eigenvectors)
dynmat2fc.run()
force_constants = ForceConstants(dynmat2fc.get_force_constants(),
supercell=fc_supercell)
# Symmetrize force constants using crystal symmetry
if symmetrize:
print('Symmetrizing force constants')
set_tensor_symmetry_PJ(force_constants.get_array(),
phonon.supercell.get_cell().T,
phonon.supercell.get_scaled_positions(),
phonon.symmetry)
return force_constants
if __name__ == "__main__":
import dynaphopy.interface.iofile as reading
input_parameters = reading.read_parameters_from_input_file(
'/home/abel/VASP/Ag2Cu2O4/MD/input_dynaphopy')
structure = reading.read_from_file_structure_poscar(
input_parameters['structure_file_name_poscar'])
structure.set_primitive_matrix(input_parameters['_primitive_matrix'])
# structure.set_supercell_phonon(input_parameters['_supercell_phonon'])
structure.set_force_set(
get_force_sets_from_file(
file_name=input_parameters['force_constants_file_name']))
obtain_phonopy_dos(structure)
def __init__(self, args, load_data=False, verbose=False, tmin=None):
input_parameters = reading.read_parameters_from_input_file(args.input_file)
if 'structure_file_name_outcar' in input_parameters:
structure = reading.read_from_file_structure_outcar(input_parameters['structure_file_name_outcar'])
else:
structure = reading.read_from_file_structure_poscar(input_parameters['structure_file_name_poscar'])
structure.get_data_from_dict(input_parameters)
if 'supercell_phonon' in input_parameters:
supercell_phonon = input_parameters['supercell_phonon']
else:
supercell_phonon = np.identity(3)
structure.set_force_constants(get_force_constants_from_file(file_name=input_parameters['force_constants_file_name'],
fc_supercell=supercell_phonon))
if '_mesh_phonopy' in input_parameters:
mesh = input_parameters['_mesh_phonopy']
else:
mesh = [20, 20, 20] # Default
print ('mesh set to: {}'.format(mesh))
if 'bands' in input_parameters is None:
self._bands = structure.get_path_using_seek_path()
else:
self._bands = input_parameters['_band_ranges']
volumes, energies = read_v_e(args.ev, factor=1.0, volume_factor=1.0, pressure=args.pressure)
self._fc_fit = ForceConstantsFitting(structure,
files_temperature=args.ct_data,
files_volume=args.cv_data,
temperatures=args.temperatures,
volumes=volumes,
mesh=mesh,
ref_temperature=args.ref_temperature,
fitting_order=args.order,
tmin=tmin,
use_NAC=True)
if not load_data:
temperatures = self._fc_fit.get_temperature_range()
free_energy = []
entropy = []
cv = []
for v, e in zip(volumes, energies):
print ('Volume: {} Ang. Energy(U): {} eV'.format(v, e))
tp_data = self._fc_fit.get_thermal_properties(volume=v)
free_energy.append(tp_data[0])
entropy.append(tp_data[1])
cv.append(tp_data[2])
free_energy = np.array(free_energy).T
entropy = np.array(entropy).T
cv = np.array(cv).T
np.save('free_energy.npy', free_energy)
np.save('temperatures.npy', temperatures)
np.save('cv.npy', cv)
np.save('entropy.npy', entropy)
else:
free_energy = np.load('free_energy.npy')
temperatures = np.load('temperatures.npy')
cv = np.load('cv.npy')
entropy = np.load('entropy.npy')
self.phonopy_qha = PhonopyQHA(volumes,
energies,
eos="vinet", # options: 'vinet', 'murnaghan' or 'birch_murnaghan'
temperatures=temperatures,
free_energy=free_energy,
cv=cv,
entropy=entropy,
t_max=self.fc_fit.get_temperature_range()[-1],
verbose=False)
# Write data files to disk
self.phonopy_qha.write_bulk_modulus_temperature()
self.phonopy_qha.write_gibbs_temperature()
self.phonopy_qha.write_heat_capacity_P_numerical()
self.phonopy_qha.write_gruneisen_temperature()
self.phonopy_qha.write_thermal_expansion()
self.phonopy_qha.write_helmholtz_volume()
self.phonopy_qha.write_volume_expansion()
self.phonopy_qha.write_volume_temperature()
if verbose:
self.phonopy_qha.plot_qha().show()
def __init__(self, args, load_data=False, verbose=False, tmin=None):
input_parameters = reading.read_parameters_from_input_file(
args.input_file)
