def _allocate_values(self):
num_band0 = len(self._pp.get_band_indices())
num_band = self._primitive.get_number_of_atoms() * 3
num_grid_points = len(self._grid_points)
num_temp = len(self._temperatures)
self._kappa = np.zeros((len(self._sigmas), num_temp, 6),
dtype='double')
self._mode_kappa = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0, 6),
dtype='double')
if not self._read_gamma:
self._gamma = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0),
dtype='double')
if self._is_gamma_detail:
self._gamma_N = np.zeros_like(self._gamma)
self._gamma_U = np.zeros_like(self._gamma)
self._gv = np.zeros((num_grid_points, num_band0, 3), dtype='double')
self._gv_sum2 = np.zeros((num_grid_points, num_band0, 6),
dtype='double')
self._cv = np.zeros((num_temp, num_grid_points, num_band0),
dtype='double')
if self._isotope is not None:
self._gamma_iso = np.zeros(
(len(self._sigmas), num_grid_points, num_band0),
dtype='double')
if self._is_full_pp or self._use_ave_pp:
self._averaged_pp_interaction = np.zeros(
(num_grid_points, num_band0), dtype='double')
self._num_ignored_phonon_modes = np.zeros(
(len(self._sigmas), num_temp), dtype='intc')
self._collision = ImagSelfEnergy(
self._pp,
with_detail=self._is_gamma_detail,
unit_conversion=self._gamma_unit_conversion)
def __init__(self,
interaction,
point_operations=None,
ir_grid_points=None,
rot_grid_points=None,
temperature=None,
sigma=None,
is_reducible_collision_matrix=False,
log_level=0,
lang='C'):
self._pp = None
self._sigma = None
self._frequency_points = None
self._temperature = None
self._grid_point = None
self._lang = None
self._imag_self_energy = None
self._collision_matrix = None
self._pp_strength = None
self._frequencies = None
self._triplets_at_q = None
self._triplets_map_at_q = None
self._weights_at_q = None
self._band_indices = None
self._unit_conversion = None
self._cutoff_frequency = None
self._g = None
self._mesh = None
self._is_collision_matrix = None
self._unit_conversion = None
self._log_level = log_level
ImagSelfEnergy.__init__(self,
interaction,
temperature=temperature,
sigma=sigma,
lang=lang)
self._is_reducible_collision_matrix = is_reducible_collision_matrix
self._is_collision_matrix = True
if not self._is_reducible_collision_matrix:
self._ir_grid_points = ir_grid_points
self._rot_grid_points = rot_grid_points
self._point_operations = point_operations
self._primitive = self._pp.get_primitive()
rec_lat = np.linalg.inv(self._primitive.get_cell())
self._rotations_cartesian = np.array([
similarity_transformation(rec_lat, r)
for r in self._point_operations
],
dtype='double',
order='C')
def __next__(self):
if self._gp_index >= len(self._grid_points):
if self._log_level:
print("-" * 74)
raise StopIteration
if self._log_level:
print(("-" * 24 + " Spectral function (%d/%d) " + "-" * 24) %
(self._gp_index + 1, len(self._grid_points)))
gp = self._grid_points[self._gp_index]
ise = ImagSelfEnergy(self._interaction)
ise.set_grid_point(gp)
if self._log_level:
print("Running ph-ph interaction calculation...")
sys.stdout.flush()
ise.run_interaction()
for sigma_i, sigma in enumerate(self._sigmas):
self._run_gamma(ise, self._gp_index, sigma, sigma_i)
self._run_delta(self._gp_index, sigma_i)
self._run_spectral_function(self._gp_index, gp, sigma_i)
self._gp_index += 1
return gp
def __next__(self):
"""Calculate at next grid point."""
if self._gp_index >= len(self._grid_points):
if self._log_level:
print("-" * 74)
raise StopIteration
gp = self._grid_points[self._gp_index]
qpoint = np.dot(
self._pp.bz_grid.addresses[gp],
self._pp.bz_grid.QDinv.T,
)
if self._log_level:
print(("-" * 24 + " Spectral function %d (%d/%d) " + "-" * 24) %
(gp, self._gp_index + 1, len(self._grid_points)))
print("q-point: (%5.2f %5.2f %5.2f)" % tuple(qpoint))
ise = ImagSelfEnergy(self._pp)
ise.set_grid_point(gp)
if self._log_level:
print("Running ph-ph interaction calculation...")
