def __init__(self,
fc4,
supercell,
primitive,
mesh,
temperatures=None,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo='L'):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._masses = np.double(self._primitive.get_masses())
self._mesh = np.intc(mesh)
if temperatures is None:
self._temperatures = np.double([0])
else:
self._temperatures = np.double(temperatures)
num_band = primitive.get_number_of_atoms() * 3
if band_indices is None:
self._band_indices = np.arange(num_band, dtype='intc')
else:
self._band_indices = np.intc(band_indices)
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
symmetry = Symmetry(primitive, symprec=symprec)
self._point_group_operations = symmetry.get_pointgroup_operations()
self._grid_address = get_grid_address(mesh)
self._grid_point = None
self._quartets_at_q = None
self._weights_at_q = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._dm = None
self._nac_q_direction = None
self._frequency_shifts = None
# Unit to THz of Gamma
self._unit_conversion = (EV / Angstrom**4 / AMU**2 /
(2 * np.pi * THz)**2 * Hbar * EV /
(2 * np.pi * THz) / 8 /
len(self._grid_address))
def __init__(self,
fc4,
supercell,
primitive,
mesh,
temperatures=None,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo='L'):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._masses = np.double(self._primitive.get_masses())
self._mesh = np.intc(mesh)
if temperatures is None:
self._temperatures = np.double([0])
else:
self._temperatures = np.double(temperatures)
num_band = primitive.get_number_of_atoms() * 3
if band_indices is None:
self._band_indices = np.arange(num_band, dtype='intc')
else:
self._band_indices = np.intc(band_indices)
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
symmetry = Symmetry(primitive, symprec=symprec)
self._point_group_operations = symmetry.get_pointgroup_operations()
self._grid_address = get_grid_address(mesh)
self._grid_point = None
self._quartets_at_q = None
self._weights_at_q = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._dm = None
self._nac_q_direction = None
self._frequency_shifts = None
# Unit to THz of Gamma
self._unit_conversion = (EV / Angstrom ** 4 / AMU ** 2
/ (2 * np.pi * THz) ** 2
* Hbar * EV / (2 * np.pi * THz) / 8
/ len(self._grid_address))
def get_linewidth_at_paths(self,
ise,
sigmas,
temperatures,
band_paths,
is_nu,
scattering_class=None,
filename=None):
if self._is_nosym:
grid_address, grid_mapping =get_grid_address([x + (x % 2 == 0) for x in self._mesh], is_return_map=True)
else:
grids, weights, grid_address, grid_mapping = get_ir_grid_points([x + (x % 2 == 0) for x in self._mesh],
self._primitive,
is_return_map=True)
qpoints_address=grid_address / np.array(self._mesh, dtype=float)
print "Paths in reciprocal reduced coordinates:"
for sigma in sigmas:
self._sigma = sigma
lws_paths=[]
distances=[]
frequencies=[]
new_paths = []
for path in band_paths:
print "[%5.2f %5.2f %5.2f] --> [%5.2f %5.2f %5.2f]" % (tuple(path[0]) + tuple(path[-1]))
(new_path,
dists,
freqs,
lws)=self.path(path,
qpoints_address,
grid_mapping,
ise,
temperatures,
scattering_class)
new_paths.append(new_path)
distances.append(dists)
frequencies.append(freqs)
lws_paths.append(lws)
self._distances=distances
self._freqs_on_path=frequencies
self._lws_on_path=lws_paths
write_linewidth_band_csv(self._mesh,
new_paths,
distances=self._distances,
lws=self._lws_on_path,
band_indices=self._band_indices,
temperatures=temperatures,
frequencies=self._freqs_on_path,
scattering_class=scattering_class,
nu=is_nu,
filename=(("-s%s"%sigma) if sigma is not None else ""))
self.plot_lw()
def get_linewidth_at_paths(self,
ise,
sigmas,
temperatures,
band_paths,
is_nu,
scattering_class=None,
filename=None):
if self._is_nosym:
grid_address, grid_mapping = get_grid_address(
[x + (x % 2 == 0) for x in self._mesh], is_return_map=True)
else:
grids, weights, grid_address, grid_mapping = get_ir_grid_points(
[x + (x % 2 == 0) for x in self._mesh],
self._primitive,
is_return_map=True)
qpoints_address = grid_address / np.array(self._mesh, dtype=float)
print "Paths in reciprocal reduced coordinates:"
for sigma in sigmas:
self._sigma = sigma
lws_paths = []
distances = []
frequencies = []
new_paths = []
for path in band_paths:
print "[%5.2f %5.2f %5.2f] --> [%5.2f %5.2f %5.2f]" % (
tuple(path[0]) + tuple(path[-1]))
(new_path, dists, freqs,
lws) = self.path(path, qpoints_address, grid_mapping, ise,
temperatures, scattering_class)
new_paths.append(new_path)
distances.append(dists)
frequencies.append(freqs)
lws_paths.append(lws)
self._distances = distances
self._freqs_on_path = frequencies
self._lws_on_path = lws_paths
write_linewidth_band_csv(
self._mesh,
new_paths,
distances=self._distances,
lws=self._lws_on_path,
band_indices=self._band_indices,
temperatures=temperatures,
frequencies=self._freqs_on_path,
scattering_class=scattering_class,
nu=is_nu,
filename=(("-s%s" % sigma) if sigma is not None else ""))
self.plot_lw()
def _set_grid_properties(self, grid_points):
self._grid_address = self._pp.get_grid_address()
