def nacl_pbe_cutoff_fc3(request):
"""Return Phono3py instance of NaCl 2x2x2.
* cutoff pair with 5
"""
yaml_filename = os.path.join(current_dir,
"phono3py_params_NaCl222.yaml.xz")
enable_v2 = request.config.getoption("--v1")
ph3 = phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
produce_fc=False,
log_level=1,
)
forces = ph3.forces
ph3.generate_displacements(cutoff_pair_distance=5)
dataset = ph3.dataset
dataset["first_atoms"][0]["forces"] = forces[0]
dataset["first_atoms"][1]["forces"] = forces[1]
count = 2
for first_atoms in dataset["first_atoms"]:
for second_atoms in first_atoms["second_atoms"]:
assert second_atoms["id"] == count + 1
second_atoms["forces"] = forces[count]
count += 1
ph3.dataset = dataset
ph3.produce_fc3(symmetrize_fc3r=True)
return ph3
def run_thermal_conductivity():
"""Run RTA thermal conductivity calculation from input files."""
ph3 = phono3py.load("phono3py_disp.yaml", log_level=2)
ph3.mesh_numbers = [11, 11, 11]
ph3.init_phph_interaction()
ph3.run_thermal_conductivity(temperatures=range(0, 1001, 10),
write_kappa=True)
# Conductivity_RTA object
print(ph3.thermal_conductivity.kappa)
def aln_lda(request):
"""Return Phono3py instance of AlN 3x3x2.
* with symmetry
* full fc.
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_AlN332.yaml.xz")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
def si_pbesol_111(request):
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* full fc
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_Si111.yaml")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
def nacl_pbe(request):
"""Return Phono3py instance of NaCl 2x2x2.
* with symmetry
* compact fc
"""
yaml_filename = os.path.join(current_dir,
"phono3py_params_NaCl222.yaml.xz")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
def si_pbesol(request):
"""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")
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,
log_level=1,
)
def si_pbesol_111_alm(request):
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* full fc
* use alm if available on test side
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si111.yaml")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm",
log_level=1,
)
def test_duplicates_agno2(agno2_cell):
"""Test duplicated pairs of displacements."""
ph3 = phono3py.load(unitcell=agno2_cell, supercell_matrix=[1, 1, 1])
ph3.generate_displacements()
duplicates_ref = [
[106, 22],
[220, 80],
[252, 81],
[221, 96],
[253, 97],
[290, 142],
[348, 244],
[364, 245],
[349, 276],
[365, 277],
[119, 0],
[261, 0],
[229, 0],
[260, 0],
[228, 0],
]
np.testing.assert_equal(duplicates_ref, ph3.dataset["duplicates"])
def si_pbesol():
yaml_filename = os.path.join(current_dir, "phono3py_si_pbesol.yaml")
forces_fc3_filename = os.path.join(current_dir, "FORCES_FC3_si_pbesol")
return phono3py.load(yaml_filename,
forces_fc3_filename=forces_fc3_filename,
log_level=1)
def nacl_pbe():
yaml_filename = os.path.join(current_dir,
"phono3py_params_NaCl222.yaml.xz")
return phono3py.load(yaml_filename, log_level=1)
def si_pbesol_111():
yaml_filename = os.path.join(current_dir, "phono3py_params_Si111.yaml")
return phono3py.load(yaml_filename, log_level=1)