@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.
- package/package.json +9 -5
- package/.babelrc +0 -10
- package/.eslintrc.json +0 -11
- package/.gitattributes +0 -1
- package/.husky/post-checkout +0 -3
- package/.husky/post-commit +0 -3
- package/.husky/post-merge +0 -3
- package/.husky/pre-commit +0 -6
- package/.husky/pre-push +0 -3
- package/.mocharc.json +0 -5
- package/.pre-commit-config.yaml +0 -26
- package/.prettierignore +0 -2
- package/.prettierrc +0 -6
- package/AGENTS.md +0 -133
- package/MANIFEST.in +0 -1
- package/data/constants.json +0 -13
- package/data/reciprocal_paths.json +0 -111
- package/images/made/tools/tools_diagram_general.png +0 -3
- package/images/made/tools/tools_diagram_interface.png +0 -3
- package/pyproject.toml +0 -123
- package/scripts/generate-mixins.ts +0 -28
- package/src/__init__.py +0 -0
- package/src/js/Material.ts +0 -618
- package/src/js/basis/basis.ts +0 -634
- package/src/js/basis/constrained_basis.ts +0 -115
- package/src/js/basis/coordinates.ts +0 -92
- package/src/js/basis/elements.ts +0 -24
- package/src/js/basis/helpers.ts +0 -20
- package/src/js/basis/labels.ts +0 -6
- package/src/js/cell/cell.ts +0 -149
- package/src/js/cell/conventional_cell.ts +0 -86
- package/src/js/cell/primitive_cell.ts +0 -166
- package/src/js/constants/molecule.ts +0 -18
- package/src/js/constants.ts +0 -4
- package/src/js/constraints/constraints.ts +0 -45
- package/src/js/generated/MaterialSchemaMixin.ts +0 -79
- package/src/js/lattice/lattice.ts +0 -308
- package/src/js/lattice/lattice_types.ts +0 -134
- package/src/js/lattice/reciprocal/lattice_reciprocal.ts +0 -206
- package/src/js/lattice/reciprocal/paths.ts +0 -39
- package/src/js/lattice/reciprocal/symmetry_points.ts +0 -886
- package/src/js/lattice/unit_cell.ts +0 -66
- package/src/js/made.ts +0 -62
- package/src/js/parsers/cif.ts +0 -25
- package/src/js/parsers/errors.ts +0 -6
- package/src/js/parsers/espresso.ts +0 -29
- package/src/js/parsers/native_format_parsers.ts +0 -52
- package/src/js/parsers/parsers.ts +0 -13
- package/src/js/parsers/poscar.ts +0 -218
- package/src/js/parsers/xyz.ts +0 -190
- package/src/js/parsers/xyz_combinatorial_basis.ts +0 -268
- package/src/js/tools/basis.ts +0 -131
- package/src/js/tools/cell.ts +0 -40
- package/src/js/tools/index.ts +0 -11
- package/src/js/tools/material.ts +0 -64
- package/src/js/tools/supercell.ts +0 -89
- package/src/js/tools/surface.ts +0 -213
- package/src/py/__init__.py +0 -0
- package/src/py/mat3ra/__init__.py +0 -1
- package/src/py/mat3ra/made/__init__.py +0 -7
- package/src/py/mat3ra/made/basis/__init__.py +0 -255
- package/src/py/mat3ra/made/basis/coordinates.py +0 -43
- package/src/py/mat3ra/made/cell/__init__.py +0 -55
- package/src/py/mat3ra/made/cell/primitive_cell.py +0 -156
- package/src/py/mat3ra/made/data_helper.py +0 -5
- package/src/py/mat3ra/made/lattice.py +0 -195
- package/src/py/mat3ra/made/material.py +0 -135
- package/src/py/mat3ra/made/metadata.py +0 -45
- package/src/py/mat3ra/made/reciprocal/__init__.py +0 -5
- package/src/py/mat3ra/made/reciprocal/lattice_reciprocal.py +0 -147
- package/src/py/mat3ra/made/reciprocal/paths.py +0 -30
- package/src/py/mat3ra/made/reciprocal/symmetry_points.py +0 -385
- package/src/py/mat3ra/made/tools/README.md +0 -173
- package/src/py/mat3ra/made/tools/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/analyze/__init__.py +0 -31
- package/src/py/mat3ra/made/tools/analyze/basis/__init__.py +0 -3
- package/src/py/mat3ra/made/tools/analyze/basis/analyzer.py +0 -50
- package/src/py/mat3ra/made/tools/analyze/build_metadata_analyzer.py +0 -32
- package/src/py/mat3ra/made/tools/analyze/build_metadata_analyzer_factory.py +0 -31
- package/src/py/mat3ra/made/tools/analyze/coordination.py +0 -56
- package/src/py/mat3ra/made/tools/analyze/crystal_site/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_crystal_site_material_analyzer.py +0 -35
- package/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_material_analyzer.py +0 -49
- package/src/py/mat3ra/made/tools/analyze/crystal_site/crystal_site_analyzer.py +0 -65
- package/src/py/mat3ra/made/tools/analyze/crystal_site/voronoi_crystal_site_analyzer.py +0 -47
- package/src/py/mat3ra/made/tools/analyze/enums.py +0 -33
- package/src/py/mat3ra/made/tools/analyze/fingerprint/__init__.py +0 -4
- package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/layered_fingerprint_along_axis.py +0 -83
- package/src/py/mat3ra/made/tools/analyze/fingerprint/layers/unique_element_string_per_layer.py +0 -9
- package/src/py/mat3ra/made/tools/analyze/interface/__init__.py +0 -20
- package/src/py/mat3ra/made/tools/analyze/interface/commensurate.py +0 -156
- package/src/py/mat3ra/made/tools/analyze/interface/enums.py +0 -60
- package/src/py/mat3ra/made/tools/analyze/interface/grain_boundary.py +0 -80
- package/src/py/mat3ra/made/tools/analyze/interface/simple.py +0 -251
- package/src/py/mat3ra/made/tools/analyze/interface/twisted_nanoribbons.py +0 -91
- package/src/py/mat3ra/made/tools/analyze/interface/utils/__init__.py +0 -77
- package/src/py/mat3ra/made/tools/analyze/interface/utils/holders.py +0 -14
- package/src/py/mat3ra/made/tools/analyze/interface/utils/vector.py +0 -56
- package/src/py/mat3ra/made/tools/analyze/interface/zsl.py +0 -259
- package/src/py/mat3ra/made/tools/analyze/interface_material.py +0 -45
- package/src/py/mat3ra/made/tools/analyze/lattice/__init__.py +0 -2
- package/src/py/mat3ra/made/tools/analyze/lattice/analyzer.py +0 -126
- package/src/py/mat3ra/made/tools/analyze/lattice/helpers.py +0 -31
- package/src/py/mat3ra/made/tools/analyze/lattice_lines.py +0 -30
- package/src/py/mat3ra/made/tools/analyze/lattice_planes.py +0 -192
- package/src/py/mat3ra/made/tools/analyze/lattice_swap_analyzer.py +0 -105
- package/src/py/mat3ra/made/tools/analyze/material.py +0 -276