sys.stdout.flush()
ise.run_interaction()
for sigma_i, sigma in enumerate(self._sigmas):
self._run_gamma(ise, self._gp_index, sigma, sigma_i)
self._run_delta(self._gp_index, sigma_i)
self._run_spectral_function(self._gp_index, gp, sigma_i)
self._gp_index += 1
return gp
class Conductivity_RTA(Conductivity):
def __init__(
self,
interaction,
symmetry,
grid_points=None,
temperatures=None,
sigmas=None,
sigma_cutoff=None,
is_isotope=False,
mass_variances=None,
boundary_mfp=None, # in micrometre
use_ave_pp=False,
gamma_unit_conversion=None,
mesh_divisors=None,
coarse_mesh_shifts=None,
is_kappa_star=True,
gv_delta_q=None,
is_full_pp=False,
read_pp=False,
store_pp=False,
pp_filename=None,
is_N_U=False,
is_gamma_detail=False,
log_level=0):
self._pp = None
self._temperatures = None
self._sigmas = None
self._sigma_cutoff = None
self._is_kappa_star = None
self._gv_delta_q = None
self._is_full_pp = None
self._is_N_U = is_N_U
self._is_gamma_detail = is_gamma_detail
self._log_level = None
self._primitive = None
self._dm = None
self._frequency_factor_to_THz = None
self._cutoff_frequency = None
self._boundary_mfp = None
self._symmetry = None
self._point_operations = None
self._rotations_cartesian = None
self._grid_points = None
self._grid_weights = None
self._grid_address = None
self._read_gamma = False
self._read_gamma_iso = False
self._frequencies = None
self._cv = None
self._gv = None
self._gv_sum2 = None
self._gamma = None
self._gamma_iso = None
self._gamma_N = None
self._gamma_U = None
self._gamma_detail_at_q = None
self._gamma_unit_conversion = gamma_unit_conversion
self._use_ave_pp = use_ave_pp
self._use_const_ave_pp = None
self._averaged_pp_interaction = None
self._num_ignored_phonon_modes = None
self._num_sampling_grid_points = None
self._mesh = None
self._conversion_factor = None
self._is_isotope = None
self._isotope = None
self._mass_variances = None
self._grid_point_count = None
Conductivity.__init__(self,
interaction,
symmetry,
grid_points=grid_points,
temperatures=temperatures,
sigmas=sigmas,
sigma_cutoff=sigma_cutoff,
is_isotope=is_isotope,
mass_variances=mass_variances,
mesh_divisors=mesh_divisors,
coarse_mesh_shifts=coarse_mesh_shifts,
boundary_mfp=boundary_mfp,
is_kappa_star=is_kappa_star,
gv_delta_q=gv_delta_q,
is_full_pp=is_full_pp,
log_level=log_level)
self._use_const_ave_pp = self._pp.get_constant_averaged_interaction()
self._read_pp = read_pp
self._store_pp = store_pp
self._pp_filename = pp_filename
if self._temperatures is not None:
self._allocate_values()
def set_kappa_at_sigmas(self):
num_band = self._primitive.get_number_of_atoms() * 3
for i, grid_point in enumerate(self._grid_points):
cv = self._cv[:, i, :]
gp = self._grid_points[i]
frequencies = self._frequencies[gp]
# Kappa
for j in range(len(self._sigmas)):
for k in range(len(self._temperatures)):
g_sum = self._get_main_diagonal(i, j, k)
for l in range(num_band):
if frequencies[l] < self._cutoff_frequency:
self._num_ignored_phonon_modes[j, k] += 1
continue
old_settings = np.seterr(all='raise')
try:
self._mode_kappa[j, k, i,
l] = (self._gv_sum2[i, l] *
cv[k, l] / (g_sum[l] * 2) *
self._conversion_factor)
except FloatingPointError:
# supposed that g is almost 0 and |gv|=0
pass
except:
print("=" * 26 + " Warning " + "=" * 26)
print(" Unexpected physical condition of ph-ph "
"interaction calculation was found.")
print(" g=%f at gp=%d, band=%d, freq=%f" %
(g_sum[l], gp, l + 1, frequencies[l]))
print("=" * 61)
np.seterr(**old_settings)
N = self._num_sampling_grid_points
self._kappa = self._mode_kappa.sum(axis=2).sum(axis=2) / N
def get_gamma_N_U(self):
return (self._gamma_N, self._gamma_U)
def set_gamma_N_U(self, gamma_N, gamma_U):
self._gamma_N = gamma_N
self._gamma_U = gamma_U
def get_gamma_detail_at_q(self):
return self._gamma_detail_at_q
def get_number_of_ignored_phonon_modes(self):
return self._num_ignored_phonon_modes
def get_number_of_sampling_grid_points(self):
return self._num_sampling_grid_points
def set_averaged_pp_interaction(self, ave_pp):
self._averaged_pp_interaction = ave_pp
def _run_at_grid_point(self):
i = self._grid_point_count
self._show_log_header(i)
grid_point = self._grid_points[i]
self._set_harmonic_properties(i, i)
if self._read_gamma:
if self._use_ave_pp:
self._collision.set_grid_point(grid_point)
self._set_gamma_at_sigmas(i)
else:
self._collision.set_grid_point(
grid_point,
stores_triplets_map=(self._is_full_pp
or self._is_gamma_detail))
num_triplets = len(self._pp.get_triplets_at_q()[0])
if self._log_level:
print("Number of triplets: %d" % num_triplets)
if (self._is_full_pp or self._read_pp or self._store_pp
or self._use_ave_pp or self._use_const_ave_pp
or self._is_gamma_detail):
self._set_gamma_at_sigmas(i)
else: # can save memory space
self._set_gamma_at_sigmas_lowmem(i)
if self._isotope is not None and not self._read_gamma_iso:
gamma_iso = self._get_gamma_isotope_at_sigmas(i)
self._gamma_iso[:, i, :] = gamma_iso[:,
self._pp.get_band_indices()]
if self._log_level:
self._show_log(self._qpoints[i], i)
def _allocate_values(self):
num_band0 = len(self._pp.get_band_indices())
num_grid_points = len(self._grid_points)
num_temp = len(self._temperatures)
self._kappa = np.zeros((len(self._sigmas), num_temp, 6),
order='C',
dtype='double')
self._mode_kappa = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0, 6),
order='C',
dtype='double')
if not self._read_gamma:
self._gamma = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0),
order='C',
dtype='double')
if self._is_gamma_detail or self._is_N_U:
self._gamma_N = np.zeros_like(self._gamma)
self._gamma_U = np.zeros_like(self._gamma)
self._gv = np.zeros((num_grid_points, num_band0, 3),
order='C',
dtype='double')
self._gv_sum2 = np.zeros((num_grid_points, num_band0, 6),
order='C',
dtype='double')
self._cv = np.zeros((num_temp, num_grid_points, num_band0),
order='C',
dtype='double')
if self._isotope is not None:
self._gamma_iso = np.zeros(
(len(self._sigmas), num_grid_points, num_band0),
order='C',
dtype='double')
if self._is_full_pp or self._use_ave_pp or self._use_const_ave_pp:
self._averaged_pp_interaction = np.zeros(
(num_grid_points, num_band0), order='C', dtype='double')
self._num_ignored_phonon_modes = np.zeros(
(len(self._sigmas), num_temp), order='C', dtype='intc')
self._collision = ImagSelfEnergy(
self._pp,
with_detail=(self._is_gamma_detail or self._is_N_U),
unit_conversion=self._gamma_unit_conversion)
def _set_gamma_at_sigmas(self, i):
for j, sigma in enumerate(self._sigmas):
self._collision.set_sigma(sigma, sigma_cutoff=self._sigma_cutoff)
self._collision.set_integration_weights()
if self._log_level:
text = "Collisions will be calculated with "
if sigma is None:
text += "tetrahedron method."
