import numpy as np import pytest from ase import Atoms from ase.build import molecule from mat3ra.code.array_with_ids import ArrayWithIds from mat3ra.made.material import Material from mat3ra.made.tools.convert import from_ase, from_poscar, from_pymatgen, to_ase, to_poscar, to_pymatgen from mat3ra.made.tools.convert.utils import ( DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE, calculate_padded_cell_simple_cubic, ) from mat3ra.utils import assertion as assertion_utils from pymatgen.core.structure import Element, Lattice, Structure from .fixtures.monolayer import GRAPHENE from .fixtures.thrid_party.ase_atoms import ( ASE_MOLECULE_H2O, BULK_SI_LABELS, BULK_SI_LATTICE_A, BULK_SI_LATTICE_ALPHA, ASE_BULK_Si, ) PYMATGEN_LATTICE = Lattice.from_parameters(a=3.84, b=3.84, c=3.84, alpha=120, beta=90, gamma=60) PYMATGEN_STRUCTURE = Structure(PYMATGEN_LATTICE, ["Si", "Si"], [[0, 0, 0], [0.75, 0.5, 0.75]]) POSCAR_CONTENT = """Si2 1.0 3.3489202364344242 0.0000000000000000 1.9335000000000004 1.1163067454781415 3.1573922784475164 1.9335000000000004 0.0000000000000000 0.0000000000000000 3.8670000000000000 Si 2 direct 0.0000000000000000 0.0000000000000000 0.0000000000000000 Si 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si """ @pytest.mark.parametrize( "material_config, expected_lattice_params, expected_species, expected_frac_coords", [ ( Material.__default_config__, {"a": 3.867, "b": 3.867, "c": 3.867, "alpha": 60, "beta": 60, "gamma": 60}, [Element("Si"), Element("Si")], [[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]], ), ( GRAPHENE, {"a": 2.467291, "b": 2.467291, "c": 20.0, "alpha": 90, "beta": 90, "gamma": 120}, [Element("C"), Element("C")], [[0.0, 0.0, 0.0], [0.333333, 0.666667, 0.0]], ), ], ) def test_to_pymatgen(material_config, expected_lattice_params, expected_species, expected_frac_coords): material = Material.create(material_config) structure = to_pymatgen(material) assert isinstance(structure, Structure) assert np.allclose(structure.lattice.parameters, tuple(expected_lattice_params.values()), atol=1e-6) assert structure.species == expected_species assert np.allclose(structure.frac_coords, expected_frac_coords, atol=1e-6) structure_to_poscar_str = structure.to(fmt="poscar") material_to_poscar_str = to_poscar(material) assert structure_to_poscar_str == material_to_poscar_str def test_from_pymatgen(): material_data = from_pymatgen(PYMATGEN_STRUCTURE) assert material_data["lattice"]["a"] == 3.84 assert material_data["lattice"]["alpha"] == 120 assert material_data["basis"]["elements"] == [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}] converted_material = Material.create(material_data) default_material = Material.create_default() assertion_utils.assert_deep_almost_equal(converted_material, default_material) def test_to_poscar(): material = Material.create_default() poscar = to_poscar(material) assert poscar == POSCAR_CONTENT def test_from_poscar(): material_data = from_poscar(POSCAR_CONTENT) assert material_data["lattice"]["a"] == 3.867 assert material_data["lattice"]["alpha"] == 60 def test_to_ase(): material = Material.create_default() labels_array = [{"id": 0, "value": 0}, {"id": 1, "value": 1}] material.basis.labels = ArrayWithIds.from_list_of_dicts(labels_array) ase_atoms = to_ase(material) assert isinstance(ase_atoms, Atoms) assert np.allclose( ase_atoms.get_cell().tolist(), [ [3.3489202364344242, 0.0, 1.9335000000000004], [1.1163067454781415, 3.1573922784475164, 1.9335000000000004], [0.0, 0.0, 3.8670000000000000], ], ) assert ase_atoms.get_chemical_symbols() == ["Si", "Si"] assert np.allclose(ase_atoms.get_scaled_positions().tolist(), [[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]]) assert ase_atoms.get_tags().tolist() == [0, 1] @pytest.mark.parametrize( "ase_atoms, expected_lattice_a, expected_lattice_alpha, expected_labels," + " expected_is_non_periodic, expected_lattice_type", [ ( ASE_BULK_Si, BULK_SI_LATTICE_A, BULK_SI_LATTICE_ALPHA, BULK_SI_LABELS, False, None, ), ( ASE_MOLECULE_H2O, None, None, [], True, "CUB", ), ], ) def test_from_ase( ase_atoms, expected_lattice_a, expected_lattice_alpha, expected_labels, expected_is_non_periodic, expected_lattice_type, ): material_data = from_ase(ase_atoms) if expected_lattice_a is not None: assertion_utils.assert_almost_equal_numbers(material_data["lattice"]["a"], expected_lattice_a, atol=1e-4) if expected_lattice_alpha is not None: assert material_data["lattice"]["alpha"] == expected_lattice_alpha assert material_data["basis"]["labels"] == expected_labels assert material_data["isNonPeriodic"] == expected_is_non_periodic if expected_lattice_type is not None: assert material_data["lattice"]["type"] == expected_lattice_type TOLERANCE = 1e-4 H2_EXPECTED_LATTICE_A = DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE O2_EXPECTED_LATTICE_A = 3.7379 H2O_EXPECTED_LATTICE_A = 3.0530 C2H4_EXPECTED_LATTICE_A = 6.1754 @pytest.mark.parametrize( "molecule_name, expected_lattice_a", [ ("H2", H2_EXPECTED_LATTICE_A), ("O2", O2_EXPECTED_LATTICE_A), ("H2O", H2O_EXPECTED_LATTICE_A), ("C2H4", C2H4_EXPECTED_LATTICE_A), ], ) def test_calculate_padded_cell_simple_cubic(molecule_name, expected_lattice_a): atoms = molecule(molecule_name) cell_vectors = calculate_padded_cell_simple_cubic(atoms.get_positions().tolist()) lattice_a = cell_vectors[0][0] assert np.isclose(lattice_a, expected_lattice_a, atol=TOLERANCE) assert lattice_a >= DEFAULT_NON_PERIODIC_MIN_LATTICE_SIZE assert np.isclose(cell_vectors[0][0], cell_vectors[1][1], atol=TOLERANCE) assert np.isclose(cell_vectors[0][0], cell_vectors[2][2], atol=TOLERANCE)