def get_force_constants(phonon_origin, gruneisen, commensurate, volumes):
from phonopy.harmonic.dynmat_to_fc import DynmatToForceConstants
from phonopy.units import VaspToTHz
from copy import deepcopy
phonon = deepcopy(phonon_origin)
phonon.set_qpoints_phonon(commensurate,
is_eigenvectors=True)
frequencies, eigenvectors = phonon.get_qpoints_phonon()
primitive = phonon.get_primitive()
supercell = phonon.get_supercell()
dynmat2fc = DynmatToForceConstants(primitive, supercell)
volume_ref = phonon.get_unitcell().get_volume()
force_constants_list = []
for volume in volumes:
renormalized_frequencies = []
for freq, g in zip(frequencies, gruneisen):
renormalized_frequencies.append(freq + (freq * (np.exp(-g*np.log(volume/volume_ref))-1)))
renormalized_frequencies = np.array(renormalized_frequencies)
# Fixing Gamma point data
renormalized_frequencies[0][0:3] = [0.0, 0.0, 0.0]
dynmat2fc.set_dynamical_matrices(renormalized_frequencies / VaspToTHz, eigenvectors)
dynmat2fc.run()
force_constants_list.append(np.array(dynmat2fc.get_force_constants()))
return force_constants_list
def get_renormalized_force_constants(renormalized_frequencies, eigenvectors, structure, fc_supercell, symmetrize=False):
phonon = get_phonon(structure, setup_forces=False, custom_supercell=fc_supercell)
primitive = phonon.get_primitive()
supercell = phonon.get_supercell()
dynmat2fc = DynmatToForceConstants(primitive, supercell)
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)
try:
dynmat2fc.set_dynamical_matrices(renormalized_frequencies / VaspToTHz, eigenvectors)
except TypeError:
dynmat2fc.create_dynamical_matrices(frequencies=renormalized_frequencies / VaspToTHz,
eigenvalues=None,
eigenvectors=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
def get_renormalized_force_constants(renormalized_frequencies, eigenvectors, structure, fc_supercell, symmetrize=False):
phonon = get_phonon(structure, setup_forces=False, custom_supercell=fc_supercell)
primitive = phonon.get_primitive()
supercell = phonon.get_supercell()
dynmat2fc = DynmatToForceConstants(primitive, supercell)
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
def _set_Gonze_force_constants(self):
d2f = DynmatToForceConstants(self._pcell,
self._scell,
symprec=self._symprec)
dynmat = []
num_q = len(d2f.get_commensurate_points())
for i, q_red in enumerate(d2f.get_commensurate_points()):
if self._log_level > 1:
print("%d/%d %s" % (i + 1, num_q, q_red))
self._set_dynamical_matrix(q_red)
dm_dd = self._get_Gonze_dipole_dipole(q_red, None)
self._dynamical_matrix -= dm_dd
dynmat.append(self._dynamical_matrix)
d2f.set_dynamical_matrices(dynmat=dynmat)
d2f.run()
self._Gonze_force_constants = d2f.get_force_constants()
def _set_Gonze_force_constants(self):
d2f = DynmatToForceConstants(self._pcell,
self._scell,
symprec=self._symprec)
self._force_constants = self._bare_force_constants
dynmat = []
num_q = len(d2f.get_commensurate_points())
for i, q_red in enumerate(d2f.get_commensurate_points()):
print("%d/%d %s" % (i + 1, num_q, q_red))
self._set_dynamical_matrix(q_red)
dm_dd = self._get_Gonze_dipole_dipole(q_red, None)
self._dynamical_matrix -= dm_dd
dynmat.append(self._dynamical_matrix)
d2f.set_dynamical_matrices(dynmat=dynmat)
d2f.run()
self._Gonze_force_constants = d2f.get_force_constants()
def _set_Gonze_force_constants(self):
fc_shape = self._force_constants.shape
d2f = DynmatToForceConstants(self._pcell,
self._scell,
is_full_fc=(fc_shape[0] == fc_shape[1]),
symprec=self._symprec)
dynmat = []
num_q = len(d2f.get_commensurate_points())
for i, q_red in enumerate(d2f.get_commensurate_points()):
if self._log_level > 2:
print("%d/%d %s" % (i + 1, num_q, q_red))
self._set_dynamical_matrix(q_red)
dm_dd = self._get_Gonze_dipole_dipole(q_red, None)
self._dynamical_matrix -= dm_dd
dynmat.append(self._dynamical_matrix)
d2f.set_dynamical_matrices(dynmat=dynmat)
d2f.run()
self._Gonze_force_constants = d2f.get_force_constants()
def phonopy_merge(**kwargs):
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
from phonopy.units import VaspToTHz
