@mat3ra/made 2026.8.7-0 → 2026.8.18-0

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 (522) hide show
  1. package/dist/js/Material.d.ts +219 -0
  2. package/dist/js/Material.js +457 -0
  3. package/dist/js/basis/basis.d.ts +14 -9
  4. package/dist/js/basis/basis.js +15 -13
  5. package/dist/js/basis/constrained_basis.d.ts +9 -7
  6. package/dist/js/basis/constrained_basis.js +4 -4
  7. package/dist/js/generated/MaterialSchemaMixin.d.ts +5 -0
  8. package/dist/js/generated/MaterialSchemaMixin.js +69 -0
  9. package/dist/js/lattice/lattice.d.ts +4 -3
  10. package/dist/js/lattice/lattice.js +1 -2
  11. package/dist/js/made.d.ts +12 -12
  12. package/dist/js/made.js +38 -5
  13. package/dist/js/parsers/espresso.d.ts +2 -3
  14. package/dist/js/parsers/espresso.js +0 -1
  15. package/dist/js/parsers/native_format_parsers.d.ts +9 -8
  16. package/dist/js/parsers/native_format_parsers.js +6 -6
  17. package/dist/js/parsers/parsers.d.ts +6 -6
  18. package/dist/js/parsers/poscar.d.ts +5 -4
  19. package/dist/js/parsers/poscar.js +3 -2
  20. package/dist/js/parsers/xyz.d.ts +3 -5
  21. package/dist/js/parsers/xyz.js +3 -4
  22. package/dist/js/parsers/xyz_combinatorial_basis.js +3 -1
  23. package/dist/js/tools/basis.d.ts +1 -1
  24. package/dist/js/tools/index.d.ts +7 -7
  25. package/dist/js/tools/material.d.ts +1 -1
  26. package/dist/js/tools/material.js +8 -7
  27. package/dist/js/tools/supercell.d.ts +4 -5
  28. package/dist/js/tools/supercell.js +2 -4
  29. package/dist/js/tools/surface.d.ts +4 -4
  30. package/dist/js/tools/surface.js +2 -7
  31. package/package.json +12 -8
  32. package/.babelrc +0 -10
  33. package/.eslintrc.json +0 -11
  34. package/.gitattributes +0 -1
  35. package/.husky/post-checkout +0 -3
  36. package/.husky/post-commit +0 -3
  37. package/.husky/post-merge +0 -3
  38. package/.husky/pre-commit +0 -6
  39. package/.husky/pre-push +0 -3
  40. package/.mocharc.json +0 -5
  41. package/.pre-commit-config.yaml +0 -26
  42. package/.prettierignore +0 -2
  43. package/.prettierrc +0 -6
  44. package/AGENTS.md +0 -133
  45. package/MANIFEST.in +0 -1
  46. package/data/constants.json +0 -13
  47. package/data/reciprocal_paths.json +0 -111
  48. package/dist/js/material.d.ts +0 -169
  49. package/dist/js/material.js +0 -362
  50. package/images/made/tools/tools_diagram_general.png +0 -3
  51. package/images/made/tools/tools_diagram_interface.png +0 -3
  52. package/pyproject.toml +0 -123
  53. package/src/__init__.py +0 -0
  54. package/src/js/basis/basis.ts +0 -621
  55. package/src/js/basis/constrained_basis.ts +0 -114
  56. package/src/js/basis/coordinates.ts +0 -93
  57. package/src/js/basis/elements.ts +0 -24
  58. package/src/js/basis/helpers.ts +0 -20
  59. package/src/js/basis/labels.ts +0 -6
  60. package/src/js/cell/cell.ts +0 -150
  61. package/src/js/cell/conventional_cell.ts +0 -86
  62. package/src/js/cell/primitive_cell.ts +0 -166
  63. package/src/js/constants/molecule.ts +0 -18
  64. package/src/js/constants.ts +0 -4
  65. package/src/js/constraints/constraints.ts +0 -45
  66. package/src/js/lattice/lattice.ts +0 -306
  67. package/src/js/lattice/lattice_types.ts +0 -134
  68. package/src/js/lattice/reciprocal/lattice_reciprocal.ts +0 -193
  69. package/src/js/lattice/reciprocal/paths.ts +0 -39
  70. package/src/js/lattice/reciprocal/symmetry_points.ts +0 -886
  71. package/src/js/lattice/unit_cell.ts +0 -66
  72. package/src/js/made.ts +0 -62
  73. package/src/js/material.ts +0 -458
  74. package/src/js/parsers/cif.ts +0 -25
  75. package/src/js/parsers/errors.ts +0 -6
  76. package/src/js/parsers/espresso.ts +0 -30
  77. package/src/js/parsers/native_format_parsers.ts +0 -51
  78. package/src/js/parsers/parsers.ts +0 -13
  79. package/src/js/parsers/poscar.ts +0 -212
  80. package/src/js/parsers/xyz.ts +0 -187
  81. package/src/js/parsers/xyz_combinatorial_basis.ts +0 -265
  82. package/src/js/tools/basis.ts +0 -132
  83. package/src/js/tools/cell.ts +0 -41
  84. package/src/js/tools/index.ts +0 -11
  85. package/src/js/tools/material.ts +0 -62
  86. package/src/js/tools/supercell.ts +0 -88
  87. package/src/js/tools/surface.ts +0 -223
  88. package/src/py/__init__.py +0 -0
  89. package/src/py/mat3ra/__init__.py +0 -1
  90. package/src/py/mat3ra/made/__init__.py +0 -7
  91. package/src/py/mat3ra/made/basis/__init__.py +0 -255
  92. package/src/py/mat3ra/made/basis/coordinates.py +0 -43
  93. package/src/py/mat3ra/made/cell/__init__.py +0 -55
  94. package/src/py/mat3ra/made/cell/primitive_cell.py +0 -156
  95. package/src/py/mat3ra/made/data_helper.py +0 -5
  96. package/src/py/mat3ra/made/lattice.py +0 -195
  97. package/src/py/mat3ra/made/material.py +0 -134
  98. package/src/py/mat3ra/made/metadata.py +0 -45
  99. package/src/py/mat3ra/made/reciprocal/__init__.py +0 -5
  100. package/src/py/mat3ra/made/reciprocal/lattice_reciprocal.py +0 -147
  101. package/src/py/mat3ra/made/reciprocal/paths.py +0 -30
  102. package/src/py/mat3ra/made/reciprocal/symmetry_points.py +0 -385
  103. package/src/py/mat3ra/made/tools/README.md +0 -173
  104. package/src/py/mat3ra/made/tools/__init__.py +0 -0
  105. package/src/py/mat3ra/made/tools/analyze/__init__.py +0 -31
  106. package/src/py/mat3ra/made/tools/analyze/basis/__init__.py +0 -3
  107. package/src/py/mat3ra/made/tools/analyze/basis/analyzer.py +0 -50
  108. package/src/py/mat3ra/made/tools/analyze/build_metadata_analyzer.py +0 -32
  109. package/src/py/mat3ra/made/tools/analyze/build_metadata_analyzer_factory.py +0 -31
