def test_get_grid_point_from_address(self):
self._mesh = (10, 10, 10)
print("Compare get_grid_point_from_address from spglib and that " "written in python")
print("with mesh numbers [%d %d %d]" % self._mesh)
for address in list(np.ndindex(self._mesh)):
gp_spglib = get_grid_point_from_address(address, self._mesh)
gp_py = get_grid_point_from_address_py(address, self._mesh)
# print("%s %d %d" % (address, gp_spglib, gp_py))
self.assertEqual(gp_spglib, gp_py)
def test_get_grid_point_from_address(self):
self._mesh = (10, 10, 10)
print("Compare get_grid_point_from_address from spglib and that "
"written in python")
print("with mesh numbers [%d %d %d]" % self._mesh)
for address in list(np.ndindex(self._mesh)):
gp_spglib = get_grid_point_from_address(address, self._mesh)
gp_py = get_grid_point_from_address_py(address, self._mesh)
# print("%s %d %d" % (address, gp_spglib, gp_py))
self.assertEqual(gp_spglib, gp_py)
def get_rotations_for_stars(self):
"Finding the equivalent qpoints as the original q-star and their corresponding rotation matrices"
if os.path.exists("reverse_mapping-m%d%d%d"%tuple(self._mesh)) and os.path.exists("kpt_rotations_at_stars-m%d%d%d"%tuple(self._mesh)):
self._reverse_mapping=pickle.load(open("reverse_mapping-m%d%d%d"%tuple(self._mesh),"rb"))
self._kpt_rotations_at_stars=pickle.load(open("kpt_rotations_at_stars-m%d%d%d"%tuple(self._mesh),"rb"))
else:
try:
kpt_rotations_at_stars=[]
reverse_mapping=[]
for index, grid_point in enumerate(np.unique(self._mapping)):
equi_pos = np.where(self._mapping == grid_point)
kpt_rotations_at_stars.append([np.linalg.inv(rot) for rot in self._rot_mappings[equi_pos]])
reverse_mapping.append(equi_pos[0])
assert len(kpt_rotations_at_stars[index]) == self._weight[index]
self._kpt_rotations_at_stars = kpt_rotations_at_stars
self._reverse_mapping = reverse_mapping
except ImportError:
all_orbits=[]
kpt_rotations_at_stars=[]
for index, grid_point in enumerate(np.unique(self._mapping)):
orig_address = self._grid[grid_point]
orbits = []
rotations = []
for rot in self._kpoint_operations:
rot_address = np.dot(rot, orig_address) % self._mesh
in_orbits = False
for orbit in orbits:
if (rot_address == orbit).all():
in_orbits = True
break
if not in_orbits:
orbits.append(rot_address)
rotations.append(rot)
# check if the number of rotations is correct.
assert len(rotations) == self._weight[index], \
"Num rotations %d, weight %d" % (
len(rotations), self._weight[index])
all_orbits.append(orbits)
kpt_rotations_at_stars.append(rotations)
self._reverse_mapping=[[get_grid_point_from_address(o, self._mesh) for o in p]for p in all_orbits]
assert len(sum(self._reverse_mapping, []))==len(self._mapping)
self._kpt_rotations_at_stars=kpt_rotations_at_stars
pickle.dump(self._reverse_mapping, open("reverse_mapping-m%d%d%d"%tuple(self._mesh),"wb"))
pickle.dump(self._kpt_rotations_at_stars, open("kpt_rotations_at_stars-m%d%d%d"%tuple(self._mesh),"wb"))
def get_phono3py_configurations(settings, options):
primitive_matrix = settings.get_primitive_matrix()
supercell_matrix = settings.get_supercell_matrix()
phonon_supercell_matrix = settings.get_phonon_supercell_matrix()
masses = settings.get_masses()
mesh = settings.get_mesh_numbers()
mesh_divs = settings.get_mesh_divisors()
coarse_mesh_shifts = settings.get_coarse_mesh_shifts()
grid_points = settings.get_grid_points()
grid_addresses = settings.get_grid_addresses()
if grid_addresses is not None:
grid_points = [get_grid_point_from_address(ga, mesh)
for ga in grid_addresses]
band_indices = settings.get_band_indices()
# Brillouin zone integration: Tetrahedron (default) or smearing method
sigma = settings.get_sigma()
if sigma is None:
sigmas = []
elif isinstance(sigma, float):
sigmas = [sigma]
else:
sigmas = sigma
if settings.get_is_tetrahedron_method():
sigmas = [None] + sigmas
if len(sigmas) == 0:
sigmas = [None]
if settings.get_temperatures() is None:
if settings.get_is_joint_dos():
temperature_points = None
temperatures = None
else:
t_max = settings.get_max_temperature()
t_min = settings.get_min_temperature()
t_step = settings.get_temperature_step()
temperature_points = [0.0, 300.0] # For spectra
temperatures = np.arange(t_min, t_max + float(t_step) / 10, t_step)
else:
temperature_points = settings.get_temperatures() # For spectra
temperatures = settings.get_temperatures() # For others
