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GR-grid matrices are saved in hdf5 files

This commit is contained in:
Atsushi Togo 2022-02-15 17:47:16 +09:00
parent 9df898e2f8
commit 098b7e0e2a
9 changed files with 147 additions and 15 deletions
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44
phono3py/file_IO.py
View File

@ -453,7 +453,12 @@ def write_grid_address(grid_address, mesh, filename=None):
def write_grid_address_to_hdf5(
grid_address, mesh, grid_mapping_table, compression="gzip", filename=None
grid_address,
mesh,
grid_mapping_table,
bz_grid=None,
compression="gzip",
filename=None,
):
"""Write grid addresses to grid_address.hdf5."""
suffix = _get_filename_suffix(mesh, filename=filename)
@ -461,6 +466,10 @@ def write_grid_address_to_hdf5(
with h5py.File(full_filename, "w") as w:
w.create_dataset("version", data=np.string_(__version__))
w.create_dataset("mesh", data=mesh)
if bz_grid is not None and bz_grid.grid_matrix is not None:
w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
w.create_dataset("P_matrix", data=bz_grid.P)
w.create_dataset("Q_matrix", data=bz_grid.Q)
w.create_dataset("grid_address", data=grid_address, compression=compression)
w.create_dataset(
"grid_mapping_table", data=grid_mapping_table, compression=compression
@ -618,6 +627,7 @@ def write_real_self_energy_to_hdf5(
deltas,
mesh,
epsilon,
bz_grid=None,
frequency_points=None,
frequencies=None,
filename=None,
@ -649,6 +659,10 @@ def write_real_self_energy_to_hdf5(
w.create_dataset("version", data=np.string_(__version__))
w.create_dataset("grid_point", data=grid_point)
w.create_dataset("mesh", data=mesh)
if bz_grid is not None and bz_grid.grid_matrix is not None:
w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
w.create_dataset("P_matrix", data=bz_grid.P)
w.create_dataset("Q_matrix", data=bz_grid.Q)
w.create_dataset("band_index", data=_band_indices)
w.create_dataset("delta", data=deltas)
w.create_dataset("temperature", data=temperatures)
@ -700,6 +714,7 @@ def write_spectral_function_to_hdf5(
shifts,
half_linewidths,
mesh,
bz_grid=None,
sigma=None,
frequency_points=None,
frequencies=None,
@ -724,6 +739,10 @@ def write_spectral_function_to_hdf5(
w.create_dataset("version", data=np.string_(__version__))
w.create_dataset("grid_point", data=grid_point)
w.create_dataset("mesh", data=mesh)
if bz_grid is not None and bz_grid.grid_matrix is not None:
w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
w.create_dataset("P_matrix", data=bz_grid.P)
w.create_dataset("Q_matrix", data=bz_grid.Q)
w.create_dataset("band_index", data=_band_indices)
w.create_dataset("spectral_function", data=spectral_functions)
w.create_dataset("shift", data=shifts)
@ -884,6 +903,7 @@ def write_collision_eigenvalues_to_hdf5(
def write_kappa_to_hdf5(
temperature,
mesh,
bz_grid=None,
frequency=None,
group_velocity=None,
gv_by_gv=None,
@ -928,7 +948,10 @@ def write_kappa_to_hdf5(
w.create_dataset("version", data=np.string_(__version__))
w.create_dataset("temperature", data=temperature)
w.create_dataset("mesh", data=mesh)
if bz_grid is not None and bz_grid.grid_matrix is not None:
w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
w.create_dataset("P_matrix", data=bz_grid.P)
w.create_dataset("Q_matrix", data=bz_grid.Q)
if frequency is not None:
if isinstance(frequency, np.floating):
w.create_dataset("frequency", data=frequency)
@ -1299,6 +1322,7 @@ def read_pp_from_hdf5(
def write_gamma_detail_to_hdf5(
temperature,
mesh,
bz_grid=None,
gamma_detail=None,
grid_point=None,
triplet=None,
@ -1332,6 +1356,10 @@ def write_gamma_detail_to_hdf5(
w.create_dataset("version", data=np.string_(__version__))
w.create_dataset("temperature", data=temperature)
w.create_dataset("mesh", data=mesh)
if bz_grid is not None and bz_grid.grid_matrix is not None:
w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
w.create_dataset("P_matrix", data=bz_grid.P)
w.create_dataset("Q_matrix", data=bz_grid.Q)
if gamma_detail is not None:
w.create_dataset("gamma_detail", data=gamma_detail, compression=compression)
if triplet is not None:
@ -1384,7 +1412,13 @@ def write_gamma_detail_to_hdf5(
def write_phonon_to_hdf5(
frequency, eigenvector, grid_address, mesh, compression="gzip", filename=None
frequency,
eigenvector,
grid_address,
mesh,
bz_grid=None,
compression="gzip",
filename=None,
):
"""Write phonon on grid in its hdf5 file."""
suffix = _get_filename_suffix(mesh, filename=filename)
@ -1393,6 +1427,10 @@ def write_phonon_to_hdf5(
with h5py.File(full_filename, "w") as w:
w.create_dataset("version", data=np.string_(__version__))
w.create_dataset("mesh", data=mesh)
if bz_grid is not None and bz_grid.grid_matrix is not None:
w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
w.create_dataset("P_matrix", data=bz_grid.P)
w.create_dataset("Q_matrix", data=bz_grid.Q)
w.create_dataset("grid_address", data=grid_address, compression=compression)
w.create_dataset("frequency", data=frequency, compression=compression)
w.create_dataset("eigenvector", data=eigenvector, compression=compression)

