": 90,
56
- "gamma": 90,
57
- "units": {"length": "angstrom", "angle": "degree"},
58
- "type": "TRI",
59
- },
60
- }
@@ -1,162 +0,0 @@
1
- from typing import Any, Dict
2
-
3
- from mat3ra.standata.materials import Materials
4
-
5
- BULK_SrTiO3 = Materials.get_by_name_first_match("SrTiO3")
6
- BULK_GRAPHITE = Materials.get_by_name_first_match("Graphite")
7
- BULK_SiO2 = Materials.get_by_name_first_match("SiO2")
8
- BULK_Hf2O_MCL = Materials.get_by_name_first_match("Hafnium IV Oxide, MCL")
9
- BULK_TiN = Materials.get_by_name_first_match("TiN")
10
- BULK_Ni_PRIMITIVE = Materials.get_by_name_first_match("Nickel")
11
- BULK_GRAPHENE = Materials.get_by_name_first_match("Graphene")
12
-
13
- BULK_Si_PRIMITIVE: Dict[str, Any] = {
14
- "name": "Silicon FCC",
15
- "basis": {
16
- "constraints": [],
17
- "coordinates": [{"id": 0, "value": [0.0, 0.0, 0.0]}, {"id": 1, "value": [0.25, 0.25, 0.25]}],
18
- "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
19
- "labels": [],
20
- "units": "crystal",
21
- },
22
- "lattice": {
23
- "a": 3.867,
24
- "alpha": 60.0,
25
- "b": 3.867,
26
- "beta": 60.0,
27
- "c": 3.867,
28
- "gamma": 60.0,
29
- "type": "FCC",
30
- "units": {"angle": "degree", "length": "angstrom"},
31
- },
32
- }
33
-
34
- BULK_Si_PRIMITIVIZED = {
35
- "metadata": {"build": [], "boundaryConditions": {"type": "pbc", "offset": 0}},
36
- "name": "Si2",
37
- "basis": {
38
- "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
39
- "coordinates": [{"id": 0, "value": [0.5, 0.5, 0.5]}, {"id": 1, "value": [0.75, 0.75, 0.75]}],
40
- "units": "crystal",
41
- "labels": [],
42
- "constraints": [],
43
- },
44
- "lattice": {
45
- "a": 3.867,
46
- "b": 3.867,
47
- "c": 3.867,
48
- "alpha": 60.0,
49
- "beta": 60.0,
50
- "gamma": 60.0,
51
- "units": {"length": "angstrom", "angle": "degree"},
52
- "type": "TRI",
53
- },
54
- }
55
-
56
-
57
- BULK_Si_CONVENTIONAL: Dict[str, Any] = {
58
- "name": "Si8",
59
- "basis": {
60
- "elements": [
61
- {"id": 0, "value": "Si"},
62
- {"id": 1, "value": "Si"},
63
- {"id": 2, "value": "Si"},
64
- {"id": 3, "value": "Si"},
65
- {"id": 4, "value": "Si"},
66
- {"id": 5, "value": "Si"},
67
- {"id": 6, "value": "Si"},
68
- {"id": 7, "value": "Si"},
69
- ],
70
- "coordinates": [
71
- {"id": 0, "value": [0.5, 0.0, 0.0]},
72
- {"id": 1, "value": [0.25, 0.25, 0.75]},
73
- {"id": 2, "value": [0.5, 0.5, 0.5]},
74
- {"id": 3, "value": [0.25, 0.75, 0.25]},
75
- {"id": 4, "value": [0.0, 0.0, 0.5]},
76
- {"id": 5, "value": [0.75, 0.25, 0.25]},
77
- {"id": 6, "value": [0.0, 0.5, 0.0]},
78
- {"id": 7, "value": [0.75, 0.75, 0.75]},
79
- ],
80
- "units": "crystal",
81
- "constraints": [],
82
- "labels": [],
83
- },
84
