def init_dynamical_matrix(
self,
fc2,
supercell,
primitive,
nac_params=None,
decimals=None,
):
"""Prepare for phonon calculation on grid.
solve_dynamical_matrices : bool
When False, phonon calculation will be postponed.
"""
self._nac_params = nac_params
self._dm = get_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=self._frequency_scale_factor,
decimals=decimals,
symprec=self._symprec,
)
self._allocate_phonon()
def init_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
solve_dynamical_matrices=True,
decimals=None,
verbose=False):
self._nac_params = nac_params
self._dm = get_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=self._frequency_scale_factor,
decimals=decimals,
symprec=self._symprec)
if solve_dynamical_matrices:
self.run_phonon_solver(verbose=verbose)
else:
self.run_phonon_solver(np.array([0], dtype='uintp'),
verbose=verbose)
if (self._grid_address[0] == 0).all():
if np.sum(self._frequencies[0] < self._cutoff_frequency) < 3:
for i, f in enumerate(self._frequencies[0, :3]):
if not (f < self._cutoff_frequency):
self._frequencies[0, i] = 0
print("=" * 26 + " Warning " + "=" * 26)
print(" Phonon frequency of band index %d at Gamma "
"is calculated to be %f." % (i + 1, f))
print(" But this frequency is forced to be zero.")
print("=" * 61)
def set_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
frequency_scale_factor=None,
decimals=None):
self._dm = get_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor,
decimals=decimals,
symprec=self._symprec)
self.set_phonons(np.arange(len(self._grid_address), dtype='intc'))
if (self._grid_address[0] == 0).all():
if np.sum(self._frequencies[0] < self._cutoff_frequency) < 3:
for i, f in enumerate(self._frequencies[0, :3]):
if not (f < self._cutoff_frequency):
self._frequencies[0, i] = 0
print("=" * 26 + " Warning " + "=" * 26)
print(" Phonon frequency of band index %d at Gamma "
"is calculated to be %f." % (i + 1, f))
print(" But this frequency is forced to be zero.")
print("=" * 61)
def _set_dynamical_matrix(self):
self._dm = get_dynamical_matrix(
self._fc2,
self._supercell,
self._primitive,
nac_params=self._nac_params,
frequency_scale_factor=self._frequency_scale_factor,
symprec=self._symprec)
def _init_dynamical_matrix(self):
self._dm = get_dynamical_matrix(
self._fc2,
self._supercell,
self._primitive,
nac_params=self._nac_params,
frequency_scale_factor=self._frequency_scale_factor,
symprec=self._symprec)
def __init__(
self,
fc2,
fc3,
supercell,
primitive,
nac_params=None,
nac_q_direction=None,
ion_clamped=False,
factor=VaspToTHz,
symprec=1e-5,
):
"""Init method."""
self._fc2 = fc2
self._fc3 = fc3
self._scell = supercell
self._pcell = primitive
self._ion_clamped = ion_clamped
self._factor = factor
self._symprec = symprec
self._dm = get_dynamical_matrix(
self._fc2,
self._scell,
self._pcell,
nac_params=nac_params,
symprec=self._symprec,
)
self._nac_q_direction = nac_q_direction
svecs, multi = self._pcell.get_smallest_vectors()
if self._pcell.store_dense_svecs:
self._svecs = svecs
self._multi = multi
else:
self._svecs, self._multi = sparse_to_dense_svecs(svecs, multi)
if self._ion_clamped:
num_atom_prim = self._pcell.get_number_of_atoms()
self._X = np.zeros((num_atom_prim, 3, 3, 3), dtype=float)
else:
self._X = self._get_X()
self._dPhidu = self._get_dPhidu()
self._gruneisen_parameters = None
self._frequencies = None
self._qpoints = None
self._mesh = None
self._band_paths = None
self._band_distances = None
self._run_mode = None
self._weights = None
def set_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
frequency_scale_factor=None,
decimals=None):
self._dm = get_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor,
decimals=decimals,
symprec=self._symprec)
def set_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
frequency_scale_factor=None,
decimals=None):
self._dm = get_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor,
decimals=decimals,
symprec=self._symprec)
def init_dynamical_matrix(
self,
fc2,
supercell,
primitive,
nac_params=None,
frequency_scale_factor=None,
decimals=None,
):
"""Initialize dynamical matrix."""