  110. package/src/py/mat3ra/made/tools/analyze/coordination.py +0 -56
  111. package/src/py/mat3ra/made/tools/analyze/crystal_site/__init__.py +0 -0
  112. package/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_crystal_site_material_analyzer.py +0 -35
  113. package/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_material_analyzer.py +0 -49
  114. package/src/py/mat3ra/made/tools/analyze/crystal_site/crystal_site_analyzer.py +0 -65
  115. package/src/py/mat3ra/made/tools/analyze/crystal_site/voronoi_crystal_site_analyzer.py +0 -47
  116. package/src/py/mat3ra/made/tools/analyze/enums.py +0 -33
  117. package/src/py/mat3ra/made/tools/analyze/fingerprint/__init__.py +0 -4
  118. package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/__init__.py +0 -0
  119. package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/layered_fingerprint_along_axis.py +0 -83
  120. package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/unique_element_string_per_layer.py +0 -9
  121. package/src/py/mat3ra/made/tools/analyze/interface/__init__.py +0 -20
  122. package/src/py/mat3ra/made/tools/analyze/interface/commensurate.py +0 -156
  123. package/src/py/mat3ra/made/tools/analyze/interface/enums.py +0 -60
  124. package/src/py/mat3ra/made/tools/analyze/interface/grain_boundary.py +0 -80
  125. package/src/py/mat3ra/made/tools/analyze/interface/simple.py +0 -251
  126. package/src/py/mat3ra/made/tools/analyze/interface/twisted_nanoribbons.py +0 -91
  127. package/src/py/mat3ra/made/tools/analyze/interface/utils/__init__.py +0 -77
  128. package/src/py/mat3ra/made/tools/analyze/interface/utils/holders.py +0 -14
  129. package/src/py/mat3ra/made/tools/analyze/interface/utils/vector.py +0 -56
  130. package/src/py/mat3ra/made/tools/analyze/interface/zsl.py +0 -259
  131. package/src/py/mat3ra/made/tools/analyze/interface_material.py +0 -45
  132. package/src/py/mat3ra/made/tools/analyze/lattice/__init__.py +0 -2
  133. package/src/py/mat3ra/made/tools/analyze/lattice/analyzer.py +0 -126
  134. package/src/py/mat3ra/made/tools/analyze/lattice/helpers.py +0 -31
  135. package/src/py/mat3ra/made/tools/analyze/lattice_lines.py +0 -30
  136. package/src/py/mat3ra/made/tools/analyze/lattice_planes.py +0 -192
  137. package/src/py/mat3ra/made/tools/analyze/lattice_swap_analyzer.py +0 -105
  138. package/src/py/mat3ra/made/tools/analyze/material.py +0 -276
  139. package/src/py/mat3ra/made/tools/analyze/other.py +0 -434
  140. package/src/py/mat3ra/made/tools/analyze/rdf.py +0 -74
  141. package/src/py/mat3ra/made/tools/analyze/slab.py +0 -76
  142. package/src/py/mat3ra/made/tools/analyze/solid_solution_analyzer.py +0 -171
  143. package/src/py/mat3ra/made/tools/analyze/terrace.py +0 -105
  144. package/src/py/mat3ra/made/tools/analyze/utils.py +0 -162
  145. package/src/py/mat3ra/made/tools/bond_directions/__init__.py +0 -0
  146. package/src/py/mat3ra/made/tools/bond_directions/bond_directions.py +0 -150
  147. package/src/py/mat3ra/made/tools/bond_directions/bond_directions_for_element_list.py +0 -7
  148. package/src/py/mat3ra/made/tools/bond_directions/bond_directions_templates_enum.py +0 -8
  149. package/src/py/mat3ra/made/tools/bond_directions/bond_directions_templates_for_element.py +0 -16
  150. package/src/py/mat3ra/made/tools/build/__init__.py +0 -25
  151. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/__init__.py +0 -7
  152. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/helpers.py +0 -59
  153. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/types.py +0 -26
  154. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/utils.py +0 -139
  155. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/__init__.py +0 -47
  156. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/__init__.py +0 -11
  157. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/build_parameters.py +0 -5
  158. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/builder.py +0 -164
  159. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/configuration.py +0 -48
  160. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/helpers.py +0 -134
  161. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/__init__.py +0 -6
  162. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/helpers.py +0 -157
  163. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/enums.py +0 -7
  164. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/__init__.py +0 -7
  165. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/configuration.py +0 -13
  166. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/helpers.py +0 -70
  167. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/utils.py +0 -87
  168. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/zsl/__init__.py +0 -6
  169. package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/zsl/helpers.py +0 -129
  170. package/src/py/mat3ra/made/tools/build/defective_structures/__init__.py +0 -0
  171. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/__init__.py +0 -0
  172. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/__init__.py +0 -0
  173. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/build_parameters.py +0 -12
  174. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/builder.py +0 -17
  175. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/configuration.py +0 -40
  176. package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/helpers.py +0 -82
  177. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/__init__.py +0 -1
  178. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/__init__.py +0 -9
