def _get_irt(ph3: Phono3py,
mesh,
nac_params=None,
solve_dynamical_matrices=True):
ph3.mesh_numbers = mesh
itr = Interaction(ph3.primitive,
ph3.grid,
ph3.primitive_symmetry,
ph3.fc3,
cutoff_frequency=1e-4)
if nac_params is None:
itr.init_dynamical_matrix(
ph3.fc2,
ph3.phonon_supercell,
ph3.phonon_primitive,
)
else:
itr.init_dynamical_matrix(
ph3.fc2,
ph3.phonon_supercell,
ph3.phonon_primitive,
nac_params=nac_params,
)
if solve_dynamical_matrices:
itr.run_phonon_solver()
return itr
def test_real_self_energy_with_frequency_points(si_pbesol: Phono3py):
"""Real part of self energy spectrum of Si.
* specified frquency points
"""
si_pbesol.mesh_numbers = [9, 9, 9]
si_pbesol.init_phph_interaction()
frequency_points = [1.469947, 3.085309, 14.997187, 15.129080]
fps, delta = si_pbesol.run_real_self_energy(
si_pbesol.grid.grg2bzg[[1, 103]],
[
300,
],
frequency_points=frequency_points,
write_hdf5=False,
frequency_points_at_bands=False,
)
np.testing.assert_allclose(frequency_points, fps, atol=1e-5)
np.testing.assert_allclose(si_pbesol_Delta_fps[0],
delta[0, 0, 0].ravel(),
atol=0.01)
np.testing.assert_allclose(si_pbesol_Delta_fps[1],
delta[0, 0, 1].ravel(),
atol=0.01)
def test_jdos_nacl_nac_gamma_at_300K_npoints(nacl_pbe: Phono3py):
"""Real part of self energy spectrum of NaCl.
* at 10 frequency points sampled uniformly.
* at q->0
"""
nacl_pbe.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
nacl_pbe.phonon_supercell,
nacl_pbe.phonon_primitive,
nacl_pbe.fc2,
mesh=nacl_pbe.mesh_numbers,
nac_params=nacl_pbe.nac_params,
nac_q_direction=[1, 0, 0],
num_frequency_points=10,
temperatures=[
300,
],
log_level=1,
)
jdos.run([nacl_pbe.grid.gp_Gamma])
# print(", ".join(["%.7f" % fp for fp in jdos.frequency_points]))
np.testing.assert_allclose(nacl_freq_points_gamma_at_300K,
jdos.frequency_points,
atol=1e-5)
# print(", ".join(["%.7f" % jd for jd in jdos.joint_dos.ravel()]))
np.testing.assert_allclose(nacl_jdos_gamma_at_300K[2:],
jdos.joint_dos.ravel()[2:],
rtol=1e-2,
atol=1e-5)
def test_jdos_nacl_at_300K(nacl_pbe: Phono3py, gp: int,
store_dense_gp_map: bool):
"""Test joint-DOS at 300K by NaCl."""
nacl_pbe.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
nacl_pbe.phonon_supercell,
nacl_pbe.phonon_primitive,
nacl_pbe.fc2,
mesh=nacl_pbe.mesh_numbers,
nac_params=nacl_pbe.nac_params,
num_frequency_points=10,
temperatures=[
300,
],
store_dense_gp_map=store_dense_gp_map,
log_level=1,
)
jdos.run([gp])
# print(", ".join(["%.7f" % fp for fp in jdos.frequency_points]))
np.testing.assert_allclose(nacl_freq_points_at_300K,
jdos.frequency_points,
atol=1e-5)
# print(", ".join(["%.7f" % jd for jd in jdos.joint_dos.ravel()]))
np.testing.assert_allclose(nacl_jdos_12_at_300K[2:],
jdos.joint_dos.ravel()[2:],
rtol=1e-2,
atol=1e-5)
def test_jdos_si(si_pbesol: Phono3py, gp: int, store_dense_gp_map: bool):
"""Test joint-DOS by Si.
store_dense_gp_map=False : 103
store_dense_gp_map=True : 105
"""
si_pbesol.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
si_pbesol.phonon_supercell,
si_pbesol.phonon_primitive,
si_pbesol.fc2,
mesh=si_pbesol.mesh_numbers,
num_frequency_points=10,
store_dense_gp_map=store_dense_gp_map,
log_level=1,
)
jdos.run([gp])
# print(", ".join(["%.7f" % fp for fp in jdos.frequency_points]))
np.testing.assert_allclose(si_freq_points,
jdos.frequency_points,
atol=1e-5)
# print(", ".join(["%.7f" % jd for jd in jdos.joint_dos.ravel()]))
np.testing.assert_allclose(si_jdos_12[2:],
jdos.joint_dos.ravel()[2:],
rtol=1e-2,
atol=1e-5)
def test_SpectralFunction_band_indices(si_pbesol: Phono3py):
"""Spectral function of Si."""
