def get_thermal_properties(structure, ph_settings, force_constants_list):
from phonopy import Phonopy
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
free_energy_list = []
entropy_list = []
cv_list = []
temperature = None
for fc in force_constants_list:
phonon = Phonopy(phonopy_bulk_from_structure(structure),
ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision)
# Normalization factor primitive to unit cell
normalization_factor = phonon.unitcell.get_number_of_atoms()/phonon.primitive.get_number_of_atoms()
phonon.set_force_constants(fc)
phonon.set_mesh(ph_settings.dict.mesh, is_eigenvectors=True, is_mesh_symmetry=False)
phonon.set_thermal_properties()
temperature, free_energy, entropy, cv = phonon.get_thermal_properties()
free_energy_list.append(np.array(free_energy) * normalization_factor)
entropy_list.append(np.array(entropy) * normalization_factor)
cv_list.append(np.array(cv) * normalization_factor)
return np.array(free_energy_list), np.array(entropy_list).T, np.array(cv_list).T, temperature
def get_force_constants3(data_sets, structure, ph_settings):
from phono3py.phonon3 import Phono3py
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
# Generate phonopy phonon object
phono3py = Phono3py(phonopy_bulk_from_structure(structure),
supercell_matrix=ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision,
log_level=1)
phono3py.produce_fc3(data_sets.get_forces3(),
displacement_dataset=data_sets.get_data_sets3(),
is_translational_symmetry=True,
is_permutation_symmetry=True,
is_permutation_symmetry_fc2=True)
fc3 = phono3py.get_fc3()
fc2 = phono3py.get_fc2()
force_constants_2 = ForceConstantsData(data=fc2)
force_constants_3 = ForceConstantsData(data=fc3)
return {'force_constants_2order': force_constants_2,
'force_constants_3order': force_constants_3}
def create_supercells_with_displacements_using_phono3py(structure, ph_settings, cutoff):
"""
Use phono3py to create the supercells with displacements to calculate the force constants by using
finite displacements methodology
:param structure: StructureData object
:param phonopy_input: ParametersData object containing a dictionary with the data needed for phonopy
:param cutoff: FloatData object containing the value of the cutoff for 3rd order FC in Angstroms (if 0 no cutoff is applied)
:return: A set of StructureData Objects containing the supercells with displacements
"""
from phono3py.phonon3 import Phono3py
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
# Generate phonopy phonon object
phono3py = Phono3py(phonopy_bulk_from_structure(structure),
supercell_matrix=ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision,
log_level=1)
if float(cutoff) == 0:
cutoff = None
else:
cutoff = float(cutoff)
phono3py.generate_displacements(distance=ph_settings.dict.distance,
cutoff_pair_distance=cutoff)
cells_with_disp = phono3py.get_supercells_with_displacements()
# Transform cells to StructureData and set them ready to return
data_sets = phono3py.get_displacement_dataset()
data_sets_object = ForceSetsData(data_sets3=data_sets)
disp_cells = {'data_sets': data_sets_object}
for i, phonopy_supercell in enumerate(cells_with_disp):
if phonopy_supercell is None:
print ('structure_{} cutoff skip'.format(i))
continue
supercell = StructureData(cell=phonopy_supercell.get_cell())
for symbol, position in zip(phonopy_supercell.get_chemical_symbols(),
phonopy_supercell.get_positions()):
supercell.append_atom(position=position, symbols=symbol)
disp_cells['structure_{}'.format(i)] = supercell
return disp_cells
def get_commensurate(structure, ph_settings):
from phonopy import Phonopy
from phonopy.harmonic.dynmat_to_fc import DynmatToForceConstants
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
phonon = Phonopy(phonopy_bulk_from_structure(structure),
ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision)
primitive = phonon.get_primitive()
supercell = phonon.get_supercell()
dynmat2fc = DynmatToForceConstants(primitive, supercell)
commensurate = dynmat2fc.get_commensurate_points()
return dynmat2fc, commensurate
def get_phonon(structure, force_constants, ph_settings, nac_data=None):
from phonopy import Phonopy
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
phonon = Phonopy(phonopy_bulk_from_structure(structure),
ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision)
if force_constants is not None:
phonon.set_force_constants(force_constants.get_data())
if nac_data is not None:
primitive = phonon.get_primitive()
nac_parameters = nac_data.get_born_parameters_phonopy(primitive_cell=primitive.get_cell())
phonon.set_nac_params(nac_parameters)
return phonon
def get_grid_points(structure, parameters):
from phono3py.phonon3 import Phono3py
from phono3py.cui.triplets_info import get_coarse_ir_grid_points
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
# Generate phonopy phonon object
phono3py = Phono3py(phonopy_bulk_from_structure(structure),
supercell_matrix=parameters.dict.supercell,
