def _validate_euphonic_input_file(cls, filename_full_path: str) -> dict:
logger.information("Validate force constants file for interpolation.")
from dos.load_euphonic import euphonic_available
if euphonic_available():
try:
from euphonic.cli.utils import force_constants_from_file
force_constants_from_file(filename_full_path)
return dict(Invalid=False, Comment="")
except Exception as error:
if hasattr(error, 'message'):
message = error.message
else:
message = str(error)
return dict(
Invalid=True,
Comment=
f"Problem opening force constants file with Euphonic.: {message}"
)
else:
return dict(
Invalid=True,
Comment=
("Could not import Euphonic module. "
"Try running user/AdamJackson/install_euphonic.py from the Script Repository."
))
def _read_file(self):
"""
Decides if a castep or phonon file should be read then reads the file data
Raises RuntimeError if no valid file is found.
@return file_data dictionary holding all required data from the castep or phonon file
"""
castep_filename = self.getPropertyValue('CASTEPFile')
phonon_filename = self.getPropertyValue('PHONONFile')
euphonic_filename = self.getPropertyValue('ForceConstantsFile')
if phonon_filename and self._spec_type != 'BondTable':
return self._read_data_from_file(phonon_filename)
elif castep_filename:
return self._read_data_from_file(castep_filename)
elif euphonic_filename:
if euphonic_available():
file_data, self._element_isotope = get_data_with_euphonic(
euphonic_filename,
cutoff=float(self.getPropertyValue('ForceConstantsSampling')),
acoustic_sum_rule=None)
else:
raise ValueError("Could not load file using Euphonic: you may need to install this library.")
self._num_ions = file_data['num_ions']
return file_data
else:
raise RuntimeError('No valid data file')
def validateInputs(self):
"""
Performs input validation.
Used to ensure the user is requesting a valid mode.
"""
issues = dict()
castep_filename = self.getPropertyValue('CASTEPFile')
phonon_filename = self.getPropertyValue('PHONONFile')
euphonic_filename = self.getPropertyValue('ForceConstantsFile')
pdos_available = bool(phonon_filename or euphonic_filename)
if not any((castep_filename, phonon_filename, euphonic_filename)):
msg = 'Must have at least one input file'
issues['CASTEPFile'] = msg
issues['PHONONFile'] = msg
issues['ForceConstantsFile'] = msg
spec_type = self.getPropertyValue('SpectrumType')
sum_contributions = self.getProperty('SumContributions').value
scale_by_cross_section = self.getPropertyValue('ScaleByCrossSection') != 'None'
ions = self.getProperty('Ions').value
calc_partial = len(ions) > 0
if euphonic_filename and not euphonic_available():
issues['ForceConstantsFile'] = ('Cannot import the Euphonic library for force constants import. '
'This will be included in a future version of Mantid. '
'Until then, it can be installed using users/AdamJackson/install_euphonic.py '
'from the Script Repository.')
if spec_type == 'IonTable' and not pdos_available:
issues['SpectrumType'] = 'Cannot produce ion table when only .castep file is provided'
if spec_type == 'BondAnalysis' and phonon_filename == '' and castep_filename == '':
issues['SpectrumType'] = 'Require both a .phonon and .castep file for bond analysis'
if spec_type == 'BondTable' and castep_filename == '':
issues['SpectrumType'] = 'Require a .castep file for bond table output'
if spec_type != 'DOS' and calc_partial:
issues['Ions'] = 'Cannot calculate partial density of states when using %s' % spec_type
if spec_type != 'DOS' and scale_by_cross_section:
issues['ScaleByCrossSection'] = 'Cannot scale contributions by cross sections when using %s' % spec_type
if scale_by_cross_section and not pdos_available:
issues['ScaleByCrossSection'] = 'Cannot scale by cross sections when only .castep file is provided'
if not calc_partial and sum_contributions:
issues['SumContributions'] = 'Cannot sum contributions when not calculating partial density of states'
return issues
def runTest(self):
with tempfile.TemporaryDirectory() as tmp_prefix:
if not euphonic_available():
self._install_euphonic_to_tmp_prefix(tmp_prefix)
import pint # noqa: F401
import euphonic # noqa: F401
SimulatedDensityOfStates(ForceConstantsFile=find_file('phonopy-Al.yaml'),
Function='Gaussian',
SpectrumType='DOS',
OutputWorkspace='phonopy-Al_DOS')
def read_vibrational_or_phonon_data(self):
"""Get AbinsData (structure and modes) from force constants data.
Frequencies/displacements are interpolated using the Euphonic library
over a regular q-point mesh. The mesh is determined by a Moreno-Soler
realspace cutoff, related to the size of an equivalent
supercell. Meshes are rounded up so a very small cutoff will yield
gamma-point-only sampling.
"""
if not euphonic_available():
raise ImportError("Could not import Euphonic library; this is "
"required to import force constants from Phonopy or .castep_bin.")
cutoff = sampling_parameters['force_constants']['qpt_cutoff']
modes = euphonic_calculate_modes(filename=self._clerk.get_input_filename(), cutoff=cutoff)
unit_cell = modes.crystal.cell_vectors.to('angstrom').magnitude
atoms = {f'atom_{atom_index}': {'symbol': str(atom_type),
'sort': atom_index,
'coord': unit_cell.T.dot(atom_r),
'mass': mass}
for atom_index, atom_type, atom_r, mass in zip(range(modes.crystal.n_atoms),
modes.crystal.atom_type,
modes.crystal.atom_r,
modes.crystal.atom_mass.to('amu').magnitude)}
file_data = {'frequencies': modes.frequencies.to('1/cm').magnitude,
'weights': modes.weights,
'k_vectors': modes.qpts,
'atomic_displacements': np.swapaxes(modes.eigenvectors, 1, 2),
'unit_cell': unit_cell,
'atoms': atoms}
# save stuff to hdf file
save_keys = ["frequencies", "weights", "k_vectors", "atomic_displacements", "unit_cell", "atoms"]
data_to_save = {key: file_data[key] for key in save_keys}
self.save_ab_initio_data(data=data_to_save)
return self._rearrange_data(data=file_data)
class AbinsLoadPhonopyTest(unittest.TestCase, abins.input.Tester):
def setUp(self):
# A small cutoff is used to limit number of data files
self.default_cutoff = abins.parameters.sampling['force_constants'][
'qpt_cutoff']
abins.parameters.sampling['force_constants']['qpt_cutoff'] = 4.
def tearDown(self):
abins.test_helpers.remove_output_files(list_of_names=["_LoadPhonopy"])
abins.parameters.sampling['force_constants'][
'qpt_cutoff'] = self.default_cutoff
@unittest.skipUnless(euphonic_available(),
'Optional dependency (euphonic) not available')
def test_non_existing_file(self):
with self.assertRaises(IOError):
bad_phonopy_reader = EuphonicLoader(
input_ab_initio_filename="NonExistingFile.yaml")
bad_phonopy_reader.read_vibrational_or_phonon_data()
with self.assertRaises(TypeError):
_ = EuphonicLoader(input_ab_initio_filename=1)
