def set_group_velocity(self, q_length=None):
self._set_dynamical_matrix()
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
def set_group_velocity(self, q_points=None, q_length=1e-4):
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_points=q_points,
symmetry=self._symmetry,
q_length=q_length,
frequency_factor_to_THz=self._factor)
def test_gv_nacl(ph_nacl: Phonopy):
"""Test of GroupVelocity by NaCl.
This test should pass _get_dD_FD.
"""
gv_ref = [
14.90162220,
14.90162220,
14.90162220,
14.90162220,
14.90162220,
14.90162220,
24.77046520,
24.77046520,
24.77046520,
-2.17239664,
-2.17239664,
-2.17239664,
-2.17239664,
-2.17239664,
-2.17239664,
-3.05277585,
-3.05277585,
-3.05277585,
]
gv = GroupVelocity(ph_nacl.dynamical_matrix,
symmetry=ph_nacl.primitive_symmetry)
gv.run([[0.1, 0.1, 0.1]])
np.testing.assert_allclose(gv.group_velocities[0].ravel(),
gv_ref,
atol=1e-5)
def __init__(
self,
dynamical_matrix,
q_length=None,
symmetry=None,
frequency_factor_to_THz=VaspToTHz,
cutoff_frequency=1e-4,
):
"""Init method.
See details of parameters at phonopy `GroupVelocity` class.
"""
self._dynmat = None
self._reciprocal_lattice = None
self._q_length = None
self._ddm = None
self._symmetry = None
self._factor = None
self._cutoff_frequency = None
self._directions = None
self._q_points = None
self._perturbation = None
GroupVelocity.__init__(
self,
dynamical_matrix,
q_length=q_length,
symmetry=symmetry,
frequency_factor_to_THz=frequency_factor_to_THz,
cutoff_frequency=cutoff_frequency,
)
self._group_velocity_matrices = None
self._complex_dtype = "c%d" % (np.dtype("double").itemsize * 2)
def test_gv_si(ph_si: Phonopy):
"""Test of GroupVelocity by Si.
This test should pass _get_dD_analytical.
"""
gv_ref = [
17.06443768,
17.06443768,
17.06443768,
17.06443768,
17.06443768,
17.06443768,
46.95145125,
46.95145125,
46.95145125,
-3.59278449,
-3.59278449,
-3.59278449,
-2.39847202,
-2.39847202,
-2.39847202,
-2.39847202,
-2.39847202,
-2.39847202,
]
gv = GroupVelocity(ph_si.dynamical_matrix,
symmetry=ph_si.primitive_symmetry)
gv.run([[0.1, 0.1, 0.1]])
np.testing.assert_allclose(gv.group_velocities[0].ravel(),
gv_ref,
atol=1e-5)
def _init_group_velocity(self):
self._group_velocity = GroupVelocity(
self._pp.get_dynamical_matrix(),
symmetry=self._pp._symmetry,
q_length=self._gv_delta_q,
frequency_factor_to_THz=self._pp.get_frequency_factor_to_THz())
num_grids_all, num_band = self._pp._frequencies.shape
self._gv_all = np.zeros((num_grids_all, num_band, 3), dtype="double")
self._gv_done_all = np.zeros(num_grids_all, dtype="bool")
def set_group_velocity(self, q_length=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._group_velocity = None
return False
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
return True
def set_group_velocity(self, q_length=None):
self._set_dynamical_matrix()
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
def _init_group_velocity(self):
self._group_velocity = GroupVelocity(
self._pp.get_dynamical_matrix(),
symmetry=self._pp._symmetry,
q_length=self._gv_delta_q,
frequency_factor_to_THz=self._pp.get_frequency_factor_to_THz())
num_grids_all, num_band = self._pp._frequencies.shape
self._gv_all = np.zeros((num_grids_all, num_band, 3), dtype="double")
self._gv_done_all = np.zeros(num_grids_all, dtype="bool")
def set_group_velocity(self,
q_points=None,
q_length=1e-4):
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_points=q_points,
symmetry=self._symmetry,
q_length=q_length,
frequency_factor_to_THz=self._factor)
def set_group_velocity(self, q_length=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._group_velocity = None
return False
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
return True
def __init__(self,
interaction,
symmetry,
grid_points=None,
temperatures=None,
sigmas=None,
sigma_cutoff=None,
is_isotope=False,
mass_variances=None,
mesh_divisors=None,
coarse_mesh_shifts=None,
boundary_mfp=None, # in micrometre
is_kappa_star=True,
gv_delta_q=None, # finite difference for group veolocity
is_full_pp=False,
log_level=0):
if sigmas is None:
self._sigmas = []
else:
self._sigmas = sigmas
self._sigma_cutoff = sigma_cutoff
self._pp = interaction
self._is_full_pp = is_full_pp
self._collision = None # has to be set derived class
if temperatures is None:
self._temperatures = None
else:
self._temperatures = np.array(temperatures, dtype='double')
self._is_kappa_star = is_kappa_star
self._gv_delta_q = gv_delta_q
self._log_level = log_level
self._primitive = self._pp.get_primitive()
self._dm = self._pp.get_dynamical_matrix()
self._frequency_factor_to_THz = self._pp.get_frequency_factor_to_THz()
self._cutoff_frequency = self._pp.get_cutoff_frequency()
self._boundary_mfp = boundary_mfp
self._symmetry = symmetry
if not self._is_kappa_star:
self._point_operations = np.array([np.eye(3, dtype='intc')],
dtype='intc')
else:
self._point_operations = symmetry.get_reciprocal_operations()
rec_lat = np.linalg.inv(self._primitive.get_cell())
self._rotations_cartesian = np.array(
[similarity_transformation(rec_lat, r)
for r in self._point_operations], dtype='double')
self._grid_points = None
self._grid_weights = None
self._grid_address = None
self._ir_grid_points = None
self._ir_grid_weights = None
self._read_gamma = False
self._read_gamma_iso = False
self._kappa = None
self._mode_kappa = None
self._frequencies = None
self._cv = None
self._gv = None
self._gv_sum2 = None
self._gamma = None
self._gamma_iso = None
self._num_sampling_grid_points = 0
self._mesh = None
self._mesh_divisors = None
self._coarse_mesh = None
self._coarse_mesh_shifts = None
self._set_mesh_numbers(mesh_divisors=mesh_divisors,
coarse_mesh_shifts=coarse_mesh_shifts)
volume = self._primitive.get_volume()
self._conversion_factor = unit_to_WmK / volume
self._isotope = None
self._mass_variances = None
self._is_isotope = is_isotope
if mass_variances is not None:
self._is_isotope = True
if self._is_isotope:
self._set_isotope(mass_variances)
self._grid_point_count = None
self._set_grid_properties(grid_points)
if (self._dm.is_nac() and
self._dm.get_nac_method() == 'gonze' and
self._gv_delta_q is None):
self._gv_delta_q = 1e-5
if self._log_level:
msg = "Group velocity calculation:\n"
text = ("Analytical derivative of dynamical matrix is not "
"implemented for NAC by Gonze et al. Instead "
"numerical derivative of it is used with dq=1e-5 "
"for group velocity calculation.")