- package/src/py/mat3ra/made/tools/analyze/other.py +0 -434
- package/src/py/mat3ra/made/tools/analyze/rdf.py +0 -74
- package/src/py/mat3ra/made/tools/analyze/slab.py +0 -76
- package/src/py/mat3ra/made/tools/analyze/solid_solution_analyzer.py +0 -171
- package/src/py/mat3ra/made/tools/analyze/terrace.py +0 -105
- package/src/py/mat3ra/made/tools/analyze/utils.py +0 -162
- package/src/py/mat3ra/made/tools/bond_directions/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/bond_directions/bond_directions.py +0 -150
- package/src/py/mat3ra/made/tools/bond_directions/bond_directions_for_element_list.py +0 -7
- package/src/py/mat3ra/made/tools/bond_directions/bond_directions_templates_enum.py +0 -8
- package/src/py/mat3ra/made/tools/bond_directions/bond_directions_templates_for_element.py +0 -16
- package/src/py/mat3ra/made/tools/build/__init__.py +0 -25
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/helpers.py +0 -59
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/types.py +0 -26
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/heterostructure/utils.py +0 -139
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/__init__.py +0 -47
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/__init__.py +0 -11
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/build_parameters.py +0 -5
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/builder.py +0 -164
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/configuration.py +0 -48
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/base/helpers.py +0 -134
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/__init__.py +0 -6
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/helpers.py +0 -157
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/enums.py +0 -7
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/configuration.py +0 -13
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/twisted/helpers.py +0 -70
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/utils.py +0 -87
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/zsl/__init__.py +0 -6
- package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/zsl/helpers.py +0 -129
- package/src/py/mat3ra/made/tools/build/defective_structures/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/build_parameters.py +0 -12
- package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/builder.py +0 -17
- package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/configuration.py +0 -40
- package/src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/helpers.py +0 -82
- package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/__init__.py +0 -1
- package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/__init__.py +0 -9
- package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/builder.py +0 -37
- package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/configuration.py +0 -30
- package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/enums.py +0 -8
- package/src/py/mat3ra/made/tools/build/defective_structures/three_dimensional/solid_solution/helpers.py +0 -76
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/builder.py +0 -11
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/configuration.py +0 -18
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/helpers.py +0 -137
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/adatom/types.py +0 -22
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/builder.py +0 -28
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/configuration.py +0 -55
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/helpers.py +0 -75
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/builder.py +0 -15
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/configuration.py +0 -16
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/island/helpers.py +0 -116
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/build_parameters.py +0 -10
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/builder.py +0 -30
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/configuration.py +0 -11
- package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/helpers.py +0 -78
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/builder.py +0 -31
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/configuration.py +0 -45
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/helpers.py +0 -80
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/__init__.py +0 -40
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/atom_placement_method_enum.py +0 -14
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/builder.py +0 -42
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/configuration.py +0 -27
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/complex_defect_type_enum.py +0 -5
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/factories.py +0 -69
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/helpers.py +0 -92
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/builder.py +0 -8
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/configuration.py +0 -29
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/helpers.py +0 -48
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/interstitial_placement_method_enum.py +0 -8
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/point_defect_type_enum.py +0 -8
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/builder.py +0 -6
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/configuration.py +0 -41
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/helpers.py +0 -43
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/substitutional/substitution_placement_method_enum.py +0 -7
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/types.py +0 -24
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/builder.py +0 -19