  179. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/builder.py +0 -37
  180. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/configuration.py +0 -30
  181. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/enums.py +0 -8
  182. package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/helpers.py +0 -76
  183. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/__init__.py +0 -0
  184. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/__init__.py +0 -0
  185. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/builder.py +0 -11
  186. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/configuration.py +0 -18
  187. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/helpers.py +0 -137
  188. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/types.py +0 -22
  189. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/__init__.py +0 -0
  190. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/builder.py +0 -28
  191. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/configuration.py +0 -55
  192. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/helpers.py +0 -75
  193. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/builder.py +0 -15
  194. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/configuration.py +0 -16
  195. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/helpers.py +0 -116
  196. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/build_parameters.py +0 -10
  197. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/builder.py +0 -30
  198. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/configuration.py +0 -11
  199. package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/helpers.py +0 -78
  200. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/__init__.py +0 -0
  201. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/__init__.py +0 -0
  202. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/builder.py +0 -31
  203. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/configuration.py +0 -45
  204. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/helpers.py +0 -80
  205. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/__init__.py +0 -40
  206. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/atom_placement_method_enum.py +0 -14
  207. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/__init__.py +0 -7
  208. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/builder.py +0 -42
  209. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/configuration.py +0 -27
  210. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/complex_defect_type_enum.py +0 -5
  211. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/factories.py +0 -69
  212. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/helpers.py +0 -92
  213. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/__init__.py +0 -7
  214. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/builder.py +0 -8
  215. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/configuration.py +0 -29
  216. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/helpers.py +0 -48
  217. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/interstitial_placement_method_enum.py +0 -8
  218. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/point_defect_type_enum.py +0 -8
  219. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/__init__.py +0 -7
  220. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/builder.py +0 -6
  221. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/configuration.py +0 -41
  222. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/helpers.py +0 -43
  223. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/substitution_placement_method_enum.py +0 -7
  224. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/types.py +0 -24
  225. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/__init__.py +0 -7
  226. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/builder.py +0 -19
  227. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/configuration.py +0 -27
  228. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/helpers.py +0 -42
  229. package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/vacancy_placement_method_enum.py +0 -7
  230. package/src/py/mat3ra/made/tools/build/pristine_structures/__init__.py +0 -0
  231. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/__init__.py +0 -0
  232. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/builder.py +0 -80
  233. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/configurations.py +0 -22
  234. package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/helpers.py +0 -40
  235. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/__init__.py +0 -0
  236. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/__init__.py +0 -29
  237. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/build_parameters.py +0 -5
  238. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/builders.py +0 -56
  239. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/configuration.py +0 -33
  240. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/helpers.py +0 -76
  241. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/__init__.py +0 -11
  242. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/build_parameters.py +0 -9
  243. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/builders.py +0 -83
  244. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/configuration.py +0 -35
  245. package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/helpers.py +0 -62
