@mat3ra/esse 2025.7.1-0 → 2025.7.29-0

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Files changed (143) hide show
  1. package/README.md +4 -4
  2. package/dist/js/example/core/abstract/vector_2d.json +4 -0
  3. package/dist/js/example/materials_category/compound_pristine_structures/two_dimensional/interface/configuration.json +693 -0
  4. package/dist/js/example/materials_category/defective_structures/one_dimensional/grain_boundary_linear/configuration.json +566 -0
  5. package/dist/js/example/materials_category/defective_structures/two_dimensional/adatom/configuration.json +553 -0
  6. package/dist/js/example/materials_category/defective_structures/two_dimensional/grain_boundary_planar/configuration.json +693 -0
  7. package/dist/js/example/materials_category/defective_structures/two_dimensional/island/configuration.json +841 -0
  8. package/dist/js/example/materials_category/defective_structures/two_dimensional/terrace/configuration.json +846 -0
  9. package/dist/js/example/materials_category/defective_structures/zero_dimensional/point_defect/base_configuration.json +271 -0
  10. package/dist/js/example/materials_category/defective_structures/zero_dimensional/point_defect/interstitial.json +271 -0
  11. package/dist/js/example/materials_category/defective_structures/zero_dimensional/point_defect/substitutional.json +271 -0
  12. package/dist/js/example/materials_category/defective_structures/zero_dimensional/point_defect/vacancy.json +136 -0
  13. package/dist/js/example/materials_category/pristine_structures/two_dimensional/nanoribbon.json +419 -0
  14. package/dist/js/example/materials_category/pristine_structures/two_dimensional/nanotape.json +282 -0
  15. package/dist/js/example/materials_category/pristine_structures/two_dimensional/slab.json +1 -11
  16. package/dist/js/example/materials_category/pristine_structures/two_dimensional/slab_strained_supercell.json +305 -0
  17. package/dist/js/example/materials_category/pristine_structures/two_dimensional/slab_strained_supercell_with_gap.json +306 -0
  18. package/dist/js/example/materials_category/processed_structures/two_dimensional/passivation/configuration.json +551 -0
  19. package/dist/js/example/materials_category_components/entities/auxiliary/one_dimensional/miller_indices_2d.json +4 -0
  20. package/dist/js/example/materials_category_components/entities/auxiliary/zero_dimensional/crystal_site.json +128 -0
  21. package/dist/js/example/materials_category_components/entities/auxiliary/zero_dimensional/point_defect_site.json +138 -0
  22. package/dist/js/example/materials_category_components/entities/reusable/one_dimensional/crystal_lattice_lines.json +135 -0
  23. package/dist/js/example/materials_category_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated.json +145 -0
  24. package/dist/js/example/materials_category_components/entities/reusable/two_dimensional/slab_stack_configuration.json +547 -0
  25. package/dist/js/example/materials_category_components/operations/core/combinations/merge.json +1 -1
  26. package/dist/js/example/materials_category_components/operations/core/modifications/perturb.json +131 -0
  27. package/dist/js/schema/core/abstract/vector_2d.json +11 -0
  28. package/dist/js/schema/core/primitive/array_of_2_numbers.json +11 -0
  29. package/dist/js/schema/job.json +14 -0
  30. package/dist/js/schema/materials_category/compound_pristine_structures/two_dimensional/interface/configuration.json +11616 -0
  31. package/dist/js/schema/materials_category/defective_structures/one_dimensional/grain_boundary_linear/configuration.json +11622 -0
  32. package/dist/js/schema/materials_category/defective_structures/two_dimensional/adatom/configuration.json +3517 -0
  33. package/dist/js/schema/materials_category/defective_structures/two_dimensional/grain_boundary_planar/configuration.json +11616 -0
  34. package/dist/js/schema/materials_category/defective_structures/two_dimensional/island/configuration.json +5197 -0
  35. package/dist/js/schema/materials_category/defective_structures/two_dimensional/terrace/configuration.json +5214 -0
  36. package/dist/js/schema/materials_category/defective_structures/zero_dimensional/point_defect/base_configuration.json +787 -0
  37. package/dist/js/schema/materials_category/defective_structures/zero_dimensional/point_defect/interstitial.json +1722 -0
  38. package/dist/js/schema/materials_category/defective_structures/zero_dimensional/point_defect/substitutional.json +1722 -0