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/configuration.py +0 -27
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/helpers.py +0 -42
- package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/vacancy/vacancy_placement_method_enum.py +0 -7
- package/src/py/mat3ra/made/tools/build/pristine_structures/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/builder.py +0 -80
- package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/configurations.py +0 -22
- package/src/py/mat3ra/made/tools/build/pristine_structures/three_dimensional/ideal_crystal/helpers.py +0 -40
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/__init__.py +0 -29
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/build_parameters.py +0 -5
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/builders.py +0 -56
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/configuration.py +0 -33
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/helpers.py +0 -76
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/__init__.py +0 -11
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/build_parameters.py +0 -9
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/builders.py +0 -83
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/configuration.py +0 -35
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/helpers.py +0 -62
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/__init__.py +0 -9
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/build_parameters.py +0 -8
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/builder.py +0 -42
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/configuration.py +0 -99
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- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/termination_utils.py +0 -14
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/utils.py +0 -61
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab_strained_supercell/builder.py +0 -22
- package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab_strained_supercell/configuration.py +0 -17
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/__init__.py +0 -19
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/analyzer.py +0 -86
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/ase_based/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/ase_based/builder.py +0 -54
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/ase_based/configuration.py +0 -19
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/enums.py +0 -42
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/helpers.py +0 -127
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/merge_based/__init__.py +0 -7
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/merge_based/builder.py +0 -33
- package/src/py/mat3ra/made/tools/build/pristine_structures/zero_dimensional/nanoparticle/merge_based/configuration.py +0 -16
- package/src/py/mat3ra/made/tools/build/processed_structures/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/__init__.py +0 -0
- package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/__init__.py +0 -9
- package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/coordination_based_passivation_material_analyzer.py +0 -112
- package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/passivation_material_analyzer.py +0 -16
- package/src/py/mat3ra/made/tools/build/processed_structures/two_dimensional/passivation/analyzers/surface_passivation_material_analyzer.py +0 -32
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assert isinstance(material.basis, Basis)
|
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27
|
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assert isinstance(material.basis.coordinates, Coordinates)
|
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28
|
-
assert isinstance(material.lattice, Lattice)
|
|
29
|
-
assert material.name == Material.__default_config__["name"]
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
def test_create():
|
|
33
|
-
material = Material.create(BULK_Si_CONVENTIONAL)
|
|
34
|
-
assert isinstance(material.basis, Basis)
|
|
35
|
-
assert isinstance(material.basis.coordinates, Coordinates)
|
|
36
|
-
assert isinstance(material.lattice, Lattice)
|
|
37
|
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assert_two_entities_deep_almost_equal(material, BULK_Si_CONVENTIONAL)
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
def test_create_with_cell_as_list():
|
|
41
|
-
# The key cell should be ignored and Basis.Cell created from Lattice by Material
|
|
42
|
-
cell = [
|
|
43
|
-
[1.0, 0.0, 0.0],
|
|
44
|
-
[0.0, 1.0, 0.0],
|
|
45
|
-
[0.0, 0.0, 1.0],
|
|
46
|
-
]
|
|
47
|
-
config = {**Material.__default_config__, "basis": {**Material.__default_config__["basis"], "cell": cell}}
|
|
48
|
-
|
|
49
|
-
material = Material.create(config)
|
|
50
|
-
assert isinstance(material.basis, Basis)
|
|
51
|
-
assert material.basis.cell.vector_arrays == material.lattice.vector_arrays
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
def test_material_to_json():
|
|
55
|
-
material = Material.create_default()
|
|
56
|
-
# Remove all keys that are null in the config
|
|
57
|
-
assert_two_entities_deep_almost_equal(material, Material.__default_config__)
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
def test_material_clone():
|
|
61
|
-
material = Material.create_default()
|
|
62
|
-
clone = material.clone()
|
|
63
|
-
assert_two_entities_deep_almost_equal(material, clone)
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
def test_material_to_from_cartesian():
|
|
67
|
-
material = Material.create_default()
|
|
68
|
-
assert material.basis.is_in_crystal_units is True
|
|
69
|
-
assert material.basis.is_in_cartesian_units is False
|
|
70
|
-
material.to_cartesian()
|
|
71
|
-
