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Merge pull request #200 from phonopy/remove-v1-compativility 

Remove v1 compatibility
This commit is contained in:
Atsushi Togo 2023-12-25 10:15:50 +09:00 committed by GitHub
parent 17c0fbda52 225692ed0e
commit 7f55f9bee9
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GPG Key ID: 4AEE18F83AFDEB23
17 changed files with 97 additions and 272 deletions
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11
phono3py/api_isotope.py
View File

@ -33,8 +33,6 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import warnings
import numpy as np
from phonopy.units import VaspToTHz
@ -53,7 +51,6 @@ class Phono3pyIsotope:
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",
@ -66,13 +63,6 @@ class Phono3pyIsotope:
else:
self._sigmas = sigmas
if not store_dense_gp_map:
warnings.warn(
"Phono3pyIsotope init parameter of store_dense_gp_map is deprecated. "
"This will be always set True.",
DeprecationWarning,
)
self._iso = Isotope(
mesh,
primitive,
@ -80,7 +70,6 @@ class Phono3pyIsotope:
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,

14
phono3py/api_jointdos.py
View File

@ -33,8 +33,6 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import warnings
import numpy as np
from phonopy.structure.cells import Primitive, Supercell
from phonopy.structure.symmetry import Symmetry
@ -72,7 +70,6 @@ class Phono3pyJointDos:
SNF_coordinates="reciprocal",
is_mesh_symmetry=True,
is_symmetry=True,
store_dense_gp_map=True,
symprec=1e-5,
output_filename=None,
log_level=0,
@ -94,14 +91,6 @@ class Phono3pyJointDos:
self._is_mesh_symmetry = is_mesh_symmetry
self._is_symmetry = is_symmetry
if not store_dense_gp_map:
warnings.warn(
"Phono3pyJointDos init parameter of store_dense_gp_map is deprecated. "
"This will be set always True.",
DeprecationWarning,
)
self._store_dense_gp_map = store_dense_gp_map
self._use_grg = use_grg
self._SNF_coordinates = SNF_coordinates
self._symprec = symprec
@ -165,7 +154,7 @@ class Phono3pyJointDos:
use_grg=self._use_grg,
force_SNF=False,
SNF_coordinates=self._SNF_coordinates,
store_dense_gp_map=self._store_dense_gp_map,
store_dense_gp_map=True,
)
def initialize(self, mesh_numbers):
@ -180,7 +169,6 @@ class Phono3pyJointDos:
frequency_factor_to_THz=self._frequency_factor_to_THz,
frequency_scale_factor=self._frequency_scale_factor,
is_mesh_symmetry=self._is_mesh_symmetry,
store_dense_gp_map=self._store_dense_gp_map,
symprec=self._symprec,
filename=self._filename,
log_level=self._log_level,