msg += textwrap.fill(text,
initial_indent=" ",
subsequent_indent=" ",
width=70)
print(msg)
self._gv_obj = GroupVelocity(
self._dm,
q_length=self._gv_delta_q,
symmetry=self._symmetry,
frequency_factor_to_THz=self._frequency_factor_to_THz)
# gv_delta_q may be changed.
self._gv_delta_q = self._gv_obj.get_q_length()
class Conductivity(object):
def __init__(self,
interaction,
symmetry,
grid_points=None,
temperatures=None,
sigmas=None,
sigma_cutoff=None,
is_isotope=False,
mass_variances=None,
mesh_divisors=None,
coarse_mesh_shifts=None,
boundary_mfp=None, # in micrometre
is_kappa_star=True,
gv_delta_q=None, # finite difference for group veolocity
is_full_pp=False,
log_level=0):
if sigmas is None:
self._sigmas = []
else:
self._sigmas = sigmas
self._sigma_cutoff = sigma_cutoff
self._pp = interaction
self._is_full_pp = is_full_pp
self._collision = None # has to be set derived class
if temperatures is None:
self._temperatures = None
else:
self._temperatures = np.array(temperatures, dtype='double')
self._is_kappa_star = is_kappa_star
self._gv_delta_q = gv_delta_q
self._log_level = log_level
self._primitive = self._pp.get_primitive()
self._dm = self._pp.get_dynamical_matrix()
self._frequency_factor_to_THz = self._pp.get_frequency_factor_to_THz()
self._cutoff_frequency = self._pp.get_cutoff_frequency()
self._boundary_mfp = boundary_mfp
self._symmetry = symmetry
if not self._is_kappa_star:
self._point_operations = np.array([np.eye(3, dtype='intc')],
dtype='intc')
else:
self._point_operations = symmetry.get_reciprocal_operations()
rec_lat = np.linalg.inv(self._primitive.get_cell())
self._rotations_cartesian = np.array(
[similarity_transformation(rec_lat, r)
for r in self._point_operations], dtype='double')
self._grid_points = None
self._grid_weights = None
self._grid_address = None
self._ir_grid_points = None
self._ir_grid_weights = None
self._read_gamma = False
self._read_gamma_iso = False
self._kappa = None
self._mode_kappa = None
self._frequencies = None
self._cv = None
self._gv = None
self._gv_sum2 = None
self._gamma = None
self._gamma_iso = None
self._num_sampling_grid_points = 0
self._mesh = None
self._mesh_divisors = None
self._coarse_mesh = None
self._coarse_mesh_shifts = None
self._set_mesh_numbers(mesh_divisors=mesh_divisors,
coarse_mesh_shifts=coarse_mesh_shifts)
volume = self._primitive.get_volume()
self._conversion_factor = unit_to_WmK / volume
self._isotope = None
self._mass_variances = None
self._is_isotope = is_isotope
if mass_variances is not None:
self._is_isotope = True
if self._is_isotope:
self._set_isotope(mass_variances)
self._grid_point_count = None
self._set_grid_properties(grid_points)
if (self._dm.is_nac() and
self._dm.get_nac_method() == 'gonze' and
self._gv_delta_q is None):
self._gv_delta_q = 1e-5
if self._log_level:
msg = "Group velocity calculation:\n"
text = ("Analytical derivative of dynamical matrix is not "
"implemented for NAC by Gonze et al. Instead "
"numerical derivative of it is used with dq=1e-5 "
"for group velocity calculation.")
msg += textwrap.fill(text,
initial_indent=" ",
subsequent_indent=" ",
width=70)
print(msg)
self._gv_obj = GroupVelocity(
self._dm,
q_length=self._gv_delta_q,
symmetry=self._symmetry,
frequency_factor_to_THz=self._frequency_factor_to_THz)
