from types import SimpleNamespace from typing import Final import numpy as np import pytest from mat3ra.made.tools.analyze.interface.zsl import ZSLInterfaceAnalyzer from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabConfiguration from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab_strained_supercell.builder import ( SlabStrainedSupercellBuilder, ) from mat3ra.made.tools.utils import supercell_matrix_2d_schema_to_list, unwrap from mat3ra.utils.matrix import convert_2x2_to_3x3 from unit.fixtures.bulk import BULK_Ge_CONVENTIONAL, BULK_Ni_PRIMITIVE, BULK_Si_CONVENTIONAL from .fixtures.monolayer import GRAPHENE from .utils import OSPlatform, get_platform_specific_value SUBSTRATE_SI_001: Final = SimpleNamespace( bulk_config=BULK_Si_CONVENTIONAL, miller_indices=(0, 0, 1), number_of_layers=2, vacuum=0.0, ) FILM_GE_001: Final = SimpleNamespace( bulk_config=BULK_Ge_CONVENTIONAL, miller_indices=(0, 0, 1), number_of_layers=2, vacuum=0.0, ) EXPECTED_PROPERTIES_SI_GE_001: Final = SimpleNamespace( substrate_strain_matrix=np.identity(3).tolist(), substrate_supercell_matrix=[[1.0, 0.0], [0.0, 1.0]], film_strain_matrix=[[0.9643, 0.0, 0.0], [0.0, 0.9643, 0.0], [0.0, 0.0, 1.0]], film_supercell_matrix=[[1.0, 0.0], [0.0, 1.0]], ) @pytest.mark.parametrize( "substrate, film, zsl_params, expected_matches_min", [ ( SUBSTRATE_SI_001, FILM_GE_001, {"max_area": 350.0, "max_area_ratio_tol": 0.09, "max_length_tol": 0.03, "max_angle_tol": 0.01}, 1, ), ( SimpleNamespace( bulk_config=BULK_Ni_PRIMITIVE, miller_indices=(0, 0, 1), number_of_layers=2, vacuum=0.0, ), SimpleNamespace( bulk_config=GRAPHENE, miller_indices=(0, 0, 1), number_of_layers=1, vacuum=0.0, ), {"max_area": 120.0, "max_area_ratio_tol": 0.09, "max_length_tol": 0.03, "max_angle_tol": 0.01}, 1, ), ], ) def test_zsl_interface_analyzer(substrate, film, zsl_params, expected_matches_min): substrate_slab_config = SlabConfiguration.from_parameters( substrate.bulk_config, substrate.miller_indices, substrate.number_of_layers, vacuum=0.0, termination_top_formula=None, termination_bottom_formula=None, ) film_slab_config = SlabConfiguration.from_parameters( film.bulk_config, film.miller_indices, film.number_of_layers, vacuum=0.0 ) analyzer = ZSLInterfaceAnalyzer( substrate_slab_configuration=substrate_slab_config, film_slab_configuration=film_slab_config, **zsl_params, ) # Test ZSL match generation match_holders = analyzer.zsl_match_holders assert len(match_holders) >= expected_matches_min match = analyzer.get_strained_configuration_by_match_id(0) sub_config = match.substrate_configuration film_config = match.film_configuration film_vectors = np.array(analyzer.film_slab.lattice.vector_arrays) substrate_vectors = np.array(analyzer.substrate_slab.lattice.vector_arrays) film_sl_vectors = ( np.array(unwrap(film_config.strain_matrix.root)) @ np.array(convert_2x2_to_3x3(supercell_matrix_2d_schema_to_list(film_config.xy_supercell_matrix))) @ film_vectors ) substrate_sl_vectors = ( np.array(convert_2x2_to_3x3(supercell_matrix_2d_schema_to_list(sub_config.xy_supercell_matrix))) @ substrate_vectors ) substrate_material = SlabStrainedSupercellBuilder().get_material(sub_config) film_material = SlabStrainedSupercellBuilder().get_material(film_config) # Check that the lattice vectors have the same magnitudes (allowing for orientation differences) film_a = np.linalg.norm(film_sl_vectors[0]) film_b = np.linalg.norm(film_sl_vectors[1]) substrate_a = np.linalg.norm(substrate_sl_vectors[0]) substrate_b = np.linalg.norm(substrate_sl_vectors[1]) assert np.isclose(film_a, substrate_a, atol=0.1) assert np.isclose(film_b, substrate_b, atol=0.1) # Check that the unit cell areas match film_area = abs(np.cross(film_sl_vectors[0][:2], film_sl_vectors[1][:2])) substrate_area = abs(np.cross(substrate_sl_vectors[0][:2], substrate_sl_vectors[1][:2])) assert np.isclose(film_area, substrate_area, atol=1e-4) assert np.isclose(substrate_material.lattice.a, film_material.lattice.a, atol=1e-4) assert np.isclose(substrate_material.lattice.b, film_material.lattice.b, atol=1e-4) @pytest.mark.parametrize( "substrate, film, zsl_parameters, expected_number_of_matches, expected_properties", [ ( SimpleNamespace( bulk_config=BULK_Ni_PRIMITIVE, miller_indices=(1, 1, 1), number_of_layers=3, vacuum=0.0, ), SimpleNamespace( bulk_config=GRAPHENE, miller_indices=(0, 0, 1), number_of_layers=1, vacuum=0.0, ), {"max_area": 90.0, "max_area_ratio_tol": 0.1, "max_length_tol": 0.1, "max_angle_tol": 0.1}, {OSPlatform.DARWIN: 26, OSPlatform.OTHER: 29}, { OSPlatform.DARWIN: {"strain_percentage": 0.474, "match_id": 0}, OSPlatform.OTHER: {"strain_percentage": 25.629, "match_id": 0}, }, # NOTE: the following values are expected for the DARWIN platform. # {"max_area": 90.0, "max_area_ratio_tol": 0.09, "max_length_tol": 0.03, "max_angle_tol": 0.01}, # 31, # {"strain_percentage": 25.122, "match_id": 0}, ), ], ) def test_zsl_interface_analyzer_sort_by_strain_then_area( substrate, film, zsl_parameters, expected_number_of_matches, expected_properties ): expected_number_of_matches = get_platform_specific_value(expected_number_of_matches) expected_properties = get_platform_specific_value(expected_properties) analyzer = ZSLInterfaceAnalyzer( substrate_slab_configuration=SlabConfiguration.from_parameters( substrate.bulk_config, substrate.miller_indices, substrate.number_of_layers, vacuum=0.0, termination_top_formula=None, termination_bottom_formula=None, ), film_slab_configuration=SlabConfiguration.from_parameters( film.bulk_config, film.miller_indices, film.number_of_layers, vacuum=0.0 ), **zsl_parameters, ) sorted_match_holders = analyzer.zsl_match_holders assert len(sorted_match_holders) == expected_number_of_matches index_to_check = expected_properties["match_id"] match_to_check = sorted_match_holders[index_to_check] expected_strain_percentage = expected_properties["strain_percentage"] assert np.isclose(match_to_check.total_strain_percentage, expected_strain_percentage, atol=1e-3)