85
phono3py/api_phono3py.py
View File

@ -153,13 +153,10 @@ class Phono3py:
is_mesh_symmetry=True,
use_grg=False,
SNF_coordinates="reciprocal",
symmetrize_fc3q=None,
store_dense_gp_map=True,
store_dense_svecs=True,
make_r0_average: bool = False,
symprec=1e-5,
calculator: Optional[str] = None,
log_level=0,
lapack_zheev_uplo=None,
):
"""Init method.
@ -213,14 +210,11 @@ class Phono3py:
`reciprocal` or `direct`. Space of coordinates to generate grid
generating matrix either in direct or reciprocal space. The default
is `reciprocal`.
symmetrize_fc3q : Deprecated.
See Phono3py.init_phph_interaction().
store_dense_gp_map : bool, optional, Deprecated.
Use dense format of BZ grid system. Default is True.
store_dense_svecs : bool, optional, Deprecated.
Shortest vectors are stored in the dense array format. This is
expected to be always True. Setting False is for rough compatibility
with v1.x. Default is True.
make_r0_average : bool, optional
fc3 transformation from real to reciprocal space is done
around three atoms and averaged when True. Default is False, i.e.,
only around the first atom. Setting False is for rough compatibility
with v2.x. Default is True.
symprec : float, optional
Tolerance used to find crystal symmetry. Default is 1e-5.
calculator : str, optional.
@ -228,8 +222,6 @@ class Phono3py:
of physical units. Default is None, which is equivalent to "vasp".
log_level : int, optional
Verbosity control. Default is 0. This can be 0, 1, or 2.
lapack_zheev_uplo : Deprecated.
See Phono3py.init_phph_interaction().
"""
self._symprec = symprec
@ -239,21 +231,13 @@ class Phono3py:
self._use_grg = use_grg
self._SNF_coordinates = SNF_coordinates
if not store_dense_gp_map:
if not make_r0_average:
warnings.warn(
"Phono3py init parameter of store_dense_gp_map is deprecated. "
"This will be set always True.",
"Phono3py init parameter of make_r0_average is deprecated. "
"This is always True but exists for backward compatibility.",
DeprecationWarning,
)
self._store_dense_gp_map = store_dense_gp_map
if not store_dense_svecs:
warnings.warn(
"Phono3py init parameter of store_dense_svecs is deprecated. "
"This will be set always True.",
DeprecationWarning,
)
self._store_dense_svecs = store_dense_svecs
self._make_r0_average = make_r0_average
self._cutoff_frequency = cutoff_frequency
self._calculator: Optional[str] = calculator
@ -361,26 +345,6 @@ class Phono3py:
)
self.sigma_cutoff = sigma_cutoff
if symmetrize_fc3q is not None:
warnings.warn(
"Phono3py init parameter of symmetrize_fc3q is deprecated. "
"Set this at Phono3py.init_phph_interaction().",
DeprecationWarning,
)
self._symmetrize_fc3q = symmetrize_fc3q
else:
self._symmetrize_fc3q = None
if lapack_zheev_uplo is not None:
warnings.warn(
"Phono3py init parameter of lapack_zheev_uplo is deprecated. "
"Set this at Phono3py.init_phph_interaction().",
DeprecationWarning,
)
self._lapack_zheev_uplo = lapack_zheev_uplo
else:
self._lapack_zheev_uplo = None
@property
def version(self):
"""Return phono3py release version number.
@ -1331,8 +1295,7 @@ class Phono3py:
nac_q_direction=None,
constant_averaged_interaction=None,
frequency_scale_factor=None,
symmetrize_fc3q=False,
make_r0_average=False,
symmetrize_fc3q: bool = False,
lapack_zheev_uplo="L",
openmp_per_triplets=None,
):
@ -1367,10 +1330,6 @@ class Phono3py:
symmetrize_fc3q : bool, optional
fc3 in phonon space is symmetrized by permutation symmetry.
Default is False.
make_r0_average : bool, optional
fc3 transformation from real to reciprocal space is done
around three atoms and averaged when True. Default is False, i.e.,
only around the first atom.
lapack_zheev_uplo : str, optional
'L' or 'U'. Default is 'L'. This is passed to LAPACK zheev
used for phonon solver.
@ -1389,16 +1348,6 @@ class Phono3py:
msg = "Phono3py.fc2 of instance is not found."
raise RuntimeError(msg)
if self._symmetrize_fc3q is None:
_symmetrize_fc3q = symmetrize_fc3q
else:
_symmetrize_fc3q = self._symmetrize_fc3q
if self._lapack_zheev_uplo is None:
_lapack_zheev_uplo = lapack_zheev_uplo
else:
_lapack_zheev_uplo = self._lapack_zheev_uplo
self._interaction = Interaction(
self._primitive,
self._bz_grid,
@ -1410,9 +1359,9 @@ class Phono3py:
frequency_scale_factor=frequency_scale_factor,
cutoff_frequency=self._cutoff_frequency,
is_mesh_symmetry=self._is_mesh_symmetry,
symmetrize_fc3q=_symmetrize_fc3q,
make_r0_average=make_r0_average,
lapack_zheev_uplo=_lapack_zheev_uplo,
symmetrize_fc3q=symmetrize_fc3q,
make_r0_average=self._make_r0_average,
lapack_zheev_uplo=lapack_zheev_uplo,
openmp_per_triplets=openmp_per_triplets,
)
self._interaction.nac_q_direction = nac_q_direction
@ -2545,9 +2494,7 @@ class Phono3py:
else:
t_mat = np.dot(inv_supercell_matrix, primitive_matrix)
return get_primitive(
supercell, t_mat, self._symprec, store_dense_svecs=self._store_dense_svecs
)
return get_primitive(supercell, t_mat, self._symprec, store_dense_svecs=True)
def _determine_primitive_matrix(self, primitive_matrix):
pmat = get_primitive_matrix(primitive_matrix, symprec=self._symprec)
@ -2571,7 +2518,7 @@ class Phono3py:
use_grg=self._use_grg,
force_SNF=False,
SNF_coordinates=self._SNF_coordinates,
store_dense_gp_map=self._store_dense_gp_map,
store_dense_gp_map=True,
)
def _init_dynamical_matrix(self):

