materialsproject/pymatgen | Build 4075885785 | pymatgen/io/tests/test_ase.py | Coveralls

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from __future__ import annotations

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import os

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import unittest

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import numpy as np

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import pytest

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import pymatgen.io.ase as aio

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from pymatgen.core.composition import Composition

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from pymatgen.core.structure import Molecule, StructureError

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from pymatgen.io.vasp.inputs import Poscar

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from pymatgen.util.testing import PymatgenTest

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class AseAtomsAdaptorTest(unittest.TestCase):

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_structure(self):

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        ase_composition = Composition(atoms.get_chemical_formula())

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        assert ase_composition == structure.composition

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        assert atoms.cell is not None and atoms.cell.any()

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        assert atoms.get_pbc() is not None and atoms.get_pbc().all()

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        assert atoms.get_chemical_symbols() == [s.species_string for s in structure]

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        assert not atoms.has("initial_magmoms")

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        assert atoms.calc is None

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        prop = [3.14] * len(structure)

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        structure.add_site_property("prop", prop)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert atoms.get_array("prop").tolist() == prop

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_structure_mags(self):

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        mags = [1.0] * len(structure)

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        structure.add_site_property("final_magmom", mags)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert not atoms.has("initial_magmoms")

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        assert atoms.get_magnetic_moments().tolist() == mags

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        initial_mags = [0.5] * len(structure)

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        structure.add_site_property("magmom", initial_mags)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert atoms.get_initial_magnetic_moments().tolist() == initial_mags

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        assert atoms.calc is None

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        mags = [1.0] * len(structure)

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        structure.add_site_property("final_magmom", mags)

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        initial_mags = [2.0] * len(structure)

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        structure.add_site_property("magmom", initial_mags)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert atoms.get_initial_magnetic_moments().tolist(), initial_mags

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        assert atoms.get_magnetic_moments().tolist(), mags

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_structure_charge(self):

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        charges = [1.0] * len(structure)

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        structure.add_site_property("final_charge", charges)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert not atoms.has("initial_charges")

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        assert atoms.get_charges().tolist() == charges

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        charges = [0.5] * len(structure)

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        structure.add_site_property("charge", charges)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert atoms.calc is None

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        assert atoms.get_initial_charges().tolist() == charges

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        charges = [1.0] * len(structure)

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        structure.add_site_property("final_charge", charges)

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        initial_charges = [2.0] * len(structure)

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        structure.add_site_property("charge", initial_charges)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert atoms.get_initial_charges().tolist(), initial_charges

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        assert atoms.get_charges().tolist(), charges

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_structure_oxistates(self):

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        oxi_states = [1.0] * len(structure)

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        structure.add_oxidation_state_by_site(oxi_states)

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert atoms.get_array("oxi_states").tolist() == oxi_states

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_structure_dyn(self):

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        p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        structure = p.structure

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        structure.add_site_property("selective_dynamics", [[False] * 3] * len(structure))

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        atoms = aio.AseAtomsAdaptor.get_atoms(structure)

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        assert atoms.constraints[0].get_indices().tolist() == [atom.index for atom in atoms]

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_molecule(self):

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        m = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))

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        atoms = aio.AseAtomsAdaptor.get_atoms(m)

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        ase_composition = Composition(atoms.get_chemical_formula())

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        assert ase_composition == m.composition

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        assert atoms.cell is None or not atoms.cell.any()

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        assert atoms.get_pbc() is None or not atoms.get_pbc().any()

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        assert atoms.get_chemical_symbols() == [s.species_string for s in m]

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        assert not atoms.has("initial_magmoms")

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        assert atoms.calc is None

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_molecule_mags(self):

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        molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))

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        atoms = aio.AseAtomsAdaptor.get_atoms(molecule)

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        mags = [1.0] * len(molecule)

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        molecule.add_site_property("final_magmom", mags)

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        atoms = aio.AseAtomsAdaptor.get_atoms(molecule)

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        assert not atoms.has("initial_magmoms")

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        assert atoms.get_magnetic_moments().tolist() == mags

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        molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))