else:
text += "sigma=%s" % sigma
if self._sigma_cutoff is None:
text += "."
else:
text += "(%4.2f SD)." % self._sigma_cutoff
print(text)
if self._read_pp:
pp, _g_zero = read_pp_from_hdf5(
self._mesh,
grid_point=self._grid_points[i],
sigma=sigma,
sigma_cutoff=self._sigma_cutoff,
filename=self._pp_filename,
verbose=(self._log_level > 0))
_, g_zero = self._collision.get_integration_weights()
if self._log_level:
if len(self._sigmas) > 1:
print("Multiple sigmas or mixing smearing and "
"tetrahedron method is not supported.")
if _g_zero is not None and (_g_zero != g_zero).any():
raise ValueError("Inconsistency found in g_zero.")
self._collision.set_interaction_strength(pp)
elif self._use_ave_pp:
self._collision.set_averaged_pp_interaction(
self._averaged_pp_interaction[i])
elif self._use_const_ave_pp:
if self._log_level:
print("Constant ph-ph interaction of %6.3e is used." %
self._pp.get_constant_averaged_interaction())
self._collision.run_interaction()
self._averaged_pp_interaction[i] = (
self._pp.get_averaged_interaction())
elif j != 0 and (self._is_full_pp or self._sigma_cutoff is None):
if self._log_level:
print("Existing ph-ph interaction is used.")
else:
if self._log_level:
print("Calculating ph-ph interaction...")
self._collision.run_interaction(is_full_pp=self._is_full_pp)
if self._is_full_pp:
self._averaged_pp_interaction[i] = (
self._pp.get_averaged_interaction())
# Number of triplets depends on q-point.
# So this is allocated each time.
if self._is_gamma_detail:
num_temp = len(self._temperatures)
self._gamma_detail_at_q = np.empty(
((num_temp, ) + self._pp.get_interaction_strength().shape),
dtype='double',
order='C')
self._gamma_detail_at_q[:] = 0
if self._log_level:
print("Calculating collisions at temperatures...")
for k, t in enumerate(self._temperatures):
self._collision.set_temperature(t)
self._collision.run()
self._gamma[j, k, i] = self._collision.get_imag_self_energy()
if self._is_N_U or self._is_gamma_detail:
g_N, g_U = self._collision.get_imag_self_energy_N_and_U()
self._gamma_N[j, k, i] = g_N
self._gamma_U[j, k, i] = g_U
if self._is_gamma_detail:
self._gamma_detail_at_q[k] = (
self._collision.get_detailed_imag_self_energy())
def _set_gamma_at_sigmas_lowmem(self, i):
band_indices = self._pp.get_band_indices()
(svecs, multiplicity, p2s, s2p,
masses) = self._pp.get_primitive_and_supercell_correspondence()
fc3 = self._pp.get_fc3()
triplets_at_q, weights_at_q, _, _ = self._pp.get_triplets_at_q()
bz_map = self._pp.get_bz_map()
symmetrize_fc3_q = 0
if None in self._sigmas:
reclat = np.linalg.inv(self._pp.get_primitive().get_cell())
thm = TetrahedronMethod(reclat, mesh=self._mesh)
# It is assumed that self._sigmas = [None].
for j, sigma in enumerate(self._sigmas):
self._collision.set_sigma(sigma)
if self._is_N_U:
collisions = np.zeros(
(2, len(self._temperatures), len(band_indices)),
dtype='double',
order='C')
else:
collisions = np.zeros(
(len(self._temperatures), len(band_indices)),
dtype='double',
order='C')
import phono3py._phono3py as phono3c
if sigma is None:
phono3c.pp_collision(collisions, thm.get_tetrahedra(),
self._frequencies, self._eigenvectors,
triplets_at_q, weights_at_q,
self._grid_address, bz_map, self._mesh,
fc3, svecs, multiplicity, masses, p2s,
s2p, band_indices, self._temperatures,
self._is_N_U * 1, symmetrize_fc3_q,
self._cutoff_frequency)
else:
if self._sigma_cutoff is None:
sigma_cutoff = -1
else:
sigma_cutoff = float(self._sigma_cutoff)
phono3c.pp_collision_with_sigma(
collisions, sigma, sigma_cutoff, self._frequencies,
self._eigenvectors, triplets_at_q, weights_at_q,
self._grid_address, self._mesh, fc3, svecs, multiplicity,
masses, p2s, s2p, band_indices, self._temperatures,
self._is_N_U * 1, symmetrize_fc3_q, self._cutoff_frequency)
col_unit_conv = self._collision.get_unit_conversion_factor()
pp_unit_conv = self._pp.get_unit_conversion_factor()
if self._is_N_U:
col = collisions.sum(axis=0)
col_N = collisions[0]
col_U = collisions[1]
else:
col = collisions
for k in range(len(self._temperatures)):
self._gamma[j, k, i, :] = average_by_degeneracy(
col[k] * col_unit_conv * pp_unit_conv, band_indices,
self._frequencies[self._grid_points[i]])
if self._is_N_U:
self._gamma_N[j, k, i, :] = average_by_degeneracy(
col_N[k] * col_unit_conv * pp_unit_conv, band_indices,
self._frequencies[self._grid_points[i]])
self._gamma_U[j, k, i, :] = average_by_degeneracy(
col_U[k] * col_unit_conv * pp_unit_conv, band_indices,
self._frequencies[self._grid_points[i]])
def _show_log(self, q, i):
gp = self._grid_points[i]
frequencies = self._frequencies[gp][self._pp.get_band_indices()]
gv = self._gv[i]
if self._averaged_pp_interaction is not None:
ave_pp = self._averaged_pp_interaction[i]