10
phono3py/cui/load.py
View File

@ -77,8 +77,6 @@ def load(
is_mesh_symmetry=True,
is_compact_fc=False,
use_grg=False,
store_dense_gp_map=True,
store_dense_svecs=True,
symprec=1e-5,
log_level=0,
) -> Phono3py:
@ -229,12 +227,6 @@ def load(
cells. Default is False.
use_grg : bool, optional
Use generalized regular grid when True. Default is False.
store_dense_gp_map : bool, optional, Deprecated
Use new format of BZ grid system. Default is True.
store_dense_svecs : bool, optional, Deprecated
Shortest vectors are stored in the dense array format. This is expected
to be always True. Setting False is for rough compatibility with v1.x.
Default is True.
symprec : float, optional
Tolerance used to find crystal symmetry. Default is 1e-5.
log_level : int, optional
@ -305,8 +297,6 @@ def load(
is_symmetry=is_symmetry,
is_mesh_symmetry=is_mesh_symmetry,
use_grg=use_grg,
store_dense_gp_map=store_dense_gp_map,
store_dense_svecs=store_dense_svecs,
calculator=calculator,
log_level=log_level,
)

2
phono3py/cui/phono3py_script.py
View File

@ -741,6 +741,7 @@ def init_phono3py(
is_symmetry=settings.is_symmetry,
is_mesh_symmetry=settings.is_mesh_symmetry,
use_grg=settings.use_grg,
make_r0_average=settings.is_fc3_r0_average,
symprec=symprec,
calculator=interface_mode,
log_level=log_level,
@ -1036,7 +1037,6 @@ def init_phph_interaction(
constant_averaged_interaction=ave_pp,
frequency_scale_factor=updated_settings["frequency_scale_factor"],
symmetrize_fc3q=settings.is_symmetrize_fc3_q,
make_r0_average=settings.is_fc3_r0_average,
lapack_zheev_uplo=settings.lapack_zheev_uplo,
)

3
phono3py/other/isotope.py
View File

@ -100,7 +100,6 @@ class Isotope:
bz_grid=None,
frequency_factor_to_THz=VaspToTHz,
use_grg=False,
store_dense_gp_map=True,
symprec=1e-5,
cutoff_frequency=None,
lapack_zheev_uplo="L",
@ -146,7 +145,7 @@ class Isotope:
lattice=self._primitive.cell,
symmetry_dataset=primitive_symmetry.dataset,
use_grg=use_grg,
store_dense_gp_map=store_dense_gp_map,
store_dense_gp_map=True,
)
def set_grid_point(self, grid_point):

6
phono3py/other/tetrahedron_method.py
View File

@ -36,8 +36,10 @@
import numpy as np
from phonopy.structure.tetrahedron_method import TetrahedronMethod
from phono3py.phonon.grid import BZGrid
def get_unique_grid_points(grid_points, bz_grid):
def get_unique_grid_points(grid_points, bz_grid: BZGrid):
"""Collect grid points on tetrahedron vertices around input grid points.
Find grid points of 24 tetrahedra around each grid point and
@ -88,7 +90,7 @@ def get_unique_grid_points(grid_points, bz_grid):
def get_integration_weights(
sampling_points,
grid_values,
bz_grid,
bz_grid: BZGrid,
grid_points=None,
bzgp2irgp_map=None,
function="I",