# gv_delta_q may be changed.
self._gv_delta_q = self._gv_obj.get_q_length()
def __iter__(self):
return self
def __next__(self):
if self._grid_point_count == len(self._grid_points):
if self._log_level:
print("=================== End of collection of collisions "
"===================")
raise StopIteration
else:
self._run_at_grid_point()
self._grid_point_count += 1
return self._grid_point_count - 1
def next(self):
return self.__next__()
def get_mesh_divisors(self):
return self._mesh_divisors
def get_mesh_numbers(self):
return self._mesh
def get_mode_heat_capacities(self):
return self._cv
def get_group_velocities(self):
return self._gv
def get_gv_by_gv(self):
return self._gv_sum2
def get_frequencies(self):
return self._frequencies[self._grid_points]
def get_qpoints(self):
return self._qpoints
def get_grid_points(self):
return self._grid_points
def get_grid_weights(self):
return self._grid_weights
def get_temperatures(self):
return self._temperatures
def set_temperatures(self, temperatures):
self._temperatures = temperatures
self._allocate_values()
def set_gamma(self, gamma):
self._gamma = gamma
self._read_gamma = True
def set_gamma_isotope(self, gamma_iso):
self._gamma_iso = gamma_iso
self._read_gamma_iso = True
def get_gamma(self):
return self._gamma
def get_gamma_isotope(self):
return self._gamma_iso
def get_kappa(self):
return self._kappa
def get_mode_kappa(self):
return self._mode_kappa
def get_sigmas(self):
return self._sigmas
def get_sigma_cutoff_width(self):
return self._sigma_cutoff
def get_grid_point_count(self):
return self._grid_point_count
def get_averaged_pp_interaction(self):
return self._averaged_pp_interaction
def _run_at_grid_point(self):
"""This has to be implementated in the derived class"""
pass
def _allocate_values(self):
"""This has to be implementated in the derived class"""
pass
def _set_grid_properties(self, grid_points):
self._grid_address = self._pp.get_grid_address()
self._pp.set_nac_q_direction(nac_q_direction=None)
if grid_points is not None: # Specify grid points
self._grid_points = reduce_grid_points(
self._mesh_divisors,
self._grid_address,
grid_points,
coarse_mesh_shifts=self._coarse_mesh_shifts)
(self._ir_grid_points,
self._ir_grid_weights) = self._get_ir_grid_points()
elif not self._is_kappa_star: # All grid points
coarse_grid_address = get_grid_address(self._coarse_mesh)
coarse_grid_points = np.arange(np.prod(self._coarse_mesh),
dtype='uintp')
self._grid_points = from_coarse_to_dense_grid_points(
self._mesh,
self._mesh_divisors,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=self._coarse_mesh_shifts)
self._grid_weights = np.ones(len(self._grid_points), dtype='intc')
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
else: # Automatic sampling
self._grid_points, self._grid_weights = self._get_ir_grid_points()
self._ir_grid_points = self._grid_points
self._ir_grid_weights = self._grid_weights
self._qpoints = np.array(self._grid_address[self._grid_points] /
self._mesh.astype('double'),
dtype='double', order='C')
self._grid_point_count = 0
# set_phonons is unnecessary now because all phonons are calculated in
# self._pp.set_dynamical_matrix, though Gamma-point is an exception,
# which is treatd at self._pp.set_grid_point.
# self._pp.set_phonons(self._grid_points)
self._frequencies, self._eigenvectors, _ = self._pp.get_phonons()
def _get_gamma_isotope_at_sigmas(self, i):
gamma_iso = []
bz_map = self._pp.get_bz_map()
pp_freqs, pp_eigvecs, pp_phonon_done = self._pp.get_phonons()
for j, sigma in enumerate(self._sigmas):
if self._log_level:
text = "Calculating Gamma of ph-isotope with "
if sigma is None:
text += "tetrahedron method"
else:
text += "sigma=%s" % sigma
print(text)
self._isotope.set_sigma(sigma)
self._isotope.set_phonons(self._grid_address,
bz_map,
pp_freqs,
pp_eigvecs,
pp_phonon_done,
dm=self._dm)
gp = self._grid_points[i]
self._isotope.set_grid_point(gp)
self._isotope.run()
gamma_iso.append(self._isotope.get_gamma())
return np.array(gamma_iso, dtype='double', order='C')
def _set_mesh_numbers(self, mesh_divisors=None, coarse_mesh_shifts=None):
self._mesh = self._pp.get_mesh_numbers()
if mesh_divisors is None:
self._mesh_divisors = np.array([1, 1, 1], dtype='intc')
else:
self._mesh_divisors = []
for i, (m, n) in enumerate(zip(self._mesh, mesh_divisors)):
if m % n == 0:
self._mesh_divisors.append(n)
else:
self._mesh_divisors.append(1)
print(("Mesh number %d for the " +
["first", "second", "third"][i] +
" axis is not dividable by divisor %d.") % (m, n))
self._mesh_divisors = np.array(self._mesh_divisors, dtype='intc')
if coarse_mesh_shifts is None:
self._coarse_mesh_shifts = [False, False, False]
else:
self._coarse_mesh_shifts = coarse_mesh_shifts
for i in range(3):
if (self._coarse_mesh_shifts[i] and
(self._mesh_divisors[i] % 2 != 0)):
print("Coarse grid along " +
["first", "second", "third"][i] +
" axis can not be shifted. Set False.")
self._coarse_mesh_shifts[i] = False
self._coarse_mesh = self._mesh // self._mesh_divisors
if self._log_level:
print("Lifetime sampling mesh: [ %d %d %d ]" %
tuple(self._mesh // self._mesh_divisors))
def _get_ir_grid_points(self):
if self._coarse_mesh_shifts is None:
mesh_shifts = [False, False, False]
else:
mesh_shifts = self._coarse_mesh_shifts
(coarse_grid_points,
coarse_grid_weights,
coarse_grid_address, _) = get_ir_grid_points(
self._coarse_mesh,
self._symmetry.get_pointgroup_operations(),
mesh_shifts=mesh_shifts)
grid_points = from_coarse_to_dense_grid_points(
self._mesh,
self._mesh_divisors,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=self._coarse_mesh_shifts)
grid_weights = coarse_grid_weights
assert grid_weights.sum() == np.prod(self._mesh // self._mesh_divisors)
return grid_points, grid_weights
def _set_isotope(self, mass_variances):
if mass_variances is True:
mv = None
else:
mv = mass_variances
self._isotope = Isotope(
self._mesh,
self._primitive,
mass_variances=mv,
frequency_factor_to_THz=self._frequency_factor_to_THz,
symprec=self._symmetry.get_symmetry_tolerance(),
cutoff_frequency=self._cutoff_frequency,
lapack_zheev_uplo=self._pp.get_lapack_zheev_uplo())
self._mass_variances = self._isotope.get_mass_variances()
def _set_harmonic_properties(self, i_irgp, i_data):
grid_point = self._grid_points[i_irgp]
freqs = self._frequencies[grid_point][self._pp.get_band_indices()]
self._cv[:, i_data, :] = self._get_cv(freqs)
gv = self._get_gv(self._qpoints[i_irgp])
self._gv[i_data] = gv[self._pp.get_band_indices(), :]
# Outer product of group velocities (v x v) [num_k*, num_freqs, 3, 3]
gv_by_gv_tensor, order_kstar = self._get_gv_by_gv(i_irgp, i_data)
self._num_sampling_grid_points += order_kstar
# Sum all vxv at k*
for j, vxv in enumerate(
([0, 0], [1, 1], [2, 2], [1, 2], [0, 2], [0, 1])):
self._gv_sum2[i_data, :, j] = gv_by_gv_tensor[:, vxv[0], vxv[1]]
def _get_gv(self, q):
self._gv_obj.set_q_points([q])
return self._gv_obj.get_group_velocity()[0]
def _get_gv_by_gv(self, i_irgp, i_data):
rotation_map = get_grid_points_by_rotations(
self._grid_address[self._grid_points[i_irgp]],
self._point_operations,
self._mesh)
gv = self._gv[i_data]
gv_by_gv = np.zeros((len(gv), 3, 3), dtype='double')
for r in self._rotations_cartesian:
gvs_rot = np.dot(gv, r.T)
gv_by_gv += [np.outer(r_gv, r_gv) for r_gv in gvs_rot]
gv_by_gv /= len(rotation_map) // len(np.unique(rotation_map))
order_kstar = len(np.unique(rotation_map))
if self._grid_weights is not None:
if order_kstar != self._grid_weights[i_irgp]:
if self._log_level:
print("*" * 33 + "Warning" + "*" * 33)
print(" Number of elements in k* is unequal "
"to number of equivalent grid-points.")
