def get_properties_from_phonopy(structure, phonopy_input, force_constants):
"""
Calculate DOS and thermal properties using phonopy (locally)
:param structure: Aiida StructureData Object
:param phonopy_input: Aiida Parametersdata object containing a dictionary with the data needed to run phonopy:
supercells matrix, primitive matrix and q-points mesh.
:param force_constants:
:return:
"""
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
# Generate phonopy phonon object
bulk = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
phonopy_input = phonopy_input.get_dict()
force_constants = force_constants.get_array('force_constants')
phonon = Phonopy(bulk,
phonopy_input['supercell'],
primitive_matrix=phonopy_input['primitive'])
phonon.set_force_constants(force_constants)
#Normalization factor primitive to unit cell
normalization_factor = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
phonon.set_mesh(phonopy_input['mesh'],
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS()
phonon.set_partial_DOS()
# get DOS (normalized to unit cell)
total_dos = phonon.get_total_DOS() * normalization_factor
partial_dos = phonon.get_partial_DOS() * normalization_factor
# Stores DOS data in DB as a workflow result
dos = ArrayData()
dos.set_array('frequency', total_dos[0])
dos.set_array('total_dos', total_dos[1])
dos.set_array('partial_dos', partial_dos[1])
#THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per unit cell) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * normalization_factor)
thermal_properties.set_array('entropy', entropy * normalization_factor)
thermal_properties.set_array('cv', cv * normalization_factor)
return {'thermal_properties': thermal_properties, 'dos': dos}
def phonopy_calculation_inline(**kwargs):
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
structure = kwargs.pop('structure')
phonopy_input = kwargs.pop('phonopy_input').get_dict()
force_constants = kwargs.pop('force_constants').get_array(
'force_constants')
# Generate phonopy phonon object
bulk = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
phonon = Phonopy(bulk,
phonopy_input['supercell'],
primitive_matrix=phonopy_input['primitive'],
distance=phonopy_input['distance'])
phonon.set_force_constants(force_constants)
# Normalization factor primitive to unit cell
normalization_factor = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
phonon.set_mesh(phonopy_input['mesh'],
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS()
phonon.set_partial_DOS()
# get DOS (normalized to unit cell)
total_dos = phonon.get_total_DOS() * normalization_factor
partial_dos = phonon.get_partial_DOS() * normalization_factor
# Stores DOS data in DB as a workflow result
dos = ArrayData()
dos.set_array('frequency', total_dos[0])
dos.set_array('total_dos', total_dos[1])
dos.set_array('partial_dos', partial_dos[1])
# THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per unit cell) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * normalization_factor)
thermal_properties.set_array('entropy', entropy * normalization_factor)
thermal_properties.set_array('cv', cv * normalization_factor)
return {'thermal_properties': thermal_properties, 'dos': dos}
for q, d, freq in zip(q_points, distances, frequencies):
print q, d, freq
phonon.plot_band_structure().show()
# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10,
t_max=1000,
t_min=0)
# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
print "%15.7f%15.7f" % (omega, dos)
phonon.plot_total_DOS().show()
# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
phonon.plot_thermal_properties().show()
# PDOS
phonon.set_mesh([10, 10, 10],
is_mesh_symmetry=False,
is_eigenvectors=True)
phonon.set_partial_DOS(tetrahedron_method=True)
omegas, pdos = phonon.get_partial_DOS()
pdos_indices = [[0], [1]]
phonon.plot_partial_DOS(pdos_indices=pdos_indices,
legend=pdos_indices).show()
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
append_band(bands, [0.5, 0.5, 0.0], [0.0, 0.0, 0.0])
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon.set_band_structure(bands)
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
for q, d, freq in zip(q_points, distances, frequencies):
print q, d, freq
phonon.plot_band_structure().show()
# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10, t_max=1000, t_min=0)
# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
print "%15.7f%15.7f" % (omega, dos)
phonon.plot_total_DOS().show()
# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
print("%12.3f " + "%15.7f" * 3) % (t, free_energy, entropy, cv)
phonon.plot_thermal_properties().show()
# PDOS
phonon.set_mesh([10, 10, 10], is_mesh_symmetry=False, is_eigenvectors=True)
phonon.set_partial_DOS(tetrahedron_method=True)
omegas, pdos = phonon.get_partial_DOS()
pdos_indices = [[0], [1]]
phonon.plot_partial_DOS(pdos_indices=pdos_indices, legend=pdos_indices).show()
def phonopy_calculation_inline(**kwargs):
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
structure = kwargs.pop('structure')
phonopy_input = kwargs.pop('phonopy_input').get_dict()
force_constants = kwargs.pop('force_constants').get_array(
'force_constants')
bands = get_path_using_seekpath(structure)
# Generate phonopy phonon object
bulk = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