assert material.basis.is_in_crystal_units is False
|
|
72
|
-
assert material.basis.is_in_cartesian_units is True
|
|
73
|
-
assert np.allclose(material.basis.coordinates.values[1], [1.1163, 0.7893, 1.9335], atol=1e-4)
|
|
74
|
-
material.to_crystal()
|
|
75
|
-
assert material.basis.is_in_crystal_units is True
|
|
76
|
-
assert material.basis.is_in_cartesian_units is False
|
|
77
|
-
assert np.allclose(material.basis.coordinates.values[1], [0.25, 0.25, 0.25], atol=1e-4)
|
|
78
|
-
assert_two_entities_deep_almost_equal(material, Material.__default_config__)
|
|
79
|
-
|
|
80
|
-
|
|
81
|
-
def test_material_to_cartesian_to_crystal_repeated():
|
|
82
|
-
material = Material.create_default()
|
|
83
|
-
material.to_cartesian()
|
|
84
|
-
material.to_cartesian()
|
|
85
|
-
assert np.allclose(material.basis.coordinates.values[1], [1.1163, 0.7893, 1.9335], atol=1e-4)
|
|
86
|
-
material.to_crystal()
|
|
87
|
-
material.to_crystal()
|
|
88
|
-
assert_two_entities_deep_almost_equal(material, Material.__default_config__)
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
def test_basis_to_json():
|
|
92
|
-
material = Material.create_default()
|
|
93
|
-
basis = material.basis
|
|
94
|
-
assert_two_entities_deep_almost_equal(basis, Material.__default_config__["basis"])
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
def test_basis_cell_lattice_sync():
|
|
98
|
-
"""Test synchronization between basis.cell and material.lattice"""
|
|
99
|
-
material = Material.create_default()
|
|
100
|
-
# Change lattice vectors
|
|
101
|
-
new_vectors = [[1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]
|
|
102
|
-
new_lattice = Lattice.from_vectors_array(new_vectors)
|
|
103
|
-
material.set_lattice(new_lattice)
|
|
104
|
-
# Verify basis.cell matches new lattice vectors
|
|
105
|
-
assertion_utils.assert_deep_almost_equal(new_vectors, material.basis.cell.vector_arrays)
|
|
106
|
-
assertion_utils.assert_deep_almost_equal(new_vectors, material.lattice.vector_arrays)
|
|
107
|
-
# Verify basis coordinates are still correct
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
@pytest.mark.parametrize(
|
|
111
|
-
"initial_labels, reset_labels, expected_final",
|
|
112
|
-
[
|
|
113
|
-
# Test resetting with empty list
|
|
114
|
-
([1, 2], [], []),
|
|
115
|
-
# Test resetting with None
|
|
116
|
-
([1, 2], None, []),
|
|
117
|
-
# Test normal behavior with non-empty lists
|
|
118
|
-
([], [1, 2], [1, 2]),
|
|
119
|
-
],
|
|
120
|
-
)
|
|
121
|
-
def test_set_labels_from_list(initial_labels, reset_labels, expected_final):
|
|
122
|
-
material = Material.create(BULK_Si_PRIMITIVE)
|
|
123
|
-
|
|
124
|
-
if initial_labels:
|
|
125
|
-
material.basis.set_labels_from_list(initial_labels)
|
|
126
|
-
assert len(material.basis.labels.values) == len(initial_labels)
|
|
127
|
-
assert material.basis.labels.values == initial_labels
|
|
128
|
-
|
|
129
|
-
material.basis.set_labels_from_list(reset_labels)
|
|
130
|
-
|
|
131
|
-
assert len(material.basis.labels.values) == len(expected_final)
|
|
132
|
-
assert material.basis.labels.values == expected_final
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
@pytest.mark.parametrize("fixture_file", ["si-standata.json", "Graphene.json"])
|
|
136
|
-
def test_calculate_hash(fixture_file):
|
|
137
|
-
fixture = load_fixture(fixture_file)
|
|
138
|
-
material = Material.create(fixture)
|
|
139
|
-
assert material.hash == fixture["hash"]
|
|
140
|
-
assert material.scaled_hash == fixture["scaledHash"]
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
def test_calculate_hash_feo_standata():
|
|
144
|
-
from mat3ra.standata.materials import Materials
|
|
145
|
-
|
|
146
|
-
expected_hashes = load_fixture("hashes.json")["FeO"]
|
|
147
|
-
data = Materials.get_by_name_first_match("FeO")
|
|
148
|
-
material = Material.create(data)
|
|
149
|
-
assert material.hash == expected_hashes["hash"]
|
|
150
|
-
assert material.scaled_hash == expected_hashes["scaledHash"]
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
def test_model_dump_includes_hashes():
|
|
154
|
-
material = Material.create_default()
|
|
155
|
-
serialized_material = material.model_dump()
|
|
156
|
-
|
|
157
|
-
assert serialized_material[HASH_KEY] == material.hash
|
|
158
|
-
assert serialized_material[SCALED_HASH_KEY] == material.scaled_hash
|
|
@@ -1,126 +0,0 @@
|
|
|
1
|
-
import math
|
|
2
|
-
|
|
3
|
-
import numpy as np
|
|
4
|
-
import pytest
|
|
5
|
-
from mat3ra.esse.models.core.abstract.matrix_3x3 import Matrix3x3Schema
|
|
6
|
-
from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
|
|
7
|
-
from mat3ra.made.material import Material
|
|
8
|
-
from mat3ra.made.tools.build_components.operations.core.modifications.perturb import (
|
|
9
|
-
SineWavePerturbationFunctionHolder,
|
|
10
|
-
)
|
|
11
|
-
from mat3ra.made.tools.operations.core.binary import stack_two_materials
|
|
12
|
-
from mat3ra.made.tools.operations.core.unary import perturb, strain, translate_atoms
|
|
13
|
-
from mat3ra.made.tools.operations.reusable.unary import transform_material_by_matrix
|
|
14
|
-
from unit.fixtures.bulk import BULK_Si_CONVENTIONAL
|
|
15
|
-
from unit.fixtures.strain import BULK_Si_CONVENTIONAL_STRAINED
|
|
16
|
-
from unit.utils import assert_two_entities_deep_almost_equal
|
|
17
|
-
|
|
18
|
-
from .fixtures.bulk import BULK_Si_PRIMITIVE
|
|
19
|
-
from .fixtures.nanoribbon.nanoribbon import GRAPHENE_ZIGZAG_NANORIBBON
|
|
20
|
-
from .fixtures.slab import SI_CONVENTIONAL_SLAB_001
|
|
21
|
-
|
|
22
|
-
STRAIN_TEST_CASES = [
|
|
23
|
-
(BULK_Si_CONVENTIONAL, [[1.1, 0, 0], [0, 1.1, 0], [0, 0, 1.0]], BULK_Si_CONVENTIONAL_STRAINED),
|
|
24
|
-
]
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
@pytest.mark.parametrize("material_config, strain_matrix, expected_material_config", STRAIN_TEST_CASES)
