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Spectral function implementation updated

This commit is contained in:
Atsushi Togo 2020-09-06 13:21:16 +09:00
parent f9ffcc90fa
commit 41ce7fe379
6 changed files with 96 additions and 73 deletions
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118
phono3py/api_phono3py.py
View File

@ -1421,7 +1421,7 @@ class Phono3py(object):
raise RuntimeError(msg)
if temperatures is None:
self._temperatures = [0.0, 300.0]
self._temperatures = [300.0, ]
else:
self._temperatures = temperatures
self._grid_points = grid_points
@ -1440,11 +1440,11 @@ class Phono3py(object):
output_filename=output_filename,
log_level=self._log_level)
if keep_gamma_detail:
(self._gammas,
self._detailed_gammas,
self._frequency_points) = vals
(self._frequency_points,
self._gammas,
self._detailed_gammas) = vals
else:
self._gammas, self._frequency_points = vals
self._frequency_points, self._gammas = vals
def write_imag_self_energy(self, filename=None):
write_imag_self_energy(
@ -1459,6 +1459,60 @@ class Phono3py(object):
filename=filename,
is_mesh_symmetry=self._is_mesh_symmetry)
def run_frequency_shift(
self,
grid_points,
run_on_bands=False,
frequency_points=None,
frequency_step=None,
num_frequency_points=None,
temperatures=None,
epsilons=None,
write_hdf5=True,
output_filename=None):
"""Frequency shift from lowest order diagram is calculated.
Parameters
----------
epsilons : array_like
The value to avoid divergence. When multiple values are given
frequency shifts for those values are returned.
dtype=float, shape=(epsilons,)
"""
if self._interaction is None:
msg = ("Phono3py.init_phph_interaction has to be called "
"before running this method.")
raise RuntimeError(msg)
if epsilons is not None:
_epsilons = epsilons
else:
if len(self._sigmas) == 1 and self._sigmas[0] is None:
_epsilons = None
elif self._sigmas[0] is None:
_epsilons = self._sigmas[1:]
else:
_epsilons = self._sigmas
self._grid_points = grid_points
# (epsilon, grid_point, temperature, band)
self._frequency_points, self._frequency_shifts = get_frequency_shift(
self._interaction,
self._grid_points,
temperatures,
run_on_bands=run_on_bands,
frequency_points=frequency_points,
frequency_step=frequency_step,
num_frequency_points=num_frequency_points,
epsilons=_epsilons,
write_hdf5=write_hdf5,
output_filename=output_filename,
log_level=self._log_level)
return self._frequency_points, self._frequency_shifts
def run_thermal_conductivity(
self,
is_LBTE=False,
@ -1562,60 +1616,6 @@ class Phono3py(object):
output_filename=output_filename,
log_level=self._log_level)
def run_frequency_shift(
self,
grid_points,
run_on_bands=False,
frequency_points=None,
frequency_step=None,
num_frequency_points=None,
temperatures=None,
epsilons=None,
write_Delta_hdf5=True,
output_filename=None):
"""Frequency shift from lowest order diagram is calculated.
Parameters
----------
epsilons : array_like
The value to avoid divergence. When multiple values are given
frequency shifts for those values are returned.
dtype=float, shape=(epsilons,)
"""
if self._interaction is None:
msg = ("Phono3py.init_phph_interaction has to be called "
"before running this method.")
raise RuntimeError(msg)
if epsilons is not None:
_epsilons = epsilons
else:
if len(self._sigmas) == 1 and self._sigmas[0] is None:
_epsilons = None
elif self._sigmas[0] is None:
_epsilons = self._sigmas[1:]
else:
_epsilons = self._sigmas
self._grid_points = grid_points
# (epsilon, grid_point, temperature, band)
self._frequency_shift = get_frequency_shift(
self._interaction,
self._grid_points,
run_on_bands=run_on_bands,
frequency_points=frequency_points,
frequency_step=frequency_step,
num_frequency_points=num_frequency_points,
epsilons=_epsilons,
temperatures=temperatures,
write_Delta_hdf5=write_Delta_hdf5,
output_filename=output_filename,
log_level=self._log_level)
return self._frequency_shift
def save(self,
filename="phono3py_params.yaml",
settings=None):

