def _get_band_qpoints():
band_paths = [
[[0, 0, 0], [0.5, 0.5, 0.5]],
[[0.5, 0.5, 0], [0, 0, 0], [0.5, 0.25, 0.75]],
]
qpoints = get_band_qpoints(band_paths, npoints=11)
return qpoints
def run_task(self, fw_spec):
create_FORCE_CONSTANTS("vasprun.xml", False, 1)
(Keylist, Coordslist, prims,
transmat) = get_highsympath("POSCAR-unitcell")
phonon = phonopy.load(supercell_matrix=self.get("supercell"),
primitive_matrix=transmat,
unitcell_filename="POSCAR-unitcell",
calculator="vasp",
is_nac=False,
force_constants_filename="FORCE_CONSTANTS")
points = get_band_qpoints([np.array(Coordslist)], 51)
phonon.run_band_structure(points, with_group_velocities=True)
phonon.write_yaml_band_structure()
def run_gruneisen_then_exit(phono3py, settings, output_filename, log_level):
"""Run mode Grueneisen parameter calculation from fc3."""
if (settings.mesh_numbers is None and settings.band_paths is None
and settings.qpoints is None):
print("An option of --mesh, --band, or --qpoints has to be specified.")
if log_level:
print_error()
sys.exit(1)
if len(phono3py.fc2) != len(phono3py.fc3):
print("Supercells used for fc2 and fc3 have to be same.")
if log_level:
print_error()
sys.exit(1)
if settings.band_paths is not None:
if settings.band_points is None:
npoints = 51
else:
npoints = settings.band_points
band_paths = settings.band_paths
bands = get_band_qpoints(band_paths, npoints=npoints)
else:
bands = None
rotations = phono3py.primitive_symmetry.pointgroup_operations
run_gruneisen_parameters(
phono3py.fc2,
phono3py.fc3,
phono3py.supercell,
phono3py.primitive,
bands,
settings.mesh_numbers,
rotations,
settings.qpoints,
nac_params=phono3py.nac_params,
nac_q_direction=settings.nac_q_direction,
ion_clamped=settings.ion_clamped,
factor=VaspToTHz,
symprec=phono3py.symmetry.tolerance,
output_filename=output_filename,
log_level=log_level,
)
if log_level:
print_end()
sys.exit(0)
def testBand(self):
band_paths = [[[0, 0, 0], [0.5, 0.5, 0.5]],
[[0.5, 0.5, 0], [0, 0, 0], [0.5, 0.25, 0.75]]]
qpoints = get_band_qpoints(band_paths, npoints=11)
phonon = self._get_phonon()
phonon.run_band_structure(qpoints, with_group_velocities=True)
band_structure = phonon.band_structure
phonon.get_band_structure_dict()
self.assertTrue(id(band_structure.distances),
id(band_structure.get_distances()))
self.assertTrue(id(band_structure.qpoints),
id(band_structure.get_qpoints()))
self.assertTrue(id(band_structure.frequencies),
id(band_structure.get_frequencies()))
self.assertTrue(id(band_structure.eigenvectors),
id(band_structure.get_eigenvectors()))
self.assertTrue(id(band_structure.group_velocities),
id(band_structure.get_group_velocities()))
def testBand(self):
band_paths = [[[0, 0, 0], [0.5, 0.5, 0.5]],
[[0.5, 0.5, 0], [0, 0, 0], [0.5, 0.25, 0.75]]]
qpoints = get_band_qpoints(band_paths, npoints=11)
phonon = self._get_phonon()
phonon.run_band_structure(qpoints, with_group_velocities=True)
band_structure = phonon.band_structure
phonon.get_band_structure_dict()
self.assertTrue(id(band_structure.distances),
id(band_structure.get_distances()))
self.assertTrue(id(band_structure.qpoints),
id(band_structure.get_qpoints()))
self.assertTrue(id(band_structure.frequencies),
id(band_structure.get_frequencies()))
self.assertTrue(id(band_structure.eigenvectors),
id(band_structure.get_eigenvectors()))
self.assertTrue(id(band_structure.group_velocities),
id(band_structure.get_group_velocities()))
def run_task(self, fw_spec):
files_to_copy = [
"POSCAR-unitcell", "INCAR", "vasprun.xml", "FORCE_CONSTANTS",
"band.yaml"
]
path_dict = dict()
calc_loc_orig = get_calc_loc("orig phonon band", fw_spec["calc_locs"])
path_dict["orig"] = calc_loc_orig["path"]
calc_loc_minus = get_calc_loc("minus phonon band",
fw_spec["calc_locs"])
path_dict["minus"] = calc_loc_minus["path"]
calc_loc_plus = get_calc_loc("plus phonon band", fw_spec["calc_locs"])
path_dict["plus"] = calc_loc_plus["path"]
curr_dir = os.getcwd()
for key, path in path_dict.items():
new_dir = os.path.join(curr_dir, key)
os.makedirs(new_dir)
copy = CopyFiles(from_dir=path,
to_dir=new_dir,
files_to_copy=files_to_copy)
copy.run_task(fw_spec)
phonons = {}
for vol in ("orig", "plus", "minus"):
(Keylist, Coordslist, prims,
transmat) = get_highsympath("%s/POSCAR-unitcell" % vol)
phonon = phonopy.load(
supercell_matrix=self.get("supercell"),
primitive_matrix=transmat,
unitcell_filename="%s/POSCAR-unitcell" % vol,
calculator="vasp",
is_nac=False,
force_constants_filename="%s/FORCE_CONSTANTS" % vol)
phonons[vol] = phonon
gruneisen = PhonopyGruneisen(phonons["orig"], phonons["plus"],
phonons["minus"])
bands = get_band_qpoints([np.array(Coordslist)], 51)
gruneisen.set_band_structure(bands)
gruneisen.write_yaml_band_structure()
def test_gruneisen_band(ph_nacl_gruneisen):
"""Test of mode Grueneisen parameter calculation along band paths."""