|
|
28
|
-
def test_strain(material_config, strain_matrix, expected_material_config):
|
|
29
|
-
material = Material.create(material_config)
|
|
30
|
-
strain_matrix_obj = Matrix3x3Schema(root=strain_matrix)
|
|
31
|
-
expected_material = Material.create(expected_material_config)
|
|
32
|
-
|
|
33
|
-
strained_material = strain(material, strain_matrix_obj)
|
|
34
|
-
|
|
35
|
-
assert_two_entities_deep_almost_equal(strained_material, expected_material)
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
@pytest.mark.parametrize(
|
|
39
|
-
"material1_config, material2_config, stacking_axis, expected_a, expected_b, expected_c",
|
|
40
|
-
[
|
|
41
|
-
(BULK_Si_PRIMITIVE, BULK_Si_PRIMITIVE, AxisEnum.z, 3.867, 3.867, 7.734),
|
|
42
|
-
(BULK_Si_PRIMITIVE, BULK_Si_PRIMITIVE, AxisEnum.x, 7.734, 3.867, 3.867),
|
|
43
|
-
],
|
|
44
|
-
)
|
|
45
|
-
def test_stack_two_materials(
|
|
46
|
-
material1_config: dict,
|
|
47
|
-
material2_config: dict,
|
|
48
|
-
stacking_axis: AxisEnum,
|
|
49
|
-
expected_a: float,
|
|
50
|
-
expected_b: float,
|
|
51
|
-
expected_c: float,
|
|
52
|
-
):
|
|
53
|
-
material1 = Material.create(material1_config)
|
|
54
|
-
material2 = Material.create(material2_config)
|
|
55
|
-
|
|
56
|
-
original_atom_count1 = len(material1.basis.coordinates.values)
|
|
57
|
-
original_atom_count2 = len(material2.basis.coordinates.values)
|
|
58
|
-
|
|
59
|
-
stacked_material = stack_two_materials(material1, material2, stacking_axis)
|
|
60
|
-
|
|
61
|
-
assert len(stacked_material.basis.coordinates.values) == original_atom_count1 + original_atom_count2
|
|
62
|
-
|
|
63
|
-
assert math.isclose(stacked_material.lattice.a, expected_a)
|
|
64
|
-
assert math.isclose(stacked_material.lattice.b, expected_b)
|
|
65
|
-
assert math.isclose(stacked_material.lattice.c, expected_c)
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
@pytest.mark.parametrize(
|
|
69
|
-
"material_config, perturbation_function, expected_coord_changes",
|
|
70
|
-
[
|
|
71
|
-
(
|
|
72
|
-
GRAPHENE_ZIGZAG_NANORIBBON,
|
|
73
|
-
SineWavePerturbationFunctionHolder(amplitude=0.1, wavelength=1.0, phase=0.0, axis="x"),
|
|
74
|
-
[0.0, 0.0, -0.0383],
|
|
75
|
-
),
|
|
76
|
-
],
|
|
77
|
-
)
|
|
78
|
-
def test_perturb(material_config, perturbation_function, expected_coord_changes):
|
|
79
|
-
material = Material.create(material_config)
|
|
80
|
-
original_coords = [coord[:] for coord in material.basis.coordinates.values]
|
|
81
|
-
|
|
82
|
-
perturbed_material = perturb(material, perturbation_function)
|
|
83
|
-
actual_delta = np.array(original_coords[0]) - np.array(perturbed_material.basis.coordinates.values[0])
|
|
84
|
-
assert np.isclose(actual_delta, expected_coord_changes, atol=1e-4).all()
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
@pytest.mark.parametrize(
|
|
88
|
-
"matrix, expected_a, expected_b, expected_c",
|
|
89
|
-
[
|
|
90
|
-
(np.eye(3), 5.468763846, 5.468763846, 15.937527692),
|
|
91
|
-
(np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]]), 5.468763846, 5.468763846, 15.937527692),
|
|
92
|
-
(np.array([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), 5.468763846, 15.937527692, 5.468763846),
|
|
93
|
-
(np.array([[0, 0, 1], [0, 1, 0], [1, 0, 0]]), 15.937527692, 5.468763846, 5.468763846),
|
|
94
|
-
],
|
|
95
|
-
)
|
|
96
|
-
def test_transform_material_by_matrix(matrix, expected_a, expected_b, expected_c):
|
|
97
|
-
material = Material.create(SI_CONVENTIONAL_SLAB_001)
|
|
98
|
-
transformed_material = transform_material_by_matrix(material, matrix)
|
|
99
|
-
|
|
100
|
-
assert len(transformed_material.basis.coordinates.values) == len(material.basis.coordinates.values)
|
|
101
|
-
assert len(transformed_material.basis.elements.values) == len(material.basis.elements.values)
|
|
102
|
-
assert transformed_material.lattice.a == pytest.approx(expected_a, abs=1e-6)
|
|
103
|
-
assert transformed_material.lattice.b == pytest.approx(expected_b, abs=1e-6)
|
|
104
|
-
assert transformed_material.lattice.c == pytest.approx(expected_c, abs=1e-6)
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
@pytest.mark.parametrize(
|
|
108
|
-
"material_config, atom_ids, vector, expected_coord_change",
|
|
109
|
-
[
|
|
110
|
-
(SI_CONVENTIONAL_SLAB_001, [3], [0.0, 0.0, -1.5], [0.0, 0.0, -1.5]),
|
|
111
|
-
],
|
|
112
|
-
)
|
|
113
|
-
def test_translate_atoms(material_config, atom_ids, vector, expected_coord_change):
|
|
114
|
-
material = Material.create(material_config)
|
|
115
|
-
original_coords = [coord[:] for coord in material.basis.coordinates.values]
|
|
116
|
-
|
|
117
|
-
translated_material = translate_atoms(material, atom_ids, vector)
|
|
118
|
-
lattice_vectors = np.array(material.lattice.vector_arrays)
|
|
119
|
-
|
|
120
|
-
actual_delta = (
|
|
121
|
-
np.array(translated_material.basis.coordinates.values[atom_ids[0]]) - np.array(original_coords[atom_ids[0]])
|
|
122
|
-
) @ lattice_vectors
|
|
123
|
-
assert np.isclose(actual_delta, expected_coord_change, atol=1e-4).all()
|
|
124
|
-
|
|
125
|
-
untouched_id = atom_ids[0] - 1
|
|
126
|
-
assert np.allclose(translated_material.basis.coordinates.values[untouched_id], original_coords[untouched_id])
|
|
@@ -1,118 +0,0 @@
|
|
|
1
|
-
import math
|
|
2
|
-
import pytest
|
|
3
|
-
|
|
4
|
-
from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
|
|
5
|
-
from mat3ra.made.lattice import Lattice, LatticeTypeEnum
|
|
6
|
-
from unit.utils import assert_two_entities_deep_almost_equal
|
|
7
|
-
|
|
8
|
-
EXPECTED_PRIMITIVE_CELL_NA4CL4 = [
|
|
9
|
-
[5.691694, 0.0, 0.0],
|
|
10
|
-
[0.0, 5.691694, 0.0],
|
|
11
|
-
[0.0, 0.0, 5.691694],
|
|
12
|
-
]
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
def test_primitive_lattice_vectors_na4cl4():
|
|
16
|
-
"""
|
|
17
|
-
Replicates the TypeScript test for Na4Cl4 (CUB cell).
