def get_data_from_node_id(node_id):
n = load_node(node_id.value)
if 'structure' in n.inputs:
cell = phonopy_atoms_from_structure(n.inputs.structure)
structure = phonopy_atoms_to_structure(cell)
else:
raise RuntimeError("Crystal structure could not be found.")
if 'born_charges' in n.outputs and 'dielectrics' in n.outputs:
born = DataFactory('array')()
born.set_array('born_charges',
n.outputs.born_charges.get_array('born_charges'))
born.label = 'born_charges'
epsilon = DataFactory('array')()
epsilon.set_array('epsilon',
n.outputs.dielectrics.get_array('epsilon'))
epsilon.label = 'epsilon'
return {
'born_charges': born,
'dielectrics': epsilon,
'structure': structure
}
elif 'forces' in n.outputs:
forces = DataFactory('array')()
forces.set_array('final', n.outputs.forces.get_array('final'))
forces.label = 'forces'
return {'forces': forces, 'structure': structure}
else:
raise RuntimeError("Forces or NAC params were not found.")
def get_phonon_setting_info(phonon_settings,
structure,
symmetry_tolerance,
displacement_dataset=None):
return_vals = {}
ph_settings = {}
ph_settings.update(phonon_settings.get_dict())
dim = ph_settings['supercell_matrix']
if len(np.ravel(dim)) == 3:
smat = np.diag(dim)
else:
smat = np.array(dim)
if not np.issubdtype(smat.dtype, np.integer):
raise TypeError("supercell_matrix is not integer matrix.")
else:
ph_settings['supercell_matrix'] = smat.tolist()
if 'mesh' not in ph_settings:
ph_settings['mesh'] = 100.0
if 'distance' not in ph_settings:
ph_settings['distance'] = 0.01
tolerance = symmetry_tolerance.value
ph_settings['symmetry_tolerance'] = tolerance
ph = get_phonopy_instance(structure, ph_settings, {})
ph_settings['primitive_matrix'] = ph.primitive_matrix
ph_settings['symmetry'] = {
'number': ph.symmetry.dataset['number'],
'international': ph.symmetry.dataset['international']
}
if displacement_dataset is None:
ph.generate_displacements(distance=ph_settings['distance'])
else:
ph.dataset = displacement_dataset.get_dict()
ph_settings['displacement_dataset'] = ph.dataset
settings = DataFactory('dict')(dict=ph_settings)
settings.label = 'phonon_setting_info'
return_vals['phonon_setting_info'] = settings
# Supercells and primitive cell
for i, scell in enumerate(ph.supercells_with_displacements):
structure = phonopy_atoms_to_structure(scell)
label = "supercell_%03d" % (i + 1)
structure.label = "%s %s" % (structure.get_formula(
mode='hill_compact'), label)
return_vals[label] = structure
supercell_structure = phonopy_atoms_to_structure(ph.supercell)
supercell_structure.label = "%s %s" % (supercell_structure.get_formula(
mode='hill_compact'), 'supercell')
return_vals['supercell'] = supercell_structure
primitive_structure = phonopy_atoms_to_structure(ph.primitive)
primitive_structure.label = "%s %s" % (primitive_structure.get_formula(
mode='hill_compact'), 'primitive cell')
return_vals['primitive'] = primitive_structure
return return_vals
def get_thermal_properties(thermal_properties):
tprops = DataFactory('array.xy')()
tprops.set_x(thermal_properties['temperatures'], 'Temperature', 'K')
tprops.set_y([
thermal_properties['free_energy'], thermal_properties['entropy'],
thermal_properties['heat_capacity']
], ['Helmholtz free energy', 'Entropy', 'Cv'],
['kJ/mol', 'J/K/mol', 'J/K/mol'])
tprops.label = 'Thermal properties'
return tprops
def get_projected_dos(projected_dos):
pdos = DataFactory('array.xy')()
pdos_list = [pd for pd in projected_dos['projected_dos']]
pdos.set_x(projected_dos['frequency_points'], 'Frequency', 'THz')
pdos.set_y(pdos_list, [
'Projected DOS',
] * len(pdos_list), [
'1/THz',
] * len(pdos_list))
pdos.label = 'Projected DOS'
return pdos
def get_force_constants(structure, phonon_settings, force_sets):
params = {}