print("*" * 73)
return gv_by_gv, order_kstar
def _get_cv(self, freqs):
cv = np.zeros((len(self._temperatures), len(freqs)), dtype='double')
# T/freq has to be large enough to avoid divergence.
# Otherwise just set 0.
for i, f in enumerate(freqs):
finite_t = (self._temperatures > f / 100)
if f > self._cutoff_frequency:
cv[:, i] = np.where(
finite_t, get_mode_cv(
np.where(finite_t, self._temperatures, 10000),
f * THzToEv), 0)
return cv
def _get_main_diagonal(self, i, j, k):
num_band = self._primitive.get_number_of_atoms() * 3
main_diagonal = self._gamma[j, k, i].copy()
if self._gamma_iso is not None:
main_diagonal += self._gamma_iso[j, i]
if self._boundary_mfp is not None:
main_diagonal += self._get_boundary_scattering(i)
# if self._boundary_mfp is not None:
# for l in range(num_band):
# # Acoustic modes at Gamma are avoided.
# if i == 0 and l < 3:
# continue
# gv_norm = np.linalg.norm(self._gv[i, l])
# mean_free_path = (gv_norm * Angstrom * 1e6 /
# (4 * np.pi * main_diagonal[l]))
# if mean_free_path > self._boundary_mfp:
# main_diagonal[l] = (
# gv_norm / (4 * np.pi * self._boundary_mfp))
return main_diagonal
def _get_boundary_scattering(self, i):
num_band = self._primitive.get_number_of_atoms() * 3
g_boundary = np.zeros(num_band, dtype='double')
for l in range(num_band):
g_boundary[l] = (np.linalg.norm(self._gv[i, l]) * Angstrom * 1e6 /
(4 * np.pi * self._boundary_mfp))
return g_boundary
def _show_log_header(self, i):
if self._log_level:
gp = self._grid_points[i]
print("======================= Grid point %d (%d/%d) "
"=======================" %
(gp, i + 1, len(self._grid_points)))
print("q-point: (%5.2f %5.2f %5.2f)" % tuple(self._qpoints[i]))
if self._boundary_mfp is not None:
if self._boundary_mfp > 1000:
print("Boundary mean free path (millimetre): %.3f" %
(self._boundary_mfp / 1000.0))
else:
print("Boundary mean free path (micrometre): %.5f" %
self._boundary_mfp)
if self._is_isotope:
print(("Mass variance parameters: " +
"%5.2e " * len(self._mass_variances)) %
tuple(self._mass_variances))
class Collision():
def __init__(self,
interaction,
sigmas=np.array([0.1]),
temperatures=None,
lang="C",
is_tetrahedron_method=False,
mass_variances=None,
length=None,
gv_delta_q = None,
is_adaptive_sigma=False,
is_group_velocity=False, # Use gv to determine smearing factor
write=False,
read=False,
cutoff_frequency = 1e-4): #unit: THz
self._pp = interaction
self._sigmas = sigmas
self._temperatures = temperatures
self._mesh = self._pp.get_mesh_numbers()
self._is_nosym = self._pp._is_nosym
if interaction._is_nosym:
self._point_operations = np.array([[1,0,0],[0,1,0],[0,0,1]], dtype="intc")
else:
self._point_operations = self._pp.get_point_group_operations()
self._kpoint_operations = self._pp._kpoint_operations
self._is_dispersed=self._pp.get_is_dispersed()
self._cutoff_frequency = cutoff_frequency
self._grid_point = None
self._grid_point_triplets = None
self._triplet_weights = None
self._is_thm = is_tetrahedron_method
self._lang = lang
self._frequencies_all = None
self._eigenvectors_all = None
self._band_indices = None
self._fc3_normal_squared = None
self._occupations_all = None
self._sigma =None
self._temperature = None
self._isigma = None
self._itemp = None
self._is_group_velocity = is_group_velocity
self._write_col=write
self._read_col=read
self._is_adaptive_sigma =is_adaptive_sigma
self._is_on_iteration = False
self._asigma = None
self._gamma_all=None
self._irr_mapping_indices = None
self._collision_in = None
self._collision_out = None
self._collision_in_all = None
self._is_read_error = None
self._unit_conversion = np.pi / 4 * ((Hbar * EV) ** 3 # Hbar * EV : hbar
* EV ** 2 / Angstrom ** 6
/ (2 * np.pi * THz) ** 3
/ AMU ** 3
/ (Hbar * EV) ** 2
/ (2 * np.pi * THz) ** 2
/ np.prod(self._mesh))
self._init_grids_properties()
self._length = length
self._gv_delta_q = gv_delta_q
if is_group_velocity or self._length is not None:
self._init_group_velocity()
if mass_variances is not None:
self._collision_iso = \
CollisionIso(self._mesh,
self._pp._primitive,
mass_variances,
self._band_indices,
self._sigma)
self._collision_iso.set_dynamical_matrix(dynamical_matrix=self._pp.get_dynamical_matrix())
else:
self._collision_iso = None
def _init_group_velocity(self):
self._group_velocity = GroupVelocity(
self._pp.get_dynamical_matrix(),
symmetry=self._pp._symmetry,
q_length=self._gv_delta_q,
frequency_factor_to_THz=self._pp.get_frequency_factor_to_THz())
num_grids_all, num_band = self._pp._frequencies.shape
self._gv_all = np.zeros((num_grids_all, num_band, 3), dtype="double")
self._gv_done_all = np.zeros(num_grids_all, dtype="bool")
def _init_grids_properties(self):
num_grids_all, num_band = self._pp._frequencies.shape
num_temp = len(self._temperatures)
num_sigma = len(self._sigmas)
self._occupations_all = np.zeros((num_grids_all, num_temp, num_band), dtype="double")
self._collision_out_all = np.zeros((num_sigma, num_grids_all, num_temp, num_band), dtype="double")
self._gamma_all = np.zeros_like(self._collision_out_all)
self._n_done = np.zeros((num_grids_all, num_temp), dtype="bool")
def set_grid(self, grid_point):
