def modes_from_file(filename: Union[str, os.PathLike]
) -> QpointPhononModes:
"""
Load phonon mode data from file
Parameters
----------
filename
Data file
Returns
-------
QpointPhononmodes
"""
path = pathlib.Path(filename)
if path.suffix == '.phonon':
return QpointPhononModes.from_castep(path)
elif path.suffix == '.json':
return QpointPhononModes.from_json_file(path)
elif path.suffix in ('.yaml', '.hdf5'):
return QpointPhononModes.from_phonopy(path=path.parent,
phonon_name=path.name)
else:
raise ValueError("File not recognised. Should have extension "
".yaml or .hdf5 (phonopy), "
".phonon (castep) or .json (JSON from Euphonic).")
def test_calculate_dos(self, material, qpt_ph_modes_file,
expected_dos_json, ebins):
if qpt_ph_modes_file.endswith('.phonon'):
qpt_ph_modes = QpointPhononModes.from_castep(
get_castep_path(material, qpt_ph_modes_file))
else:
qpt_ph_modes = QpointPhononModes.from_phonopy(
phonon_name=get_phonopy_path(material, qpt_ph_modes_file))
dos = qpt_ph_modes.calculate_dos(ebins)
expected_dos = get_expected_spectrum1d(expected_dos_json)
check_spectrum1d(dos, expected_dos)
def test_calculate_debye_waller(self, material, qpt_ph_modes_file,
expected_dw_json, temperature, kwargs):
if qpt_ph_modes_file.endswith('.phonon'):
qpt_ph_modes = QpointPhononModes.from_castep(
get_castep_path(material, qpt_ph_modes_file))
else:
qpt_ph_modes = QpointPhononModes.from_phonopy(
phonon_name=get_phonopy_path(material, qpt_ph_modes_file))
dw = qpt_ph_modes.calculate_debye_waller(temperature * ureg('K'),
**kwargs)
expected_dw = get_expected_dw(material, expected_dw_json)
check_debye_waller(dw, expected_dw, dw_atol=1e-12)
def test_create_from_phonopy_without_installed_modules_raises_err(
self, material, subdir, phonopy_args, mocker):
phonopy_args['path'] = get_phonopy_path(material, subdir)
# Mock import of yaml, h5py to raise ModuleNotFoundError
import builtins
real_import = builtins.__import__
def mocked_import(name, *args, **kwargs):
if name == 'h5py' or name == 'yaml':
raise ModuleNotFoundError
return real_import(name, *args, **kwargs)
mocker.patch('builtins.__import__', side_effect=mocked_import)
with pytest.raises(ImportPhonopyReaderError):
QpointPhononModes.from_phonopy(**phonopy_args)
def create_from_phonopy(self, request):
material, subdir, phonopy_args, json_file = request.param
phonopy_args['path'] = get_phonopy_path(material, subdir)
qpt_ph_modes = QpointPhononModes.from_phonopy(**phonopy_args)
json_path = os.path.join(get_qpt_ph_modes_dir(material), json_file)
expected_qpt_ph_modes = ExpectedQpointPhononModes(json_path)
return qpt_ph_modes, expected_qpt_ph_modes
def create_from_castep(self, request):
material, phonon_file, json_file = request.param
qpt_ph_modes = QpointPhononModes.from_castep(
get_castep_path(material, phonon_file))
expected_qpt_ph_modes = ExpectedQpointPhononModes(
os.path.join(get_qpt_ph_modes_dir(material), json_file))
return qpt_ph_modes, expected_qpt_ph_modes
def test_serialise_to_json_file(self, qpt_ph_modes, tmpdir):
output_file = str(tmpdir.join('tmp.test'))
qpt_ph_modes.to_json_file(output_file)
check_json_metadata(output_file, 'QpointPhononModes')
deserialised_qpt_ph_modes = QpointPhononModes.from_json_file(
output_file)
check_qpt_ph_modes(qpt_ph_modes,
deserialised_qpt_ph_modes,
check_evecs=True)
def test_create_from_phonopy_without_cloader_is_ok(self, material, subdir,
phonopy_args, json_file,
mocker):
# Mock 'from yaml import CLoader as Loader' to raise ImportError
import builtins
real_import = builtins.__import__
def mocked_import(name, globals, locals, fromlist, level):
if name == 'yaml':
if fromlist is not None and fromlist[0] == 'CSafeLoader':
raise ImportError
return real_import(name, globals, locals, fromlist, level)
mocker.patch('builtins.__import__', side_effect=mocked_import)
phonopy_args['path'] = get_phonopy_path(material, subdir)
qpt_ph_modes = QpointPhononModes.from_phonopy(**phonopy_args)
json_path = os.path.join(get_qpt_ph_modes_dir(material), json_file)
expected_qpt_ph_modes = ExpectedQpointPhononModes(json_path)
check_qpt_ph_modes(qpt_ph_modes,
expected_qpt_ph_modes,
check_evecs=True)
def get_quartz_qpt_ph_modes():
return QpointPhononModes.from_castep(
get_castep_path('quartz', 'quartz_nosplit.phonon'))
def serialise_to_dict(self, request):
qpt_ph_modes = get_qpt_ph_modes(request.param)
# Convert to dict, then back to object to test
qpt_ph_modes_dict = qpt_ph_modes.to_dict()
qpt_ph_modes_from_dict = QpointPhononModes.from_dict(qpt_ph_modes_dict)
return qpt_ph_modes, qpt_ph_modes_from_dict
def get_qpt_ph_modes_from_json(material, file):
return QpointPhononModes.from_json_file(
os.path.join(get_qpt_ph_modes_dir(material), file))
def test_faulty_object_creation(self, inject_faulty_elements):
faulty_args, faulty_kwargs, expected_exception = inject_faulty_elements
with pytest.raises(expected_exception):
QpointPhononModes(*faulty_args, **faulty_kwargs)
def create_from_dict(self, request):
material = request.param
expected_qpt_ph_modes = get_expected_qpt_ph_modes(material)
qpt_ph_modes = QpointPhononModes.from_dict(
expected_qpt_ph_modes.to_dict())
return qpt_ph_modes, expected_qpt_ph_modes
def create_from_constructor_without_weights(self, request):
expected_qpt_ph_modes = request.param
args, kwargs = expected_qpt_ph_modes.to_constructor_args(weights=False)
qpt_ph_modes = QpointPhononModes(*args, **kwargs)
return qpt_ph_modes, expected_qpt_ph_modes
def get_si2_qpt_ph_modes():
return QpointPhononModes.from_castep(
get_castep_path('Si2-sc-skew', 'Si2-sc-skew.phonon'))
def get_cahgo2_qpt_ph_modes():
return QpointPhononModes.from_phonopy(
path=get_phonopy_path('CaHgO2', ''),
summary_name='mp-7041-20180417.yaml',
phonon_name='qpoints.yaml')
def test_create_from_phonopy_with_bad_inputs_raises_err(
self, material, subdir, phonopy_args, err):
phonopy_args['path'] = get_phonopy_path(material, subdir)
with pytest.raises(err):
QpointPhononModes.from_phonopy(**phonopy_args)