5
phono3py/phonon3/conductivity.py
View File

@ -278,6 +278,11 @@ class Conductivity(ConductivityBase):
)
return self.mesh_numbers
@property
def bz_grid(self):
"""Return GR-grid."""
return self._pp.bz_grid
@property
def mode_heat_capacities(self):
"""Return mode heat capacity at constant volume at grid points.

2
phono3py/phonon3/conductivity_LBTE.py
View File

@ -1486,6 +1486,7 @@ def _write_kappa(
sigmas = lbte.sigmas
sigma_cutoff = lbte.sigma_cutoff_width
mesh = lbte.mesh_numbers
bz_grid = lbte.bz_grid
weights = lbte.grid_weights
frequencies = lbte.frequencies
ave_pp = lbte.averaged_pp_interaction
@ -1519,6 +1520,7 @@ def _write_kappa(
write_kappa_to_hdf5(
temperatures,
mesh,
bz_grid=bz_grid,
frequency=frequencies,
group_velocity=gv,
gv_by_gv=gv_by_gv,

45
phono3py/phonon3/conductivity_RTA.py
View File

@ -35,6 +35,7 @@
import sys
from typing import Optional
import numpy as np
from phonopy.phonon.group_velocity import GroupVelocity
from phonopy.structure.tetrahedron_method import TetrahedronMethod
@ -50,7 +51,7 @@ from phono3py.phonon3.conductivity import write_pp as _write_pp
from phono3py.phonon3.imag_self_energy import ImagSelfEnergy, average_by_degeneracy
from phono3py.phonon3.interaction import Interaction
from phono3py.phonon3.triplets import get_all_triplets
from phono3py.phonon.grid import get_grid_points_by_rotations
from phono3py.phonon.grid import _get_ir_grid_map, get_grid_points_by_rotations
class ConductivityRTA(Conductivity):
@ -676,15 +677,21 @@ def get_thermal_conductivity_RTA(
def _write_gamma_detail(
br, interaction, i, compression="gzip", filename=None, verbose=True
br: ConductivityRTA,
interaction: Interaction,
i: int,
compression: str = "gzip",
filename: Optional[str] = None,
verbose: bool = True,
):
gamma_detail = br.get_gamma_detail_at_q()
temperatures = br.get_temperatures()
mesh = br.get_mesh_numbers()
grid_points = br.get_grid_points()
temperatures = br.temperatures
mesh = br.mesh_numbers
bz_grid = br.bz_grid
grid_points = br.grid_points
gp = grid_points[i]
sigmas = br.get_sigmas()
sigma_cutoff = br.get_sigma_cutoff_width()
sigmas = br.sigmas
sigma_cutoff = br.sigma_cutoff_width
triplets, weights, _, _ = interaction.get_triplets_at_q()
all_triplets = get_all_triplets(gp, interaction.bz_grid)
@ -693,6 +700,7 @@ def _write_gamma_detail(
write_gamma_detail_to_hdf5(
temperatures,
mesh,
bz_grid=bz_grid,
gamma_detail=gamma_detail,
grid_point=gp,
triplet=triplets,
@ -710,6 +718,7 @@ def _write_gamma_detail(
write_gamma_detail_to_hdf5(
temperatures,
mesh,
bz_grid=bz_grid,
gamma_detail=gamma_detail[:, :, k, :, :],
grid_point=gp,
triplet=triplets,
@ -723,7 +732,14 @@ def _write_gamma_detail(
)
def _write_gamma(br, interaction, i, compression="gzip", filename=None, verbose=True):
def _write_gamma(
br: ConductivityRTA,
interaction: Interaction,
i: int,
compression: str = "gzip",
filename: Optional[str] = None,
verbose: bool = True,
):
"""Write mode kappa related properties into a hdf5 file."""
grid_points = br.grid_points
group_velocities = br.group_velocities
@ -731,6 +747,7 @@ def _write_gamma(br, interaction, i, compression="gzip", filename=None, verbose=