else:
ave_pp = None
self._show_log_value_names()
if self._log_level > 1:
self._show_log_values_on_kstar(frequencies, gv, ave_pp, gp, q)
else:
self._show_log_values(frequencies, gv, ave_pp)
sys.stdout.flush()
def _show_log_values(self, frequencies, gv, ave_pp):
if self._is_full_pp or self._use_ave_pp or self._use_const_ave_pp:
for f, v, pp in zip(frequencies, gv, ave_pp):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f %11.3e" %
(f, v[0], v[1], v[2], np.linalg.norm(v), pp))
else:
for f, v in zip(frequencies, gv):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f" %
(f, v[0], v[1], v[2], np.linalg.norm(v)))
def _show_log_values_on_kstar(self, frequencies, gv, ave_pp, gp, q):
rotation_map = get_grid_points_by_rotations(self._grid_address[gp],
self._point_operations,
self._mesh)
for i, j in enumerate(np.unique(rotation_map)):
for k, (rot, rot_c) in enumerate(
zip(self._point_operations, self._rotations_cartesian)):
if rotation_map[k] != j:
continue
print(" k*%-2d (%5.2f %5.2f %5.2f)" %
((i + 1, ) + tuple(np.dot(rot, q))))
if (self._is_full_pp or self._use_ave_pp
or self._use_const_ave_pp):
for f, v, pp in zip(frequencies,
np.dot(rot_c, gv.T).T, ave_pp):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f %11.3e" %
(f, v[0], v[1], v[2], np.linalg.norm(v), pp))
else:
for f, v in zip(frequencies, np.dot(rot_c, gv.T).T):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f" %
(f, v[0], v[1], v[2], np.linalg.norm(v)))
print('')
def _show_log_value_names(self):
if self._is_full_pp or self._use_ave_pp or self._use_const_ave_pp:
text = "Frequency group velocity (x, y, z) |gv| Pqj"
else:
text = "Frequency group velocity (x, y, z) |gv|"
if self._gv_delta_q is None:
pass
else:
text += " (dq=%3.1e)" % self._gv_delta_q
print(text)
def __init__(
self,
interaction: Interaction,
grid_points=None,
temperatures=None,
sigmas=None,
sigma_cutoff=None,
is_isotope=False,
mass_variances=None,
boundary_mfp=None, # in micrometre
use_ave_pp=False,
is_kappa_star=True,
gv_delta_q=None,
is_full_pp=False,
read_pp=False,
store_pp=False,
pp_filename=None,
is_N_U=False,
is_gamma_detail=False,
is_frequency_shift_by_bubble=False,
log_level=0,
):
"""Init method."""
self._is_N_U = is_N_U
self._is_gamma_detail = is_gamma_detail
self._is_frequency_shift_by_bubble = is_frequency_shift_by_bubble
self._gamma_N = None
self._gamma_U = None
self._gamma_detail_at_q = None
self._use_ave_pp = use_ave_pp
self._use_const_ave_pp = None
self._averaged_pp_interaction = None
self._num_ignored_phonon_modes = None
super().__init__(
interaction,
grid_points=grid_points,
temperatures=temperatures,
sigmas=sigmas,
sigma_cutoff=sigma_cutoff,
is_isotope=is_isotope,
mass_variances=mass_variances,
boundary_mfp=boundary_mfp,
is_kappa_star=is_kappa_star,
gv_delta_q=gv_delta_q,
is_full_pp=is_full_pp,
log_level=log_level,
)
self._use_const_ave_pp = self._pp.get_constant_averaged_interaction()
self._read_pp = read_pp
self._store_pp = store_pp
self._pp_filename = pp_filename
if self._temperatures is not None:
self._allocate_values()
self._collision = ImagSelfEnergy(
self._pp, with_detail=(self._is_gamma_detail or self._is_N_U)
)
class ConductivityRTABase(ConductivityBase):
"""Base class of ConductivityRTA*.
This is a base class of RTA classes.
"""
def __init__(
self,
interaction: Interaction,
grid_points=None,
temperatures=None,
sigmas=None,
sigma_cutoff=None,
is_isotope=False,
mass_variances=None,
boundary_mfp=None, # in micrometre
use_ave_pp=False,
is_kappa_star=True,
gv_delta_q=None,
is_full_pp=False,
read_pp=False,
store_pp=False,
pp_filename=None,
is_N_U=False,
is_gamma_detail=False,
is_frequency_shift_by_bubble=False,
log_level=0,
):
"""Init method."""
self._is_N_U = is_N_U
self._is_gamma_detail = is_gamma_detail
self._is_frequency_shift_by_bubble = is_frequency_shift_by_bubble
self._gamma_N = None
self._gamma_U = None
self._gamma_detail_at_q = None
self._use_ave_pp = use_ave_pp
self._use_const_ave_pp = None
self._averaged_pp_interaction = None
self._num_ignored_phonon_modes = None
super().__init__(
interaction,
grid_points=grid_points,
temperatures=temperatures,
sigmas=sigmas,
sigma_cutoff=sigma_cutoff,
is_isotope=is_isotope,
mass_variances=mass_variances,
boundary_mfp=boundary_mfp,
is_kappa_star=is_kappa_star,
gv_delta_q=gv_delta_q,
is_full_pp=is_full_pp,
log_level=log_level,
)
self._use_const_ave_pp = self._pp.get_constant_averaged_interaction()
self._read_pp = read_pp
self._store_pp = store_pp
self._pp_filename = pp_filename
if self._temperatures is not None:
self._allocate_values()
self._collision = ImagSelfEnergy(
self._pp, with_detail=(self._is_gamma_detail or self._is_N_U)
)
def get_gamma_N_U(self):
"""Return N and U parts of gamma."""