14
phono3py/phonon3/gruneisen.py
View File

@ -37,7 +37,8 @@ import sys
import numpy as np
from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
from phonopy.structure.cells import sparse_to_dense_svecs
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import Primitive
from phonopy.structure.grid_points import get_qpoints
from phonopy.units import VaspToTHz
@ -126,8 +127,8 @@ class Gruneisen:
self,
fc2,
fc3,
supercell,
primitive,
supercell: PhonopyAtoms,
primitive: Primitive,
nac_params=None,
nac_q_direction=None,
ion_clamped=False,
@ -151,12 +152,7 @@ class Gruneisen:
)
self._nac_q_direction = nac_q_direction
svecs, multi = self._pcell.get_smallest_vectors()
if self._pcell.store_dense_svecs:
self._svecs = svecs
self._multi = multi
else:
self._svecs, self._multi = sparse_to_dense_svecs(svecs, multi)
self._svecs, self._multi = self._pcell.get_smallest_vectors()
if self._ion_clamped:
num_atom_prim = len(self._pcell)

13
phono3py/phonon3/interaction.py
View File

@ -40,11 +40,7 @@ from typing import Literal, Optional, Union
import numpy as np
from phonopy.harmonic.dynamical_matrix import DynamicalMatrix, get_dynamical_matrix
from phonopy.structure.cells import (
Primitive,
compute_all_sg_permutations,
sparse_to_dense_svecs,
)
from phonopy.structure.cells import Primitive, compute_all_sg_permutations
from phonopy.structure.symmetry import Symmetry
from phonopy.units import AMU, EV, Angstrom, Hbar, THz, VaspToTHz
@ -171,12 +167,7 @@ class Interaction:
self._band_index_count = 0
svecs, multi = self._primitive.get_smallest_vectors()
if self._primitive.store_dense_svecs:
self._svecs = svecs
self._multi = multi
else:
self._svecs, self._multi = sparse_to_dense_svecs(svecs, multi)
self._svecs, self._multi = self._primitive.get_smallest_vectors()
self._masses = np.array(self._primitive.masses, dtype="double")
self._p2s = np.array(self._primitive.p2s_map, dtype="int_")
self._s2p = np.array(self._primitive.s2p_map, dtype="int_")

2
phono3py/phonon3/joint_dos.py
View File

@ -68,7 +68,6 @@ class JointDos:
frequency_factor_to_THz=VaspToTHz,
frequency_scale_factor=1.0,
is_mesh_symmetry=True,
store_dense_gp_map=False,
symprec=1e-5,
filename=None,
log_level=False,
@ -93,7 +92,6 @@ class JointDos:
self._frequency_factor_to_THz = frequency_factor_to_THz
self._frequency_scale_factor = frequency_scale_factor
self._is_mesh_symmetry = is_mesh_symmetry
self._store_dense_gp_map = store_dense_gp_map
self._symprec = symprec
self._filename = filename
self._log_level = log_level

8
phono3py/phonon3/real_to_reciprocal.py
View File

@ -34,7 +34,6 @@
# POSSIBILITY OF SUCH DAMAGE.
import numpy as np
from phonopy.structure.cells import sparse_to_dense_svecs
class RealToReciprocal:
@ -50,12 +49,7 @@ class RealToReciprocal:
self._p2s_map = primitive.p2s_map
self._s2p_map = primitive.s2p_map
# Reduce supercell atom index to primitive index
svecs, multi = self._primitive.get_smallest_vectors()
if self._primitive.store_dense_svecs:
self._svecs = svecs
self._multi = multi
else:
self._svecs, self._multi = sparse_to_dense_svecs(svecs, multi)
self._svecs, self._multi = self._primitive.get_smallest_vectors()
self._fc3_reciprocal = None
def run(self, triplet):

7
phono3py/phonon3/triplets.py
View File

@ -70,8 +70,6 @@ def get_triplets_at_q(
Inversion symemtry is added if it doesn't exist. Default is True.
swappable : bool, optional
q1 and q2 among (q0, q1, q2) can be swapped. Deafult is True.
store_dense_gp_map : bool, optional
See the detail in the docstring of ``_relocate_BZ_grid_address``.
Returns
-------
@ -343,7 +341,10 @@ def _get_BZ_triplets_at_q(bz_grid_index, bz_grid: BZGrid, map_triplets):
def _set_triplets_integration_weights_c(
g, g_zero, pp: Union["Interaction", "JointDos"], frequency_points
g: np.ndarray,
g_zero: np.ndarray,
pp: Union["Interaction", "JointDos"],
frequency_points,
):
import phono3py._phono3py as phono3c