|
|
18
|
-
Translates from: tests/js/cell/primitive_cell.ts
|
|
19
|
-
"""
|
|
20
|
-
lattice = Lattice(type=LatticeTypeEnum.CUB, a=5.691694)
|
|
21
|
-
actual_primitive_cell = get_primitive_lattice_vectors_from_config(lattice)
|
|
22
|
-
|
|
23
|
-
assert_two_entities_deep_almost_equal(EXPECTED_PRIMITIVE_CELL_NA4CL4, actual_primitive_cell)
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
@pytest.mark.parametrize(
|
|
27
|
-
"l_type, kwargs, expected",
|
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28
|
-
[
|
|
29
|
-
(LatticeTypeEnum.CUB, {"a": 2.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]),
|
|
30
|
-
(LatticeTypeEnum.FCC, {"a": 2.0}, [[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 0.0]]),
|
|
31
|
-
(LatticeTypeEnum.BCC, {"a": 2.0}, [[-1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0]]),
|
|
32
|
-
(LatticeTypeEnum.TET, {"a": 2.0, "c": 3.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]),
|
|
33
|
-
(LatticeTypeEnum.BCT, {"a": 2.0, "c": 3.0}, [[-1.0, 1.0, 1.5], [1.0, -1.0, 1.5], [1.0, 1.0, -1.5]]),
|
|
34
|
-
(LatticeTypeEnum.ORC, {"a": 2.0, "b": 3.0, "c": 4.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]),
|
|
35
|
-
(
|
|
36
|
-
LatticeTypeEnum.ORCF,
|
|
37
|
-
{"a": 2.0, "b": 3.0, "c": 4.0},
|
|
38
|
-
[[0.0, 1.5, 2.0], [1.0, 0.0, 2.0], [1.0, 1.5, 0.0]],
|
|
39
|
-
),
|
|
40
|
-
(
|
|
41
|
-
LatticeTypeEnum.ORCI,
|
|
42
|
-
{"a": 2.0, "b": 3.0, "c": 4.0},
|
|
43
|
-
[[-1.0, 1.5, 2.0], [1.0, -1.5, 2.0], [1.0, 1.5, -2.0]],
|
|
44
|
-
),
|
|
45
|
-
(
|
|
46
|
-
LatticeTypeEnum.ORCC,
|
|
47
|
-
{"a": 2.0, "b": 3.0, "c": 4.0},
|
|
48
|
-
[[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 0.0, 4.0]],
|
|
49
|
-
),
|
|
50
|
-
(
|
|
51
|
-
LatticeTypeEnum.HEX,
|
|
52
|
-
{"a": 2.0, "c": 3.0},
|
|
53
|
-
[[1.0, -math.sqrt(3), 0.0], [1.0, math.sqrt(3), 0.0], [0.0, 0.0, 3.0]],
|
|
54
|
-
),
|
|
55
|
-
(
|
|
56
|
-
LatticeTypeEnum.RHL,
|
|
57
|
-
{"a": 2.0, "alpha": 60.0},
|
|
58
|
-
[[1.7320508, -1.0, 0.0], [1.7320508, 1.0, 0.0], [1.1547005, 0.0, 1.6329931]],
|
|
59
|
-
),
|
|
60
|
-
(
|
|
61
|
-
LatticeTypeEnum.MCL,
|
|
62
|
-
{"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0},
|
|
63
|
-
[[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 2.0, 3.4641016]],
|
|
64
|
-
),
|
|
65
|
-
(
|
|
66
|
-
LatticeTypeEnum.MCLC,
|
|
67
|
-
{"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0},
|
|
68
|
-
[[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 2.0, 3.4641016]],
|
|
69
|
-
),
|
|
70
|
-
(
|
|
71
|
-
LatticeTypeEnum.TRI,
|
|
72
|
-
{"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 90.0, "beta": 90.0, "gamma": 90.0},
|
|
73
|
-
[[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]],
|
|
74
|
-
),
|
|
75
|
-
],
|
|
76
|
-
)
|
|
77
|
-
def test_primitive_lattice_generators(l_type, kwargs, expected):
|
|
78
|
-
"""Validates the math generators for all 14 Bravais lattice scenarios."""