return (self._gamma_N, self._gamma_U)
def set_gamma_N_U(self, gamma_N, gamma_U):
"""Set N and U parts of gamma."""
self._gamma_N = gamma_N
self._gamma_U = gamma_U
def get_gamma_detail_at_q(self):
"""Return contribution of each triplet to gamma at current q-point."""
return self._gamma_detail_at_q
def get_number_of_ignored_phonon_modes(self):
"""Return number of ignored phonon modes."""
return self._num_ignored_phonon_modes
def set_averaged_pp_interaction(self, ave_pp):
"""Set averaged ph-ph interaction."""
self._averaged_pp_interaction = ave_pp
@abstractmethod
def set_kappa_at_sigmas(self):
"""Must be implementated in the inherited class."""
raise NotImplementedError()
def _allocate_values(self):
num_band0 = len(self._pp.band_indices)
num_grid_points = len(self._grid_points)
num_temp = len(self._temperatures)
if not self._read_gamma:
self._gamma = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0),
order="C",
dtype="double",
)
if self._is_gamma_detail or self._is_N_U:
self._gamma_N = np.zeros_like(self._gamma)
self._gamma_U = np.zeros_like(self._gamma)
self._gv = np.zeros((num_grid_points, num_band0, 3), order="C", dtype="double")
if self._is_isotope:
self._gamma_iso = np.zeros(
(len(self._sigmas), num_grid_points, num_band0),
order="C",
dtype="double",
)
if self._is_full_pp or self._use_ave_pp or self._use_const_ave_pp:
self._averaged_pp_interaction = np.zeros(
(num_grid_points, num_band0), order="C", dtype="double"
)
self._num_ignored_phonon_modes = np.zeros(
(len(self._sigmas), num_temp), order="C", dtype="intc"
)
def _run_at_grid_point(self):
i_gp = self._grid_point_count
self._show_log_header(i_gp)
grid_point = self._grid_points[i_gp]
self._set_cv(i_gp, i_gp)
self._set_velocities(i_gp, i_gp)
if self._read_gamma:
if self._use_ave_pp:
self._collision.set_grid_point(grid_point)
self._set_gamma_at_sigmas(i_gp)
else:
self._collision.set_grid_point(grid_point)
num_triplets = len(self._pp.get_triplets_at_q()[0])
if self._log_level:
print("Number of triplets: %d" % num_triplets)
if (
self._is_full_pp
or self._read_pp
or self._store_pp
or self._use_ave_pp
or self._use_const_ave_pp
or self._is_gamma_detail
):
self._set_gamma_at_sigmas(i_gp)
else: # can save memory space
self._set_gamma_at_sigmas_lowmem(i_gp)
if self._is_isotope and not self._read_gamma_iso:
gamma_iso = self._get_gamma_isotope_at_sigmas(i_gp)
self._gamma_iso[:, i_gp, :] = gamma_iso[:, self._pp.band_indices]
if self._log_level:
self._show_log(i_gp)
def _set_gamma_at_sigmas(self, i):
for j, sigma in enumerate(self._sigmas):
self._collision.set_sigma(sigma, sigma_cutoff=self._sigma_cutoff)
self._collision.run_integration_weights()
if self._log_level:
text = "Collisions will be calculated with "
if sigma is None:
text += "tetrahedron method."
else:
text += "sigma=%s" % sigma
if self._sigma_cutoff is None:
text += "."
else:
text += "(%4.2f SD)." % self._sigma_cutoff
print(text)
if self._read_pp:
pp, _g_zero = read_pp_from_hdf5(
self._pp.mesh_numbers,
grid_point=self._grid_points[i],
sigma=sigma,
sigma_cutoff=self._sigma_cutoff,
filename=self._pp_filename,
verbose=(self._log_level > 0),
)
_, g_zero = self._collision.get_integration_weights()
if self._log_level:
if len(self._sigmas) > 1:
print(
"Multiple sigmas or mixing smearing and "
"tetrahedron method is not supported."
)
if _g_zero is not None and (_g_zero != g_zero).any():
raise ValueError("Inconsistency found in g_zero.")
self._collision.set_interaction_strength(pp)
elif self._use_ave_pp:
self._collision.set_averaged_pp_interaction(
self._averaged_pp_interaction[i]
)
elif self._use_const_ave_pp:
if self._log_level:
print(
"Constant ph-ph interaction of %6.3e is used."
% self._pp.get_constant_averaged_interaction()
)
self._collision.run_interaction()
self._averaged_pp_interaction[i] = self._pp.get_averaged_interaction()
elif j != 0 and (self._is_full_pp or self._sigma_cutoff is None):
if self._log_level:
print("Existing ph-ph interaction is used.")
else:
if self._log_level:
print("Calculating ph-ph interaction...")
self._collision.run_interaction(is_full_pp=self._is_full_pp)
if self._is_full_pp:
self._averaged_pp_interaction[
i
] = self._pp.get_averaged_interaction()
# Number of triplets depends on q-point.
# So this is allocated each time.
if self._is_gamma_detail:
num_temp = len(self._temperatures)
self._gamma_detail_at_q = np.empty(
((num_temp,) + self._pp.get_interaction_strength().shape),
dtype="double",
order="C",
)
self._gamma_detail_at_q[:] = 0
if self._log_level:
print("Calculating collisions at temperatures...")
for k, t in enumerate(self._temperatures):
self._collision.temperature = t
self._collision.run()
self._gamma[j, k, i] = self._collision.imag_self_energy
if self._is_N_U or self._is_gamma_detail:
g_N, g_U = self._collision.get_imag_self_energy_N_and_U()
self._gamma_N[j, k, i] = g_N
self._gamma_U[j, k, i] = g_U
if self._is_gamma_detail:
self._gamma_detail_at_q[
k
] = self._collision.get_detailed_imag_self_energy()
def _set_gamma_at_sigmas_lowmem(self, i):
"""Calculate gamma without storing ph-ph interaction strength.