if 'structure_file_name_outcar' in input_parameters:
structure = reading.read_from_file_structure_outcar(
input_parameters['structure_file_name_outcar'])
else:
structure = reading.read_from_file_structure_poscar(
input_parameters['structure_file_name_poscar'])
structure.get_data_from_dict(input_parameters)
if 'supercell_phonon' in input_parameters:
supercell_phonon = input_parameters['supercell_phonon']
else:
supercell_phonon = np.identity(3)
structure.set_force_constants(
get_force_constants_from_file(
file_name=input_parameters['force_constants_file_name'],
fc_supercell=supercell_phonon))
if '_mesh_phonopy' in input_parameters:
mesh = input_parameters['_mesh_phonopy']
else:
mesh = [20, 20, 20] # Default
print('mesh set to: {}'.format(mesh))
if 'bands' in input_parameters is None:
self._bands = structure.get_path_using_seek_path()
else:
self._bands = input_parameters['_band_ranges']
volumes, energies = read_v_e(args.ev,
factor=1.0,
volume_factor=1.0,
pressure=args.pressure)
self._fc_fit = ForceConstantsFitting(
structure,
files_temperature=args.ct_data,
files_volume=args.cv_data,
temperatures=args.temperatures,
volumes=volumes,
mesh=mesh,
ref_temperature=args.ref_temperature,
fitting_order=args.order,
tmin=tmin,
use_NAC=True)
if not load_data:
temperatures = self._fc_fit.get_temperature_range()
free_energy = []
entropy = []
cv = []
for v, e in zip(volumes, energies):
print('Volume: {} Ang. Energy(U): {} eV'.format(v, e))
tp_data = self._fc_fit.get_thermal_properties(volume=v)
free_energy.append(tp_data[0])
entropy.append(tp_data[1])
cv.append(tp_data[2])
free_energy = np.array(free_energy).T
entropy = np.array(entropy).T
cv = np.array(cv).T
np.save('free_energy.npy', free_energy)
np.save('temperatures.npy', temperatures)
np.save('cv.npy', cv)
np.save('entropy.npy', entropy)
else:
free_energy = np.load('free_energy.npy')
temperatures = np.load('temperatures.npy')
cv = np.load('cv.npy')
entropy = np.load('entropy.npy')
self.phonopy_qha = PhonopyQHA(
volumes,
energies,
eos="vinet", # options: 'vinet', 'murnaghan' or 'birch_murnaghan'
temperatures=temperatures,
free_energy=free_energy,
cv=cv,
entropy=entropy,
t_max=self.fc_fit.get_temperature_range()[-1],
verbose=False)
# Write data files to disk
self.phonopy_qha.write_bulk_modulus_temperature()
self.phonopy_qha.write_gibbs_temperature()
self.phonopy_qha.write_heat_capacity_P_numerical()
self.phonopy_qha.write_gruneisen_temperature()
self.phonopy_qha.write_thermal_expansion()
self.phonopy_qha.write_helmholtz_volume()
self.phonopy_qha.write_volume_expansion()
self.phonopy_qha.write_volume_temperature()
if verbose:
self.phonopy_qha.plot_qha().show()
size = structure.get_number_of_dimensions() * structure.get_number_of_primitive_atoms()
eigenvectors = np.array([eigenvector.reshape(size, size, order='C').T for eigenvector in eigenvectors ])
renormalized_frequencies = np.array(renormalized_frequencies)
dynmat2fc.set_dynamical_matrices(renormalized_frequencies / VaspToTHz, eigenvectors)
dynmat2fc.run()
force_constants = ForceConstants(dynmat2fc.get_force_constants(), supercell=fc_supercell)
# Symmetrize force constants using crystal symmetry
if symmetrize:
print('Symmetrizing force constants')
set_tensor_symmetry_PJ(force_constants.get_array(),
phonon.supercell.get_cell(),
phonon.supercell.get_scaled_positions(),
phonon.symmetry)
return force_constants
if __name__ == "__main__":
import dynaphopy.interface.iofile as reading
input_parameters = reading.read_parameters_from_input_file('/home/abel/VASP/Ag2Cu2O4/MD/input_dynaphopy')
structure = reading.read_from_file_structure_poscar(input_parameters['structure_file_name_poscar'])
structure.set_primitive_matrix(input_parameters['_primitive_matrix'])
# structure.set_supercell_phonon(input_parameters['_supercell_phonon'])
structure.set_force_set(get_force_sets_from_file(file_name=input_parameters['force_constants_file_name']))
obtain_phonopy_dos(structure)