- "lattice": {
85
- "a": 5.468763846,
86
- "b": 5.468763846,
87
- "c": 5.468763846,
88
- "alpha": 90.0,
89
- "beta": 90.0,
90
- "gamma": 90.0,
91
- "units": {"length": "angstrom", "angle": "degree"},
92
- "type": "TRI",
93
- },
94
- "isNonPeriodic": False,
95
- "metadata": {"boundaryConditions": {"type": "pbc", "offset": 0}},
96
- }
97
-
98
- BULK_Si_CONVENTIONAL_FILTERED: Dict[str, Any] = {
99
- "name": "Si",
100
- "basis": {
101
- "elements": [
102
- {"id": 0, "value": "Si"},
103
- {"id": 2, "value": "Si"},
104
- ],
105
- "coordinates": [
106
- {"id": 0, "value": [0.5, 0.0, 0.0]},
107
- {"id": 2, "value": [0.5, 0.5, 0.5]},
108
- ],
109
- "units": "crystal",
110
- "labels": [],
111
- "constraints": [],
112
- },
113
- "lattice": {
114
- "a": 5.468763846,
115
- "b": 5.468763846,
116
- "c": 5.468763846,
117
- "alpha": 90.0,
118
- "beta": 90.0,
119
- "gamma": 90.0,
120
- "units": {"length": "angstrom", "angle": "degree"},
121
- "type": "TRI",
122
- },
123
- }
124
-
125
- BULK_Ge_CONVENTIONAL: Dict[str, Any] = {
126
- "name": "Germanium FCC",
127
- "basis": {
128
- "units": "crystal",
129
- "elements": [
130
- {"id": 0, "value": "Ge"},
131
- {"id": 1, "value": "Ge"},
132
- {"id": 2, "value": "Ge"},
133
- {"id": 3, "value": "Ge"},
134
- {"id": 4, "value": "Ge"},
135
- {"id": 5, "value": "Ge"},
136
- {"id": 6, "value": "Ge"},
137
- {"id": 7, "value": "Ge"},
138
- ],
139
- "coordinates": [
140
- {"id": 0, "value": [0, 0, 0]},
141
- {"id": 1, "value": [0.5, 0.5, 0]},
142
- {"id": 2, "value": [0.5, 0, 0.5]},
143
- {"id": 3, "value": [0, 0.5, 0.5]},
144
- {"id": 4, "value": [0.25, 0.25, 0.25]},
145
- {"id": 5, "value": [0.75, 0.75, 0.25]},
146
- {"id": 6, "value": [0.75, 0.25, 0.75]},
147
- {"id": 7, "value": [0.25, 0.75, 0.75]},
148
- ],
149
- "constraints": [],
150
- },
151
- "lattice": {
152
- "a": 5.67099638511611,
153
- "b": 5.67099638511611,
154
- "c": 5.67099638511611,
155
- "alpha": 90,
156
- "beta": 90,
157
- "gamma": 90,
158
- "units": {"length": "angstrom", "angle": "degree"},
159
- "type": "CUB",
160
- "vectors": {"a": [5.671, 0, 0], "b": [0, 5.671, 0], "c": [0, 0, 5.671], "alat": 1, "units": "angstrom"},
161
- },
162
- }
@@ -1,118 +0,0 @@
1
- FULL_MATERIAL = {
2
- "basis": {
3
- "constraints": [],
4
- "coordinates": [
5
- {"id": 0, "value": [0.0, 0.0, 0.0]},
6
- {"id": 1, "value": [0.0, 0.5, 0.5]},
7
- {"id": 2, "value": [0.5, 0.0, 0.5]},
8
- {"id": 3, "value": [0.5, 0.5, 0.0]},
9
- ],
10
- "elements": [
11
- {"id": 0, "value": "Ni"},
12
- {"id": 1, "value": "Ni"},
13
- {"id": 2, "value": "Ni"},
14
- {"id": 3, "value": "Ni"},
15
- ],
16
- "labels": [],
17
- "units": "crystal",
18
- },
19
- "consistencyChecks": None,
20