5
test/conductivity/test_kappa_LBTE.py
View File

@ -57,7 +57,10 @@ def test_kappa_LBTE_aln(aln_lda: Phono3py):
def test_kappa_LBTE_aln_with_r0_ave(aln_lda: Phono3py):
"""Test direct solution by AlN."""
aln_lda.mesh_numbers = [7, 7, 5]
aln_lda.init_phph_interaction(make_r0_average=True)
make_r0_average_orig = aln_lda._make_r0_average
aln_lda._make_r0_average = True
aln_lda.init_phph_interaction()
aln_lda._make_r0_average = make_r0_average_orig
aln_lda.run_thermal_conductivity(
is_LBTE=True,
temperatures=[

9
test/conductivity/test_kappa_RTA.py
View File

@ -369,7 +369,7 @@ def test_kappa_RTA_aln_with_sigma_and_r0_ave(aln_lda: Phono3py):
def _get_kappa(
ph3,
ph3: Phono3py,
mesh,
is_isotope=False,
is_full_pp=False,
@ -377,9 +377,10 @@ def _get_kappa(
make_r0_average=False,
):
ph3.mesh_numbers = mesh
ph3.init_phph_interaction(
make_r0_average=make_r0_average, openmp_per_triplets=openmp_per_triplets
)
make_r0_average_orig = ph3._make_r0_average
ph3._make_r0_average = make_r0_average
ph3.init_phph_interaction(openmp_per_triplets=openmp_per_triplets)
ph3._make_r0_average = make_r0_average_orig
ph3.run_thermal_conductivity(
temperatures=[
300,

91
test/conftest.py
View File

@ -12,16 +12,15 @@ import phono3py
from phono3py import Phono3py
cwd = Path(__file__).parent
store_dense_gp_map = True
def pytest_addoption(parser):
"""Activate v1 emulation with --v1 option."""
"""Activate v2 emulation with --v2 option."""
parser.addoption(
"--v1",
action="store_false",
default=True,
help="Run with phono3py v1.x emulation.",
"--v2",
action="store_true",
default=False,
help="Run with phono3py v2.x emulation.",
)
@ -59,12 +58,10 @@ def si_pbesol(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
forces_fc3_filename=forces_fc3_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@ -80,12 +77,10 @@ def si_pbesol_grg(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
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,
)
@ -101,14 +96,12 @@ def si_pbesol_nosym(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
forces_fc3_filename=forces_fc3_filename,
is_symmetry=False,
produce_fc=False,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@ -123,14 +116,12 @@ def si_pbesol_nomeshsym(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
forces_fc3_filename=forces_fc3_filename,
is_mesh_symmetry=False,
produce_fc=False,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@ -145,13 +136,11 @@ def si_pbesol_compact_fc(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
forces_fc3_filename=forces_fc3_filename,
is_compact_fc=True,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@ -165,11 +154,9 @@ def si_pbesol_111(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_Si111.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@ -186,11 +173,9 @@ def si_pbesol_111_alm(request) -> Phono3py:
pytest.importorskip("alm")
yaml_filename = cwd / "phono3py_params_Si111.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm",
log_level=1,
)
@ -218,11 +203,9 @@ def si_pbesol_111_222_fd(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@ -239,11 +222,9 @@ def si_pbesol_111_222_alm(request) -> Phono3py:
pytest.importorskip("alm")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm",
log_level=1,
)
@ -261,11 +242,9 @@ def si_pbesol_111_222_alm_fd(request) -> Phono3py:
pytest.importorskip("alm")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm|",
log_level=1,
)
@ -283,11 +262,9 @@ def si_pbesol_111_222_fd_alm(request) -> Phono3py:
pytest.importorskip("alm")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="|alm",
log_level=1,
)
@ -306,11 +283,9 @@ def si_pbesol_111_222_alm_cutoff(request) -> Phono3py:
pytest.importorskip("alm")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm",
fc_calculator_options="cutoff = 3",
log_level=1,
@ -330,11 +305,9 @@ def si_pbesol_111_222_alm_cutoff_fc2(request) -> Phono3py:
pytest.importorskip("alm")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm",
fc_calculator_options="cutoff = 3|",
log_level=1,
@ -354,11 +327,9 @@ def si_pbesol_111_222_alm_cutoff_fc3(request) -> Phono3py:
pytest.importorskip("alm")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm",
fc_calculator_options="|cutoff = 3",
log_level=1,
@ -374,11 +345,9 @@ def nacl_pbe(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@ -392,11 +361,9 @@ def nacl_pbe_compact_fc(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
is_compact_fc=True,
log_level=1,
)
@ -410,11 +377,9 @@ def nacl_pbe_cutoff_fc3(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
ph3 = phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
produce_fc=False,
log_level=1,
)
@ -444,11 +409,9 @@ def nacl_pbe_cutoff_fc3_all_forces(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
ph3 = phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
produce_fc=False,
log_level=1,
)
@ -469,11 +432,9 @@ def nacl_pbe_cutoff_fc3_compact_fc(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
ph3 = phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
produce_fc=False,
log_level=1,
)
@ -493,11 +454,9 @@ def aln_lda(request) -> Phono3py:
"""
yaml_filename = cwd / "phono3py_params_AlN332.yaml.xz"
enable_v2 = request.config.getoption("--v1")
# enable_v2 = request.config.getoption("--v2")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)

