def _set_triplets_integration_weights_py(g, interaction, frequency_points):
reciprocal_lattice = np.linalg.inv(interaction.get_primitive().get_cell())
mesh = interaction.get_mesh_numbers()
thm = TetrahedronMethod(reciprocal_lattice, mesh=mesh)
grid_address = interaction.get_grid_address()
bz_map = interaction.get_bz_map()
triplets_at_q = interaction.get_triplets_at_q()[0]
unique_vertices = thm.get_unique_tetrahedra_vertices()
tetrahedra_vertices = get_tetrahedra_vertices(
thm.get_tetrahedra(),
mesh,
triplets_at_q,
grid_address,
bz_map)
interaction.set_phonon(np.unique(tetrahedra_vertices))
frequencies = interaction.get_phonons()[0]
num_band = frequencies.shape[1]
for i, vertices in enumerate(tetrahedra_vertices):
for j, k in list(np.ndindex((num_band, num_band))):
f1_v = frequencies[vertices[0], j]
f2_v = frequencies[vertices[1], k]
thm.set_tetrahedra_omegas(f1_v + f2_v)
thm.run(frequency_points)
g0 = thm.get_integration_weight()
g[0, i, :, j, k] = g0
thm.set_tetrahedra_omegas(-f1_v + f2_v)
thm.run(frequency_points)
g1 = thm.get_integration_weight()
thm.set_tetrahedra_omegas(f1_v - f2_v)
thm.run(frequency_points)
g2 = thm.get_integration_weight()
g[1, i, :, j, k] = g1 - g2
if len(g) == 3:
g[2, i, :, j, k] = g0 + g1 + g2
def _set_triplets_integration_weights_py(g, interaction, frequency_points):
reciprocal_lattice = np.linalg.inv(interaction.get_primitive().get_cell())
mesh = interaction.get_mesh_numbers()
thm = TetrahedronMethod(reciprocal_lattice, mesh=mesh)
grid_address = interaction.get_grid_address()
bz_map = interaction.get_bz_map()
triplets_at_q = interaction.get_triplets_at_q()[0]
unique_vertices = thm.get_unique_tetrahedra_vertices()
tetrahedra_vertices = get_tetrahedra_vertices(thm.get_tetrahedra(), mesh,
triplets_at_q, grid_address,
bz_map)
interaction.set_phonon(np.unique(tetrahedra_vertices))
frequencies = interaction.get_phonons()[0]
num_band = frequencies.shape[1]
for i, vertices in enumerate(tetrahedra_vertices):
for j, k in list(np.ndindex((num_band, num_band))):
f1_v = frequencies[vertices[0], j]
f2_v = frequencies[vertices[1], k]
thm.set_tetrahedra_omegas(f1_v + f2_v)
thm.run(frequency_points)
g0 = thm.get_integration_weight()
g[0, i, :, j, k] = g0
thm.set_tetrahedra_omegas(-f1_v + f2_v)
thm.run(frequency_points)
g1 = thm.get_integration_weight()
thm.set_tetrahedra_omegas(f1_v - f2_v)
thm.run(frequency_points)
g2 = thm.get_integration_weight()
g[1, i, :, j, k] = g1 - g2
if len(g) == 3:
g[2, i, :, j, k] = g0 + g1 + g2
def _set_triplets_integration_weights_py(g, pp, frequency_points):
"""Python version of _set_triplets_integration_weights_c.
Tetrahedron method engine is that implemented in phonopy written mainly in C.
