class Phono3pyIsotope(object):
def __init__(self,
mesh,
primitive,
mass_variances=None, # length of list is num_atom.
band_indices=None,
sigmas=None,
frequency_factor_to_THz=VaspToTHz,
symprec=1e-5,
cutoff_frequency=None,
lapack_zheev_uplo='L'):
if sigmas is None:
self._sigmas = [None]
else:
self._sigmas = sigmas
self._mesh = mesh
self._iso = Isotope(mesh,
primitive,
mass_variances=mass_variances,
band_indices=band_indices,
frequency_factor_to_THz=frequency_factor_to_THz,
symprec=symprec,
cutoff_frequency=cutoff_frequency,
lapack_zheev_uplo=lapack_zheev_uplo)
def run(self, grid_points):
for gp in grid_points:
self._iso.set_grid_point(gp)
print("--------------- Isotope scattering ---------------")
print("Grid point: %d" % gp)
adrs = self._iso.get_grid_address()[gp]
q = adrs.astype('double') / self._mesh
print("q-point: %s" % q)
if self._sigmas:
for sigma in self._sigmas:
if sigma is None:
print("Tetrahedron method")
else:
print("Sigma: %s" % sigma)
self._iso.set_sigma(sigma)
self._iso.run()
frequencies = self._iso.get_phonons()[0]
print('')
print("Phonon-isotope scattering rate in THz (1/4pi-tau)")
print(" Frequency Rate")
for g, f in zip(self._iso.get_gamma(), frequencies[gp]):
print("%8.3f %5.3e" % (f, g))
else:
print("sigma or tetrahedron method has to be set.")
def set_dynamical_matrix(self,
fc2,
supercell,
primitive,
nac_params=None,
frequency_scale_factor=None,
decimals=None):
self._primitive = primitive
self._iso.set_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor,
decimals=decimals)
def set_sigma(self, sigma):
self._iso.set_sigma(sigma)
class Phono3pyIsotope:
"""Class to calculate isotope scattering."""
def __init__(
self,
mesh,
primitive,
mass_variances=None, # length of list is num_atom.
band_indices=None,
sigmas=None,
frequency_factor_to_THz=VaspToTHz,
use_grg=False,
store_dense_gp_map=True,
symprec=1e-5,
cutoff_frequency=None,
lapack_zheev_uplo="L",
):
"""Init method."""
if sigmas is None:
self._sigmas = [
None,
]
else:
self._sigmas = sigmas
self._iso = Isotope(
mesh,
primitive,
mass_variances=mass_variances,
band_indices=band_indices,
frequency_factor_to_THz=frequency_factor_to_THz,
use_grg=use_grg,
store_dense_gp_map=store_dense_gp_map,
symprec=symprec,
cutoff_frequency=cutoff_frequency,
lapack_zheev_uplo=lapack_zheev_uplo,
)
@property
def dynamical_matrix(self):
"""Return dynamical matrix class instance."""
return self._iso.dynamical_matrix
@property
def grid(self):
"""Return BZGrid class instance."""
return self._iso.bz_grid
@property
def gamma(self):
"""Return calculated isotope scattering."""
return self._gamma
@property
def frequencies(self):
"""Return phonon frequencies at grid points."""
return self._iso.get_phonons()[0][self._grid_points]
@property
def grid_points(self):
"""Return grid points in BZ-grid."""
return self._grid_points
def run(self, grid_points):
"""Calculate isotope scattering."""
gamma = np.zeros(
(len(self._sigmas), len(grid_points), len(self._iso.band_indices)),
dtype="double",
)
self._grid_points = np.array(grid_points, dtype="int_")
for j, gp in enumerate(grid_points):
self._iso.set_grid_point(gp)
print("--------------- Isotope scattering ---------------")
print("Grid point: %d" % gp)
adrs = self._iso.bz_grid.addresses[gp]
bz_grid = self._iso.bz_grid
print(bz_grid.D_diag)
q = np.dot(adrs.astype("double") / bz_grid.D_diag, bz_grid.Q.T)
print("q-point: %s" % q)
if self._sigmas:
for i, sigma in enumerate(self._sigmas):
if sigma is None:
print("Tetrahedron method")
else:
print("Sigma: %s" % sigma)
self._iso.sigma = sigma
self._iso.run()
gamma[i, j] = self._iso.gamma
frequencies = self._iso.get_phonons()[0]
print("")
print("Phonon-isotope scattering rate in THz (1/4pi-tau)")
print(" Frequency Rate")
for g, f in zip(self._iso.gamma, frequencies[gp]):
print("%8.3f %5.3e" % (f, g))
else:
print("sigma or tetrahedron method has to be set.")
self._gamma = gamma
def init_dynamical_matrix(
self,
fc2,
supercell,
primitive,
nac_params=None,
frequency_scale_factor=None,
decimals=None,
):
"""Initialize dynamical matrix."""
self._primitive = primitive
self._iso.init_dynamical_matrix(
fc2,
supercell,
primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor,
decimals=decimals,
)
def set_sigma(self, sigma):
"""Set sigma. None means tetrahedron method."""
self._iso.set_sigma(sigma)