  39. package/dist/js/schema/{materials_category_components/operations/core/combinations/stack_component.json → materials_category/defective_structures/zero_dimensional/point_defect/vacancy.json} +46 -790
  40. package/dist/js/schema/materials_category/pristine_structures/two_dimensional/nanoribbon.json +2734 -0
  41. package/dist/js/schema/materials_category/pristine_structures/two_dimensional/nanotape.json +1917 -0
  42. package/dist/js/schema/materials_category/pristine_structures/two_dimensional/slab.json +1595 -1622
  43. package/dist/js/schema/materials_category/pristine_structures/two_dimensional/slab_strained_supercell.json +1810 -0
  44. package/dist/js/schema/materials_category/pristine_structures/two_dimensional/slab_strained_supercell_with_gap.json +1815 -0
  45. package/dist/js/schema/{materials_category_components/entities/reusable/two_dimensional/slab_unit_cell.json → materials_category/processed_structures/two_dimensional/passivation/configuration.json} +1003 -907
  46. package/dist/js/schema/materials_category_components/entities/auxiliary/one_dimensional/miller_indices_2d.json +12 -0
  47. package/dist/js/schema/materials_category_components/entities/auxiliary/two_dimensional/termination.json +1 -0
  48. package/dist/js/schema/materials_category_components/entities/auxiliary/zero_dimensional/crystal_site.json +757 -0
  49. package/dist/js/schema/materials_category_components/entities/auxiliary/zero_dimensional/point_defect_site.json +936 -0
  50. package/dist/js/schema/materials_category_components/entities/auxiliary/zero_dimensional/void_region.json +821 -0
  51. package/dist/js/schema/materials_category_components/entities/core/zero_dimensional/vacancy.json +20 -0
  52. package/dist/js/schema/materials_category_components/entities/reusable/one_dimensional/crystal_lattice_lines.json +785 -0
  53. package/dist/js/schema/materials_category_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated.json +1100 -0
  54. package/dist/js/schema/materials_category_components/entities/reusable/three_dimensional/crystal_lattice_base.json +773 -0
  55. package/dist/js/schema/materials_category_components/entities/reusable/two_dimensional/atomic_layers.json +18 -18
  56. package/dist/js/schema/materials_category_components/entities/reusable/two_dimensional/atomic_layers_unique.json +18 -18
  57. package/dist/js/schema/materials_category_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated.json +18 -18
  58. package/dist/js/schema/materials_category_components/entities/reusable/two_dimensional/crystal_lattice_planes.json +17 -18
  59. package/dist/js/schema/materials_category_components/entities/reusable/two_dimensional/slab_stack_configuration.json +2585 -0
  60. package/dist/js/schema/materials_category_components/operations/core/combinations/enums.json +12 -0
  61. package/dist/js/schema/materials_category_components/operations/core/combinations/merge.json +12 -1627
  62. package/dist/js/schema/materials_category_components/operations/core/combinations/stack.json +3 -1551
  63. package/dist/js/schema/materials_category_components/operations/core/modifications/perturb.json +768 -0
  64. package/dist/js/schema/software/flavor.json +7 -0
  65. package/dist/js/schema/software_directory/ml/unit/execution/evaluate/cross_validate.json +7 -0
  66. package/dist/js/schema/software_directory/ml/unit/execution/initialize.json +7 -0
  67. package/dist/js/schema/software_directory/ml/unit/execution/score.json +7 -0
  68. package/dist/js/schema/software_directory/ml/unit/execution/train.json +7 -0
  69. package/dist/js/schema/software_directory/ml/unit/execution.json +28 -0
  70. package/dist/js/schema/software_directory/modeling/unit/execution.json +7 -0
  71. package/dist/js/schema/software_directory/scripting/unit/execution.json +7 -0
  72. package/dist/js/schema/workflow/subworkflow/unit.json +7 -0
  73. package/dist/js/schema/workflow/subworkflow.json +7 -0
  74. package/dist/js/schema/workflow/unit/execution.json +7 -0
  75. package/dist/js/schema/workflow/unit.json +7 -0
  76. package/dist/js/schema/workflow.json +14 -0
  77. package/dist/js/schemas.json +1 -1
  78. package/dist/js/types.d.ts +31925 -4987
  79. package/example/core/abstract/vector_2d.json +4 -0
  80. package/example/materials_category/compound_pristine_structures/two-dimensional/interface/configuration.json +18 -0
  81. package/example/materials_category/defective_structures/one-dimensional/grain_boundary_linear/configuration.json +16 -0