`svecs` and `multi` below must not be simply replaced by
`self._pp.primitive.get_smallest_vectors()` because they must be in
dense format as always so in Interaction class instance.
`p2s`, `s2p`, and `masses` have to be also given from Interaction
class instance.
"""
band_indices = self._pp.band_indices
(
svecs,
multi,
p2s,
s2p,
masses,
) = self._pp.get_primitive_and_supercell_correspondence()
fc3 = self._pp.fc3
triplets_at_q, weights_at_q, _, _ = self._pp.get_triplets_at_q()
symmetrize_fc3_q = 0
if None in self._sigmas:
thm = TetrahedronMethod(self._pp.bz_grid.microzone_lattice)
# It is assumed that self._sigmas = [None].
for j, sigma in enumerate(self._sigmas):
self._collision.set_sigma(sigma)
if self._is_N_U:
collisions = np.zeros(
(2, len(self._temperatures), len(band_indices)),
dtype="double",
order="C",
)
else:
collisions = np.zeros(
(len(self._temperatures), len(band_indices)),
dtype="double",
order="C",
)
import phono3py._phono3py as phono3c
if sigma is None:
phono3c.pp_collision(
collisions,
np.array(
np.dot(thm.get_tetrahedra(), self._pp.bz_grid.P.T),
dtype="int_",
order="C",
),
self._frequencies,
self._eigenvectors,
triplets_at_q,
weights_at_q,
self._pp.bz_grid.addresses,
self._pp.bz_grid.gp_map,
self._pp.bz_grid.store_dense_gp_map * 1 + 1,
self._pp.bz_grid.D_diag,
self._pp.bz_grid.Q,
fc3,
svecs,
multi,
masses,
p2s,
s2p,
band_indices,
self._temperatures,
self._is_N_U * 1,
symmetrize_fc3_q,
self._pp.cutoff_frequency,
)
else:
if self._sigma_cutoff is None:
sigma_cutoff = -1
else:
sigma_cutoff = float(self._sigma_cutoff)
phono3c.pp_collision_with_sigma(
collisions,
sigma,
sigma_cutoff,
self._frequencies,
self._eigenvectors,
triplets_at_q,
weights_at_q,
self._pp.bz_grid.addresses,
self._pp.bz_grid.D_diag,
self._pp.bz_grid.Q,
fc3,
svecs,
multi,
masses,
p2s,
s2p,
band_indices,
self._temperatures,
self._is_N_U * 1,
symmetrize_fc3_q,
self._pp.cutoff_frequency,
)
col_unit_conv = self._collision.unit_conversion_factor
pp_unit_conv = self._pp.get_unit_conversion_factor()
if self._is_N_U:
col = collisions.sum(axis=0)
col_N = collisions[0]
col_U = collisions[1]
else:
col = collisions
for k in range(len(self._temperatures)):
self._gamma[j, k, i, :] = average_by_degeneracy(
col[k] * col_unit_conv * pp_unit_conv,
band_indices,
self._frequencies[self._grid_points[i]],
)
if self._is_N_U:
self._gamma_N[j, k, i, :] = average_by_degeneracy(
col_N[k] * col_unit_conv * pp_unit_conv,
band_indices,
self._frequencies[self._grid_points[i]],
)
self._gamma_U[j, k, i, :] = average_by_degeneracy(
col_U[k] * col_unit_conv * pp_unit_conv,
band_indices,
self._frequencies[self._grid_points[i]],
)
def _show_log(self, i_gp):
q = self._get_qpoint_from_gp_index(i_gp)
gp = self._grid_points[i_gp]
frequencies = self._frequencies[gp][self._pp.band_indices]
gv = self._gv[i_gp]
if self._averaged_pp_interaction is not None:
ave_pp = self._averaged_pp_interaction[i_gp]
else:
ave_pp = None
self._show_log_value_names()
if self._log_level > 2:
self._show_log_values_on_kstar(frequencies, gv, ave_pp, gp, q)
else:
self._show_log_values(frequencies, gv, ave_pp)
print("", end="", flush=True)
def _show_log_values(self, frequencies, gv, ave_pp):
if self._is_full_pp or self._use_ave_pp or self._use_const_ave_pp:
for f, v, pp in zip(frequencies, gv, ave_pp):
print(
"%8.3f (%8.3f %8.3f %8.3f) %8.3f %11.3e"
% (f, v[0], v[1], v[2], np.linalg.norm(v), pp)
)
else:
for f, v in zip(frequencies, gv):
print(
"%8.3f (%8.3f %8.3f %8.3f) %8.3f"
% (f, v[0], v[1], v[2], np.linalg.norm(v))
)
def _show_log_values_on_kstar(self, frequencies, gv, ave_pp, gp, q):
rotation_map = get_grid_points_by_rotations(gp, self._pp.bz_grid)
for i, j in enumerate(np.unique(rotation_map)):
for k, (rot, rot_c) in enumerate(
zip(self._point_operations, self._rotations_cartesian)
):
if rotation_map[k] != j:
continue
print(
" k*%-2d (%5.2f %5.2f %5.2f)" % ((i + 1,) + tuple(np.dot(rot, q)))
)
if self._is_full_pp or self._use_ave_pp or self._use_const_ave_pp:
for f, v, pp in zip(frequencies, np.dot(rot_c, gv.T).T, ave_pp):
print(
"%8.3f (%8.3f %8.3f %8.3f) %8.3f %11.3e"
% (f, v[0], v[1], v[2], np.linalg.norm(v), pp)
)
else:
for f, v in zip(frequencies, np.dot(rot_c, gv.T).T):
print(
"%8.3f (%8.3f %8.3f %8.3f) %8.3f"
% (f, v[0], v[1], v[2], np.linalg.norm(v))
)
print("")
def _show_log_value_names(self):
if self._is_full_pp or self._use_ave_pp or self._use_const_ave_pp:
text = "Frequency group velocity (x, y, z) |gv| Pqj"
else:
text = "Frequency group velocity (x, y, z) |gv|"
if self._velocity_obj.q_length is None:
pass
else:
text += " (dq=%3.1e)" % self._velocity_obj.q_length
print(text)
class Conductivity_RTA(Conductivity):
def __init__(
self,
interaction,
symmetry,
grid_points=None,
temperatures=np.arange(0, 1001, 10, dtype='double'),
sigmas=None,
is_isotope=False,
mass_variances=None,
boundary_mfp=None, # in micrometre
use_ave_pp=False,
gamma_unit_conversion=None,
mesh_divisors=None,
coarse_mesh_shifts=None,
is_kappa_star=True,
gv_delta_q=None,
run_with_g=True,
is_full_pp=False,
is_gamma_detail=False,
log_level=0):
self._pp = None
self._temperatures = None
self._sigmas = None
self._is_kappa_star = None
self._gv_delta_q = None
self._run_with_g = run_with_g
self._is_full_pp = is_full_pp
self._is_gamma_detail = is_gamma_detail
self._log_level = None
self._primitive = None
self._dm = None
self._frequency_factor_to_THz = None
self._cutoff_frequency = None
self._boundary_mfp = None
self._symmetry = None
self._point_operations = None
self._rotations_cartesian = None
self._grid_points = None
self._grid_weights = None
self._grid_address = None
self._read_gamma = False
self._read_gamma_iso = False
self._frequencies = None
self._gv = None
self._gv_sum2 = None
self._gamma = None
self._gamma_iso = None
self._gamma_N = None
self._gamma_U = None
self._gamma_detail_at_q = None
self._gamma_unit_conversion = gamma_unit_conversion
self._use_ave_pp = use_ave_pp
self._averaged_pp_interaction = None
self._num_ignored_phonon_modes = None
self._num_sampling_grid_points = None
self._mesh = None
self._mesh_divisors = None
self._coarse_mesh = None
self._coarse_mesh_shifts = None
self._conversion_factor = None
self._is_isotope = None
self._isotope = None
self._mass_variances = None
self._grid_point_count = None
Conductivity.__init__(self,
interaction,
symmetry,
grid_points=grid_points,
temperatures=temperatures,
sigmas=sigmas,
is_isotope=is_isotope,
mass_variances=mass_variances,
mesh_divisors=mesh_divisors,
coarse_mesh_shifts=coarse_mesh_shifts,
boundary_mfp=boundary_mfp,
is_kappa_star=is_kappa_star,
gv_delta_q=gv_delta_q,
log_level=log_level)
self._cv = None
if self._temperatures is not None:
self._allocate_values()
def set_kappa_at_sigmas(self):
num_band = self._primitive.get_number_of_atoms() * 3
self._num_sampling_grid_points = 0
for i, grid_point in enumerate(self._grid_points):
cv = self._cv[:, i, :]
gp = self._grid_points[i]
frequencies = self._frequencies[gp]
# Outer product of group velocities (v x v) [num_k*, num_freqs, 3, 3]
gv_by_gv_tensor, order_kstar = self._get_gv_by_gv(i)
self._num_sampling_grid_points += order_kstar
# Sum all vxv at k*
gv_sum2 = np.zeros((6, num_band), dtype='double')
for j, vxv in enumerate(
([0, 0], [1, 1], [2, 2], [1, 2], [0, 2], [0, 1])):
gv_sum2[j] = gv_by_gv_tensor[:, vxv[0], vxv[1]]
# Kappa
for j in range(len(self._sigmas)):
for k in range(len(self._temperatures)):
g_sum = self._get_main_diagonal(i, j, k)
for l in range(num_band):
if frequencies[l] < self._cutoff_frequency:
self._num_ignored_phonon_modes[j, k] += 1
continue
self._mode_kappa[j, k, i,
l] = (gv_sum2[:, l] * cv[k, l] /
(g_sum[l] * 2) *
self._conversion_factor)
self._gv_sum2[i] = gv_sum2.T
self._mode_kappa /= self._num_sampling_grid_points
self._kappa = self._mode_kappa.sum(axis=2).sum(axis=2)
def get_mode_heat_capacities(self):
return self._cv
def get_gv_by_gv(self):
return self._gv_sum2
def get_gamma_N_U(self):
return (self._gamma_N, self._gamma_U)
def get_gamma_detail_at_q(self):
return self._gamma_detail_at_q
def get_number_of_ignored_phonon_modes(self):
return self._num_ignored_phonon_modes
def get_number_of_sampling_grid_points(self):
return self._num_sampling_grid_points
def get_averaged_pp_interaction(self):
return self._averaged_pp_interaction
def set_averaged_pp_interaction(self, ave_pp):
self._averaged_pp_interaction = ave_pp
def _run_at_grid_point(self):
i = self._grid_point_count
self._show_log_header(i)
grid_point = self._grid_points[i]
if self._read_gamma:
if self._use_ave_pp:
self._collision.set_grid_point(grid_point)
self._collision.set_averaged_pp_interaction(
self._averaged_pp_interaction[i])
self._set_gamma_at_sigmas(i)
else:
self._collision.set_grid_point(grid_point)
if self._log_level:
print("Number of triplets: %d" %
len(self._pp.get_triplets_at_q()[0]))
print("Calculating ph-ph interaction...")