if grid_point is None:
self._grid_point = None
else:
self._pp.set_grid_point(grid_point)
(self._grid_point_triplets,
self._triplet_weights) = self._pp.get_triplets_at_q()
self._grid_point = self._grid_point_triplets[0, 0]
self._grid_address = self._pp.get_grid_address()
self._qpoint = self._grid_address[self._grid_point] / np.double(self._mesh)
kpg_index = get_kgp_index_at_grid(self._grid_address[grid_point], self._mesh, self._kpoint_operations)
self._inv_rot_sum = self._kpoint_operations[kpg_index].sum(axis=0)
self._kpg_at_q_index = kpg_index
self._fc3_normal_squared = None
if self._collision_iso is not None:
grid_points2 = self.get_grid_point_triplets()[:,1].astype("intc").copy()
weights2 = self.get_triplets_weights()
self._collision_iso.set_grid_point(grid_point, grid_points2=grid_points2, weights2=weights2)
def set_pp_grid_points_all(self, grid_points):
self._pp.set_grid_points(grid_points)
def set_grids(self, grid_points):
self._pp._grid_points = grid_points
self._collision_done = None
if self._pp._unique_triplets == None:
self._pp.set_grid_points(grid_points)
if not self._is_dispersed:
bi = self._pp._band_indices
nband = 3 * self._pp._primitive.get_number_of_atoms()
luniq = len(self._pp._unique_triplets)
try:
self._collision_in_all = np.zeros((luniq,3, len(bi), nband), dtype="double")
except MemoryError:
print "A memory error occurs in allocating the whole collision array"
print "--disperse is recommended as a possible solution"
sys.exit(1)
self._collision_done = np.zeros(luniq, dtype="bool")
def get_occupation(self):
return self._occupations_all
def get_grid_point_triplets(self):
return self._grid_point_triplets
def get_triplets_weights(self):
return self._triplet_weights
def get_collision_out(self):
if self._cutoff_frequency is None:
return self._collision_out
else: # Averaging imag-self-energies by degenerate bands
deg_sets = self._degeneracy_all[self._grid_point]
cout = np.zeros_like(self._collision_out)
for i, dset in enumerate(deg_sets):
cout[i] = np.average(self._collision_out[np.where(deg_sets == dset)])
return cout
def get_collision_in(self):
return self._collision_in
def read_collision_all(self, log_level=0, is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
is_error = read_collision_all_from_hdf5(self._collision_in_all,
self._mesh,
self._sigma,
self._temperature,
is_adaptive_sigma=is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
if is_error:
self.set_write_collision(True)
else:
if self._is_adaptive_sigma and (not self._is_on_iteration):
self._collision_done[:] = False
else:
self._collision_done[:] = True
def read_collision_at_grid(self, grid, log_level=0, is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
is_error = read_collision_at_grid_from_hdf5(self._collision_in,
self._mesh,
grid,
self._sigma,
self._temperature,
is_adaptive_sigma=is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
self._is_read_error = is_error
if self._is_read_error:
self.set_read_collision(False)
self.set_write_collision(True)
def write_collision_at_grid(self, grid, log_level=0, is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
write_collision_to_hdf5_at_grid(self._collision_in,
self._mesh,
grid,
self._sigma,
self._temperature,
is_adaptive_sigma=is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
if self._is_read_error: # Condition: read argument is invoked
self.set_read_collision(True)
self.set_write_collision(False)
def write_collision_all(self, log_level=0, is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
if self._write_col:
write_collision_to_hdf5_all(self._collision_in_all,
self._mesh,
self._sigma,
self._temperature,
is_adaptive_sigma = is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
def set_temperature(self, temperature):
for i, t in enumerate(self._temperatures):
if temperature == t:
self._itemp = i
break
self._temperature=temperature
def set_is_adaptive_sigma(self, is_adaptive_sigma=False):
self._is_adaptive_sigma = is_adaptive_sigma
def set_is_on_iteration(self, is_on_iteration=True):
self._is_on_iteration = is_on_iteration
def set_sigma(self, sigma):
for i, s in enumerate(self._sigmas):
if s == sigma:
self._isigma = i
break
self._sigma = sigma
if self._sigma is None:
self._is_thm = True
@total_time.timeit
def set_asigma(self, gamma_prev = None, gamma_pprev=None):
if self._is_dispersed:
if not self._read_col:
triplets = self._grid_point_triplets
elif self._is_adaptive_sigma or self._is_group_velocity:
return
else:
triplets = self._triplets_reduced
if self._is_adaptive_sigma:
if gamma_prev is not None:
if gamma_pprev is not None:
gamma_all = (self._gamma_all[self._isigma, :, self._itemp] + gamma_prev + gamma_pprev) / 3
else:
gamma_all = (self._gamma_all[self._isigma, :, self._itemp] + gamma_prev) / 2
else:
gamma_all = self._gamma_all[self._isigma, :, self._itemp]
triplet_gammas = gamma_all[triplets]
gt = (triplet_gammas * 2 * np.pi) ** 2 / (2 * np.log(2)) # 2pi comes from the definition of gamma
self._asigma = np.sqrt(gt[:,0, :, np.newaxis, np.newaxis] +
gt[:,1, np.newaxis, :, np.newaxis] +
gt[:,2, np.newaxis, np.newaxis, :])