"""
thm = TetrahedronMethod(pp.bz_grid.microzone_lattice)
triplets_at_q = pp.get_triplets_at_q()[0]
tetrahedra_vertices = _get_tetrahedra_vertices(
np.array(np.dot(thm.get_tetrahedra(), pp.bz_grid.P.T), dtype="int_", order="C"),
triplets_at_q,
pp.bz_grid,
)
pp.run_phonon_solver()
frequencies = pp.get_phonons()[0]
num_band = frequencies.shape[1]
for i, vertices in enumerate(tetrahedra_vertices):
for j, k in list(np.ndindex((num_band, num_band))):
f1_v = frequencies[vertices[0], j]
f2_v = frequencies[vertices[1], k]
thm.set_tetrahedra_omegas(f1_v + f2_v)
thm.run(frequency_points)
g0 = thm.get_integration_weight()
g[0, i, :, j, k] = g0
thm.set_tetrahedra_omegas(-f1_v + f2_v)
thm.run(frequency_points)
g1 = thm.get_integration_weight()
thm.set_tetrahedra_omegas(f1_v - f2_v)
thm.run(frequency_points)
g2 = thm.get_integration_weight()
g[1, i, :, j, k] = g1 - g2
if len(g) == 3:
g[2, i, :, j, k] = g0 + g1 + g2
def _run_py_tetrahedron_method(self):
thm = TetrahedronMethod(self._reciprocal_lattice, mesh=self._mesh)
self._vertices = get_tetrahedra_vertices(thm.get_tetrahedra(),
self._mesh,
self._triplets_at_q,
self._grid_address,
self._bz_map)
self.run_phonon_solver(self._vertices.ravel())
f_max = np.max(self._frequencies) * 2
f_max *= 1.005
f_min = 0
self._set_uniform_frequency_points(f_min, f_max)
num_freq_points = len(self._frequency_points)
jdos = np.zeros((num_freq_points, 2), dtype='double')
for vertices, w in zip(self._vertices, self._weights_at_q):
for i, j in list(np.ndindex(self._num_band, self._num_band)):
f1 = self._frequencies[vertices[0], i]
f2 = self._frequencies[vertices[1], j]
thm.set_tetrahedra_omegas(f1 + f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 1] += iw * w
thm.set_tetrahedra_omegas(f1 - f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 0] += iw * w
thm.set_tetrahedra_omegas(-f1 + f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 0] += iw * w
self._joint_dos = jdos / np.prod(self._mesh)
def _run_py_tetrahedron_method(self, is_band_freq=False):
thm = TetrahedronMethod(self._reciprocal_lattice, mesh=self._mesh)
self._vertices = get_tetrahedra_vertices(
thm.get_tetrahedra(),
self._mesh,
self._triplets_at_q,
self._grid_address)
self.set_phonons(self._vertices.ravel())
if is_band_freq:
self._frequency_points = self._frequencies[self._grid_point]
else:
f_max = np.max(self._frequencies) * 2
f_max *= 1.005
f_min = 0
self._set_frequency_points(f_min, f_max)
num_freq_points = len(self._frequency_points)
jdos = np.zeros((num_freq_points, 2), dtype='double')
for vertices, w in zip(self._vertices, self._weights_at_q):
for i, j in list(np.ndindex(self._num_band, self._num_band)):
f1 = self._frequencies[vertices[0], i]
f2 = self._frequencies[vertices[1], j]
thm.set_tetrahedra_omegas(f1 + f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 1] += iw * w
thm.set_tetrahedra_omegas(f1 - f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 0] += iw * w
thm.set_tetrahedra_omegas(-f1 + f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 0] += iw * w
self._joint_dos = jdos / np.prod(self._mesh)
def _set_integration_weights_py(self):
if self._bz_grid.store_dense_gp_map:
raise NotImplementedError("Only for type-I bz_map.")
if self._bz_grid.grid_matrix is not None:
raise NotImplementedError(
"Generalized regular grid is not supported.")