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  487. package/tests/py/unit/test_tools_analyze.py +0 -219
  488. package/tests/py/unit/test_tools_analyze_basis.py +0 -105
  489. package/tests/py/unit/test_tools_analyze_interface.py +0 -223
  490. package/tests/py/unit/test_tools_analyze_interface_material.py +0 -63
  491. package/tests/py/unit/test_tools_analyze_interface_zsl.py +0 -187
  492. package/tests/py/unit/test_tools_analyze_lattice.py +0 -74
  493. package/tests/py/unit/test_tools_analyze_swap.py +0 -80
  494. package/tests/py/unit/test_tools_build.py +0 -158
  495. package/tests/py/unit/test_tools_build_defect/__init__.py +0 -0
  496. package/tests/py/unit/test_tools_build_defect/test_adatom.py +0 -84
  497. package/tests/py/unit/test_tools_build_defect/test_island.py +0 -45
  498. package/tests/py/unit/test_tools_build_defect/test_pair_defect.py +0 -84
  499. package/tests/py/unit/test_tools_build_defect/test_point_defect.py +0 -196
  500. package/tests/py/unit/test_tools_build_defect/test_slab_stack.py +0 -30
  501. package/tests/py/unit/test_tools_build_defect/test_solid_solution.py +0 -90
  502. package/tests/py/unit/test_tools_build_defect/test_terrace.py +0 -44
  503. package/tests/py/unit/test_tools_build_grain_boundary.py +0 -133
  504. package/tests/py/unit/test_tools_build_heterostructure.py +0 -46
  505. package/tests/py/unit/test_tools_build_interface.py +0 -292
  506. package/tests/py/unit/test_tools_build_interface_zsl.py +0 -263
  507. package/tests/py/unit/test_tools_build_maxwell_disorder.py +0 -123
  508. package/tests/py/unit/test_tools_build_metadata.py +0 -79
  509. package/tests/py/unit/test_tools_build_monolayer.py +0 -33
  510. package/tests/py/unit/test_tools_build_nanoparticle.py +0 -42
  511. package/tests/py/unit/test_tools_build_nanoribbon.py +0 -45
  512. package/tests/py/unit/test_tools_build_passivation.py +0 -85
  513. package/tests/py/unit/test_tools_build_perturbation.py +0 -103
  514. package/tests/py/unit/test_tools_build_slab.py +0 -382
  515. package/tests/py/unit/test_tools_build_strain.py +0 -36
  516. package/tests/py/unit/test_tools_build_supercell.py +0 -47
  517. package/tests/py/unit/test_tools_calculate.py +0 -67
  518. package/tests/py/unit/test_tools_convert.py +0 -174
  519. package/tests/py/unit/test_tools_modify.py +0 -248
  520. package/tests/py/unit/utils.py +0 -142
  521. package/tsconfig-transpile.json +0 -3
  522. package/tsconfig.json +0 -3
@@ -1,114 +0,0 @@
1
- import { AtomicConstraintsSchema } from "@mat3ra/esse/dist/js/types";
2
-
3
- import { AtomicConstraints, AtomicConstraintValue, Constraint } from "../constraints/constraints";
4
- import { Basis, BasisConfig, ElementsAndCoordinatesConfig } from "./basis";
5
- import { AtomicCoordinateValue, Coordinate } from "./coordinates";
6
- import { AtomicElementValue } from "./elements";
7
- import { ElementWithLabel } from "./helpers";
8
- import { AtomicLabelValue } from "./labels";
9
-
10
- export interface ConstrainedBasisConfig extends BasisConfig {
11
- constraints: AtomicConstraintsSchema;
12
- }
13
-
14
- export interface ElementsCoordinatesAndConstraintsConfig extends ElementsAndCoordinatesConfig {
15
- constraints: AtomicConstraintValue[];
16
- }
17
-
18
- /**
19
- * @summary Extension of the Basis class able to deal with atomic constraints.
20
- * @extends Basis
21
- */
22
- export class ConstrainedBasis extends Basis {
23
- _constraints: AtomicConstraints;
24
-
25
- constructor(config: ConstrainedBasisConfig) {
26
- super(config);
27
- const { constraints } = config;
28
- this._constraints = AtomicConstraints.fromObjects(constraints || []); // `constraints` is an Array with ids
29
- }
30
-
31
- static fromElementsCoordinatesAndConstraints(
32
- config: ElementsCoordinatesAndConstraintsConfig,
33
- ): ConstrainedBasis {
34
- const basisConfig = this._convertValuesToConfig(config);
35
- const constraints = AtomicConstraints.fromValues(config.constraints);
36
- return new this({
37
- ...basisConfig,
38
- constraints: constraints.toJSON() as AtomicConstraintsSchema,
39
- });
40
- }
41
-
42
- get constraints() {
43
- return this._constraints.toJSON() as AtomicConstraintsSchema;
44
- }
45
-
46
- set constraints(constraints: AtomicConstraintsSchema) {
47
- this._constraints = AtomicConstraints.fromObjects(constraints);
48
- }
49
-
50
- get AtomicConstraints() {
51
- return AtomicConstraints.fromObjects(this.constraints);
52
- }
53
-
54
- override toJSON(): ConstrainedBasisConfig {
55
- return {
56
- ...super.toJSON(),
57
- constraints: this.constraints,
58
- };
59
- }
60
-
61
- getConstraintByIndex(idx: number): AtomicConstraintValue {
62
- return this._constraints.getElementValueByIndex(idx) || [true, true, true];
63
- }
64
-
65
- getConstraintById(id: number): AtomicConstraintValue {
66
- return this._constraints.getElementValueById(id) || [true, true, true];
67
- }
68
-
69
- /**
70
- * Helper function returning a nested array with [element, coordinates, constraints] as elements
71
- */
72
- get elementsCoordinatesConstraintsArray(): [
73
- AtomicElementValue,
74
- AtomicLabelValue,
75
- AtomicCoordinateValue,
76
- AtomicConstraintValue,
77
- ][] {
78
- return this._elements.values.map((element: any, idx: number) => {
79
- const coordinate = this.getCoordinateValueByIndex(idx);
80
- const constraint = this.getConstraintByIndex(idx);
81
- const label = this.atomicLabelsArray[idx];
82
- return [element, label, coordinate, constraint];
83
- });
84
- }
85
-
86
- /**
87
- * Returns an array with atomic positions (with constraints) per atom stored as strings.