- "derivedProperties": None,
21
- "description": None,
22
- "descriptionObject": None,
23
- "external": None,
24
- "field_id": None,
25
- "formula": None,
26
- "icsdId": None,
27
- "isDefault": False,
28
- "isNonPeriodic": False,
29
- "lattice": {
30
- "a": 3.52,
31
- "alpha": 90.0,
32
- "b": 3.52,
33
- "beta": 90.0,
34
- "c": 3.52,
35
- "gamma": 90.0,
36
- "type": "TRI",
37
- "units": {"angle": "degree", "length": "angstrom"},
38
- },
39
- "metadata": {"boundaryConditions": {"offset": 0, "type": "pbc"}},
40
- "name": "",
41
- "scaledHash": None,
42
- "schemaVersion": "2022.8.16",
43
- "slug": None,
44
- "src": None,
45
- "systemName": None,
46
- "unitCellFormula": None,
47
- }
48
-
49
- CAVITY_MATERIAL_BASIS = {
50
- "basis": {
51
- "constraints": [],
52
- "coordinates": [
53
- {"id": 1, "value": [0.0, 0.5, 0.5]},
54
- {"id": 2, "value": [0.5, 0.0, 0.5]},
55
- {"id": 4, "value": [0.5, 0.5, 0.0]},
56
- ],
57
- "elements": [{"id": 1, "value": "Ni"}, {"id": 2, "value": "Ni"}, {"id": 4, "value": "Au"}],
58
- "labels": [],
59
- "units": "crystal",
60
- }
61
- }
62
-
63
-
64
- SECTION_MATERIAL_BASIS = {
65
- "basis": {
66
- "constraints": [],
67
- "coordinates": [{"id": 0, "value": [0.0, 0.0, 0.0]}, {"id": 3, "value": [0.5, 0.5, 0.0]}],
68
- "elements": [{"id": 0, "value": "Ni"}, {"id": 3, "value": "Ni"}],
69
- "labels": [],
70
- "units": "crystal",
71
- }
72
- }
73
-
74
- SECTION_MATERIAL_BASIS_EXTRA_ATOM = {
75
- "basis": {
76
- "constraints": [],
77
- "coordinates": [
78
- {"id": 0, "value": [0.0, 0.0, 0.0]},
79
- {"id": 3, "value": [0.5, 0.5, 0.0]},
80
- {"id": 4, "value": [0.51, 0.51, 0.0]}, # Extra atom collides with Au in cavity material
81
- ],
82
- "elements": [{"id": 0, "value": "Ni"}, {"id": 3, "value": "Ni"}, {"id": 4, "value": "O"}],
83
- "labels": [],
84
- "units": "crystal",
85
- }
86
- }
87
-
88
- MERGED_SECTION_CAVITY_BASIS = {
89
- "elements": [
90
- {"id": 0, "value": "Ni"},
91
- {"id": 1, "value": "Ni"},
92
- {"id": 2, "value": "Ni"},
93
- {"id": 4, "value": "Au"},
94
- ],
95
- "coordinates": [
96
- {"id": 0, "value": [0.0, 0.0, 0.0]},
97
- {"id": 1, "value": [0.0, 0.5, 0.5]},
98
- {"id": 2, "value": [0.5, 0.0, 0.5]},
99
- {"id": 4, "value": [0.5, 0.5, 0.0]},
100
- ],
101
- "labels": [],
102
- }
103
-
104
- MERGED_CAVITY_SECTION_BASIS = {
105
- "elements": [
106
- {"id": 1, "value": "Ni"},
107
- {"id": 2, "value": "Ni"},
108
- {"id": 0, "value": "Ni"},
109
- {"id": 3, "value": "Ni"},
110
- ],
111
- "coordinates": [
112
- {"id": 1, "value": [0.0, 0.5, 0.5]},
113
- {"id": 2, "value": [0.5, 0.0, 0.5]},
114
- {"id": 0, "value": [0.0, 0.0, 0.0]},
115
- {"id": 3, "value": [0.5, 0.5, 0.0]},
116
- ],
117
- "labels": [],
118
- }