thm = TetrahedronMethod(self._bz_grid.microzone_lattice)
num_grid_points = len(self._grid_points)
num_band = len(self._primitive) * 3
self._integration_weights = np.zeros(
(num_grid_points, len(self._band_indices), num_band),
dtype="double")
for i, gp in enumerate(self._grid_points):
tfreqs = get_tetrahedra_frequencies(
gp,
self._bz_grid.D_diag,
self._bz_grid.addresses,
np.array(
np.dot(thm.get_tetrahedra(), self._bz_grid.P.T),
dtype="int_",
order="C",
),
self._grid_points,
self._frequencies,
grid_order=[
1,
self._bz_grid.D_diag[0],
self._bz_grid.D_diag[0] * self._bz_grid.D_diag[1],
],
lang="Py",
)
for bi, frequencies in enumerate(tfreqs):
thm.set_tetrahedra_omegas(frequencies)
thm.run(self._frequencies[self._grid_point,
self._band_indices])
iw = thm.get_integration_weight()
self._integration_weights[i, :, bi] = iw
class TetrahedronMesh:
def __init__(
self,
cell,
frequencies, # only at ir-grid-points
mesh,
grid_address,
grid_mapping_table,
grid_order=None):
self._cell = cell
self._frequencies = frequencies
self._mesh = mesh
self._grid_address = grid_address
self._grid_mapping_table = grid_mapping_table
if grid_order is None:
self._grid_order = [1, mesh[0], mesh[0] * mesh[1]]
else:
self._grid_order = grid_order
self._ir_grid_points = None
self._gp_ir_index = None
self._tm = None
self._tetrahedra_frequencies = None
self._integration_weights = None
self._relative_grid_address = None
self._prepare()
def get_integration_weights(self):
return self._integration_weights
def get_frequency_points(self):
return self._frequency_points
def run_at_frequencies(self,
value='I',
division_number=201,
frequency_points=None):
if frequency_points is None:
max_frequency = np.amax(self._frequencies)
min_frequency = np.amin(self._frequencies)
self._frequency_points = np.linspace(min_frequency, max_frequency,
division_number)
else:
self._frequency_points = frequency_points
num_ir_grid_points = len(self._ir_grid_points)
num_band = self._cell.get_number_of_atoms() * 3
num_freqs = len(self._frequency_points)
self._integration_weights = np.zeros(
(num_freqs, num_band, num_ir_grid_points), dtype='double')
reciprocal_lattice = np.linalg.inv(self._cell.get_cell())
self._tm = TetrahedronMethod(reciprocal_lattice, mesh=self._mesh)
self._relative_grid_address = self._tm.get_tetrahedra()
for i, gp in enumerate(self._ir_grid_points):
self._set_tetrahedra_frequencies(gp)
for ib, frequencies in enumerate(self._tetrahedra_frequencies):
self._tm.set_tetrahedra_omegas(frequencies)
self._tm.run(self._frequency_points, value=value)
iw = self._tm.get_integration_weight()
self._integration_weights[:, ib, i] = iw
self._integration_weights /= np.prod(self._mesh)
def _prepare(self):
(self._ir_grid_points,
ir_grid_weights) = extract_ir_grid_points(self._grid_mapping_table)
ir_gp_indices = {}
for i, gp in enumerate(self._ir_grid_points):
ir_gp_indices[gp] = i
self._gp_ir_index = np.zeros_like(self._grid_mapping_table)
for i, gp in enumerate(self._grid_mapping_table):
self._gp_ir_index[i] = ir_gp_indices[gp]
def _set_tetrahedra_frequencies(self, gp):
self._tetrahedra_frequencies = get_tetrahedra_frequencies(
gp, self._mesh, self._grid_order, self._grid_address,
self._relative_grid_address, self._gp_ir_index, self._frequencies)
class TetrahedronMesh:
def __init__(self, mesh_object):
self._mesh_object = mesh_object
self._grid_address = None
self._grid_order = None
self._ir_grid_points = None
self._ir_grid_weights = None
self._gp_ir_index = None
self._cell = None
self._frequencies = None
self._eigenvalues = None
self._eigenvectors = None
self._tm = None
self._tetrahedra_frequencies = None
self._integration_weights = None
self._relative_grid_address = None
self._total_dos = None
self._partial_dos = None
self._prepare()
def get_total_dos(self):
return self._total_dos
def get_partial_dos(self):
return self._partial_dos
def get_integration_weights(self):
return self._integration_weights
def get_frequency_points(self):
return self._frequency_points
def run_at_frequencies(self,
value='I',
division_number=201,
frequency_points=None):
if frequency_points is None:
max_frequency = np.amax(self._frequencies)
min_frequency = np.amin(self._frequencies)
self._frequency_points = np.linspace(min_frequency,
