def setUp(self):
self.structure = io.read_from_file_structure_poscar('Si_data/POSCAR')
self.structure.set_primitive_matrix([[0.0, 0.5, 0.5], [0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
self.structure.set_force_constants(
get_force_constants_from_file(file_name='Si_data/FORCE_CONSTANTS',
fc_supercell=[[2, 0, 0], [0, 2, 0],
[0, 0, 2]]))
def setUp(self):
structure = io.read_from_file_structure_poscar('MgO_data/POSCAR')
structure.set_primitive_matrix([[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
structure.set_force_constants(get_force_constants_from_file(file_name='MgO_data/FORCE_CONSTANTS',
fc_supercell=[[2, 0, 0],
[0, 2, 0],
[0, 0, 2]]))
trajectory = io.generate_test_trajectory(structure, supercell=[2, 2, 2], total_time=5, silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
def setUp(self):
self.structure = io.read_from_file_structure_poscar('GaN_data/POSCAR')
self.structure.set_primitive_matrix([[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
self.structure.set_force_constants(get_force_constants_from_file(file_name='GaN_data/FORCE_CONSTANTS',
fc_supercell=[[3, 0, 0],
[0, 3, 0],
[0, 0, 3]]))
if not os.path.exists('test_gan.h5'):
trajectory = io.generate_test_trajectory(self.structure, supercell=[3, 3, 3], total_time=8, silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.save_velocity_hdf5('test_gan.h5', save_trajectory=True)
def setUp(self):
self.structure = io.read_from_file_structure_poscar('GaN_data/POSCAR')
self.structure.set_force_constants(
parse_FORCE_CONSTANTS(filename='GaN_data/FORCE_CONSTANTS'))
self.structure.set_primitive_matrix([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
self.structure.set_supercell_phonon([[3, 0, 0], [0, 3, 0], [0, 0, 3]])
if not os.path.exists('test_gan.h5'):
trajectory = io.generate_test_trajectory(self.structure,
supercell=[3, 3, 3],
total_time=8,
silent=False)
self.calculation = dynaphopy.Quasiparticle(trajectory)
self.calculation.save_velocity_hdf5('test_gan.h5',
save_trajectory=True)
#!/usr/bin/env python
import numpy as np
import phonopy.file_IO as file_IO
import dynaphopy.interface.iofile as reading
import dynaphopy.classes.controller as controller
################################## STRUCTURE FILES #######################################
# 1. Set the directory in where the FORCE_SETS and structure OUTCAR are placed
# FORCE_SETS : force set file obtained from PHONOPY calculation
# OUTCAR : Single Point calculation of the unit cell structure used in PHONOPY calculation
directory ='/home/abel/VASP/Si-phonon/4x4x4B/'
structure = reading.read_from_file_structure_poscar(directory+'POSCAR')
structure.set_force_set(file_IO.parse_FORCE_SETS(filename=directory+'FORCE_SETS'))
############################### PHONOPY CELL INFORMATION ####################################
# 2. Set primitive matrix, this matrix fulfills that:
# Primitive_cell = Unit_cell x Primitive_matrix
# This matrix is the same needed for PHONOPY calculation
structure.set_primitive_matrix([[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]])
# 3. Set super cell phonon, this matrix denotes the super cell used in PHONOPY for creating
# the finite displacements
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)
#!/usr/bin/env python
import numpy as np
import phonopy.file_IO as file_IO
import dynaphopy.interface.iofile as io
import dynaphopy.interface.iofile.trajectory_parsers as parsers
import dynaphopy
from dynaphopy.interface.phonopy_link import get_force_sets_from_file, get_force_constants_from_file
################################## STRUCTURE FILES #######################################
# 1. Set the directory in where the FORCE_SETS and structure POSCAR are placed
directory = '/home/abel/VASP/Si/Si-FINAL3/PHONON/2x2x2/'
structure = io.read_from_file_structure_poscar(directory + 'POSCAR')
############################### PHONOPY CELL INFORMATION ####################################
# 2. Set primitive matrix that defines the primitive cell respect the unit cell
structure.set_primitive_matrix([[0.0, 0.5, 0.5], [0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
# 3. Set the hamonic phonon data (input for phonopy)
# fs_supercell: supercell matrix used in PHONOPY to obtain the force_sets
# FORCE_SETS : force set file obtained from PHONOPY calculation that contains the forces
structure.set_force_set(
get_force_sets_from_file(file_name=directory + 'FORCE_SETS',
fs_supercell=[[2, 0, 0], [0, 2, 0], [0, 0, 2]]))
# Alternatively get_force_constants_from_file function can be used to obtain the harmonic information.
# Check unittest files (unittest folder)
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)