elif self._is_group_velocity:
self._set_group_velocity(grid_points=np.unique(triplets))
triplet1, triplet2 = triplets[:, 1], triplets[:,2]
gv1, gv2 = self._gv_all[triplet1], self._gv_all[triplet2]
reciprocal_lattice = np.linalg.inv(self._pp._primitive.get_cell())
num_band = len(self._band_indices)
gvs = gv1[:, :, np.newaxis] - gv2[:, np.newaxis, :]
normalized_gvs = np.dot(gvs, reciprocal_lattice) / np.array(self._mesh)
sigmas= np.sqrt(np.sum(normalized_gvs ** 2, axis=-1) / 12)
self._asigma = np.repeat(sigmas[:, np.newaxis], repeats=num_band, axis=1)
else:
if self._read_col:
nband = self._pp._primitive.get_number_of_atoms() * 3
self._asigma = np.zeros((0,nband, nband, nband), dtype="double")
def _set_group_velocity(self, grid_points):
undone_grid_points = np.extract(self._gv_done_all[grid_points] == 0, grid_points)
qpoints = [self._grid_address[gp] / np.double(self._mesh) for gp in undone_grid_points]
if len(qpoints) != 0:
self._group_velocity.set_q_points(q_points=qpoints)
self._gv_all[undone_grid_points] = self._group_velocity.get_group_velocity()
self._gv_done_all[undone_grid_points] = True
def set_write_collision(self, is_write_col):
self._write_col = is_write_col
def set_read_collision(self, is_read_col):
self._read_col = is_read_col
def get_write_collision(self):
return self._write_col
def get_read_collision(self):
return self._read_col
def get_is_dispersed(self):
return self._is_dispersed
def get_collision_out_all(self):
return self._collision_out_all
@total_time.timeit
def run_interaction_at_grid_point(self, g_skip = None):
self.set_phonons_triplets()
if self._read_col and ((not self._is_adaptive_sigma) or self._is_on_iteration):
nband = self._pp._primitive.get_number_of_atoms() * 3
self._fc3_normal_squared = np.zeros((0,nband, nband, nband), dtype="double")
self._fc3_normal_squared_reduced = np.zeros((0,nband, nband, nband), dtype="double")
else:
self._pp.run(g_skip = g_skip, lang=self._lang)
self._fc3_normal_squared = self._pp.get_interaction_strength()
self._fc3_normal_squared_reduced= self._fc3_normal_squared[self._undone_triplet_index]
if self._collision_iso:
self._collision_iso.set_frequencies(frequencies=self._frequencies_all,
eigenvectors=self._eigenvectors_all,
phonons_done=self._pp._phonon_done,
degeneracies=self._degeneracy_all)
def set_phonons_triplets(self):
self._pp.set_phonons(lang=self._lang)
(self._frequencies_all,
self._eigenvectors_all) = self._pp.get_phonons()[:2]
self._degeneracy_all = self._pp.get_degeneracy()
self._band_indices = self._pp.get_band_indices()
def reduce_triplets(self):
num_triplets = len(self._pp.get_triplets_at_q()[0])
num_band0 = len(self._band_indices)
num_band = self._pp._primitive.get_number_of_atoms() * 3
self._collision_out = None
self._collision_in = np.zeros((num_triplets, num_band0, num_band), dtype="double")
self._triplets_mapping = self._pp.get_triplets_mapping_at_grid()
self.extract_undone_triplets()
self._collision_in_reduced = np.zeros((len(self._undone_uniq_index),
3,
num_band0,
num_band), dtype="double")
self._triplets_reduced = self._pp.get_triplets_at_q()[0][self._undone_triplet_index]
assert (self._pp._phonon_done[self._triplets_reduced] == True).all()
self._frequencies_reduced = self._frequencies_all[self._triplets_reduced]
# self.set_grid_points_occupation()
self._occu_reduced = self._occupations_all[self._triplets_reduced, self._itemp]
def set_grid_points_occupation(self, grid_points=None):
if grid_points is None:
grid_points = self._grid_point_triplets
uniq_grids = np.unique(grid_points)
for g in uniq_grids:
if not self._n_done[g, self._itemp]:
n = occupation(self._frequencies_all[g], self._temperature)
n[np.where(self._frequencies_all[g]<self._cutoff_frequency)] = 0
self._occupations_all[g, self._itemp] = n
self._n_done[g, self._itemp] = True
if self._collision_iso is not None:
self._collision_iso.set_occupation(occupations=self._occupations_all[:,self._itemp],
occupations_done=self._n_done[:,self._itemp])
def set_grid_points_group_velocity(self, grid_points=None):
if grid_points is None:
grid_points = self._grid_point_triplets
uniq_grids = np.unique(grid_points)
def extract_undone_triplets(self):
unique_map, index = np.unique(self._triplets_mapping, return_index=True)
if self._is_dispersed:
self._undone_uniq_index = unique_map
self._undone_triplet_index = index
else:
self._undone_uniq_index = np.extract(self._collision_done[unique_map]==False, unique_map)
self._undone_triplet_index = np.extract(self._collision_done[unique_map]==False, index)
def broadcast_collision_out(self):
grid_map = self._pp.get_grid_mapping()
bz_to_pp_map = self._pp.get_bz_to_pp_map()
bz_to_irred_map = grid_map[bz_to_pp_map]
equiv_pos = np.where(bz_to_irred_map == self._grid_point)
cm_out = self.get_collision_out()
self._collision_out_all[self._isigma, equiv_pos, self._itemp] = cm_out
n = self.get_occupation()[self._grid_point, self._itemp]
nn1 = n * (n + 1)
is_pass = self._frequencies_all[self._grid_point] < self._cutoff_frequency
self._gamma_all[self._isigma, equiv_pos, self._itemp] = \
cm_out * np.where(is_pass, 0, 1 / nn1) / 2.