mode_heat_capacities = br.mode_heat_capacities
ave_pp = br.averaged_pp_interaction
mesh = br.mesh_numbers
bz_grid = br.bz_grid
temperatures = br.temperatures
gamma = br.gamma
gamma_isotope = br.gamma_isotope
@ -763,6 +780,7 @@ def _write_gamma(br, interaction, i, compression="gzip", filename=None, verbose=
write_kappa_to_hdf5(
temperatures,
mesh,
bz_grid=bz_grid,
frequency=frequencies,
group_velocity=group_velocities[i],
gv_by_gv=gv_by_gv[i],
@ -803,6 +821,7 @@ def _write_gamma(br, interaction, i, compression="gzip", filename=None, verbose=
write_kappa_to_hdf5(
temperatures,
mesh,
bz_grid=bz_grid,
frequency=frequencies,
group_velocity=group_velocities[i, k],
gv_by_gv=gv_by_gv[i, k],
@ -861,7 +880,13 @@ def _show_kappa(br, log_level):
print("")
def _write_kappa(br, volume, compression="gzip", filename=None, log_level=0):
def _write_kappa(
br: ConductivityRTA,
volume: float,
compression: str = "gzip",
filename: Optional[str] = None,
log_level: int = 0,
):
temperatures = br.temperatures
sigmas = br.sigmas
sigma_cutoff = br.sigma_cutoff_width
@ -869,6 +894,7 @@ def _write_kappa(br, volume, compression="gzip", filename=None, log_level=0):
gamma_isotope = br.gamma_isotope
gamma_N, gamma_U = br.get_gamma_N_U()
mesh = br.mesh_numbers
bz_grid = br.bz_grid
frequencies = br.frequencies
gv = br.group_velocities
gv_by_gv = br.gv_by_gv
@ -897,6 +923,7 @@ def _write_kappa(br, volume, compression="gzip", filename=None, log_level=0):
write_kappa_to_hdf5(
temperatures,
mesh,
bz_grid=bz_grid,
frequency=frequencies,
group_velocity=gv,
gv_by_gv=gv_by_gv,

4
phono3py/phonon3/imag_self_energy.py
View File

@ -260,7 +260,7 @@ def _get_imag_self_energy_at_gp(
_num_frequency_points,
scattering_event_class,
num_points_in_batch,
interaction,
interaction: Interaction,
ise,
write_gamma_detail,
return_gamma_detail,
@ -270,6 +270,7 @@ def _get_imag_self_energy_at_gp(
num_band0 = len(interaction.band_indices)
frequencies = interaction.get_phonons()[0]
mesh = interaction.mesh_numbers
bz_grid = interaction.bz_grid
if write_gamma_detail or return_gamma_detail:
triplets, weights, _, _ = interaction.get_triplets_at_q()
@ -329,6 +330,7 @@ def _get_imag_self_energy_at_gp(
full_filename = write_gamma_detail_to_hdf5(
temperatures,
mesh,
bz_grid=bz_grid,
gamma_detail=detailed_gamma_at_gp[j],
grid_point=gp,
triplet=triplets,

5
phono3py/phonon3/real_self_energy.py
View File

@ -45,10 +45,11 @@ from phono3py.file_IO import (
)
from phono3py.phonon3.imag_self_energy import get_frequency_points
from phono3py.phonon.func import bose_einstein
from phono3py.phonon3.interaction import Interaction
def get_real_self_energy(
interaction,
interaction: Interaction,
grid_points,
temperatures,
epsilons=None,
@ -134,6 +135,7 @@ def get_real_self_energy(
fst = RealSelfEnergy(interaction)
mesh = interaction.mesh_numbers
bz_grid = interaction.bz_grid
frequencies = interaction.get_phonons()[0]
max_phonon_freq = np.amax(frequencies)
band_indices = interaction.band_indices
@ -228,6 +230,7 @@ def get_real_self_energy(
all_deltas[i, :, j],
mesh,
fst.epsilon,
bz_grid=bz_grid,
frequency_points=_frequency_points,
frequencies=frequencies,
filename=output_filename,