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        atoms = aio.AseAtomsAdaptor.get_atoms(molecule)

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        initial_mags = [0.5] * len(molecule)

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        molecule.add_site_property("magmom", initial_mags)

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        atoms = aio.AseAtomsAdaptor.get_atoms(molecule)

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        assert atoms.calc is None

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        assert atoms.get_initial_magnetic_moments().tolist() == initial_mags

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_atoms_from_molecule_dyn(self):

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        molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))

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        molecule.add_site_property("selective_dynamics", [[False] * 3] * len(molecule))

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        atoms = aio.AseAtomsAdaptor.get_atoms(molecule)

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        assert atoms.constraints[0].get_indices().tolist() == [atom.index for atom in atoms]

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_structure(self):

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        from ase.io import read

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        struct = aio.AseAtomsAdaptor.get_structure(atoms)

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        assert struct.formula == "Fe4 P4 O16"

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        assert [s.species_string for s in struct] == atoms.get_chemical_symbols()

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        prop = np.array([3.14] * len(atoms))

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        atoms.set_array("prop", prop)

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        struct = aio.AseAtomsAdaptor.get_structure(atoms)

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        assert struct.site_properties["prop"] == prop.tolist()

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR_overlap"))

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        struct = aio.AseAtomsAdaptor.get_structure(atoms)

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        assert [s.species_string for s in struct] == atoms.get_chemical_symbols()

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        with pytest.raises(StructureError):

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            struct = aio.AseAtomsAdaptor.get_structure(atoms, validate_proximity=True)

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_structure_mag(self):

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        from ase.io import read

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        mags = [1.0] * len(atoms)

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        atoms.set_initial_magnetic_moments(mags)

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        structure = aio.AseAtomsAdaptor.get_structure(atoms)

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        assert structure.site_properties["magmom"] == mags

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        assert "final_magmom" not in structure.site_properties

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        assert "initial_magmoms" not in structure.site_properties

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "OUTCAR"))

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        structure = aio.AseAtomsAdaptor.get_structure(atoms)

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        assert structure.site_properties["final_magmom"] == atoms.get_magnetic_moments().tolist()

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        assert "magmom" not in structure.site_properties

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        assert "initial_magmoms" not in structure.site_properties

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_structure_dyn(self):

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        from ase.constraints import FixAtoms

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        from ase.io import read

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))

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        atoms.set_constraint(FixAtoms(mask=[True] * len(atoms)))

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        structure = aio.AseAtomsAdaptor.get_structure(atoms)

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        assert structure.site_properties["selective_dynamics"][-1][0] is False

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_get_molecule(self):

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        from ase.io import read

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))

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        molecule = aio.AseAtomsAdaptor.get_molecule(atoms)

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        assert molecule.formula == "H2 C2"

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        assert [s.species_string for s in molecule] == atoms.get_chemical_symbols()

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        assert molecule.charge == 0

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        assert molecule.spin_multiplicity == 1

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))

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        initial_charges = [2.0] * len(atoms)

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        initial_mags = [1.0] * len(atoms)

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        atoms.set_initial_charges(initial_charges)

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        atoms.set_initial_magnetic_moments(initial_mags)

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        molecule = aio.AseAtomsAdaptor.get_molecule(atoms)

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        assert molecule.charge == np.sum(initial_charges)

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        assert molecule.spin_multiplicity == np.sum(initial_mags) + 1

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        assert molecule.site_properties.get("charge", None) == initial_charges

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        assert molecule.site_properties.get("magmom", None) == initial_mags

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    @unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")

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    def test_back_forth(self):

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        from ase.constraints import FixAtoms

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        from ase.io import read

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "OUTCAR"))

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        atoms.set_constraint(FixAtoms(mask=[True] * len(atoms)))

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        atoms.set_initial_charges([1.0] * len(atoms))

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        atoms.set_initial_magnetic_moments([2.0] * len(atoms))

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        atoms.set_array("prop", np.array([3.0] * len(atoms)))

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        structure = aio.AseAtomsAdaptor.get_structure(atoms)

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        atoms_back = aio.AseAtomsAdaptor.get_atoms(structure)