paths = get_band_qpoints([[[0.05, 0.05, 0.05], [0.5, 0.5, 0.5]]],
npoints=10)
ph0, ph_minus, ph_plus = ph_nacl_gruneisen
phg = PhonopyGruneisen(ph0, ph_minus, ph_plus)
phg.set_band_structure(paths)
qpoints, distances, freqs, _, gammas = phg.get_band_structure()
# print(", ".join(["%.5f" % v for v in distances[0]]))
np.testing.assert_allclose(distances[0], band_distances, atol=1e-5)
np.testing.assert_allclose(qpoints[0], band_qpoints, atol=1e-5)
# for line in freqs[0].reshape(-1, 6):
# print(", ".join(["%.5f" % v for v in line]))
for freqs_q, band_freqs_q in zip(freqs[0], band_freqs):
np.testing.assert_allclose(np.sort(freqs_q),
np.sort(band_freqs_q),
atol=1e-5)
# for line in gammas[0].reshape(-1, 6):
# print(", ".join(["%.5f" % v for v in line]))
for gammas_q, band_gammas_q in zip(gammas[0], band_gammas):
np.testing.assert_allclose(np.sort(gammas_q),
np.sort(band_gammas_q),
atol=1e-5)
"""NaCl band structure calculation example."""
import phonopy
from phonopy.phonon.band_structure import get_band_qpoints
phonon = phonopy.load(
supercell_matrix=[[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
unitcell_filename="POSCAR-unitcell",
force_sets_filename="FORCE_SETS",
born_filename="BORN",
)
points = get_band_qpoints(
[[[0.5, 0, 0.5], [0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0.25, 0.75]]], 51)
phonon.run_band_structure(points, labels=["X", r"$\Gamma$", "L", "W"])
phonon.plot_band_structure().show()
import phonopy
from phonopy.phonon.band_structure import get_band_qpoints
phonon = phonopy.load([[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
unitcell_filename="POSCAR",
force_sets_filename="FORCE_SETS",
born_filename="BORN")
points = get_band_qpoints(
[[[0.5, 0, 0.5], [0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0.25, 0.75]]], 51)
phonon.set_band_structure(points)
phonon.plot_band_structure(labels=['X', '$\Gamma$', 'L', 'W']).show()
[0.5000000000, 0.0000000000, 0.5000000000]]]
################
fid = open('results.txt', 'w')
fid.write(' System Model MAE fc2 MAE freq. MAE bands\n')
fid.write('==================== ==================== =========== =========== ===========\n')
for system in systems:
phonon_ref = phonopy.load(
unitcell_filename=system+'/POSCAR-unitcell',
supercell_matrix=supercell,
force_constants_filename=system+'/FORCE_CONSTANTS')
bands = get_band_qpoints(band_path, 100)
phonon_ref.run_band_structure(bands)
for model_file in natsorted(os.listdir(models_path)):
calc = spk_calculator(models_path+model_file, environment_provider, device)
if relax:
relax_poscar(system+'/POSCAR-unitcell', calc)
phonon = phonopy.load(
unitcell_filename='POSCAR-opt',
supercell_matrix=supercell,
produce_fc=False)
else:
phonon = phonopy.load(
unitcell_filename=system+'/POSCAR-unitcell',