if grid_points is not None: # Specify grid points
self._grid_points = reduce_grid_points(
self._mesh_divisors,
self._grid_address,
grid_points,
coarse_mesh_shifts=self._coarse_mesh_shifts)
(self._ir_grid_points,
self._ir_grid_weights) = self._get_ir_grid_points()
elif self._no_kappa_stars: # All grid points
coarse_grid_address = get_grid_address(self._coarse_mesh)
coarse_grid_points = np.arange(np.prod(self._coarse_mesh),
dtype='intc')
self._grid_points = from_coarse_to_dense_grid_points(
self._mesh,
self._mesh_divisors,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=self._coarse_mesh_shifts)
self._grid_weights = np.ones(len(self._grid_points), dtype='intc')
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
else: # Automatic sampling
self._grid_points, self._grid_weights = self._get_ir_grid_points()
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
self._qpoints = np.array(self._grid_address[self._grid_points] /
self._mesh.astype('double'),
dtype='double',
order='C')
self._grid_point_count = 0
self._pp.set_phonons(self._grid_points)
self._frequencies = self._pp.get_phonons()[0][self._grid_points]
self._eigen_vectors = self._pp.get_phonons()[1][self._grid_points]
self._degeneracies = self._pp.get_degeneracy()[self._grid_points]
if self._write_tecplot:
self._dim = np.count_nonzero(np.array(self._mesh) > 1)
#only dim=2 or 3 are implemented
assert self._dim > 1, "The dimention of the given system is %d, but only dim=2 or 3 are implemented" % self._dim
self.set_bz_grid_points()
self.tetrahedra_specify()
def set_grid_point(self, grid_point):
self._grid_point = grid_point
num_band = self._primitive.get_number_of_atoms() * 3
if self._band_indices is None:
self._band_indices = np.arange(num_band, dtype='intc')
else:
self._band_indices = np.array(self._band_indices, dtype='intc')
self._grid_points = np.arange(np.prod(self._mesh), dtype='intc')
if self._grid_address is None:
primitive_lattice = np.linalg.inv(self._primitive.get_cell())
self._grid_address = get_grid_address(self._mesh)
# self._grid_address, self._bz_map = get_bz_grid_address(
# self._mesh, primitive_lattice, with_boundary=True)
if self._phonon_done is None:
self._allocate_phonon()
def _set_grid_properties(self, grid_points):
self._grid_address = self._pp.get_grid_address()
if grid_points is not None: # Specify grid points
self._grid_points = reduce_grid_points(
self._mesh_divisors,
self._grid_address,
grid_points,
coarse_mesh_shifts=self._coarse_mesh_shifts)
(self._ir_grid_points,
self._ir_grid_weights) = self._get_ir_grid_points()
elif self._no_kappa_stars: # All grid points
coarse_grid_address = get_grid_address(self._coarse_mesh)
coarse_grid_points = np.arange(np.prod(self._coarse_mesh),
dtype='intc')
self._grid_points = from_coarse_to_dense_grid_points(
self._mesh,
self._mesh_divisors,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=self._coarse_mesh_shifts)
self._grid_weights = np.ones(len(self._grid_points), dtype='intc')
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
else: # Automatic sampling
self._grid_points, self._grid_weights = self._get_ir_grid_points()
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
self._qpoints = np.array(self._grid_address[self._grid_points] /
self._mesh.astype('double'),
dtype='double',
order='C')
self._grid_point_count = 0
self._pp.set_phonon(self._grid_points)
self._frequencies = self._pp.get_phonons()[0]
def _set_grid_properties(self, grid_points):
self._grid_address = self._pp.get_grid_address()
if grid_points is not None: # Specify grid points
self._grid_points = reduce_grid_points(
self._mesh_divisors,
self._grid_address,
grid_points,
coarse_mesh_shifts=self._coarse_mesh_shifts)
(self._ir_grid_points,
self._ir_grid_weights) = self._get_ir_grid_points()
elif self._no_kappa_stars: # All grid points
coarse_grid_address = get_grid_address(self._coarse_mesh)
coarse_grid_points = np.arange(np.prod(self._coarse_mesh),
dtype='intc')
self._grid_points = from_coarse_to_dense_grid_points(
self._mesh,
self._mesh_divisors,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=self._coarse_mesh_shifts)
self._grid_weights = np.ones(len(self._grid_points), dtype='intc')
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
else: # Automatic sampling
self._grid_points, self._grid_weights = self._get_ir_grid_points()
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
self._qpoints = np.array(self._grid_address[self._grid_points] /
self._mesh.astype('double'),
dtype='double', order='C')
self._grid_point_count = 0
self._pp.set_phonon(self._grid_points)
self._frequencies = self._pp.get_phonons()[0]
def _set_grid_address(self):
grid_address = get_grid_address(self._mesh)
self._grid_address, self._bz_map = spg.relocate_BZ_grid_address(
grid_address, self._mesh,
np.linalg.inv(self._primitive.get_cell()))
def _set_grid_address(self):
grid_address = get_grid_address(self._mesh)
self._grid_address, self._bz_map = spg.relocate_BZ_grid_address(
grid_address,
self._mesh,
np.linalg.inv(self._primitive.get_cell()))