4
phono3py/phonon3/spectral_function.py
View File

@ -46,11 +46,12 @@ from phono3py.phonon3.imag_self_energy import (
get_frequency_points,
run_ise_at_frequency_points_batch,
)
from phono3py.phonon3.interaction import Interaction
from phono3py.phonon3.real_self_energy import imag_to_real
def run_spectral_function(
interaction,
interaction: Interaction,
grid_points,
temperatures=None,
sigmas=None,
@ -157,6 +158,7 @@ def run_spectral_function(
spf.shifts[sigma_i, :, i],
spf.half_linewidths[sigma_i, :, i],
interaction.mesh_numbers,
interaction.bz_grid,
sigma=sigma,
frequency_points=spf.frequency_points,
frequencies=frequencies[gp],

22
test/conftest.py
View File

@ -48,6 +48,28 @@ def si_pbesol(request):
)
@pytest.fixture(scope="session")
def si_pbesol_grg(request):
"""Return Phono3py instance of Si 2x2x2.
* with symmetry
* full fc
* GR-grid
"""
yaml_filename = os.path.join(current_dir, "phono3py_si_pbesol.yaml")
forces_fc3_filename = os.path.join(current_dir, "FORCES_FC3_si_pbesol")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
forces_fc3_filename=forces_fc3_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
use_grg=True,
log_level=1,
)
@pytest.fixture(scope="session")
def si_pbesol_nosym(request):
"""Return Phono3py instance of Si 2x2x2.

31
test/phonon3/test_kappa_RTA.py
View File

@ -1,5 +1,6 @@
"""Test for Conductivity_RTA.py."""
import numpy as np
from phono3py import Phono3py
si_pbesol_kappa_RTA = [107.991, 107.991, 107.991, 0, 0, 0]
si_pbesol_kappa_RTA_with_sigmas = [109.6985, 109.6985, 109.6985, 0, 0, 0]
@ -14,6 +15,7 @@ si_pbesol_kappa_RTA_si_nosym = [
0.283,
]
si_pbesol_kappa_RTA_si_nomeshsym = [38.90918, 38.90918, 38.90918, 0, 0, 0]
si_pbesol_kappa_RTA_grg = [37.3176477, 37.3176477, 37.3176477, 0, 0, 0]
nacl_pbe_kappa_RTA = [7.72798252, 7.72798252, 7.72798252, 0, 0, 0]
nacl_pbe_kappa_RTA_with_sigma = [7.71913708, 7.71913708, 7.71913708, 0, 0, 0]
@ -95,6 +97,35 @@ def test_kappa_RTA_si_nomeshsym(si_pbesol, si_pbesol_nomeshsym):
np.testing.assert_allclose(kappa_ref, kappa, atol=0.5)
def test_kappa_RTA_si_grg(si_pbesol_grg: Phono3py):
"""Test RTA by Si with GR-grid."""
mesh = 10
ph3 = si_pbesol_grg
ph3.mesh_numbers = mesh
ph3.init_phph_interaction()
ph3.run_thermal_conductivity(
temperatures=[
300,
],
)
kappa = ph3.thermal_conductivity.kappa.ravel()
np.testing.assert_equal(
ph3.thermal_conductivity.bz_grid.grid_matrix,
[[-2, 2, 2], [2, -2, 2], [2, 2, -2]],
)
np.testing.assert_equal(
ph3.grid.grid_matrix,
[[-2, 2, 2], [2, -2, 2], [2, 2, -2]],
)
A = ph3.grid.grid_matrix
D_diag = ph3.grid.D_diag
P = ph3.grid.P
Q = ph3.grid.Q
np.testing.assert_equal(np.dot(P, np.dot(A, Q)), np.diag(D_diag))
np.testing.assert_allclose(si_pbesol_kappa_RTA_grg, kappa, atol=0.5)
def test_kappa_RTA_si_N_U(si_pbesol):
"""Test RTA with N and U scatterings by Si."""
ph3 = si_pbesol