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Fix isotope interface in phono3py.

This commit is contained in:
Atsushi Togo 2014-01-29 18:55:19 +09:00
parent 3501d31335
commit 5b6157267d
2 changed files with 22 additions and 24 deletions
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10
anharmonic/phonon3/__init__.py
View File

@ -466,6 +466,7 @@ class IsotopeScattering:
def __init__(self,
mesh,
mass_variances, # length of list is num_atom.
band_indices=None,
sigma=0.1,
frequency_factor_to_THz=VaspToTHz,
symprec=1e-5,
@ -473,18 +474,15 @@ class IsotopeScattering:
lapack_zheev_uplo='L'):
self._iso = Isotope(mesh,
mass_variances,
band_indices=band_indices,
sigma=sigma,
frequency_factor_to_THz=frequency_factor_to_THz,
symprec=symprec,
cutoff_frequency=cutoff_frequency,
lapack_zheev_uplo=lapack_zheev_uplo)
def run(self, grid_point, band_indices=None):
if band_indices is None:
bi = [np.arange(self._primitive.get_number_of_atoms() * 3)]
else:
bi = band_indices
self._iso.run(grid_point, bi)
def run(self, grid_point):
self._iso.run(grid_point)
g_iso = self._iso.get_gamma()
return g_iso

36
scripts/phono3py
View File

@ -780,6 +780,7 @@ if options.is_gruneisen:
if log_level:
print_end()
sys.exit(0)
#######################
# Show ph-ph settings #
@ -839,10 +840,10 @@ if log_level:
#############
if options.is_joint_dos:
joint_dos = Phono3pyJointDos(
supercell_dm,
primitive_dm,
phonon_supercell,
phonon_primitive,
mesh,
fc2,
phono3py.get_fc2(),
nac_params=nac_params,
sigmas=sigmas,
frequency_step=frequency_step,
@ -855,38 +856,37 @@ if options.is_joint_dos:
joint_dos.run(grid_points)
if log_level:
print_end()
sys.exit(0)
######################
# Isotope scattering #
######################
if options.is_isotope:
if log_level:
print "Cutoff frequency:", settings.get_cutoff_frequency()
mass_variances = settings.get_mass_variances()
if band_indices is not None:
band_indices = np.hstack(band_indices).astype('intc')
iso = IsotopeScattering(
mesh,
mass_variances,
band_indices=band_indices,
frequency_factor_to_THz=frequency_factor_to_THz,
symprec=options.symprec,
cutoff_frequency=settings.get_cutoff_frequency(),
lapack_zheev_uplo=options.uplo)
iso.set_dynamical_matrix(fc2,
supercell,
primitive,
iso.set_dynamical_matrix(phono3py.get_fc2(),
phonon_supercell,
phonon_primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor)
if settings.get_band_indices() is None:
band_indices = None
else:
band_indices = np.hstack(self._band_indices).astype('intc')
for sigma in sigmas:
if log_level:
print "Sigma:", sigma
iso.set_sigma(sigma)
print iso.run(gp, band_indices)
for sigma in sigmas:
if log_level:
print "Sigma:", sigma
iso.set_sigma(sigma)
print iso.run(gp)
if log_level:
print_end()
sys.exit(0)
#########
# Ph-ph #