8
phono3py/phonon3/frequency_shift.py
View File

@ -43,14 +43,14 @@ from phono3py.phonon3.imag_self_energy import get_frequency_points
def get_frequency_shift(interaction,
grid_points,
temperatures,
run_on_bands=False,
frequency_points=None,
frequency_step=None,
num_frequency_points=None,
epsilons=None,
temperatures=None,
output_filename=None,
write_Delta_hdf5=True,
write_hdf5=True,
log_level=0):
if epsilons is None:
_epsilons = [None, ]
@ -134,7 +134,7 @@ def get_frequency_shift(interaction,
interaction.get_phonons()[0][gp][bi_set])
sys.stdout.flush()
if write_Delta_hdf5:
if write_hdf5:
filename = write_Delta_to_hdf5(
gp,
band_indices,
@ -152,7 +152,7 @@ def get_frequency_shift(interaction,
print("\"%s\"." % filename)
sys.stdout.flush()
return all_deltas
return _frequency_points, all_deltas
class FrequencyShift(object):

8
phono3py/phonon3/imag_self_energy.py
View File

@ -101,8 +101,8 @@ def get_imag_self_energy(interaction,
Returns
-------
tuple :
(gammas, frequency_points) are returned. With return_gamma_detail=True,
(gammas, detailed_gammas, frequency_points) are returned.
(frequency_points, gammas) are returned. With return_gamma_detail=True,
(frequency_points, gammas, detailed_gammas) are returned.
"""
@ -213,9 +213,9 @@ def get_imag_self_energy(interaction,
detailed_gamma.append(detailed_gamma_at_gp)
if return_gamma_detail:
return gamma, detailed_gamma, _frequency_points
return _frequency_points, gamma, detailed_gamma
else:
return gamma, _frequency_points
return _frequency_points, gamma
def get_frequency_points(max_phonon_freq=None,

30
phono3py/phonon3/spectral_function.py
View File

@ -32,11 +32,31 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import sys
import numpy as np
from phono3py.phonon3.imag_self_energy import get_imag_self_energy
from phono3py.phonon3.frequency_shift import imag_to_real
def get_spectral_function(interaction,
grid_points,
temperatures,
frequency_points=None,
frequency_step=None,
num_frequency_points=None,
output_filename=None,
write_hdf5=True,
log_level=0):
sf = SpectralFunction(interaction,
grid_points,
frequency_points=frequency_points,
frequency_step=frequency_step,
num_frequency_points=num_frequency_points,
temperatures=temperatures)
sf.run()
return sf
class SpectralFunction(object):
"""Calculate spectral function"""
@ -81,7 +101,7 @@ class SpectralFunction(object):
def _run_gamma(self):
# gammas[grid_points, sigmas, temps, freq_points, band_indices]
gammas, self._frequency_points = get_imag_self_energy(
fpoints, gammas = get_imag_self_energy(
self._interaction,
self._grid_points,
frequency_points=self._frequency_points_in,
@ -89,6 +109,7 @@ class SpectralFunction(object):
num_frequency_points=self._num_frequency_points,
temperatures=self._temperatures)
self._gammas = np.array(gammas[:, 0], dtype='double', order='C')
self._frequency_points = fpoints
def _run_delta(self):
self._deltas = np.zeros_like(self._gammas)
@ -114,7 +135,8 @@ class SpectralFunction(object):
def _get_spectral_function(self, gammas, deltas, freq):
fpoints = self._frequency_points
vals = (4 * freq ** 2 * gammas) / (
(fpoints - freq ** 2 - 2 * freq * deltas) ** 2
+ (2 * freq * gammas) ** 2)
nums = 4 * freq ** 2 * gammas
denoms = ((fpoints - freq ** 2 - 2 * freq * deltas) ** 2
+ (2 * freq * gammas) ** 2)
vals = np.where(denoms > 0, nums / denoms, 0)
return vals

4
test/phonon3/test_frequency_shift.py
View File

@ -115,10 +115,10 @@ im_part = [
def test_frequency_shift(si_pbesol):
si_pbesol.mesh_numbers = [9, 9, 9]
si_pbesol.init_phph_interaction()
delta = si_pbesol.run_frequency_shift(
_, delta = si_pbesol.run_frequency_shift(
[1, 103],
temperatures=[300, ],
write_Delta_hdf5=False,
write_hdf5=False,
run_on_bands=True)
np.testing.assert_allclose(si_pbesol_Delta, delta[0, :, 0], atol=1e-5)

1
test/phonon3/test_spectral_function.py
View File

@ -57,6 +57,7 @@ def test_SpectralFunction(si_pbesol):
# for line in sf.spectral_functions.reshape(-1, 6):
# print(("%.7f, " * 6) % tuple(line))
# raise
print(np.where(np.abs(spec_funcs - sf.spectral_functions.ravel()) > 1e-2))
np.testing.assert_allclose(shifts, sf.shifts.ravel(), atol=1e-2)
np.testing.assert_allclose(spec_funcs, sf.spectral_functions.ravel(),
atol=1e-2)