88
- * E.g., ``` ['Si 0 0 0 0 1 0', 'Li 0.5 0.5 0.5 1 0 1']```
89
- */
90
- getAtomicPositionsWithConstraintsAsStrings(
91
- coordinatePrintFormat?: string,
92
- precision?: number,
93
- ): string[] {
94
- const omitConstraints = this._constraints.areUnconstrained;
95
- return this.elementsCoordinatesConstraintsArray.map(
96
- ([element, label, coordinate, constraint]) => {
97
- const _elementWithLabel = new ElementWithLabel({ element, label });
98
- const _coordinate = Coordinate.fromValueAndId(coordinate);
99
- const _constraint = Constraint.fromValueAndId(constraint);
100
-
101
- return [
102
- _elementWithLabel.prettyPrint(),
103
- _coordinate.prettyPrint(coordinatePrintFormat, precision),
104
- omitConstraints ? "" : _constraint.prettyPrint(),
105
- ].join(" ");
106
- },
107
- );
108
- }
109
-
110
- removeAllAtoms() {
111
- super.removeAllAtoms();
112
- this.constraints = [];
113
- }
114
- }
@@ -1,93 +0,0 @@
1
- import { RoundedArrayWithIds, RoundedValueWithId, RoundedVector3D, Vector3D } from "@mat3ra/code";
2
- import {
3
- AtomicCoordinateSchema,
4
- Coordinate3DSchema,
5
- Matrix3X3Schema,
6
- Vector3DSchema,
7
- } from "@mat3ra/esse/dist/js/types";
8
- import { Utils } from "@mat3ra/utils";
9
- import { sprintf } from "underscore.string";
10
-
11
-
12
- export type AtomicCoordinateValue = AtomicCoordinateSchema["value"];
13
-
14
- type AxisType = "x" | "y" | "z";
15
-
16
- export class Coordinate extends RoundedValueWithId<AtomicCoordinateValue> {
17
- value: AtomicCoordinateValue;
18
-
19
- constructor({ value, id }: AtomicCoordinateSchema) {
20
- super(id, value);
21
- this.value = value;
22
- }
23
-
24
- getValueAlongAxis(axis: AxisType = "z"): number {
25
- const index = { x: 0, y: 1, z: 2 }[axis];
26
- return this.value[index] as number;
27
- }
28
-
29
- translateByVector(vectorAsArray: Vector3DSchema): Coordinate {
30
- const vector3D = new Vector3D(this.value);
31
- this.value = vector3D.translateByVector(vectorAsArray).value;
32
- return this;
33
- }
34
-
35
- get valueRounded(): number[] {
36
- return new RoundedVector3D(this.value).valueRounded;
37
- }
38
-
39
- getValueRoundedWithPrecision(precision: number): number[] {
40
- const RoundedInstance = RoundedVector3D;
41
- RoundedInstance.roundPrecision = precision;
42
- return new RoundedInstance(this.value).valueRounded;
43
- }
44
-
45
- prettyPrint(format = "%14.9f", precision: number = this.precision): string {
46
- return this.getValueRoundedWithPrecision(precision)
47
- .map((x) => sprintf(format, x))
48
- .join(" ");
49
- }
50
- }
51
-
52
- export class Coordinates extends RoundedArrayWithIds<Coordinate3DSchema> {
53
- getValuesAlongAxis(axis: AxisType = "z"): number[] {
54
- return this.values.map((coord) => {
55
- const coordinate = Coordinate.fromValueAndId(coord);
56
- return coordinate.getValueAlongAxis(axis);
57
- });
58
- }
59
-
60
- getMaxValueAlongAxis(axis: AxisType = "z"): number {
61
- return Math.max(...this.getValuesAlongAxis(axis));
62
- }
63
-
64
- getMinValueAlongAxis(axis: AxisType = "z"): number {
65
- return Math.min(...this.getValuesAlongAxis(axis));
66
- }
67
-
68
- getExtremumValueAlongAxis(extremum: "max" | "min" = "max", axis: AxisType = "z"): number {
69
- return extremum === "max"
70
- ? this.getMaxValueAlongAxis(axis)
71
- : this.getMinValueAlongAxis(axis);
72
- }
73
-
74
- translateByVector(vector: Vector3DSchema): void {
75
- this.mapArrayInPlace((x) => {
76
- const coordinate = Coordinate.fromValueAndId(x);
77
- return coordinate.translateByVector(vector).value;
78
- });
79
- }
80
-
81
- getCenterPoint(): Vector3DSchema {
82
- const transposed = Utils.math.transpose(this.values) as Matrix3X3Schema;
83
- const center: Vector3DSchema = [0, 0, 0];
84
-
85
- for (let i = 0; i < 3; i++) {
86
- const axisCoords = transposed[i] as Coordinate3DSchema;
87
- const sum = axisCoords.reduce((a, b) => a + b, 0);
88
- center[i] = sum / this.values.length;
89
- }
90
-
91
- return center;
92
- }
93
- }
@@ -1,24 +0,0 @@
1
- import { ArrayWithIds, ValueWithId } from "@mat3ra/code";
2
- import { AtomicElementSchema } from "@mat3ra/esse/dist/js/types";
3
- import { uniq } from "lodash";
4
-
5
- export type AtomicElementValue = AtomicElementSchema["value"];
6
-
7
- export class Element extends ValueWithId<AtomicElementValue> {
8
- value: AtomicElementValue;
9
-
10
- constructor({ value, id }: AtomicElementSchema) {
11
- super({ id, value });
12
- this.value = value;
13
- }
14
-
15
- prettyPrint(): string {
16
- return this.value;
17
- }
18
- }
19
-
20
- export class Elements extends ArrayWithIds<AtomicElementValue> {
21
- getUnique(): string[] {
22
- return uniq(this.values.map((element) => element)) as string[];
23
- }
24
- }
@@ -1,20 +0,0 @@
1
- import s from "underscore.string";
2
-
3
- import { AtomicElementValue } from "./elements";
4
- import { AtomicLabelValue } from "./labels";
5
-
6
- export class ElementWithLabel {
7
- element: AtomicElementValue;
8
-
9
- label: AtomicLabelValue;
10
-
11
- constructor({ element, label }: { element: AtomicElementValue; label: AtomicLabelValue }) {
12