|
|
79
|
-
lattice = Lattice(type=l_type, **kwargs)
|
|
80
|
-
result = get_primitive_lattice_vectors_from_config(lattice)
|
|
81
|
-
assert_two_entities_deep_almost_equal(expected, result)
|
|
82
|
-
|
|
83
|
-
|
|
84
|
-
def test_fallback_to_tri_when_type_is_none():
|
|
85
|
-
"""Tests default fallback to 'TRI' when lattice_config.type is None."""
|
|
86
|
-
# Use a simple dummy class to bypass Pydantic's strict validation
|
|
87
|
-
# and simulate a malformed or incomplete Lattice config.
|
|
88
|
-
class MockLattice:
|
|
89
|
-
type = None
|
|
90
|
-
a, b, c = 2.0, 2.0, 2.0
|
|
91
|
-
alpha, beta, gamma = 90.0, 90.0, 90.0
|
|
92
|
-
|
|
93
|
-
lattice = MockLattice()
|
|
94
|
-
result = get_primitive_lattice_vectors_from_config(lattice)
|
|
95
|
-
expected = [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]
|
|
96
|
-
|
|
97
|
-
assert_two_entities_deep_almost_equal(expected, result)
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
def test_unsupported_lattice_type_raises_value_error():
|
|
101
|
-
"""Ensures a ValueError is raised for an unknown lattice type mapping."""
|
|
102
|
-
# Using a MagicMock specifically here to force an invalid type value
|
|
103
|
-
# since LatticeTypeEnum won't allow arbitrary strings
|
|
104
|
-
class MockType:
|
|
105
|
-
value = "INVALID_TYPE"
|
|
106
|
-
|
|
107
|
-
class MockLattice:
|
|
108
|
-
type = MockType()
|
|
109
|
-
# Provide dummy parameters just in case
|
|
110
|
-
a, b, c = 2.0, 2.0, 2.0
|
|
111
|
-
alpha, beta, gamma = 90.0, 90.0, 90.0
|
|
112
|
-
|
|
113
|
-
lattice = MockLattice()
|
|
114
|
-
|
|
115
|
-
with pytest.raises(ValueError) as exc_info:
|
|
116
|
-
get_primitive_lattice_vectors_from_config(lattice)
|
|
117
|
-
|
|
118
|
-
assert "Unsupported lattice type 'INVALID_TYPE'" in str(exc_info.value)
|
|
@@ -1,86 +0,0 @@
|
|
|
1
|
-
"""Tests for the ReciprocalLattice class."""
|
|
2
|
-
|
|
3
|
-
from mat3ra.made.reciprocal import ReciprocalLattice
|
|
4
|
-
from mat3ra.utils import assertion as assertion_utils
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
def test_reciprocal_lattice_symmetry_points_cub():
|
|
8
|
-
"""CUB lattice should have Γ, R, X, M symmetry points."""
|
|
9
|
-
lattice = ReciprocalLattice(a=5.64, b=5.64, c=5.64, type="CUB")
|
|
10
|
-
points = lattice.symmetry_points
|
|
11
|
-
labels = [p["point"] for p in points]
|
|
12
|
-
assert labels == ["Γ", "R", "X", "M"]
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
def test_reciprocal_lattice_default_kpoint_path_cub():
|
|
16
|
-
lattice = ReciprocalLattice(a=5.64, b=5.64, c=5.64, type="CUB")
|
|
17
|
-
path = lattice.default_kpoint_path
|
|
18
|
-
labels = [p["point"] for p in path]
|
|
19
|
-
assert labels == ["Γ", "X", "M", "Γ", "R", "X", "M", "R"]
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
def test_reciprocal_lattice_default_kpoint_path_bct():
|
|
23
|
-
"""BCT with c < a should use BCT-1 path."""
|
|
24
|
-
lattice = ReciprocalLattice(a=4.0, b=4.0, c=2.0, type="BCT")
|
|
25
|
-
path = lattice.default_kpoint_path
|
|
26
|
-
labels = [p["point"] for p in path]
|
|
27
|
-
assert "Z1" in labels # BCT-1 specific
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
def test_reciprocal_lattice_extract_kpoint_path():
|
|
31
|
-
lattice = ReciprocalLattice(a=5.64, b=5.64, c=5.64, type="CUB")
|
|
32
|
-
data_points = [[0, 0, 0], [0.5, 0.5, 0.5]]
|
|
33
|
-
result = lattice.extract_kpoint_path(data_points)
|
|
34
|
-
assert len(result) == 2
|
|
35
|
-
assert result[0]["point"] == "Γ"
|
|
36
|
-
assert result[0]["steps"] == 0
|
|
37
|
-
assert result[1]["point"] == "R"
|
|
38
|
-
assert result[1]["steps"] == 1
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
def test_reciprocal_lattice_extract_kpoint_path_empty():
|
|
42
|
-
lattice = ReciprocalLattice(a=5.64, b=5.64, c=5.64, type="CUB")
|
|
43
|
-
result = lattice.extract_kpoint_path([])
|
|
44
|
-
assert result == []
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
def test_reciprocal_lattice_cartesian_coordinates():
|
|
48
|
-
lattice = ReciprocalLattice(a=5.64, b=5.64, c=5.64, type="CUB")
|
|
49
|
-
cart = lattice.cartesian_coordinates([0.5, 0.5, 0.5])
|
|
50
|
-
assert len(cart) == 3
|
|
51
|
-
assert all(isinstance(c, float) for c in cart)
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
def test_reciprocal_lattice_dimensions_from_points_count():
|
|
55
|
-
"""Test grid dimension calculation from total k-point count."""