  82. package/example/materials_category/defective_structures/two-dimensional/adatom/configuration.json +24 -0
  83. package/example/materials_category/defective_structures/two-dimensional/grain_boundary_planar/configuration.json +18 -0
  84. package/example/materials_category/defective_structures/two-dimensional/island/configuration.json +37 -0
  85. package/example/materials_category/defective_structures/two-dimensional/terrace/configuration.json +42 -0
  86. package/example/materials_category/defective_structures/zero-dimensional/point_defect/base_configuration.json +19 -0
  87. package/example/materials_category/defective_structures/zero-dimensional/point_defect/interstitial.json +21 -0
  88. package/example/materials_category/defective_structures/zero-dimensional/point_defect/substitutional.json +21 -0
  89. package/example/materials_category/defective_structures/zero-dimensional/point_defect/vacancy.json +11 -0
  90. package/example/materials_category/pristine_structures/two-dimensional/nanoribbon.json +42 -0
  91. package/example/materials_category/pristine_structures/two-dimensional/nanotape.json +30 -0
  92. package/example/materials_category/pristine_structures/two-dimensional/slab.json +1 -11
  93. package/example/materials_category/pristine_structures/two-dimensional/slab_strained_supercell.json +55 -0
  94. package/example/materials_category/pristine_structures/two-dimensional/slab_strained_supercell_with_gap.json +56 -0
  95. package/example/materials_category/processed_structures/two-dimensional/passivation/configuration.json +45 -0
  96. package/example/materials_category_components/entities/auxiliary/one-dimensional/miller_indices_2d.json +2 -0
  97. package/example/materials_category_components/entities/auxiliary/zero-dimensional/crystal_site.json +7 -2
  98. package/example/materials_category_components/entities/auxiliary/zero-dimensional/point_defect_site.json +11 -0
  99. package/example/materials_category_components/entities/reusable/one-dimensional/crystal_lattice_lines.json +8 -0
  100. package/example/materials_category_components/entities/reusable/one-dimensional/crystal_lattice_lines_unique_repeated.json +18 -0
  101. package/example/materials_category_components/entities/reusable/two-dimensional/slab_stack_configuration.json +22 -0
  102. package/example/materials_category_components/operations/core/combinations/merge.json +2 -2
  103. package/example/materials_category_components/operations/core/modifications/perturb.json +6 -0
  104. package/package.json +1 -1
  105. package/schema/core/abstract/vector_2d.json +10 -0
  106. package/schema/core/primitive/array_of_2_numbers.json +11 -0
  107. package/schema/materials_category/compound_pristine_structures/two-dimensional/interface/configuration.json +65 -0
  108. package/schema/materials_category/defective_structures/one-dimensional/grain_boundary_linear/configuration.json +34 -0
  109. package/schema/materials_category/defective_structures/two-dimensional/adatom/configuration.json +26 -0
  110. package/schema/materials_category/defective_structures/two-dimensional/grain_boundary_planar/configuration.json +16 -0
  111. package/schema/materials_category/defective_structures/two-dimensional/island/configuration.json +48 -0
  112. package/schema/materials_category/defective_structures/two-dimensional/terrace/configuration.json +55 -0
  113. package/schema/materials_category/defective_structures/zero-dimensional/point_defect/base_configuration.json +30 -0
  114. package/schema/materials_category/defective_structures/zero-dimensional/point_defect/interstitial.json +23 -0
  115. package/schema/materials_category/defective_structures/zero-dimensional/point_defect/substitutional.json +23 -0
  116. package/schema/materials_category/defective_structures/zero-dimensional/point_defect/vacancy.json +23 -0
  117. package/schema/materials_category/manifest.yaml +53 -156
  118. package/schema/materials_category/pristine_structures/two-dimensional/nanoribbon.json +29 -0
  119. package/schema/materials_category/pristine_structures/two-dimensional/nanotape.json +29 -0
  120. package/schema/materials_category/pristine_structures/two-dimensional/slab.json +18 -6
  121. package/schema/materials_category/pristine_structures/two-dimensional/slab_strained_supercell.json +25 -0
  122. package/schema/materials_category/pristine_structures/two-dimensional/slab_strained_supercell_with_gap.json +18 -0
  123. package/schema/materials_category/processed_structures/two-dimensional/passivation/configuration.json +45 -0