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        structure_back = aio.AseAtomsAdaptor.get_structure(atoms)

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        assert structure == structure_back

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        atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))

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        atoms.set_constraint(FixAtoms(mask=[True] * len(atoms)))

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        atoms.set_initial_charges([1.0] * len(atoms))

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        atoms.set_initial_magnetic_moments([2.0] * len(atoms))

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        atoms.set_array("prop", np.array([3.0] * len(atoms)))

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        molecule = aio.AseAtomsAdaptor.get_molecule(atoms)

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        atoms_back = aio.AseAtomsAdaptor.get_atoms(molecule)

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        assert atoms == atoms_back

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        molecule_back = aio.AseAtomsAdaptor.get_molecule(atoms)

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        assert molecule == molecule_back

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if __name__ == "__main__":

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materialsproject / pymatgen / 4075885785

Source File
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1	# Copyright (c) Pymatgen Development Team.
2	# Distributed under the terms of the MIT License.
3
4
5	from __future__ import annotations	1✔
6
7	import os	1✔
8	import unittest	1✔
9
10	import numpy as np	1✔
11	import pytest	1✔
12
13	import pymatgen.io.ase as aio	1✔
14	from pymatgen.core.composition import Composition	1✔
15	from pymatgen.core.structure import Molecule, StructureError	1✔
16	from pymatgen.io.vasp.inputs import Poscar	1✔
17	from pymatgen.util.testing import PymatgenTest	1✔
18
19
20	class AseAtomsAdaptorTest(unittest.TestCase):	1✔
21	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
22	def test_get_atoms_from_structure(self):	1✔
23	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
24	structure = p.structure	1✔
25	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
26	ase_composition = Composition(atoms.get_chemical_formula())	1✔
27	assert ase_composition == structure.composition	1✔
28	assert atoms.cell is not None and atoms.cell.any()	1✔
29	assert atoms.get_pbc() is not None and atoms.get_pbc().all()	1✔
30	assert atoms.get_chemical_symbols() == [s.species_string for s in structure]	1✔
31	assert not atoms.has("initial_magmoms")	1✔
32	assert atoms.calc is None	1✔
33
34	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
35	structure = p.structure	1✔
36	prop = [3.14] * len(structure)	1✔
37	structure.add_site_property("prop", prop)	1✔
38	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
39	assert atoms.get_array("prop").tolist() == prop	1✔
40
41	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
42	def test_get_atoms_from_structure_mags(self):	1✔
43	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
44	structure = p.structure	1✔
45	mags = [1.0] * len(structure)	1✔
46	structure.add_site_property("final_magmom", mags)	1✔
47	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
48	assert not atoms.has("initial_magmoms")	1✔
49	assert atoms.get_magnetic_moments().tolist() == mags	1✔
50
51	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
52	structure = p.structure	1✔
53	initial_mags = [0.5] * len(structure)	1✔
54	structure.add_site_property("magmom", initial_mags)	1✔
55	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
56	assert atoms.get_initial_magnetic_moments().tolist() == initial_mags	1✔
57	assert atoms.calc is None	1✔
58
59	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
60	structure = p.structure	1✔
61	mags = [1.0] * len(structure)	1✔
62	structure.add_site_property("final_magmom", mags)	1✔
63	initial_mags = [2.0] * len(structure)	1✔
64	structure.add_site_property("magmom", initial_mags)	1✔
65	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
66	assert atoms.get_initial_magnetic_moments().tolist(), initial_mags	1✔
67	assert atoms.get_magnetic_moments().tolist(), mags	1✔
68
69	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