- this.element = element;
13
- this.label = label;
14
- }
15
-
16
- prettyPrint(): string {
17
- const elementWithLabel = `${this.element}${this.label}`;
18
- return s.sprintf("%-3s", elementWithLabel);
19
- }
20
- }
@@ -1,6 +0,0 @@
1
- import { ArrayWithIds } from "@mat3ra/code";
2
- import { AtomicLabelSchema } from "@mat3ra/esse/dist/js/types";
3
-
4
- export type AtomicLabelValue = AtomicLabelSchema["value"];
5
-
6
- export class Labels extends ArrayWithIds<AtomicLabelValue> {}
@@ -1,150 +0,0 @@
1
- import { RoundedVector3D } from "@mat3ra/code";
2
- import {
3
- Coordinate3DSchema,
4
- LatticeVectorsSchema as CellSchema,
5
- Matrix3X3Schema,
6
- Vector3DSchema,
7
- } from "@mat3ra/esse/dist/js/types";
8
- import { Utils } from "@mat3ra/utils";
9
-
10
- import constants from "../constants";
11
-
12
-
13
- const MATRIX = Utils.math.matrix;
14
- const MULT = Utils.math.multiply;
15
- const INV = Utils.math.inv;
16
- // @ts-ignore
17
- const MATRIX_MULT = (...args) => MULT(...args.map((x) => MATRIX(x))).toArray();
18
-
19
- export class Cell implements CellSchema {
20
- static RoundedVector3DClassReference = RoundedVector3D;
21
-
22
- static roundPrecision = 9;
23
-
24
- static tolerance = constants.tolerance.length; // in crystal coordinates
25
-
26
- static defaultConfig: CellSchema = {
27
- a: [1.0, 0, 0],
28
- b: [0, 1.0, 0],
29
- c: [0, 0, 1.0],
30
- };
31
-
32
- a: CellSchema["a"];
33
-
34
- b: CellSchema["b"];
35
-
36
- c: CellSchema["c"];
37
-
38
- alat = 1;
39
-
40
- units: CellSchema["units"] = "angstrom";
41
-
42
- constructor(config = Cell.defaultConfig) {
43
- const { a, b, c } = config;
44
- this.a = a;
45
- this.b = b;
46
- this.c = c;
47
- }
48
-
49
- static fromVectorsArray(vectors: Matrix3X3Schema): Cell {
50
- return new Cell({
51
- a: vectors[0],
52
- b: vectors[1],
53
- c: vectors[2],
54
- });
55
- }
56
-
57
- get _a() {
58
- return new Cell.RoundedVector3DClassReference(this.a);
59
- }
60
-
61
- get _b() {
62
- return new Cell.RoundedVector3DClassReference(this.b);
63
- }
64
-
65
- get _c() {
66
- return new Cell.RoundedVector3DClassReference(this.c);
67
- }
68
-
69
- get vectorArrays(): Matrix3X3Schema {
70
- return [this._a.value, this._b.value, this._c.value];
71
- }
72
-
73
- get vectorArraysRounded(): Matrix3X3Schema {
74
- return [this._a.valueRounded, this._b.valueRounded, this._c.valueRounded];
75
- }
76
-
77
- get volume(): number {
78
- return Utils.math.det(this.vectorArrays);
79
- }
80
-
81
- get volumeRounded(): number {
82
- return Utils.math.roundArrayOrNumber(this.volume, Cell.roundPrecision) as number;
83
- }
84
-
85
- clone(): Cell {
86
- return new Cell({ a: this.a, b: this.b, c: this.c });
87
- }
88
-
89
- cloneAndScaleByMatrix(matrix: Matrix3X3Schema) {
90
- const newCell = this.clone();
91
- newCell.scaleByMatrix(matrix);
92
- return newCell;
93
- }
94
-
95
- convertPointToCartesian(point: Coordinate3DSchema): Coordinate3DSchema {
96
- return MULT(point, this.vectorArrays) as unknown as Coordinate3DSchema;
97
- }
98
-
99
- convertPointToCrystal(point: Coordinate3DSchema): Coordinate3DSchema {
100
- return MULT(point, INV(this.vectorArrays)) as unknown as Coordinate3DSchema;
101
- }
102
-
103
- isPointInsideCellCartesian(point: Coordinate3DSchema): boolean {
104
- const { tolerance } = this.constructor as typeof Cell;
105
- return (
106
- this.convertPointToCrystal(point)
107
- .map((c: number) => Utils.math.isBetweenZeroInclusiveAndOne(c, tolerance))
108
- // @ts-ignore
109
- .reduce((a: boolean, b: boolean): boolean => a && b)
110
- );
111
- }
112
-
113
- // eslint-disable-next-line class-methods-use-this
114
- isPointInsideCellCrystal(point: Coordinate3DSchema): boolean {
115
- const { tolerance } = this.constructor as typeof Cell;
116
- return (
117
- point
118
- .map((c: number) => Utils.math.isBetweenZeroInclusiveAndOne(c, tolerance))
119
- // @ts-ignore
120
- .reduce((a: boolean, b: boolean): boolean => a && b)
121
- );
122
- }
123
-
124
- isPointInsideCell(point: Coordinate3DSchema, useCrystal = false): boolean {
125
- if (useCrystal) {
126
- return this.isPointInsideCellCrystal(point);
127
- }
128
- return this.isPointInsideCellCartesian(point);
129
- }
130
-
131
- getMostCollinearVectorIndex(testVector: Vector3DSchema): number {
132
- const angles = this.vectorArrays.map((v) => Utils.math.angleUpTo90(v, testVector, "deg"));
133
- return angles.findIndex((el: number) => el === Utils.math.min(angles));
134
- }
135
-
136
- scaleByMatrix(matrix: number[][]) {
137
- // @ts-ignore - mathjs v12 multiply return type is broader than runtime
138
- [this.a, this.b, this.c] = MATRIX_MULT(matrix, this.vectorArrays);
139
- }
140
-
141
- toJSON(): CellSchema {
142
- return {
143
- a: this._a.toJSON(),
144
- b: this._b.toJSON(),
145
- c: this._c.toJSON(),
146
- alat: this.alat,
147
- units: this.units,
148
- };
149
- }
150
- }
@@ -1,86 +0,0 @@
1
- import { LatticeSchema, LatticeTypeEnum, Matrix3X3Schema } from "@mat3ra/esse/dist/js/types";
2
-
3
- /**
4
- * Routines for calculating conventional cell vectors from primitive cell Bravais parameters.