from phonopy.harmonic.dynmat_to_fc import get_commensurate_points, DynmatToForceConstants
structure = kwargs.pop('structure')
phonopy_input = kwargs.pop('phonopy_input').get_dict()
harmonic = kwargs.pop('harmonic')
renormalized = kwargs.pop('renormalized')
eigenvectors = harmonic.get_array('eigenvectors')
frequencies = harmonic.get_array('frequencies')
shifts = renormalized.get_array('shifts')
# 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'])
primitive = phonon.get_primitive()
supercell = phonon.get_supercell()
total_frequencies = frequencies + shifts
dynmat2fc = DynmatToForceConstants(primitive, supercell)
dynmat2fc.set_dynamical_matrices(total_frequencies / VaspToTHz, eigenvectors)
dynmat2fc.run()
total_force_constants = dynmat2fc.get_force_constants()
# Stores DOS data in DB as a workflow result
total_data = ArrayData()
total_data.set_array('force_constants', total_force_constants)
return {'final_results': total_data}
# Start script here
# Workflow phonon (at given volume)
wf = load_workflow(431)
parameters = wf.get_parameters()
results = wf.get_results()
inline_params = {'structure': results['final_structure'],
'phonopy_input': parameters['phonopy_input'],
'force_constants': results['force_constants']}
harmonic = phonopy_commensurate_inline(**inline_params)
# At reference volume (at T = 0)
wf = load_workflow(432)
parameters = wf.get_parameters()
results_r = wf.get_results()
results_h = wf.get_results()
inline_params = {'structure': results_h['final_structure'],
'phonopy_input': parameters['phonopy_input'],
'force_constants': results_h['force_constants'],
'r_force_constants': results_r['r_force_constants']}
renormalized = phonopy_commensurate_shifts_inline(**inline_params)
inline_params = {'structure': results_h['final_structure'],
'phonopy_input': parameters['phonopy_input'],
'harmonic': harmonic,
'renormalized': renormalized}
total = phonopy_merge(**inline_params)
print total
inline_params = {'structure': results_h['final_structure'],
'phonopy_input': parameters['phonopy_input'],
'force_constants': total['force_constants']}
results = phonopy_calculation_inline(**inline_params)[1]
band = results['band_structure']
# Phonon Band structure plot
plot_data(results['band_structure'])
def BuildForceConstants(lattice_vectors, atom_types, atom_pos, q_pts, freqs, eigs, sc_dim, freq_units = 'thz', atom_mass = None, file_path = r"FORCE_CONSTANTS"):
"""
Use the Phonopy API to take a set of frequencies and eigenvectors, construct a dynamical matrix, transform to a set of force constants, and write out a Phonopy FORCE_CONSTANTS file.
Args:
lattice_vectors -- 3x3 matrix containing the lattice vectors
atom_types -- list of atomic symbols
atom_pos -- list of atomic positions ** in fractional coordinates **
q_pts -- list of q-point coordinates
freqs -- n_q sets of Frequencies
eigs -- n_q sets of eigenvectors
sc_dim -- (equivalent) supercell dimension for preparing force constants
freq_units -- units of freqs ('thz' or 'inv_cm' -- default: 'thz')
atom_mass -- (optional) list of atomic masses (default: taken from Phonopy internal database)
file_path -- path to FORCE_CONSTANTS file to write (default: FORCE_CONSTANTS)
"""
# Check input.
_CheckStructure(lattice_vectors, atom_types, atom_pos, atom_mass)
for param in q_pts, freqs, eigs, sc_dim:
assert param is not None
dim_1, dim_2 = np.shape(q_pts)
assert dim_1 > 0 and dim_2 == 3
n_at = len(atom_types)
n_q = dim_1
n_b = 3 * n_at
dim_1, dim_2 = np.shape(freqs)
assert dim_1 == n_q and dim_2 == n_b
dim_1, dim_2, dim_3, dim_4 = np.shape(eigs)
assert dim_1 == n_q and dim_2 == n_b and dim_3 == n_at and dim_4 == 3
dim_1, = np.shape(sc_dim)
assert dim_1 == 3
# Obtain a frequency conversion factor to "VASP units".
freq_conv_factor = None
if freq_units == 'thz':
freq_conv_factor = VaspToTHz
elif freq_units == 'inv_cm':
freq_conv_factor = VaspToCm
if freq_conv_factor is None:
raise Exception("Error: Unknown freq_units '{0}'.".format(freq_units))
# Create a Phonopy-format structure.
structure = PhonopyAtoms(
symbols = atom_types, masses = atom_mass, scaled_positions = atom_pos, cell = lattice_vectors
)