70	def test_get_atoms_from_structure_charge(self):	1✔
71	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
72	structure = p.structure	1✔
73	charges = [1.0] * len(structure)	1✔
74	structure.add_site_property("final_charge", charges)	1✔
75	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
76	assert not atoms.has("initial_charges")	1✔
77	assert atoms.get_charges().tolist() == charges	1✔
78
79	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
80	structure = p.structure	1✔
81	charges = [0.5] * len(structure)	1✔
82	structure.add_site_property("charge", charges)	1✔
83	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
84	assert atoms.calc is None	1✔
85	assert atoms.get_initial_charges().tolist() == charges	1✔
86
87	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
88	structure = p.structure	1✔
89	charges = [1.0] * len(structure)	1✔
90	structure.add_site_property("final_charge", charges)	1✔
91	initial_charges = [2.0] * len(structure)	1✔
92	structure.add_site_property("charge", initial_charges)	1✔
93	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
94	assert atoms.get_initial_charges().tolist(), initial_charges	1✔
95	assert atoms.get_charges().tolist(), charges	1✔
96
97	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
98	def test_get_atoms_from_structure_oxistates(self):	1✔
99	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
100	structure = p.structure	1✔
101	oxi_states = [1.0] * len(structure)	1✔
102	structure.add_oxidation_state_by_site(oxi_states)	1✔
103	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
104	assert atoms.get_array("oxi_states").tolist() == oxi_states	1✔
105
106	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
107	def test_get_atoms_from_structure_dyn(self):	1✔
108	p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
109	structure = p.structure	1✔
110	structure.add_site_property("selective_dynamics", [[False] * 3] * len(structure))	1✔
111	atoms = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
112	assert atoms.constraints[0].get_indices().tolist() == [atom.index for atom in atoms]	1✔
113
114	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
115	def test_get_atoms_from_molecule(self):	1✔
116	m = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))	1✔
117	atoms = aio.AseAtomsAdaptor.get_atoms(m)	1✔
118	ase_composition = Composition(atoms.get_chemical_formula())	1✔
119	assert ase_composition == m.composition	1✔
120	assert atoms.cell is None or not atoms.cell.any()	1✔
121	assert atoms.get_pbc() is None or not atoms.get_pbc().any()	1✔
122	assert atoms.get_chemical_symbols() == [s.species_string for s in m]	1✔
123	assert not atoms.has("initial_magmoms")	1✔
124	assert atoms.calc is None	1✔
125
126	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
127	def test_get_atoms_from_molecule_mags(self):	1✔
128	molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))	1✔
129	atoms = aio.AseAtomsAdaptor.get_atoms(molecule)	1✔
130	mags = [1.0] * len(molecule)	1✔
131	molecule.add_site_property("final_magmom", mags)	1✔
132	atoms = aio.AseAtomsAdaptor.get_atoms(molecule)	1✔
133	assert not atoms.has("initial_magmoms")	1✔
134	assert atoms.get_magnetic_moments().tolist() == mags	1✔
135
136	molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))	1✔
137	atoms = aio.AseAtomsAdaptor.get_atoms(molecule)	1✔
138	initial_mags = [0.5] * len(molecule)	1✔
139	molecule.add_site_property("magmom", initial_mags)	1✔
140	atoms = aio.AseAtomsAdaptor.get_atoms(molecule)	1✔
141	assert atoms.calc is None	1✔
142	assert atoms.get_initial_magnetic_moments().tolist() == initial_mags	1✔
143
144	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
145	def test_get_atoms_from_molecule_dyn(self):	1✔
146	molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))	1✔
147	molecule.add_site_property("selective_dynamics", [[False] * 3] * len(molecule))	1✔
148	atoms = aio.AseAtomsAdaptor.get_atoms(molecule)	1✔
149	assert atoms.constraints[0].get_indices().tolist() == [atom.index for atom in atoms]	1✔
150
151	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
152	def test_get_structure(self):	1✔
153	from ase.io import read	1✔
154
155	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
156	struct = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
157	assert struct.formula == "Fe4 P4 O16"	1✔
158	assert [s.species_string for s in struct] == atoms.get_chemical_symbols()	1✔
159
160	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