86
test/phonon3/test_joint_dos.py
View File

@ -205,14 +205,8 @@ nacl_jdos_gamma_at_300K = [
]
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
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
"""
def test_jdos_si(si_pbesol: Phono3py):
"""Test joint-DOS by Si."""
si_pbesol.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
si_pbesol.phonon_supercell,
@ -220,10 +214,9 @@ def test_jdos_si(si_pbesol: Phono3py, gp: int, store_dense_gp_map: bool):
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])
jdos.run([105])
# print(", ".join(["%.7f" % fp for fp in jdos.frequency_points]))
np.testing.assert_allclose(si_freq_points, jdos.frequency_points, atol=1e-5)
@ -233,8 +226,7 @@ def test_jdos_si(si_pbesol: Phono3py, gp: int, store_dense_gp_map: bool):
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
def test_jdso_si_nomeshsym(si_pbesol: Phono3py, gp: int, store_dense_gp_map: bool):
def test_jdso_si_nomeshsym(si_pbesol: Phono3py):
"""Test joint-DOS without considering mesh symmetry by Si."""
si_pbesol.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
@ -244,10 +236,9 @@ def test_jdso_si_nomeshsym(si_pbesol: Phono3py, gp: int, store_dense_gp_map: boo
mesh=si_pbesol.mesh_numbers,
num_frequency_points=10,
is_mesh_symmetry=False,
store_dense_gp_map=store_dense_gp_map,
log_level=1,
)
jdos.run([gp])
jdos.run([105])
# 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()]))
@ -256,8 +247,7 @@ def test_jdso_si_nomeshsym(si_pbesol: Phono3py, gp: int, store_dense_gp_map: boo
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
def test_jdos_nacl(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
def test_jdos_nacl(nacl_pbe: Phono3py):
"""Test joint-DOS by NaCl."""
nacl_pbe.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
@ -267,10 +257,9 @@ def test_jdos_nacl(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
mesh=nacl_pbe.mesh_numbers,
nac_params=nacl_pbe.nac_params,
num_frequency_points=10,
store_dense_gp_map=store_dense_gp_map,
log_level=1,
)
jdos.run([gp])
jdos.run([105])
# print(", ".join(["%.7f" % fp for fp in jdos.frequency_points]))
np.testing.assert_allclose(nacl_freq_points, jdos.frequency_points, atol=1e-5)
# print(", ".join(["%.7f" % jd for jd in jdos.joint_dos.ravel()]))
@ -279,8 +268,7 @@ def test_jdos_nacl(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(0, True)])
def test_jdos_nacl_gamma(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
def test_jdos_nacl_gamma(nacl_pbe: Phono3py):
"""Test joint-DOS at Gamma-point by NaCl."""
nacl_pbe.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
@ -291,10 +279,9 @@ def test_jdos_nacl_gamma(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
nac_params=nacl_pbe.nac_params,
nac_q_direction=[1, 0, 0],
num_frequency_points=10,
store_dense_gp_map=store_dense_gp_map,
log_level=1,
)
jdos.run([gp])
jdos.run([0])
# print(", ".join(["%.7f" % fp for fp in jdos.frequency_points]))
np.testing.assert_allclose(nacl_freq_points_gamma, jdos.frequency_points, atol=1e-5)