  124. package/schema/materials_category_components/entities/auxiliary/one-dimensional/miller_indices_2d.json +13 -0
  125. package/schema/materials_category_components/entities/auxiliary/two-dimensional/termination.json +1 -0
  126. package/schema/materials_category_components/entities/auxiliary/zero-dimensional/crystal_site.json +4 -0
  127. package/schema/materials_category_components/entities/auxiliary/zero-dimensional/point_defect_site.json +30 -0
  128. package/schema/materials_category_components/entities/auxiliary/zero-dimensional/void_region.json +18 -0
  129. package/schema/materials_category_components/entities/core/zero-dimensional/vacancy.json +20 -0
  130. package/schema/materials_category_components/entities/reusable/one-dimensional/crystal_lattice_lines.json +20 -0
  131. package/schema/materials_category_components/entities/reusable/one-dimensional/crystal_lattice_lines_unique_repeated.json +37 -0
  132. package/schema/materials_category_components/entities/reusable/three-dimensional/crystal_lattice_base.json +20 -0
  133. package/schema/materials_category_components/entities/reusable/two-dimensional/crystal_lattice_planes.json +6 -11
  134. package/schema/materials_category_components/entities/reusable/two-dimensional/slab_stack_configuration.json +32 -0
  135. package/schema/materials_category_components/operations/core/combinations/enums.json +12 -0
  136. package/schema/materials_category_components/operations/core/combinations/merge.json +9 -23
  137. package/schema/materials_category_components/operations/core/combinations/stack.json +3 -5
  138. package/schema/materials_category_components/operations/core/modifications/perturb.json +16 -0
  139. package/schema/software/flavor.json +7 -0
  140. package/dist/js/example/materials_category_components/operations/core/combinations/stack_component.json +0 -128
  141. package/example/materials_category_components/operations/core/combinations/stack_component.json +0 -3
  142. package/schema/materials_category_components/entities/reusable/two-dimensional/slab_unit_cell.json +0 -33
  143. package/schema/materials_category_components/operations/core/combinations/stack_component.json +0 -14
package/README.md CHANGED
@@ -116,9 +116,9 @@ When developing in python the following should be taken into account:
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  1. The modules containing the schemas and examples are generated using the [build-schemas.py](./build_schemas.py) script. There is a setup for it to be run automatically on every commit, but it is recommended to run it manually before committing to make sure that the changes are reflected in the modules. This can be done with `pre-commit run --all-files`. The pre-commit package can be installed with `pip install pre-commit`. To rebuild schemas manually, run (note `-e` in install):
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  ```bash
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- virtualenv .venv
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+ python -m venv .venv
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  source .venv/bin/activate
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- pip install -e ."[tests]"
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+ pip install -e ".[tests]"
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  pip install pre-commit
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  pre-commit --install
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  git config --unset-all core.hooksPath
@@ -128,9 +128,9 @@ When developing in python the following should be taken into account:
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  2. Tests can be run using the following commands:
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  ```bash
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- virtualenv .venv
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+ python -m venv .venv
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  source .venv/bin/activate
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- pip install ."[tests]"
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+ pip install ".[tests]"
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  python -m unittest discover --verbose --catch --start-directory tests/py/esse/
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  ```
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+ [
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