self._set_gamma_at_sigmas(i)
if self._isotope is not None and not self._read_gamma_iso:
self._set_gamma_isotope_at_sigmas(i)
freqs = self._frequencies[grid_point][self._pp.get_band_indices()]
self._cv[:, i, :] = self._get_cv(freqs)
self._set_gv(i)
if self._log_level:
self._show_log(self._qpoints[i], i)
def _allocate_values(self):
num_band0 = len(self._pp.get_band_indices())
num_band = self._primitive.get_number_of_atoms() * 3
num_grid_points = len(self._grid_points)
num_temp = len(self._temperatures)
self._kappa = np.zeros((len(self._sigmas), num_temp, 6),
dtype='double')
self._mode_kappa = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0, 6),
dtype='double')
if not self._read_gamma:
self._gamma = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0),
dtype='double')
if self._is_gamma_detail:
self._gamma_N = np.zeros_like(self._gamma)
self._gamma_U = np.zeros_like(self._gamma)
self._gv = np.zeros((num_grid_points, num_band0, 3), dtype='double')
self._gv_sum2 = np.zeros((num_grid_points, num_band0, 6),
dtype='double')
self._cv = np.zeros((num_temp, num_grid_points, num_band0),
dtype='double')
if self._isotope is not None:
self._gamma_iso = np.zeros(
(len(self._sigmas), num_grid_points, num_band0),
dtype='double')
if self._is_full_pp or self._use_ave_pp:
self._averaged_pp_interaction = np.zeros(
(num_grid_points, num_band0), dtype='double')
self._num_ignored_phonon_modes = np.zeros(
(len(self._sigmas), num_temp), dtype='intc')
self._collision = ImagSelfEnergy(
self._pp,
with_detail=self._is_gamma_detail,
unit_conversion=self._gamma_unit_conversion)
def _set_gamma_at_sigmas(self, i):
for j, sigma in enumerate(self._sigmas):
self._collision.set_sigma(sigma)
if sigma is None or self._run_with_g:
self._collision.set_integration_weights()
if not self._use_ave_pp:
if self._log_level:
text = "Calculating Gamma of ph-ph with "
if sigma is None:
text += "tetrahedron method"
else:
text += "sigma=%s" % sigma
print(text)
if self._is_full_pp and j != 0:
pass
else:
self._collision.run_interaction(
is_full_pp=self._is_full_pp)
if self._is_full_pp and j == 0:
self._averaged_pp_interaction[i] = (
self._pp.get_averaged_interaction())
# Number of triplets depends on q-point.
# So this is allocated each time.
if self._is_gamma_detail:
num_temp = len(self._temperatures)
self._gamma_detail_at_q = np.zeros(
((num_temp, ) + self._pp.get_interaction_strength().shape),
dtype='double',
order='C')
for k, t in enumerate(self._temperatures):
self._collision.set_temperature(t)
self._collision.run()
self._gamma[j, k, i] = self._collision.get_imag_self_energy()
if self._is_gamma_detail:
g_N, g_U = self._collision.get_imag_self_energy_N_and_U()
self._gamma_N[j, k, i] = g_N
self._gamma_U[j, k, i] = g_U
self._gamma_detail_at_q[k] = (
self._collision.get_detailed_imag_self_energy())
def _get_gv_by_gv(self, i):
rotation_map = get_grid_points_by_rotations(
self._grid_address[self._grid_points[i]], self._point_operations,
self._mesh)
gv_by_gv = np.zeros((len(self._gv[i]), 3, 3), dtype='double')
for r in self._rotations_cartesian:
gvs_rot = np.dot(self._gv[i], r.T)
gv_by_gv += [np.outer(r_gv, r_gv) for r_gv in gvs_rot]
gv_by_gv /= len(rotation_map) // len(np.unique(rotation_map))
order_kstar = len(np.unique(rotation_map))
if order_kstar != self._grid_weights[i]:
if self._log_level:
print("*" * 33 + "Warning" + "*" * 33)
print(" Number of elements in k* is unequal "
"to number of equivalent grid-points.")
print("*" * 73)
return gv_by_gv, order_kstar
def _get_cv(self, freqs):
cv = np.zeros((len(self._temperatures), len(freqs)), dtype='double')
# T/freq has to be large enough to avoid divergence.
# Otherwise just set 0.
for i, f in enumerate(freqs):
finite_t = (self._temperatures > f / 100)
if f > self._cutoff_frequency:
cv[:, i] = np.where(
finite_t,
get_mode_cv(np.where(finite_t, self._temperatures, 10000),
f * THzToEv), 0)
return cv
def _show_log(self, q, i):
gp = self._grid_points[i]
frequencies = self._frequencies[gp][self._pp.get_band_indices()]
gv = self._gv[i]
if self._is_full_pp or self._use_ave_pp:
ave_pp = self._averaged_pp_interaction[i]
if self._is_full_pp or self._use_ave_pp:
text = "Frequency group velocity (x, y, z) |gv| Pqj"
else:
text = "Frequency group velocity (x, y, z) |gv|"
if self._gv_delta_q is None:
pass
else:
text += " (dq=%3.1e)" % self._gv_delta_q
print(text)
if self._log_level > 1:
rotation_map = get_grid_points_by_rotations(
self._grid_address[gp], self._point_operations, self._mesh)
for i, j in enumerate(np.unique(rotation_map)):
for k, (rot, rot_c) in enumerate(
zip(self._point_operations,
self._rotations_cartesian)):
if rotation_map[k] != j:
continue
print(" k*%-2d (%5.2f %5.2f %5.2f)" %
((i + 1, ) + tuple(np.dot(rot, q))))
if self._is_full_pp or self._use_ave_pp:
for f, v, pp in zip(frequencies,
np.dot(rot_c, gv.T).T, ave_pp):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f %11.3e" %
(f, v[0], v[1], v[2], np.linalg.norm(v), pp))
else:
for f, v in zip(frequencies, np.dot(rot_c, gv.T).T):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f" %
(f, v[0], v[1], v[2], np.linalg.norm(v)))
print('')
else:
if self._is_full_pp or self._use_ave_pp:
for f, v, pp in zip(frequencies, gv, ave_pp):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f %11.3e" %
(f, v[0], v[1], v[2], np.linalg.norm(v), pp))
else:
for f, v in zip(frequencies, gv):
print("%8.3f (%8.3f %8.3f %8.3f) %8.3f" %
(f, v[0], v[1], v[2], np.linalg.norm(v)))