161	prop = np.array([3.14] * len(atoms))	1✔
162	atoms.set_array("prop", prop)	1✔
163	struct = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
164	assert struct.site_properties["prop"] == prop.tolist()	1✔
165
166	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR_overlap"))	1✔
167	struct = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
168	assert [s.species_string for s in struct] == atoms.get_chemical_symbols()	1✔
169	with pytest.raises(StructureError):	1✔
170	struct = aio.AseAtomsAdaptor.get_structure(atoms, validate_proximity=True)	1✔
171
172	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
173	def test_get_structure_mag(self):	1✔
174	from ase.io import read	1✔
175
176	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
177	mags = [1.0] * len(atoms)	1✔
178	atoms.set_initial_magnetic_moments(mags)	1✔
179	structure = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
180	assert structure.site_properties["magmom"] == mags	1✔
181	assert "final_magmom" not in structure.site_properties	1✔
182	assert "initial_magmoms" not in structure.site_properties	1✔
183
184	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "OUTCAR"))	1✔
185	structure = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
186	assert structure.site_properties["final_magmom"] == atoms.get_magnetic_moments().tolist()	1✔
187	assert "magmom" not in structure.site_properties	1✔
188	assert "initial_magmoms" not in structure.site_properties	1✔
189
190	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
191	def test_get_structure_dyn(self):	1✔
192	from ase.constraints import FixAtoms	1✔
193	from ase.io import read	1✔
194
195	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))	1✔
196	atoms.set_constraint(FixAtoms(mask=[True] * len(atoms)))	1✔
197	structure = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
198	assert structure.site_properties["selective_dynamics"][-1][0] is False	1✔
199
200	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
201	def test_get_molecule(self):	1✔
202	from ase.io import read	1✔
203
204	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))	1✔
205	molecule = aio.AseAtomsAdaptor.get_molecule(atoms)	1✔
206	assert molecule.formula == "H2 C2"	1✔
207	assert [s.species_string for s in molecule] == atoms.get_chemical_symbols()	1✔
208	assert molecule.charge == 0	1✔
209	assert molecule.spin_multiplicity == 1	1✔
210
211	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))	1✔
212	initial_charges = [2.0] * len(atoms)	1✔
213	initial_mags = [1.0] * len(atoms)	1✔
214	atoms.set_initial_charges(initial_charges)	1✔
215	atoms.set_initial_magnetic_moments(initial_mags)	1✔
216	molecule = aio.AseAtomsAdaptor.get_molecule(atoms)	1✔
217	assert molecule.charge == np.sum(initial_charges)	1✔
218	assert molecule.spin_multiplicity == np.sum(initial_mags) + 1	1✔
219	assert molecule.site_properties.get("charge", None) == initial_charges	1✔
220	assert molecule.site_properties.get("magmom", None) == initial_mags	1✔
221
222	@unittest.skipIf(not aio.ase_loaded, "ASE not loaded.")	1✔
223	def test_back_forth(self):	1✔
224	from ase.constraints import FixAtoms	1✔
225	from ase.io import read	1✔
226
227	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "OUTCAR"))	1✔
228	atoms.set_constraint(FixAtoms(mask=[True] * len(atoms)))	1✔
229	atoms.set_initial_charges([1.0] * len(atoms))	1✔
230	atoms.set_initial_magnetic_moments([2.0] * len(atoms))	1✔
231	atoms.set_array("prop", np.array([3.0] * len(atoms)))	1✔
232	structure = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
233	atoms_back = aio.AseAtomsAdaptor.get_atoms(structure)	1✔
234	structure_back = aio.AseAtomsAdaptor.get_structure(atoms)	1✔
235	assert structure == structure_back	1✔
236
237	atoms = read(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))	1✔
238	atoms.set_constraint(FixAtoms(mask=[True] * len(atoms)))	1✔
239	atoms.set_initial_charges([1.0] * len(atoms))	1✔
240	atoms.set_initial_magnetic_moments([2.0] * len(atoms))	1✔
241	atoms.set_array("prop", np.array([3.0] * len(atoms)))	1✔
242	molecule = aio.AseAtomsAdaptor.get_molecule(atoms)	1✔
243	atoms_back = aio.AseAtomsAdaptor.get_atoms(molecule)	1✔
244	assert atoms == atoms_back	1✔
245	molecule_back = aio.AseAtomsAdaptor.get_molecule(atoms)	1✔
246	assert molecule == molecule_back	1✔
247
248
249	if __name__ == "__main__":	1✔
250	unittest.main()	×

materialsproject / pymatgen / 4075885785

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