max_frequency,
division_number)
else:
self._frequency_points = frequency_points
num_ir_grid_points = len(self._ir_grid_points)
num_band = self._cell.get_number_of_atoms() * 3
num_freqs = len(self._frequency_points)
self._integration_weights = np.zeros(
(num_freqs, num_band, num_ir_grid_points), dtype='double')
reciprocal_lattice = np.linalg.inv(self._cell.get_cell())
self._tm = TetrahedronMethod(reciprocal_lattice, mesh=self._mesh)
self._relative_grid_address = self._tm.get_tetrahedra()
for i, gp in enumerate(self._ir_grid_points):
self._set_tetrahedra_frequencies(gp)
for ib, frequencies in enumerate(self._tetrahedra_frequencies):
self._tm.set_tetrahedra_omegas(frequencies)
self._tm.run(self._frequency_points, value=value)
iw = self._tm.get_integration_weight()
self._integration_weights[:, ib, i] = iw
self._integration_weights /= np.prod(self._mesh)
def _prepare(self):
mo = self._mesh_object
self._cell = mo.get_dynamical_matrix().get_primitive()
self._mesh = mo.get_mesh_numbers()
self._grid_address = mo.get_grid_address()
self._ir_grid_points = mo.get_ir_grid_points()
self._ir_grid_weights = mo.get_weights()
self._grid_order = [1, self._mesh[0], self._mesh[0] * self._mesh[1]]
grid_mapping_table = mo.get_grid_mapping_table()
self._gp_ir_index = np.zeros_like(grid_mapping_table)
count = 0
for i, gp in enumerate(grid_mapping_table):
if i == gp:
self._gp_ir_index[i] = count
count += 1
else:
self._gp_ir_index[i] = self._gp_ir_index[grid_mapping_table[i]]
self._frequencies = mo.get_frequencies()
self._eigenvectors = mo.get_eigenvectors()
def _set_tetrahedra_frequencies(self, gp):
self._tetrahedra_frequencies = get_tetrahedra_frequencies(
gp,
self._mesh,
self._grid_order,
self._grid_address,
self._relative_grid_address,
self._gp_ir_index,
self._frequencies)
class TetrahedronMesh:
def __init__(self,
cell,
frequencies, # only at ir-grid-points
mesh,
grid_address,
grid_mapping_table,
grid_order=None):
self._cell = cell
self._frequencies = frequencies
self._mesh = mesh
self._grid_address = grid_address
self._grid_mapping_table = grid_mapping_table
if grid_order is None:
self._grid_order = [1, mesh[0], mesh[0] * mesh[1]]
else:
self._grid_order = grid_order
self._ir_grid_points = None
self._gp_ir_index = None
self._tm = None
self._tetrahedra_frequencies = None
self._integration_weights = None
self._relative_grid_address = None
self._prepare()
def get_integration_weights(self):
return self._integration_weights
def get_frequency_points(self):
return self._frequency_points
def run_at_frequencies(self,
value='I',
division_number=201,
frequency_points=None):
if frequency_points is None:
max_frequency = np.amax(self._frequencies)
min_frequency = np.amin(self._frequencies)
self._frequency_points = np.linspace(min_frequency,
max_frequency,
division_number)
else:
self._frequency_points = frequency_points
num_ir_grid_points = len(self._ir_grid_points)
num_band = self._cell.get_number_of_atoms() * 3
num_freqs = len(self._frequency_points)
self._integration_weights = np.zeros(
(num_freqs, num_band, num_ir_grid_points), dtype='double')
reciprocal_lattice = np.linalg.inv(self._cell.get_cell())
self._tm = TetrahedronMethod(reciprocal_lattice, mesh=self._mesh)
self._relative_grid_address = self._tm.get_tetrahedra()
for i, gp in enumerate(self._ir_grid_points):
self._set_tetrahedra_frequencies(gp)
for ib, frequencies in enumerate(self._tetrahedra_frequencies):
self._tm.set_tetrahedra_omegas(frequencies)
self._tm.run(self._frequency_points, value=value)
iw = self._tm.get_integration_weight()
self._integration_weights[:, ib, i] = iw
self._integration_weights /= np.prod(self._mesh)
def _prepare(self):
(self._ir_grid_points,
ir_grid_weights) = extract_ir_grid_points(self._grid_mapping_table)
ir_gp_indices = {}
for i, gp in enumerate(self._ir_grid_points):
ir_gp_indices[gp] = i
self._gp_ir_index = np.zeros_like(self._grid_mapping_table)
for i, gp in enumerate(self._grid_mapping_table):
self._gp_ir_index[i] = ir_gp_indices[gp]
def _set_tetrahedra_frequencies(self, gp):
self._tetrahedra_frequencies = get_tetrahedra_frequencies(
gp,
self._mesh,
self._grid_order,
self._grid_address,
self._relative_grid_address,
self._gp_ir_index,
self._frequencies)