def test_write_phonopy_yaml_extra(ph_nacl_nofcsym: Phonopy):
"""Test PhonopyYaml.set_phonon_info, __str__, yaml_data, parse.
settings parameter controls amount of yaml output. In this test,
more data than the default are dumped and those are tested.
"""
phonon = ph_nacl_nofcsym
settings = {
"force_sets": True,
"displacements": True,
"force_constants": True,
"born_effective_charge": True,
"dielectric_constant": True,
}
phpy_yaml = PhonopyYaml(calculator="vasp", settings=settings)
phpy_yaml.set_phonon_info(phonon)
phpy_yaml_test = PhonopyYaml()
phpy_yaml_test.yaml_data = yaml.safe_load(StringIO(str(phpy_yaml)))
phpy_yaml_test.parse()
np.testing.assert_allclose(phpy_yaml.force_constants,
phpy_yaml_test.force_constants,
atol=1e-8)
np.testing.assert_allclose(phpy_yaml.nac_params["born"],
phpy_yaml_test.nac_params["born"],
atol=1e-8)
np.testing.assert_allclose(
phpy_yaml.nac_params["dielectric"],
phpy_yaml_test.nac_params["dielectric"],
atol=1e-8,
)
np.testing.assert_allclose(
phpy_yaml.nac_params["factor"],
phpy_yaml_test.nac_params["factor"],
atol=1e-8,
)
disps, forces = get_displacements_and_forces(phpy_yaml.dataset)
disps_test, forces_test = get_displacements_and_forces(
phpy_yaml_test.dataset)
np.testing.assert_allclose(forces, forces_test, atol=1e-8)
np.testing.assert_allclose(disps, disps_test, atol=1e-8)
def test_write_phonopy_yaml(ph_nacl_nofcsym: Phonopy, helper_methods):
"""Test PhonopyYaml.set_phonon_info, __str__, yaml_data, parse."""
phonon = ph_nacl_nofcsym
phpy_yaml = PhonopyYaml(calculator="vasp")
phpy_yaml.set_phonon_info(phonon)
phpy_yaml_test = PhonopyYaml()
phpy_yaml_test.yaml_data = yaml.safe_load(StringIO(str(phpy_yaml)))
phpy_yaml_test.parse()
helper_methods.compare_cells_with_order(phpy_yaml.primitive,
phpy_yaml_test.primitive)
helper_methods.compare_cells_with_order(phpy_yaml.unitcell,
phpy_yaml_test.unitcell)
helper_methods.compare_cells_with_order(phpy_yaml.supercell,
phpy_yaml_test.supercell)
assert phpy_yaml.version == phpy_yaml_test.version
np.testing.assert_allclose(phpy_yaml.supercell_matrix,
phpy_yaml_test.supercell_matrix,
atol=1e-8)
np.testing.assert_allclose(phpy_yaml.primitive_matrix,
phpy_yaml_test.primitive_matrix,
atol=1e-8)
