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Preparing GridMatrix test

This commit is contained in:
Atsushi Togo 2023-05-30 19:01:53 +09:00
parent 06914266c0
commit d5b004ea97
4 changed files with 79 additions and 67 deletions
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22
phono3py/cui/load.py
View File

@ -181,28 +181,28 @@ def load(
'dielectric': Dielectric constant matrix
(array_like, shape=(3, 3), dtype=float),
'factor': unit conversion facotr (float)}
unitcell_filename : str, optional
unitcell_filename : os.PathLike, optional
Input unit cell filename. Default is None.
supercell_filename : str, optional
supercell_filename : os.PathLike, optional
Input supercell filename. When this is specified, supercell_matrix is
ignored. Default is None.
born_filename : str, optional
born_filename : os.PathLike, optional
Filename corresponding to 'BORN', a file contains non-analytical term
correction parameters.
forces_fc3_filename : sequence or str, optional
forces_fc3_filename : sequence or os.PathLike, optional
A two-elemental sequence of filenames corresponding to
('FORCES_FC3', 'disp_fc3.yaml') in the type-1 format or a filename
(str) corresponding to 'FORCES_FC3' in the type-2 format.
(os.PathLike) corresponding to 'FORCES_FC3' in the type-2 format.
Default is None.
forces_fc2_filename : str or tuple, optional
forces_fc2_filename : os.PathLike or sequence, optional
A two-elemental sequence of filenames corresponding to
('FORCES_FC2', 'disp_fc2.yaml') in the type-1 format or a filename
(str) corresponding to 'FORCES_FC2' in the type-2 format.
(os.PathLike) corresponding to 'FORCES_FC2' in the type-2 format.
Default is None.
fc3_filename : str, optional
fc3_filename : os.PathLike, optional
Filename of a file corresponding to 'fc3.hdf5', a file contains
third-order force constants. Default is None.
fc2_filename : str, optional
fc2_filename : os.PathLike, optional
Filename of a file corresponding to 'fc2.hdf5', a file contains
second-order force constants. Default is None.
fc_calculator : str, optional
@ -378,7 +378,7 @@ def set_dataset_and_force_constants(
if log_level:
print('fc3 was read from "%s".' % fc3_filename)
elif forces_fc3_filename is not None:
if type(forces_fc3_filename) is str:
if isinstance(forces_fc3_filename, os.PathLike):
force_filename = forces_fc3_filename
disp_filename = None
else:
@ -456,7 +456,7 @@ def set_dataset_and_force_constants(
if log_level:
print('fc2 was read from "%s".' % fc2_filename)
elif forces_fc2_filename is not None:
if type(forces_fc2_filename) is str:
if isinstance(forces_fc2_filename, os.PathLike):
force_filename = forces_fc2_filename
disp_filename = None
else:

9
phono3py/phonon/grid.py
View File

@ -549,7 +549,7 @@ class GridMatrix:
Symmetry dataset of spglib (Symmetry.dataset) of primitive cell that
has `lattice`. Default is None.
transformation_matrix : array_like, optional
Transformation matrix equivalent to ``transformation_matrix`` or
Transformation matrix equivalent to ``transformation_matrix`` in
spglib-dataset. This is only used when ``use_grg=True``. Default is
None.
use_grg : bool, optional
@ -714,7 +714,12 @@ class GridMatrix:
RuntimeWarning,
)
if fall_back:
self._D_diag = length2mesh(length, self._lattice)
if symmetry_dataset is None:
self._D_diag = length2mesh(length, self._lattice)
else:
self._D_diag = length2mesh(
length, self._lattice, rotations=symmetry_dataset["rotations"]
)
elif num_values == 3:
self._D_diag = np.array(mesh, dtype="int_")