# print(", ".join(["%.7f" % jd for jd in jdos.joint_dos.ravel()]))
@ -303,8 +290,7 @@ def test_jdos_nacl_gamma(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
def test_jdos_nacl_at_300K(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
def test_jdos_nacl_at_300K(nacl_pbe: Phono3py):
"""Test joint-DOS at 300K by NaCl."""
nacl_pbe.mesh_numbers = [9, 9, 9]
jdos = Phono3pyJointDos(
@ -317,10 +303,9 @@ def test_jdos_nacl_at_300K(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool
temperatures=[
300,
],
store_dense_gp_map=store_dense_gp_map,
log_level=1,
)
jdos.run([gp])
jdos.run([105])
# 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
@ -363,29 +348,22 @@ def test_jdos_nacl_nac_gamma_at_300K_npoints(nacl_pbe: Phono3py):
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(0, False), (0, True)])
def test_jdos_nac_direction_phonon_NaCl(
nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool
):
def test_jdos_nac_direction_phonon_NaCl(nacl_pbe: Phono3py):
"""Test JDOS of NaCl with nac_q_direction."""
jdos = _get_jdos(
nacl_pbe,
[7, 7, 7],
nac_params=nacl_pbe.nac_params,
store_dense_gp_map=store_dense_gp_map,
)
jdos.nac_q_direction = [1, 0, 0]
jdos.set_grid_point(gp)
jdos.set_grid_point(0)
frequencies, _, _ = jdos.get_phonons()
np.testing.assert_allclose(
frequencies[0], [0, 0, 0, 4.59488262, 4.59488262, 7.41183870], rtol=0, atol=1e-6
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(0, False), (0, True)])
def test_jdos_nac_direction_phonon_NaCl_second_error(
nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool
):
def test_jdos_nac_direction_phonon_NaCl_second_error(nacl_pbe: Phono3py):
"""Test JDOS of NaCl with nac_q_direction.
Second setting non-gamma grid point must raise exception.
@ -395,18 +373,14 @@ def test_jdos_nac_direction_phonon_NaCl_second_error(
nacl_pbe,
[7, 7, 7],
nac_params=nacl_pbe.nac_params,
store_dense_gp_map=store_dense_gp_map,
)
jdos.nac_q_direction = [1, 0, 0]
jdos.set_grid_point(gp)
jdos.set_grid_point(0)
with pytest.raises(RuntimeError):
jdos.set_grid_point(1)
@pytest.mark.parametrize("gp1,gp2,store_dense_gp_map", [(0, 1, False), (0, 1, True)])
def test_jdos_nac_direction_phonon_NaCl_second_no_error(
nacl_pbe: Phono3py, gp1: int, gp2: int, store_dense_gp_map: bool
):
def test_jdos_nac_direction_phonon_NaCl_second_no_error(nacl_pbe: Phono3py):
"""Test JDOS of NaCl with nac_q_direction.
Second setting non-gamma grid point should not raise exception because
@ -418,28 +392,25 @@ def test_jdos_nac_direction_phonon_NaCl_second_no_error(
nacl_pbe,
[7, 7, 7],
nac_params=nacl_pbe.nac_params,
store_dense_gp_map=store_dense_gp_map,
)
jdos.nac_q_direction = [1, 0, 0]
jdos.set_grid_point(gp1)
jdos.set_grid_point(0)
jdos.nac_q_direction = None
jdos.set_grid_point(gp2)
jdos.set_grid_point(1)
frequencies, _, _ = jdos.get_phonons()
np.testing.assert_allclose(
frequencies[0], [0, 0, 0, 4.59488262, 4.59488262, 4.59488262], rtol=0, atol=1e-6
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(103, False), (105, True)])