5
- * Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010
6
- */
7
-
8
- const unitMatrix: Matrix3X3Schema = [
9
- [1, 0, 0],
10
- [0, 1, 0],
11
- [0, 0, 1],
12
- ];
13
-
14
- // (Conventional cellVectors) = (Primitive cellVectors) * (PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIER matrix)
15
- export const PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS: Record<string, Matrix3X3Schema> = {
16
- // PRIMITIVE => CONVENTIONAL
17
- CUB: unitMatrix,
18
- FCC: [
19
- [-1, 1, 1],
20
- [1, -1, 1],
21
- [1, 1, -1],
22
- ],
23
- BCC: [
24
- [0, 1, 1],
25
- [1, 0, 1],
26
- [1, 1, 0],
27
- ],
28
- TET: unitMatrix,
29
- BCT: [
30
- [0, 1, 1],
31
- [1, 0, 1],
32
- [1, 1, 0],
33
- ],
34
- ORC: unitMatrix,
35
- ORCF: [
36
- [-1, 1, 1],
37
- [1, -1, 1],
38
- [1, 1, -1],
39
- ],
40
- ORCI: [
41
- [0, 1, 1],
42
- [1, 0, 1],
43
- [1, 1, 0],
44
- ],
45
- ORCC: [
46
- [1, -1, 0],
47
- [1, 1, 0],
48
- [0, 0, 1],
49
- ],
50
- HEX: unitMatrix,
51
- RHL: unitMatrix,
52
- MCL: unitMatrix,
53
- MCLC: [
54
- [1, -1, 0],
55
- [1, 1, 0],
56
- [0, 0, 1],
57
- ],
58
- TRI: unitMatrix,
59
- };
60
-
61
- export const PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES: {
62
- [key in LatticeTypeEnum]: LatticeTypeEnum;
63
- } = {
64
- // PRIMITIVE => CONVENTIONAL
65
- CUB: "CUB",
66
- FCC: "CUB",
67
- BCC: "CUB",
68
- TET: "TET",
69
- BCT: "TET",
70
- ORC: "ORC",
71
- ORCF: "ORC",
72
- ORCI: "ORC",
73
- ORCC: "ORC",
74
- HEX: "HEX",
75
- RHL: "RHL",
76
- MCL: "MCL",
77
- MCLC: "MCL",
78
- TRI: "TRI",
79
- };
80
-
81
- export function isConventionalCellSameAsPrimitiveForLatticeType(
82
- latticeType: LatticeSchema["type"],
83
- ): boolean {
84
- const multiplier = PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[latticeType || "TRI"];
85
- return multiplier === unitMatrix;
86
- }
@@ -1,166 +0,0 @@
1
- import { LatticeSchema, Matrix3X3Schema } from "@mat3ra/esse/dist/js/types";
2
- import { Utils } from "@mat3ra/utils";
3
-
4
- /**
5
- * Routines for calculating primitive cell vectors from conventional cell Bravais parameters.
6
- * Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010
7
- */
8
- const PRIMITIVE_CELLS = {
9
- CUB: ({ a }: LatticeSchema): Matrix3X3Schema => {
10
- return [
11
- [a, 0, 0],
12
- [0, a, 0],
13
- [0, 0, a],
14
- ];
15
- },
16
-
17
- FCC: ({ a }: LatticeSchema): Matrix3X3Schema => {
18
- return [
19
- [0.0, a / 2, a / 2],
20
- [a / 2, 0.0, a / 2],
21
- [a / 2, a / 2, 0.0],
22
- ];
23
- },
24
-
25
- BCC: ({ a }: LatticeSchema): Matrix3X3Schema => {
26
- return [
27
- [-a / 2, a / 2, a / 2],
28
- [a / 2, -a / 2, a / 2],
29
- [a / 2, a / 2, -a / 2],
30
- ];
31
- },
32
-
33
- TET: ({ a, c }: LatticeSchema): Matrix3X3Schema => {
34
- return [
35
- [a, 0, 0],
36
- [0, a, 0],
37
- [0, 0, c],
38
- ];
39
- },
40
-
41
- BCT: ({ a, c }: LatticeSchema): Matrix3X3Schema => {
42
- return [
43
- [-a / 2, a / 2, c / 2],
44
- [a / 2, -a / 2, c / 2],
45
- [a / 2, a / 2, -c / 2],
46
- ];
47
- },
48
-
49
- ORC: ({ a, b, c }: LatticeSchema): Matrix3X3Schema => {
50
- return [
51
- [a, 0, 0],
52
- [0, b, 0],
53
- [0, 0, c],
54
- ];
55
- },
56
-
57
- ORCF: ({ a, b, c }: LatticeSchema): Matrix3X3Schema => {
58
- return [
59
- [0, b / 2, c / 2],
60
- [a / 2, 0, c / 2],
61
- [a / 2, b / 2, 0],
62
- ];
63
- },
64
-
65
- ORCI: ({ a, b, c }: LatticeSchema): Matrix3X3Schema => {
66
- return [
67
- [-a / 2, b / 2, c / 2],
68
- [a / 2, -b / 2, c / 2],
69
- [a / 2, b / 2, -c / 2],
70
- ];
71
- },
72
-
73
- ORCC: ({ a, b, c }: LatticeSchema): Matrix3X3Schema => {
74
- return [
75
- [a / 2, b / 2, 0],
76
- [-a / 2, b / 2, 0],
77
- [0, 0, c],
78
- ];
79
- },
80
-
81
- HEX: ({ a, c }: LatticeSchema): Matrix3X3Schema => {
82
- return [
83
- [a / 2, (-a * Number(Utils.math.sqrt(3))) / 2, 0],
84
- [a / 2, (a * Number(Utils.math.sqrt(3))) / 2, 0],