109
test/conftest.py
View File

@ -1,5 +1,5 @@
"""Pytest conftest.py."""
import os
from pathlib import Path
import numpy as np
import phonopy
@ -9,8 +9,9 @@ from phonopy.interface.phonopy_yaml import read_cell_yaml
from phonopy.structure.atoms import PhonopyAtoms
import phono3py
from phono3py import Phono3py
current_dir = os.path.dirname(os.path.abspath(__file__))
cwd = Path(__file__).parent
store_dense_gp_map = True
@ -27,7 +28,7 @@ def pytest_addoption(parser):
@pytest.fixture(scope="session")
def agno2_cell() -> PhonopyAtoms:
"""Return AgNO2 cell (Imm2)."""
cell = read_cell_yaml(os.path.join(current_dir, "AgNO2_cell.yaml"))
cell = read_cell_yaml(cwd / "AgNO2_cell.yaml")
return cell
@ -49,15 +50,15 @@ def aln_cell() -> PhonopyAtoms:
@pytest.fixture(scope="session")
def si_pbesol(request):
def si_pbesol(request) -> Phono3py:
"""Return Phono3py instance of Si 2x2x2.
* with symmetry
* full fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_si_pbesol.yaml")
forces_fc3_filename = os.path.join(current_dir, "FORCES_FC3_si_pbesol")
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -69,7 +70,7 @@ def si_pbesol(request):
@pytest.fixture(scope="session")
def si_pbesol_grg(request):
def si_pbesol_grg(request) -> Phono3py:
"""Return Phono3py instance of Si 2x2x2.
* with symmetry
@ -77,8 +78,8 @@ def si_pbesol_grg(request):
* 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")
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -91,15 +92,15 @@ def si_pbesol_grg(request):
@pytest.fixture(scope="session")
def si_pbesol_nosym(request):
def si_pbesol_nosym(request) -> Phono3py:
"""Return Phono3py instance of Si 2x2x2.
* without symmetry
* no fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_si_pbesol.yaml")
forces_fc3_filename = os.path.join(current_dir, "FORCES_FC3_si_pbesol")
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -113,15 +114,15 @@ def si_pbesol_nosym(request):
@pytest.fixture(scope="session")
def si_pbesol_nomeshsym(request):
def si_pbesol_nomeshsym(request) -> Phono3py:
"""Return Phono3py instance of Si 2x2x2.
* without mesh-symmetry
* no fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_si_pbesol.yaml")
forces_fc3_filename = os.path.join(current_dir, "FORCES_FC3_si_pbesol")
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -135,15 +136,15 @@ def si_pbesol_nomeshsym(request):
@pytest.fixture(scope="session")
def si_pbesol_compact_fc(request):
def si_pbesol_compact_fc(request) -> Phono3py:
"""Return Phono3py instance of Si 2x2x2.
* with symmetry
* compact fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_si_pbesol.yaml")
forces_fc3_filename = os.path.join(current_dir, "FORCES_FC3_si_pbesol")
yaml_filename = cwd / "phono3py_si_pbesol.yaml"
forces_fc3_filename = cwd / "FORCES_FC3_si_pbesol"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -156,14 +157,14 @@ def si_pbesol_compact_fc(request):
@pytest.fixture(scope="session")
def si_pbesol_111(request):
def si_pbesol_111(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* full fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_Si111.yaml")
yaml_filename = cwd / "phono3py_params_Si111.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -174,7 +175,7 @@ def si_pbesol_111(request):
@pytest.fixture(scope="session")
def si_pbesol_111_alm(request):
def si_pbesol_111_alm(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -184,7 +185,7 @@ def si_pbesol_111_alm(request):
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si111.yaml")
yaml_filename = cwd / "phono3py_params_Si111.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -196,19 +197,19 @@ def si_pbesol_111_alm(request):
@pytest.fixture(scope="session")
def si_pbesol_iterha_111():
def si_pbesol_iterha_111() -> Phonopy:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* no fc
"""
yaml_filename = os.path.join(current_dir, "phonopy_params-Si111-iterha.yaml.gz")
yaml_filename = cwd / "phonopy_params-Si111-iterha.yaml.gz"
return phonopy.load(yaml_filename, log_level=1, produce_fc=False)
@pytest.fixture(scope="session")
def si_pbesol_111_222_fd(request):
def si_pbesol_111_222_fd(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -216,7 +217,7 @@ def si_pbesol_111_222_fd(request):
* use alm if available on test side
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -227,7 +228,7 @@ def si_pbesol_111_222_fd(request):
@pytest.fixture(scope="session")
def si_pbesol_111_222_alm(request):
def si_pbesol_111_222_alm(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -237,7 +238,7 @@ def si_pbesol_111_222_alm(request):
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -249,7 +250,7 @@ def si_pbesol_111_222_alm(request):
@pytest.fixture(scope="session")
def si_pbesol_111_222_alm_fd(request):
def si_pbesol_111_222_alm_fd(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -259,7 +260,7 @@ def si_pbesol_111_222_alm_fd(request):
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -271,7 +272,7 @@ def si_pbesol_111_222_alm_fd(request):
@pytest.fixture(scope="session")
def si_pbesol_111_222_fd_alm(request):
def si_pbesol_111_222_fd_alm(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -281,7 +282,7 @@ def si_pbesol_111_222_fd_alm(request):