def test_jdos_nac_NaCl_300K_C(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
def test_jdos_nac_NaCl_300K_C(nacl_pbe: Phono3py):
"""Test running JDOS of NaCl in C mode."""
jdos = _get_jdos(
nacl_pbe,
[9, 9, 9],
nac_params=nacl_pbe.nac_params,
store_dense_gp_map=store_dense_gp_map,
)
jdos.set_grid_point(gp)
jdos.set_grid_point(105)
jdos.frequency_points = nacl_freq_points_at_300K
jdos.temperature = 300
jdos.run_phonon_solver()
@ -450,16 +421,14 @@ def test_jdos_nac_NaCl_300K_C(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: b
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(103, False), (105, True)])
def test_jdos_nac_NaCl_300K_Py(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
def test_jdos_nac_NaCl_300K_Py(nacl_pbe: Phono3py):
"""Test running JDOS of NaCl in Py (JDOS) mode."""
jdos = _get_jdos(
nacl_pbe,
[9, 9, 9],
nac_params=nacl_pbe.nac_params,
store_dense_gp_map=store_dense_gp_map,
)
jdos.set_grid_point(gp)
jdos.set_grid_point(105)
jdos.frequency_points = nacl_freq_points_at_300K
jdos.temperature = 300
jdos.run_phonon_solver()
@ -470,16 +439,14 @@ def test_jdos_nac_NaCl_300K_Py(nacl_pbe: Phono3py, gp: int, store_dense_gp_map:
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(103, False), (105, True)])
def test_jdos_nac_NaCl_300K_PyPy(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
def test_jdos_nac_NaCl_300K_PyPy(nacl_pbe: Phono3py):
"""Test running JDOS of NaCl in Py (JDOS) and Py (tetrahedron) mode."""
jdos = _get_jdos(
nacl_pbe,
[9, 9, 9],
nac_params=nacl_pbe.nac_params,
store_dense_gp_map=store_dense_gp_map,
)
jdos.set_grid_point(gp)
jdos.set_grid_point(105)
jdos.frequency_points = nacl_freq_points_at_300K
jdos.temperature = 300
jdos.run_phonon_solver()
@ -490,12 +457,12 @@ def test_jdos_nac_NaCl_300K_PyPy(nacl_pbe: Phono3py, gp: int, store_dense_gp_map
)
def _get_jdos(ph3: Phono3py, mesh, nac_params=None, store_dense_gp_map=False):
def _get_jdos(ph3: Phono3py, mesh, nac_params=None):
bz_grid = BZGrid(
mesh,
lattice=ph3.primitive.cell,
symmetry_dataset=ph3.primitive_symmetry.dataset,
store_dense_gp_map=store_dense_gp_map,
store_dense_gp_map=True,
)
jdos = JointDos(
ph3.primitive,
@ -503,7 +470,6 @@ def _get_jdos(ph3: Phono3py, mesh, nac_params=None, store_dense_gp_map=False):
bz_grid,
ph3.fc2,
nac_params=nac_params,
store_dense_gp_map=store_dense_gp_map,
cutoff_frequency=1e-4,
)
return jdos

3
test/phonon3/test_triplets.py
View File

@ -5,6 +5,7 @@ from phonopy import Phonopy
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.symmetry import Symmetry
from phono3py import Phono3py
from phono3py.phonon3.triplets import (
_get_BZ_triplets_at_q,
_get_triplets_reciprocal_mesh_at_q,
@ -68,7 +69,7 @@ def test_get_triplets_at_q_type1(si_pbesol_111):
np.testing.assert_equal(weights, weights_ref)
def test_get_triplets_at_q_type2(si_pbesol_111):
def test_get_triplets_at_q_type2(si_pbesol_111: Phono3py):
"""Test triplets under type2 grid."""
pcell = si_pbesol_111.primitive
psym = si_pbesol_111.primitive_symmetry