si_pbesol.mesh_numbers = [9, 9, 9]
si_pbesol.band_indices = [[4, 5]]
si_pbesol.init_phph_interaction()
sf = SpectralFunction(
si_pbesol.phph_interaction,
si_pbesol.grid.grg2bzg[[1, 103]],
temperatures=[
300,
],
num_frequency_points=10,
log_level=1,
)
sf.run()
# for line in np.swapaxes(sf.spectral_functions, -2, -1).reshape(-1, 6):
# print(("%.7f, " * 6) % tuple(line))
# raise
np.testing.assert_allclose(
np.reshape(shifts, (-1, 6))[:, [4, 5]],
np.swapaxes(sf.shifts, -2, -1).reshape(-1, 2),
atol=1e-2,
)
np.testing.assert_allclose(
np.reshape(spec_funcs, (-1, 6))[:, [4, 5]],
np.swapaxes(sf.spectral_functions, -2, -1).reshape(-1, 2),
atol=1e-2,
rtol=1e-2,
)
def test_real_self_energy_nacl_nac_npoints(nacl_pbe: Phono3py):
"""Real part of self energy spectrum of NaCl.
* at 10 frequency points sampled uniformly.
* at q->0
"""
nacl_pbe.mesh_numbers = [9, 9, 9]
nacl_pbe.init_phph_interaction(nac_q_direction=[1, 0, 0])
fps, delta = nacl_pbe.run_real_self_energy([nacl_pbe.grid.gp_Gamma], [300],
num_frequency_points=10)
# for line in np.swapaxes(delta, -1, -2).ravel().reshape(-1, 6):
# print(("%10.8f, " * 6) % tuple(line))
# print(fps.ravel())
np.testing.assert_allclose(freq_points_nacl_nac,
fps.ravel(),
rtol=0,
atol=1e-5)
np.testing.assert_allclose(delta_nacl_nac,
np.swapaxes(delta, -1, -2).ravel(),
rtol=0,
atol=1e-2)
def init_phph_interaction(
phono3py: Phono3py,
settings,
updated_settings,
input_filename,
output_filename,
log_level,
):
"""Initialize ph-ph interaction and phonons on grid."""
if log_level:
print("Generating grid system ... ", end="", flush=True)
phono3py.mesh_numbers = settings.mesh_numbers
bz_grid = phono3py.grid
if log_level:
if bz_grid.grid_matrix is None:
print("[ %d %d %d ]" % tuple(phono3py.mesh_numbers))
else:
print("")
print("Generalized regular grid: [ %d %d %d ]" %
tuple(bz_grid.D_diag))
print("Grid generation matrix:")
print(" [ %d %d %d ]" % tuple(bz_grid.grid_matrix[0]))
print(" [ %d %d %d ]" % tuple(bz_grid.grid_matrix[1]))
print(" [ %d %d %d ]" % tuple(bz_grid.grid_matrix[2]))
if settings.is_symmetrize_fc3_q:
print("Permutation symmetry of ph-ph interaction strengths: True")
ave_pp = settings.constant_averaged_pp_interaction
phono3py.init_phph_interaction(
nac_q_direction=settings.nac_q_direction,
constant_averaged_interaction=ave_pp,
frequency_scale_factor=updated_settings["frequency_scale_factor"],
symmetrize_fc3q=settings.is_symmetrize_fc3_q,
lapack_zheev_uplo=settings.lapack_zheev_uplo,
)
if not settings.read_phonon:
if log_level:
print("-" * 27 + " Phonon calculations " + "-" * 28)
dm = phono3py.dynamical_matrix
if dm.is_nac() and dm.nac_method == "gonze":
dm.show_nac_message()
print("Running harmonic phonon calculations...")
sys.stdout.flush()
phono3py.run_phonon_solver()
if settings.write_phonon:
freqs, eigvecs, grid_address = phono3py.get_phonon_data()
ir_grid_points, ir_grid_weights, _ = get_ir_grid_points(bz_grid)
ir_grid_points = np.array(bz_grid.grg2bzg[ir_grid_points],
dtype="int_")
filename = write_phonon_to_hdf5(
freqs,
eigvecs,
grid_address,
phono3py.mesh_numbers,
bz_grid=bz_grid,
ir_grid_points=ir_grid_points,
ir_grid_weights=ir_grid_weights,
compression=settings.hdf5_compression,
filename=output_filename,
)
if filename:
if log_level:
print('Phonons are written into "%s".' % filename)
else:
print("Writing phonons failed.")
if log_level:
print_error()
sys.exit(1)
if settings.read_phonon:
phonons = read_phonon_from_hdf5(phono3py.mesh_numbers,
filename=input_filename,
verbose=(log_level > 0))
if phonons is None:
print("Reading phonons failed.")
if log_level:
print_error()
sys.exit(1)
try:
phono3py.set_phonon_data(*phonons)
except RuntimeError:
if log_level:
print_error()
sys.exit(1)