phonon = get_phonopy_instance(structure, phonon_settings, params)
phonon.dataset = phonon_settings['displacement_dataset']
phonon.forces = force_sets.get_array('force_sets')
phonon.produce_force_constants()
force_constants = DataFactory('array')()
force_constants.set_array('force_constants', phonon.force_constants)
force_constants.set_array('p2s_map', phonon.primitive.p2s_map)
force_constants.label = 'force_constants'
return force_constants
def get_force_sets(**forces_dict):
forces = []
energies = []
for i in range(len(forces_dict)):
label = "forces_%03d" % (i + 1)
if label in forces_dict:
forces.append(forces_dict[label].get_array('final'))
label = "misc_%03d" % (i + 1)
if label in forces_dict:
energies.append(
forces_dict[label]['total_energies']['energy_no_entropy'])
assert len(forces) == sum(['forces' in k for k in forces_dict])
force_sets = DataFactory('array')()
force_sets.set_array('force_sets', np.array(forces))
if energies:
force_sets.set_array('energies', np.array(energies))
force_sets.label = 'force_sets'
return force_sets
def get_bands(qpoints, frequencies, labels, path_connections, label=None):
qpoints_list = list(qpoints[0])
frequencies_list = list(frequencies[0])
labels_list = [
(0, labels[0]),
]
label_index = 1
for pc, qs, fs in zip(path_connections[:-1], qpoints[1:], frequencies[1:]):
if labels[label_index] == 'GAMMA' and pc:
labels_list.append((len(qpoints_list) - 1, labels[label_index]))
if label_index < len(labels):
labels_list.append((len(qpoints_list), labels[label_index]))
label_index += 1
qpoints_list += list(qs)
frequencies_list += list(fs)
elif pc:
labels_list.append((len(qpoints_list) - 1, labels[label_index]))
label_index += 1
qpoints_list += list(qs[1:])
frequencies_list += list(fs[1:])
else:
labels_list.append((len(qpoints_list) - 1, labels[label_index]))
label_index += 1
if label_index < len(labels):
labels_list.append((len(qpoints_list), labels[label_index]))
label_index += 1
qpoints_list += list(qs)
frequencies_list += list(fs)
labels_list.append((len(qpoints_list) - 1, labels[-1]))
bs = DataFactory('array.bands')()
bs.set_kpoints(np.array(qpoints_list))
bs.set_bands(np.array(frequencies_list), units='THz')
bs.labels = labels_list
if label is not None:
bs.label = label
return bs
def get_nac_params(born_charges, epsilon, nac_structure, **params):
"""Obtain Born effective charges and dielectric constants in primitive cell
When Born effective charges and dielectric constants are calculated within
phonopy workchain, those values are calculated in the primitive cell.
However using immigrant, the cell may not be primitive cell and can be
unit cell. In this case, conversion of data is necessary. This conversion
needs information of the structure where those values were calcualted and
the target primitive cell structure.
Two kargs parameters
primitive : StructureData
symmetry_tolerance : Float
"""
from phonopy.structure.symmetry import symmetrize_borns_and_epsilon
borns = born_charges.get_array('born_charges')
eps = epsilon.get_array('epsilon')
nac_cell = phonopy_atoms_from_structure(nac_structure)
kargs = {}
if 'symmetry_tolerance' in params:
kargs['symprec'] = params['symmetry_tolerance'].value
if 'primitive' in params:
pcell = phonopy_atoms_from_structure(params['primitive'])
kargs['primitive'] = pcell
borns_, epsilon_ = symmetrize_borns_and_epsilon(borns, eps, nac_cell,
**kargs)
nac_params = DataFactory('array')()
nac_params.set_array('born_charges', borns_)
nac_params.set_array('epsilon', epsilon_)
nac_params.label = 'born_charges & epsilon'
return nac_params
def get_total_dos(total_dos):
dos = DataFactory('array.xy')()
dos.set_x(total_dos['frequency_points'], 'Frequency', 'THz')
dos.set_y(total_dos['total_dos'], 'Total DOS', '1/THz')
dos.label = 'Total DOS'
return dos