self._primitive = primitive
self._dm = get_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor,
decimals=decimals,
symprec=self._symprec,
)
def __init__(self,
supercell,
primitive,
force_constants,
dist_func=None,
cutoff_frequency=None,
factor=VaspToTHz):
"""
Parameters
----------
supercell : Supercell
Supercell.
primitive : Primitive
Primitive cell
force_constants : array_like
Force constants matrix. See the details at docstring of
DynamialMatrix.
dist_func : str or None
Harmonic oscillator distribution function either by 'quantum'
or 'classical'. The starndard deviation of normal distribution
is determined following the choice. Default is None, corresponding
to 'quantum'.
cutoff_frequency : float
Lowest phonon frequency below which frequency the phonon mode
is treated specially. See _get_sigma. Default is None, which
means 0.01.
factor : float
Phonon frequency unit conversion factor to THz
"""
if cutoff_frequency is None or cutoff_frequency < 0:
self._cutoff_frequency = 0.01
else:
self._cutoff_frequency = cutoff_frequency
self._factor = factor
self._T = None
self.u = None
if dist_func is None or dist_func == 'quantum':
self._dist_func = 'quantum'
elif dist_func == 'classical':
self._dist_func = 'classical'
else:
raise RuntimeError("Either 'quantum' or 'classical' is required.")
self._unit_conversion = (Hbar * EV / AMU / THz / (2 * np.pi) /
Angstrom**2)
self._unit_conversion_classical = (Kb * EV / AMU / (THz *
(2 * np.pi))**2 /
Angstrom**2)
# Dynamical matrix without NAC because of commensurate points only
self._dynmat = get_dynamical_matrix(force_constants, supercell,
primitive)
self._setup_sampling_qpoints(supercell.cell, primitive.cell)
s2p = primitive.s2p_map
p2p = primitive.p2p_map
self._s2pp = [p2p[i] for i in s2p]
self._eigvals_ii = []
self._eigvecs_ii = []
self._phase_ii = []
self._eigvals_ij = []
self._eigvecs_ij = []
self._phase_ij = []
self._prepare()
# This is set when running run_d2f.
# The aim is to produce force constants from modified frequencies.
self._force_constants = None
def __init__(self,
supercell,
primitive,
force_constants,
cutoff_frequency=None,
factor=VaspToTHz):
"""
Parameters
----------
supercell : Supercell
Supercell.
primitive : Primitive
Primitive cell
force_constants : array_like
Force constants matrix. See the details at docstring of
DynamialMatrix.
cutoff_frequency : float
Lowest phonon frequency below which frequency the phonon mode
is treated specially. See _get_sigma. Default is None, which
means 0.01.
factor : float
Phonon frequency unit conversion factor to THz
"""
# Dynamical matrix without NAC because of commensurate points only
self._dynmat = get_dynamical_matrix(force_constants, supercell,
primitive)
if cutoff_frequency is None or cutoff_frequency < 0:
self._cutoff_frequency = 0.01
else:
self._cutoff_frequency = cutoff_frequency
self._factor = factor
self._T = None
self.u = None
self._unit_conversion = (Hbar * EV / AMU / THz / (2 * np.pi) /
Angstrom**2)
slat = supercell.cell
self._rec_lat = np.linalg.inv(primitive.cell)
smat = np.rint(np.dot(slat, self._rec_lat).T).astype(int)
self._comm_points = get_commensurate_points_in_integers(smat)
self._ii, self._ij = self._categorize_points()
assert len(self._ii) + len(self._ij) * 2 == len(self._comm_points)
s2p = primitive.s2p_map
p2p = primitive.p2p_map
self._s2pp = [p2p[i] for i in s2p]
self._eigvals_ii = []
self._eigvecs_ii = []
self._phase_ii = []
self._eigvals_ij = []
self._eigvecs_ij = []
self._phase_ij = []
self._prepare()
# This is set when running run_d2f.
# The aim is to produce force constants from modified frequencies.
self._force_constants = None