85
- [0, 0, c],
86
- ];
87
- },
88
-
89
- RHL: ({ a, alpha }: LatticeSchema): Matrix3X3Schema => {
90
- const cosAlpha = Number(Utils.math.cos((alpha / 180) * Number(Utils.math.PI)));
91
- const cosHalfAlpha = Number(Utils.math.sqrt((1 / 2) * (1 + cosAlpha)));
92
- const sinHalfAlpha = Number(Utils.math.sqrt((1 / 2) * (1 - cosAlpha)));
93
- return [
94
- [a * cosHalfAlpha, -a * sinHalfAlpha, 0.0],
95
- [a * cosHalfAlpha, a * sinHalfAlpha, 0.0],
96
- [
97
- (a * cosAlpha) / cosHalfAlpha,
98
- 0.0,
99
- a *
100
- Number(
101
- Utils.math.sqrt(1 - (cosAlpha * cosAlpha) / (cosHalfAlpha * cosHalfAlpha)),
102
- ),
103
- ],
104
- ];
105
- },
106
-
107
- MCL: ({ a, b, c, alpha }: LatticeSchema): Matrix3X3Schema => {
108
- const cosAlpha = Number(Utils.math.cos((alpha / 180) * Number(Utils.math.PI)));
109
- return [
110
- [a, 0, 0],
111
- [0, b, 0],
112
- [0, c * cosAlpha, c * Number(Utils.math.sqrt(1 - cosAlpha * cosAlpha))],
113
- ];
114
- },
115
-
116
- MCLC: ({ a, b, c, alpha }: LatticeSchema): Matrix3X3Schema => {
117
- const cosAlpha = Number(Utils.math.cos((alpha / 180) * Number(Utils.math.PI)));
118
- return [
119
- [a / 2, b / 2, 0],
120
- [-a / 2, b / 2, 0],
121
- [0, c * cosAlpha, c * Number(Utils.math.sqrt(1 - cosAlpha * cosAlpha))],
122
- ];
123
- },
124
-
125
- // Algorithm from http://pymatgen.org/_modules/pymatgen/core/lattice.html (from_params)
126
- TRI: ({ a, b, c, alpha, beta, gamma }: LatticeSchema): Matrix3X3Schema => {
127
- // convert angles to Radians
128
- // eslint-disable-next-line no-param-reassign
129
- [alpha, beta, gamma] = [alpha, beta, gamma].map((x) =>
130
- Number(Utils.math.unit(x, "degree").to("rad").value),
131
- );
132
-
133
- const [cosAlpha, cosBeta, cosGamma] = [alpha, beta, gamma].map((x) =>
134
- Number(Utils.math.cos(x)),
135
- );
136
- const [sinAlpha, sinBeta] = [alpha, beta].map((x) => Number(Utils.math.sin(x)));
137
- let acosArg = (cosAlpha * cosBeta - cosGamma) / (sinAlpha * sinBeta);
138
- if (acosArg < -1) {
139
- acosArg = -1;
140
- } else if (acosArg > 1) {
141
- acosArg = 1;
142
- }
143
- const gammaStar = Number(Utils.math.acos(acosArg));
144
- const cosGammaStar = Number(Utils.math.cos(gammaStar));
145
- const sinGammaStar = Number(Utils.math.sin(gammaStar));
146
-
147
- return [
148
- [a * sinBeta, 0.0, a * cosBeta],
149
- [-b * sinAlpha * cosGammaStar, b * sinAlpha * sinGammaStar, b * cosAlpha],
150
- [0.0, 0.0, c],
151
- ];
152
- },
153
- };
154
-
155
- /**
156
- * Returns lattice vectors for a primitive cell for a lattice.
157
- * @param latticeConfig - Lattice config.
158
- * @return Cell.vectorsAsArray
159
- */
160
- export function getPrimitiveLatticeVectorsFromConfig(
161
- latticeConfig: LatticeSchema,
162
- ): Matrix3X3Schema {
163
- const primitiveCellGenerator = PRIMITIVE_CELLS[latticeConfig.type || "TRI"];
164
- const [vectorA, vectorB, vectorC] = primitiveCellGenerator(latticeConfig);
165
- return [vectorA, vectorB, vectorC];
166
- }
@@ -1,18 +0,0 @@
1
- /**
2
- * Constants for molecule handling and precision.
3
- * Source of truth: /constants.json at repository root
4
- *
5
- * These values are duplicated here for TypeScript compilation.
6
- * When updating these, also update constants.json.
7
- */
8
-
9
- export const defaultNonPeriodicMinimumLatticeSize = 3.0;
10
- export const diatomicLatticePaddingFactor = 3.0;
11
- export const molecularLatticePaddingFactor = 2.0;
12
-
13
- export const PRECISION_MAP = {
14
- coordinatesCrystal: 9,
15
- coordinatesCartesian: 6,
16
- latticeLengths: 6,
17
- latticeAngles: 4,
18
- };
@@ -1,4 +0,0 @@
1
- // TODO: adjust the imports and remove the need for re-exporting
2
- export * from "@mat3ra/code/dist/js/constants";
3
- // eslint-disable-next-line no-restricted-exports
4
- export { default } from "@mat3ra/code/dist/js/constants";