phonon = Phonopy(bulk,
phonopy_input['supercell'],
primitive_matrix=phonopy_input['primitive'],
symprec=phonopy_input['symmetry_precision'])
phonon.set_force_constants(force_constants)
try:
print('trying born')
nac_data = kwargs.pop('nac_data')
born = nac_data.get_array('born_charges')
epsilon = nac_data.get_array('epsilon')
phonon.set_nac_params(get_born_parameters(phonon, born, epsilon))
print('born succeed')
except:
pass
# Normalization factor primitive to unit cell
norm_primitive_to_unitcell = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
phonon.set_band_structure(bands['ranges'])
phonon.set_mesh(phonopy_input['mesh'],
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS(tetrahedron_method=True)
phonon.set_partial_DOS(tetrahedron_method=True)
# get band structure
band_structure_phonopy = phonon.get_band_structure()
q_points = np.array(band_structure_phonopy[0])
q_path = np.array(band_structure_phonopy[1])
frequencies = np.array(band_structure_phonopy[2])
band_labels = np.array(bands['labels'])
# stores band structure
band_structure = ArrayData()
band_structure.set_array('q_points', q_points)
band_structure.set_array('q_path', q_path)
band_structure.set_array('frequencies', frequencies)
band_structure.set_array('labels', band_labels)
# get DOS (normalized to unit cell)
total_dos = phonon.get_total_DOS() * norm_primitive_to_unitcell
partial_dos = phonon.get_partial_DOS() * norm_primitive_to_unitcell
# Stores DOS data in DB as a workflow result
dos = ArrayData()
dos.set_array('frequency', total_dos[0])
dos.set_array('total_dos', total_dos[1] * norm_primitive_to_unitcell)
dos.set_array('partial_dos', partial_dos[1] * norm_primitive_to_unitcell)
dos.set_array('partial_symbols', np.array(phonon.primitive.symbols))
# THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per mol) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * norm_primitive_to_unitcell)
thermal_properties.set_array('entropy',
entropy * norm_primitive_to_unitcell)
thermal_properties.set_array('cv', cv * norm_primitive_to_unitcell)
return {
'thermal_properties': thermal_properties,
'dos': dos,
'band_structure': band_structure
}
def get_properties_from_phonopy(**kwargs):
"""
Calculate DOS and thermal properties using phonopy (locally)
:param structure: StructureData Object
:param ph_settings: Parametersdata object containing a dictionary with the data needed to run phonopy:
supercells matrix, primitive matrix and q-points mesh.
:param force_constants: (optional)ForceConstantsData object containing the 2nd order force constants
:param force_sets: (optional) ForceSetsData object containing the phonopy force sets
:param nac: (optional) ArrayData object from a single point calculation data containing dielectric tensor and Born charges
:return: phonon band structure, force constants, thermal properties and DOS
"""
structure = kwargs.pop('structure')
ph_settings = kwargs.pop('ph_settings')
bands = kwargs.pop('bands')
from phonopy import Phonopy
phonon = Phonopy(phonopy_bulk_from_structure(structure),
supercell_matrix=ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision)
if 'force_constants' in kwargs:
force_constants = kwargs.pop('force_constants')
phonon.set_force_constants(force_constants.get_data())
else:
force_sets = kwargs.pop('force_sets')
phonon.set_displacement_dataset(force_sets.get_force_sets())
phonon.produce_force_constants()
force_constants = ForceConstantsData(data=phonon.get_force_constants())
if 'nac_data' in kwargs:
print('use born charges')
nac_data = kwargs.pop('nac_data')
primitive = phonon.get_primitive()
nac_parameters = nac_data.get_born_parameters_phonopy(
primitive_cell=primitive.get_cell())
phonon.set_nac_params(nac_parameters)
# Normalization factor primitive to unit cell
normalization_factor = phonon.unitcell.get_number_of_atoms(
) / phonon.primitive.get_number_of_atoms()
# DOS
phonon.set_mesh(ph_settings.dict.mesh,
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS(tetrahedron_method=True)
phonon.set_partial_DOS(tetrahedron_method=True)
total_dos = phonon.get_total_DOS()
partial_dos = phonon.get_partial_DOS()
dos = PhononDosData(
frequencies=total_dos[0],
dos=total_dos[1] * normalization_factor,
partial_dos=np.array(partial_dos[1]) * normalization_factor,
atom_labels=np.array(phonon.primitive.get_chemical_symbols()))
# THERMAL PROPERTIES (per primtive cell)
phonon.set_thermal_properties()
t, free_energy, entropy, cv = phonon.get_thermal_properties()
# Stores thermal properties (per unit cell) data in DB as a workflow result
thermal_properties = ArrayData()
thermal_properties.set_array('temperature', t)
thermal_properties.set_array('free_energy',
free_energy * normalization_factor)
thermal_properties.set_array('entropy', entropy * normalization_factor)
thermal_properties.set_array('heat_capacity', cv * normalization_factor)
# BAND STRUCTURE
phonon.set_band_structure(bands.get_bands())
band_structure = BandStructureData(bands=bands.get_bands(),
labels=bands.get_labels(),
unitcell=bands.get_unitcell())
band_structure.set_band_structure_phonopy(phonon.get_band_structure())
return {
'thermal_properties': thermal_properties,
'dos': dos,
'band_structure': band_structure,
'force_constants': force_constants
}