# Convert supercell expansion to a supercell matrix.
dim_1, dim_2, dim_3 = sc_dim
if dim_1 != dim_2 != dim_2 != 1:
warnings.warn("The dynamical matrix -> force constants transform has only been tested at the Gamma point; please report issues to the developer.", RuntimeWarning)
sc_matrix = [[dim_1, 0, 0], [0, dim_2, 0], [0, 0, dim_3]]
# Use the main Phonopy object to obtain the primitive cell and supercell.
calculator = Phonopy(structure, sc_matrix)
primitive = calculator.get_primitive();
supercell = calculator.get_supercell();
# Use the DynmatToForceConstants object to convert frequencies/eigenvectors -> dynamical matrices -> force constants.
dynmat_to_fc = DynmatToForceConstants(primitive, supercell)
commensurate_points = dynmat_to_fc.get_commensurate_points()
# If an input code does not use crystal symmetry or outputs data at all q-points in a sampling mesh, data may be provided for more q-points than there are commensurate points.
# However, for most codes this would be an odd situation -> issue a warning.
if len(commensurate_points) != n_q:
warnings.warn("The number of entries in the q_pts list does not equal the number of commensurate points expected for the supplied supercell matrix.", RuntimeWarning)
# Map commensurate points in Phonopy setup to q-points in input data.
map_indices = []
for qx_1, qy_1, qz_1 in commensurate_points:
map_index = None
for i, (qx_2, qy_2, qz_2) in enumerate(q_pts):
if math.fabs(qx_2 - qx_1) < _SymPrec and math.fabs(qy_2 - qy_1) < _SymPrec and math.fabs(qz_2 - qz_1) < _SymPrec:
map_index = i
break
if map_index is None:
raise Exception("Error: Expected q = ({0: >6.3f}, {1: >6.3f}, {2: >6.3f}) in the q_pts list (this may be a bug; please report to the developer).".format(qx_1, qy_1, qz_1))
# Sanity check.
assert map_index not in map_indices
map_indices.append(map_index)
# Arrange the frequencies and eigenvectors to the layout required by Phonopy.
freq_sets, eig_sets = [], []
for index in map_indices:
freq_sets.append(
[freq / freq_conv_factor for freq in freqs[index]]
)
eig = eigs[index]
# Eigenvectors need to be a 3Nx3N matrix in the format:
# 1_x -> [ m_1, ..., m_3N ]
# 1_y -> [ m_1, ..., m_3N ]
# ...
# N_z -> [ m_1, ..., m_3N ]
eig_rows = []
for i in range(0, n_at):
for j in range(0, 3):
eig_row = []
for k in range(0, n_b):
eig_row.append(eig[k][i][j])
eig_rows.append(eig_row)
eig_sets.append(eig_rows)
freq_sets = np.array(freq_sets, dtype = np.float64)
eig_sets = np.array(eig_sets, dtype = np.complex128)
# Use the DynmatToForceConstants object to build the dynamical matrices, reverse transform to the force constants, and write a Phonopy FORCE_CONSTANTS file.
dynmat_to_fc.set_dynamical_matrices(freq_sets, eig_sets)
dynmat_to_fc.run()
write_FORCE_CONSTANTS(
dynmat_to_fc.get_force_constants(), filename = file_path
)
primitive = phonon.get_primitive()
supercell = phonon.get_supercell()
dynmat2fc = DynmatToForceConstants(primitive, supercell)
com_points = dynmat2fc.get_commensurate_points()
print "Commensurate points"
for i, q in enumerate(com_points):
print i + 1, q
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonon.set_qpoints_phonon(com_points,
is_eigenvectors=True)
frequencies, eigenvectors = phonon.get_qpoints_phonon()
dynmat2fc.set_dynamical_matrices(frequencies / VaspToTHz, eigenvectors)
dynmat2fc.run()
fc = dynmat2fc.get_force_constants()
phonon2 = Phonopy(bulk,
[[2, 0, 0],
[0, 2, 0],
[0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
is_auto_displacements=False)
phonon2.set_force_constants(fc)
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
primitive = phonon.get_primitive()
supercell = phonon.get_supercell()
dynmat2fc = DynmatToForceConstants(primitive, supercell)
com_points = dynmat2fc.get_commensurate_points()
print "Commensurate points"
for i, q in enumerate(com_points):
print i + 1, q
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonon.set_qpoints_phonon(com_points, is_eigenvectors=True)
frequencies, eigenvectors = phonon.get_qpoints_phonon()
dynmat2fc.set_dynamical_matrices(frequencies / VaspToTHz, eigenvectors)
dynmat2fc.run()
fc = dynmat2fc.get_force_constants()
phonon2 = Phonopy(bulk, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0]],
is_auto_displacements=False)
phonon2.set_force_constants(fc)
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
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])
phonon2.set_band_structure(bands)
phonon2.plot_band_structure().show()