primitive_matrix=parameters.dict.primitive,
symprec=parameters.dict.symmetry_precision,
log_level=1)
primitive = phono3py.get_primitive()
(ir_grid_points, grid_weights, bz_grid_address,
grid_mapping_table) = get_coarse_ir_grid_points(primitive,
parameters.dict.mesh,
None,
None,
is_kappa_star=True,
symprec=1e-5)
return ir_grid_points
def get_disp_fc3_txt(structure, parameters_data, force_sets):
from phono3py.file_IO import write_cell_yaml
from phonopy.structure.cells import get_supercell
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
import StringIO
dataset = force_sets.get_data_sets3()
supercell = get_supercell(phonopy_bulk_from_structure(structure),
parameters_data.dict.supercell,
symprec=parameters_data.dict.symmetry_precision)
w = StringIO.StringIO()
w.write("natom: %d\n" % dataset['natom'])
num_first = len(dataset['first_atoms'])
w.write("num_first_displacements: %d\n" % num_first)
if 'cutoff_distance' in dataset:
w.write("cutoff_distance: %f\n" % dataset['cutoff_distance'])
num_second = 0
num_disp_files = 0
for d1 in dataset['first_atoms']:
num_disp_files += 1
num_second += len(d1['second_atoms'])
for d2 in d1['second_atoms']:
if 'included' in d2:
if d2['included']:
num_disp_files += 1
else:
num_disp_files += 1
w.write("num_second_displacements: %d\n" % num_second)
w.write("num_displacements_created: %d\n" % num_disp_files)
w.write("first_atoms:\n")
count1 = 1
count2 = num_first + 1
for disp1 in dataset['first_atoms']:
disp_cart1 = disp1['displacement']
w.write("- number: %5d\n" % (disp1['number'] + 1))
w.write(" displacement:\n")
w.write(" [%20.16f,%20.16f,%20.16f ] # %05d\n" %
(disp_cart1[0], disp_cart1[1], disp_cart1[2], count1))
w.write(" second_atoms:\n")
count1 += 1
included = None
distance = 0.0
atom2 = -1
for disp2 in disp1['second_atoms']:
if atom2 != disp2['number']:
atom2 = disp2['number']
if 'included' in disp2:
included = disp2['included']
pair_distance = disp2['pair_distance']
w.write(" - number: %5d\n" % (atom2 + 1))
w.write(" distance: %f\n" % pair_distance)
if included is not None:
if included:
w.write(" included: %s\n" % "true")
else:
w.write(" included: %s\n" % "false")
w.write(" displacements:\n")
disp_cart2 = disp2['displacement']
w.write(" - [%20.16f,%20.16f,%20.16f ] # %05d\n" %
(disp_cart2[0], disp_cart2[1], disp_cart2[2], count2))
count2 += 1
write_cell_yaml(w, supercell)
w.seek(0)
lines = w.read()
w.close()
return lines
################################
wc = load_node(int(sys.argv[1]))
################################
# get phono3py data from database
force_sets = wc.out.force_sets
structure = wc.out.final_structure
ph_settings = wc.inp.ph_settings
# If modifications in phonon parameters are necessary
ph_settings_dict = ph_settings.get_dict()
ph_settings_dict['mesh'] = [40, 40, 40]
ph_settings = ParameterData(dict=ph_settings_dict)
# Create phono3py and calculate as usual
phono3py = Phono3py(phonopy_bulk_from_structure(structure),
supercell_matrix=ph_settings.dict.supercell,
primitive_matrix=ph_settings.dict.primitive,
symprec=ph_settings.dict.symmetry_precision,
mesh=ph_settings.dict.mesh,
log_level=1)
phono3py.produce_fc3(force_sets.get_forces3(),
displacement_dataset=force_sets.get_data_sets3(),
is_translational_symmetry=True,
is_permutation_symmetry=True,
is_permutation_symmetry_fc2=True)
fc3 = phono3py.get_fc3()
fc2 = phono3py.get_fc2()
if len(sys.argv) < 2:
print('use: python get_phonon3py_inputs.py {pk_number}')
exit()
# Set WorkChain phonon3 PK number
################################
wc = load_node(int(sys.argv[1]))
################################
# get phono3py data from database
force_sets = wc.out.force_sets
structure = wc.out.final_structure
ph_settings = wc.inp.ph_settings
supercell = get_supercell(phonopy_bulk_from_structure(structure),
ph_settings.dict.supercell,
symprec=ph_settings.dict.symmetry_precision)
write_disp_fc3_yaml(force_sets.get_data_sets3(),
supercell,
filename='disp_fc3.yaml')
write_FORCES_FC3(force_sets.get_data_sets3(),
force_sets.get_forces3(),
filename='FORCES_FC3')
with open('POSCAR-unitcell', mode='w') as f:
f.writelines(get_poscar_txt(structure))
if 'nac_data' in wc.get_outputs_dict():
mode_kappa = wc.out.kappa.get_array('mode_kappa')[:]
mesh = wc.out.kappa.get_array('mesh')
qpoint = wc.out.kappa.get_array('qpoint')
print mode_kappa.shape
structure = wc.out.final_structure
from phono3py.phonon3.triplets import (get_ir_grid_points,
get_grid_points_by_rotations,
get_grid_address,
from_coarse_to_dense_grid_points)
# May change
grid_address = get_grid_address(mesh)
ir_grid_points = np.arange(np.prod(mesh), dtype='intc')
grid_mapping_table = np.arange(np.prod(mesh), dtype='intc')
from aiida_phonopy.workchains.phonon import phonopy_bulk_from_structure
kappados = KappaDOS(mode_kappa=mode_kappa,
cell=phonopy_bulk_from_structure(structure),
frequencies=frequency,
mesh=mesh,
grid_address=grid_address,
ir_grid_points=ir_grid_points,
grid_mapping_table=grid_mapping_table,
num_sampling_points=100)
print kappados.get_kdos()