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 get_force_sets_wien2k(num_displacements,
force_filenames,
disp_filename,
supercell,
disp_dataset,
wien2k_P1_mode=False,
symmetry_tolerance=None,
verbose=False):
from phonopy.interface.wien2k import parse_set_of_forces
disps, _ = get_displacements_and_forces(disp_dataset)
force_sets = parse_set_of_forces(disps,
force_filenames,
supercell,
wien2k_P1_mode=wien2k_P1_mode,
symmetry_tolerance=symmetry_tolerance,
verbose=verbose)
return force_sets
def _extract_dataset_from_db(forces_in_db, ph_info_in_db):
nitems = len(forces_in_db)
displacements = []
forces = []
energies = []
for i in range(nitems):
force_sets = forces_in_db[i].get_array('force_sets')
dataset = ph_info_in_db[i]['displacement_dataset']
disps, _ = get_displacements_and_forces(dataset)
forces.append(force_sets)
if 'energies' in forces_in_db[i].get_arraynames():
energy_sets = forces_in_db[i].get_array('energies')
energies.append(energy_sets)
displacements.append(disps)
return displacements, forces, energies
def _get_dataset(f, natom=None, to_type2=False):
first_line_ary = _get_line_ignore_blank(f).split()
f.seek(0)
if len(first_line_ary) == 1:
if natom is None or int(first_line_ary[0]) == natom:
dataset = _get_dataset_type1(f)
else:
msg = "Number of forces is not consistent with supercell setting."
raise RuntimeError(msg)
if to_type2:
disps, forces = get_displacements_and_forces(dataset)
return {"displacements": disps, "forces": forces}
else:
return dataset
elif len(first_line_ary) == 6:
return get_dataset_type2(f, natom)
def get_force_sets_wien2k(
force_filenames,
supercell,
disp_dataset,
wien2k_P1_mode=False,
symmetry_tolerance=None,
verbose=False,
):
"""Read Wien2k output files and parse force sets."""
from phonopy.interface.wien2k import parse_set_of_forces
disps, _ = get_displacements_and_forces(disp_dataset)
force_sets = parse_set_of_forces(
disps,
force_filenames,
supercell,
wien2k_P1_mode=wien2k_P1_mode,
symmetry_tolerance=symmetry_tolerance,
verbose=verbose,
)
return force_sets