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -293,7 +294,7 @@ def si_pbesol_111_222_fd_alm(request):
@pytest.fixture(scope="session")
def si_pbesol_111_222_alm_cutoff(request):
def si_pbesol_111_222_alm_cutoff(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -304,7 +305,7 @@ def si_pbesol_111_222_alm_cutoff(request):
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -317,7 +318,7 @@ def si_pbesol_111_222_alm_cutoff(request):
@pytest.fixture(scope="session")
def si_pbesol_111_222_alm_cutoff_fc2(request):
def si_pbesol_111_222_alm_cutoff_fc2(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -328,7 +329,7 @@ def si_pbesol_111_222_alm_cutoff_fc2(request):
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -341,7 +342,7 @@ def si_pbesol_111_222_alm_cutoff_fc2(request):
@pytest.fixture(scope="session")
def si_pbesol_111_222_alm_cutoff_fc3(request):
def si_pbesol_111_222_alm_cutoff_fc3(request) -> Phono3py:
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
@ -352,7 +353,7 @@ def si_pbesol_111_222_alm_cutoff_fc3(request):
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -365,14 +366,14 @@ def si_pbesol_111_222_alm_cutoff_fc3(request):
@pytest.fixture(scope="session")
def nacl_pbe(request):
def nacl_pbe(request) -> Phono3py:
"""Return Phono3py instance of NaCl 2x2x2.
* with symmetry
* full fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_NaCl222.yaml.xz")
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -383,14 +384,14 @@ def nacl_pbe(request):
@pytest.fixture(scope="session")
def nacl_pbe_compact_fc(request):
def nacl_pbe_compact_fc(request) -> Phono3py:
"""Return Phono3py instance of NaCl 2x2x2.
* with symmetry
* compact fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_NaCl222.yaml.xz")
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -402,13 +403,13 @@ def nacl_pbe_compact_fc(request):
@pytest.fixture(scope="session")
def nacl_pbe_cutoff_fc3(request):
def nacl_pbe_cutoff_fc3(request) -> Phono3py:
"""Return Phono3py instance of NaCl 2x2x2 with cutoff-pair-distance.
* cutoff pair with 5
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_NaCl222.yaml.xz")
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
ph3 = phono3py.load(
yaml_filename,
@ -435,14 +436,14 @@ def nacl_pbe_cutoff_fc3(request):
@pytest.fixture(scope="session")
def nacl_pbe_cutoff_fc3_all_forces(request):
def nacl_pbe_cutoff_fc3_all_forces(request) -> Phono3py:
"""Return Phono3py instance of NaCl 2x2x2 with cutoff-pair-distance.
* cutoff pair with 5
* All forces are set.
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_NaCl222.yaml.xz")
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
ph3 = phono3py.load(
yaml_filename,
@ -459,7 +460,7 @@ def nacl_pbe_cutoff_fc3_all_forces(request):
@pytest.fixture(scope="session")
def nacl_pbe_cutoff_fc3_compact_fc(request):
def nacl_pbe_cutoff_fc3_compact_fc(request) -> Phono3py:
"""Return Phono3py instance of NaCl 2x2x2 with cutoff-pair-distance.
* cutoff pair with 5
@ -467,7 +468,7 @@ def nacl_pbe_cutoff_fc3_compact_fc(request):
* Compact FC
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_NaCl222.yaml.xz")
yaml_filename = cwd / "phono3py_params_NaCl222.yaml.xz"
enable_v2 = request.config.getoption("--v1")
ph3 = phono3py.load(
yaml_filename,
@ -484,14 +485,14 @@ def nacl_pbe_cutoff_fc3_compact_fc(request):
@pytest.fixture(scope="session")
def aln_lda(request):
def aln_lda(request) -> Phono3py:
"""Return Phono3py instance of AlN 3x3x2.
* with symmetry
* full fc.
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_AlN332.yaml.xz")
yaml_filename = cwd / "phono3py_params_AlN332.yaml.xz"
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
@ -504,9 +505,9 @@ def aln_lda(request):
@pytest.fixture(scope="session")
def ph_nacl() -> Phonopy:
"""Return Phonopy class instance of NaCl 2x2x2."""
yaml_filename = os.path.join(current_dir, "phonopy_disp_NaCl.yaml")
force_sets_filename = os.path.join(current_dir, "FORCE_SETS_NaCl")
born_filename = os.path.join(current_dir, "BORN_NaCl")
yaml_filename = cwd / "phonopy_disp_NaCl.yaml"
force_sets_filename = cwd / "FORCE_SETS_NaCl"
born_filename = cwd / "BORN_NaCl"
return phonopy.load(
yaml_filename,
force_sets_filename=force_sets_filename,
@ -520,7 +521,7 @@ def ph_nacl() -> Phonopy:
@pytest.fixture(scope="session")
def ph_si() -> Phonopy:
"""Return Phonopy class instance of Si-prim 2x2x2."""
yaml_filename = os.path.join(current_dir, "phonopy_params_Si.yaml")
yaml_filename = cwd / "phonopy_params_Si.yaml"
return phonopy.load(
yaml_filename,
is_compact_fc=False,

6
test/phonon/test_grid.py
View File

@ -11,6 +11,7 @@ from phono3py import Phono3py
from phono3py.other.tetrahedron_method import get_tetrahedra_relative_grid_address
from phono3py.phonon.grid import (
BZGrid,
GridMatrix,
_get_grid_points_by_bz_rotations_c,
_get_grid_points_by_bz_rotations_py,
_get_grid_points_by_rotations,
@ -2384,3 +2385,8 @@ def test_relocate_BZ_grid_address_aln_compare():
# print(np.dot(bzgrid.P, shifts.T).T)
# return bzgrid
def test_GridMatrix_without_symmetry():
"""Test of GridMatrix."""
GridMatrix(50, np.eye(3) * 5)