|
|
56
|
-
lattice = ReciprocalLattice(a=2.0, b=3.0, c=4.0, type="ORC")
|
|
57
|
-
dims = lattice.get_dimensions_from_points_count(500)
|
|
58
|
-
assert len(dims) == 3
|
|
59
|
-
assert all(d >= 1 for d in dims)
|
|
60
|
-
# Product should be close to 500
|
|
61
|
-
product = dims[0] * dims[1] * dims[2]
|
|
62
|
-
assert product >= 500 # Should be at least 500 due to ceiling
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
def test_reciprocal_lattice_dimensions_from_spacing():
|
|
66
|
-
lattice = ReciprocalLattice(a=2.0, b=3.0, c=4.0, type="ORC")
|
|
67
|
-
dims = lattice.get_dimensions_from_spacing(0.1)
|
|
68
|
-
assert len(dims) == 3
|
|
69
|
-
assert all(d >= 1 for d in dims)
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
def test_reciprocal_lattice_spacing_from_dimensions():
|
|
73
|
-
lattice = ReciprocalLattice(a=2.0, b=3.0, c=4.0, type="ORC")
|
|
74
|
-
dims = [10, 7, 5]
|
|
75
|
-
spacing = lattice.get_spacing_from_dimensions(dims)
|
|
76
|
-
assert isinstance(spacing, float)
|
|
77
|
-
assert spacing > 0
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
def test_reciprocal_lattice_reciprocal_vectors_inherited():
|
|
81
|
-
"""ReciprocalLattice should inherit reciprocal_vectors from Lattice."""
|
|
82
|
-
lattice = ReciprocalLattice(a=2.0, b=3.0, c=4.0, type="ORC")
|
|
83
|
-
vecs = lattice.reciprocal_vectors
|
|
84
|
-
assert len(vecs) == 3
|
|
85
|
-
expected = [[0.5, 0.0, 0.0], [0.0, 1 / 3, 0.0], [0.0, 0.0, 0.25]]
|
|
86
|
-
assertion_utils.assert_deep_almost_equal(vecs, expected)
|
|
@@ -1,64 +0,0 @@
|
|
|
1
|
-
"""Tests for reciprocal paths data."""
|
|
2
|
-
|
|
3
|
-
from mat3ra.made.reciprocal import RECIPROCAL_PATHS
|
|
4
|
-
|
|
5
|
-
EXPECTED_KEYS = [
|
|
6
|
-
"CUB",
|
|
7
|
-
"BCC",
|
|
8
|
-
"FCC",
|
|
9
|
-
"TET",
|
|
10
|
-
"BCT-1",
|
|
11
|
-
"BCT-2",
|
|
12
|
-
"ORC",
|
|
13
|
-
"ORCF-1",
|
|
14
|
-
"ORCF-2",
|
|
15
|
-
"ORCF-3",
|
|
16
|
-
"ORCI",
|
|
17
|
-
"ORCC",
|
|
18
|
-
"HEX",
|
|
19
|
-
"RHL-1",
|
|
20
|
-
"RHL-2",
|
|
21
|
-
"MCL",
|
|
22
|
-
"MCLC-1",
|
|
23
|
-
"MCLC-2",
|
|
24
|
-
"MCLC-3",
|
|
25
|
-
"MCLC-4",
|
|
26
|
-
"MCLC-5",
|
|
27
|
-
"TRI",
|
|
28
|
-
]
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
def test_reciprocal_paths_all_keys_present():
|
|
32
|
-
for key in EXPECTED_KEYS:
|
|
33
|
-
assert key in RECIPROCAL_PATHS, f"Missing path key: {key}"
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
def test_reciprocal_paths_count():
|
|
37
|
-
assert len(RECIPROCAL_PATHS) == len(EXPECTED_KEYS)
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
def test_reciprocal_paths_entry_structure():
|
|
41
|
-
for key, path in RECIPROCAL_PATHS.items():
|
|
42
|
-
assert isinstance(path, list), f"Path {key} should be a list"
|
|
43
|
-
for entry in path:
|
|
44
|
-
assert "point" in entry, f"Entry in {key} missing 'point'"
|
|
45
|
-
assert "steps" in entry, f"Entry in {key} missing 'steps'"
|
|
46
|
-
assert entry["steps"] == 10, f"Entry in {key} should have steps=10"
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
def test_reciprocal_paths_cub():
|
|
50
|
-
path = RECIPROCAL_PATHS["CUB"]
|
|
51
|
-
labels = [p["point"] for p in path]
|
|
52
|
-
assert labels == ["Γ", "X", "M", "Γ", "R", "X", "M", "R"]
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
def test_reciprocal_paths_fcc():
|
|
56
|
-
path = RECIPROCAL_PATHS["FCC"]
|
|
57
|
-
labels = [p["point"] for p in path]
|
|
58
|
-
assert labels == ["Γ", "X", "W", "K", "Γ", "L", "U", "W", "L", "U", "X"]
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
def test_reciprocal_paths_hex():
|
|
62
|
-
path = RECIPROCAL_PATHS["HEX"]
|
|
63
|
-
labels = [p["point"] for p in path]
|
|
64
|
-
assert labels == ["Γ", "M", "K", "Γ", "A", "L", "H", "A", "L", "M", "K", "H"]
|