if options.factor is None:
frequency_factor_to_THz = VaspToTHz
else:
frequency_factor_to_THz = options.factor
if settings.get_num_frequency_points() is None:
if settings.get_frequency_pitch() is None:
num_frequency_points = 201
frequency_step = None
else:
num_frequency_points = None
frequency_step = settings.get_frequency_pitch()
else:
num_frequency_points = settings.get_num_frequency_points()
frequency_step = None
if options.freq_scale is None:
frequency_scale_factor = 1.0
else:
frequency_scale_factor = options.freq_scale
if settings.get_cutoff_frequency() is None:
cutoff_frequency = 1e-2
else:
cutoff_frequency = settings.get_cutoff_frequency()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
conf = {}
conf['primitive_matrix'] = primitive_matrix
conf['supercell_matrix'] = supercell_matrix
conf['phonon_supercell_matrix'] = phonon_supercell_matrix
conf['masses'] = masses
conf['mesh'] = mesh
conf['mesh_divs'] = mesh_divs
conf['coarse_mesh_shifts'] = coarse_mesh_shifts
conf['grid_points'] = grid_points
conf['band_indices'] = band_indices
conf['sigmas'] = sigmas
conf['temperature_points'] = temperature_points
conf['temperatures'] = temperatures
conf['frequency_factor_to_THz'] = frequency_factor_to_THz
conf['num_frequency_points'] = num_frequency_points
conf['frequency_step'] = frequency_step
conf['frequency_scale_factor'] = frequency_scale_factor
conf['cutoff_frequency'] = cutoff_frequency
conf['tsym_type'] = tsym_type
return conf
def get_phono3py_configurations(settings, options):
primitive_matrix = settings.get_primitive_matrix()
supercell_matrix = settings.get_supercell_matrix()
phonon_supercell_matrix = settings.get_phonon_supercell_matrix()
masses = settings.get_masses()
mesh = settings.get_mesh_numbers()
mesh_divs = settings.get_mesh_divisors()
coarse_mesh_shifts = settings.get_coarse_mesh_shifts()
grid_points = settings.get_grid_points()
grid_addresses = settings.get_grid_addresses()
if grid_addresses is not None:
grid_points = [
get_grid_point_from_address(ga, mesh) for ga in grid_addresses
]
band_indices = settings.get_band_indices()
# Brillouin zone integration: Tetrahedron (default) or smearing method
sigma = settings.get_sigma()
if sigma is None:
sigmas = []
elif isinstance(sigma, float):
sigmas = [sigma]
else:
sigmas = sigma
if settings.get_is_tetrahedron_method():
sigmas = [None] + sigmas
if len(sigmas) == 0:
sigmas = [None]
if settings.get_temperatures() is None:
if settings.get_is_joint_dos():
temperature_points = None
temperatures = None
else:
t_max = settings.get_max_temperature()
t_min = settings.get_min_temperature()
t_step = settings.get_temperature_step()
temperature_points = [0.0, 300.0] # For spectra
temperatures = np.arange(t_min, t_max + float(t_step) / 10, t_step)
else:
temperature_points = settings.get_temperatures() # For spectra
temperatures = settings.get_temperatures() # For others
if options.factor is None:
frequency_factor_to_THz = VaspToTHz
else:
frequency_factor_to_THz = options.factor
if settings.get_num_frequency_points() is None:
if settings.get_frequency_pitch() is None:
num_frequency_points = 201
frequency_step = None
else:
num_frequency_points = None
frequency_step = settings.get_frequency_pitch()
else:
num_frequency_points = settings.get_num_frequency_points()
frequency_step = None
if options.freq_scale is None:
frequency_scale_factor = 1.0
else:
frequency_scale_factor = options.freq_scale
if settings.get_cutoff_frequency() is None:
cutoff_frequency = 1e-2
else:
cutoff_frequency = settings.get_cutoff_frequency()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
conf = {}
conf['primitive_matrix'] = primitive_matrix
conf['supercell_matrix'] = supercell_matrix
conf['phonon_supercell_matrix'] = phonon_supercell_matrix
conf['masses'] = masses
conf['mesh'] = mesh
conf['mesh_divs'] = mesh_divs
conf['coarse_mesh_shifts'] = coarse_mesh_shifts
conf['grid_points'] = grid_points
conf['band_indices'] = band_indices
conf['sigmas'] = sigmas
conf['temperature_points'] = temperature_points
conf['temperatures'] = temperatures
conf['frequency_factor_to_THz'] = frequency_factor_to_THz
conf['num_frequency_points'] = num_frequency_points
conf['frequency_step'] = frequency_step
conf['frequency_scale_factor'] = frequency_scale_factor
conf['cutoff_frequency'] = cutoff_frequency
conf['tsym_type'] = tsym_type
return conf