def run(self):
if self._is_dispersed and self._read_col:
self.read_collision_at_grid(self._grid_point)
if self._lang=="C":
self.run_c()
else:
self.run_py()
if self._is_dispersed and self._write_col:
self.write_collision_at_grid(self._grid_point)
# self._collision_in *= self._unit_conversion # unit in THz
summation = np.sum(self._collision_in, axis=-1)
self._collision_out = np.dot(self._triplet_weights, summation) / 2.0
# Set the diagonal part in A_in as 0
# bz_to_pp = self._pp._bz_to_pp_map
# triplets = bz_to_pp[self.get_grid_point_triplets()]
# diag_pos = np.where(triplets[:, 1] == triplets[0,0])[0][0]
# self._collision_out += self._collision_in[diag_pos].diagonal()
# np.fill_diagonal(self._collision_in[diag_pos], 0)
# Set the diagonal part in A_in as 0
if self._collision_iso is not None:
self._collision_iso.run()
self._collision_out += self._collision_iso._collision_out
self._collision_in += self._collision_iso._collision_in
if self._length is not None:
self._collision_out += self.get_boundary_scattering_strength()
self.broadcast_collision_out()
@total_time.timeit
def get_boundary_scattering_strength(self):
self._set_group_velocity(grid_points=[self._grid_point])
bnd_collision_unit = 100. / 1e-6 / THz / (2 * np.pi) # unit in THz, unit of length is micron
gv = self._gv_all[self._grid_point]
dm = self._pp.get_dynamical_matrix()
gv1 = get_group_velocity(self._qpoint,
dm,
symmetry=self._pp._symmetry,
q_length=self._gv_delta_q,
frequency_factor_to_THz=self._pp.get_frequency_factor_to_THz())
gv_average = np.sqrt(np.sum(gv ** 2, axis=-1))
n = self._occupations_all[self._grid_point, self._itemp]
cout_bnd = gv_average / self._length * n * (n + 1)
return cout_bnd * bnd_collision_unit
def run_py(self):
for i, triplet in enumerate(self._grid_point_triplets):
occu = occupation(self._frequencies_all[triplet], self._temperature)
freq = self._frequencies_all[triplet]
for (j,k,l) in np.ndindex(self._fc3_normal_squared.shape[1:]):
if self._asigma:
sigma=self._asigma[i,j,k,l]
else:
sigma = self._sigma
f0 = freq[0, j]; f1 = freq[1, k]; f2 = freq[2, l]
if (f0<self._cutoff_frequency or f1 < self._cutoff_frequency or f2 < self._cutoff_frequency):
continue
n0 = occu[0, j]; n1 = occu[1, k]; n2 = occu[2, l]
delta1 = gaussian(f0+f1-f2, sigma)
delta2 = gaussian(f0+f2-f1, sigma)
delta3 = gaussian(f0-f1-f2, sigma)
self._collision_in[i,j,k] += self._fc3_normal_squared[i,j,k,l] * ((n0 + 1) * n1 * n2 * delta3 +
(n1 + 1) * n0 * n2 * delta2 +
(n2 + 1) * n0 * n1 * delta1)
self._collision_in *= self._unit_conversion
def set_integration_weights(self, cutoff_g = 1e-8):
f_points = self._frequencies_all[self._grid_point][self._band_indices]
is_read_g = False; is_write_g = False
if not self._is_adaptive_sigma and len(self._temperatures) > 1:
if self._pp.get_is_read_amplitude() or self._pp.get_is_write_amplitude():
if self._itemp == 0:
is_write_g = True; is_read_g = False
else:
is_write_g = False; is_read_g = True
if self._asigma is not None:
sigma_object = self._asigma
cutoff_g = np.where(self._asigma > 0, cutoff_g / self._asigma, 0)
if self._is_dispersed and not self._read_col:
cutoff_g = cutoff_g[self._undone_triplet_index]
else:
sigma_object = self._sigma
if sigma_object is not None:
cutoff_g = cutoff_g / self._sigma
if self._is_dispersed:
if is_read_g:
self._g = read_integration_weight_from_hdf5_at_grid(self._mesh, self._sigma, self._grid_point)
elif not self._read_col:
self._g = get_triplets_integration_weights(
self._pp,
np.array(f_points, dtype='double'),
sigma_object,
band_indices=self._band_indices,
triplets = self._grid_point_triplets,
is_triplet_symmetry=self._pp._symmetrize_fc3_q)
# when all the integration weights are smaller than the cutoff value
# the interaction strength will not be calculated
if is_write_g:
write_integration_weight_to_hdf5_at_grid(self._mesh, self._sigma, self._grid_point, self._g)
self._g_skip = np.array(self._g[:, self._undone_triplet_index].sum(axis=0) < cutoff_g, dtype="bool")
else:
self._g_skip = None
else:
if is_read_g:
self._g = read_integration_weight_from_hdf5_at_grid(self._mesh, self._sigma, self._grid_point)
else:
self._g = get_triplets_integration_weights(
self._pp,
np.array(f_points, dtype='double'),
sigma_object,
band_indices=self._band_indices,
triplets = self._triplets_reduced,
is_triplet_symmetry=self._pp._symmetrize_fc3_q)
if is_write_g:
write_integration_weight_to_hdf5_at_grid(self._mesh, self._sigma, self._grid_point, self._g)
if self._pp.get_triplets_done().all(): #when the interaction strengths are all done
self._g_skip = None
else:
self._g_skip = np.array(np.abs(self._g).sum(axis=0) < cutoff_g, dtype="bool")
def get_integration_weights(self):
return self._g
def get_interaction_skip(self):
return self._g_skip
@total_time.timeit
def run_c(self):
import anharmonic._phono3py as phono3c
freq = self._frequencies_all[self._grid_point_triplets]
if self._is_dispersed:
if not self._read_col:
phono3c.collision(self._collision_in,
self._fc3_normal_squared.copy(),
freq.copy(),
self._g.copy(),
self._temperature,
self._cutoff_frequency)
phono3c.collision_degeneracy(self._collision_in,
self._degeneracy_all.astype('intc'),
self._grid_point_triplets.astype("intc"),
False)
self._collision_in *= self._unit_conversion # unit in THz
else:
phono3c.collision_all_permute(self._collision_in_reduced,
self._fc3_normal_squared_reduced.copy(),
self._occu_reduced.copy(),
self._frequencies_reduced.copy(),
self._g.copy(),
self._cutoff_frequency)
self._collision_in_reduced *= self._unit_conversion # unit in THz
phono3c.collision_degeneracy(self._collision_in_reduced,
self._degeneracy_all.astype('intc'),
self._triplets_reduced.astype('intc').copy(),
True)
self._collision_in_all[self._undone_uniq_index] = self._collision_in_reduced[:]
self._collision_done[self._undone_uniq_index] = True
phono3c.collision_from_reduced(self._collision_in,
self._collision_in_all,
self._pp.get_triplets_mapping_at_grid().astype("intc"),
self._pp.get_triplets_sequence_at_grid().astype("byte"))
# #############debugging############################
# f_points = self._frequencies_all[self._grid_point][self._band_indices]
# if self._asigma is not None:
# sigma_object = self._asigma
# else:
# sigma_object = self._sigma
# self._g = get_triplets_integration_weights(
# self._pp,
# np.array(f_points, dtype='double'),
# sigma_object,
# triplets = self._grid_point_triplets)
# collision_in = np.zeros_like(self._collision_in)
#
# phono3c.collision(collision_in,
# self._fc3_normal_squared.copy(),
# freq.copy(),
# self._g.copy(),
# self._temperature,
# self._cutoff_frequency)
# grid_points2 = self._grid_point_triplets[:, 1]
# phono3c.collision_degeneracy_grid(collision_in,
# self._degeneracy_all.astype('intc'),
# grid_points2.astype('intc').copy(),
# self._grid_point)
# collision_in *= self._unit_conversion # unit in THz
# diff = np.abs(collision_in - self._collision_in)
# if len(diff)>0:
# print diff.max()
# tt, bb0, bb1 = np.unravel_index(diff.argmax(), diff.shape)
# grid0, grid1, grid2 = self._grid_point_triplets[tt]
# n0 = self._occupations_all[grid0, self._itemp, bb0]
# n1 = self._occupations_all[grid1, self._itemp, bb1]
# n2 = self._occupations_all[grid2, self._itemp]
# g0 = self._g[0, tt, bb0, bb1]
# g1 = self._g[1, tt, bb0, bb1]
# g2 = self._g[2, tt, bb0, bb1]
# ng = n0 * n1 * (n2 + 1) * g2 + n0 * (n1 + 1) * n2 * g1 + (n0 + 1) * n1 * n2 * g0
# nga = ng * self._fc3_normal_squared[tt, bb0, bb1] * self._unit_conversion
# print
@total_time.timeit
def calculate_collision(self,grid_point, sigma=None, temperature=None):
"On behalf of the limited memory, each time only one temperature and one sigma is calculated"
if sigma is not None:
self.set_sigma(sigma)
if temperature is not None:
self.set_temperature(temperature)
self.set_grid(grid_point)
self.set_phonons_triplets()
self.set_grid_points_occupation()
self.reduce_triplets()
self.set_asigma()
self.set_integration_weights()
self.run_interaction_at_grid_point(g_skip = self._g_skip)
self.run()
class Phonopy:
def __init__(self,
unitcell,
supercell_matrix,
distance=0.01,
factor=VaspToTHz,
is_auto_displacements=True,
symprec=1e-5,
is_symmetry=True,
log_level=0):
self._symprec = symprec
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._factor = factor
self._is_symmetry = is_symmetry
self._log_level = log_level
self._supercell = None
self._set_supercell()
self._symmetry = None
self._set_symmetry()
# set_displacements (used only in preprocess)
self._displacements = None
self._displacement_directions = None
self._supercells_with_displacements = None
if is_auto_displacements:
self.generate_displacements(distance)
# set_post_process
self._primitive = None
self._dynamical_matrix = None
self._is_nac = False
# set_force_constants or set_forces
self._set_of_forces_objects = None
self._force_constants = None
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
def get_primitive(self):
return self._primitive
primitive = property(get_primitive)
def set_primitive(self, primitive):
self._primitive = primitive
def get_unitcell(self):
return self._unitcell
unitcell = property(get_unitcell)
def get_supercell(self):
return self._supercell
supercell = property(get_supercell)
def set_supercell(self, supercell):
self._supercell = supercell
def get_symmetry(self):
return self._symmetry
symmetry = property(get_symmetry)
def get_unit_conversion_factor(self):
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacements automatically
displacements:
List of displacements in Cartesian coordinates.
See 'set_displacements'
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[0, 1, 0, 0],
[7, 1, 0, 1], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
lattice = self._supercell.get_cell()
self._displacements = []
self._displacement_directions = \
get_least_displacements(self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
log_level=self._log_level)
for disp in self._displacement_directions:
atom_num = disp[0]
disp_cartesian = np.dot(disp[1:], lattice)
disp_cartesian *= distance / np.linalg.norm(disp_cartesian)
self._displacements.append([
atom_num, disp_cartesian[0], disp_cartesian[1],
disp_cartesian[2]
])
self._set_supercells_with_displacements()
def set_displacements(self, displacements):
"""Set displacements manually
displacemsts: List of disctionaries
[[0, 0.01, 0.00, 0.00], ...]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
"""
self._displacements = displacements
self._set_supercells_with_displacements()
def get_displacements(self):
return self._displacements
displacements = property(get_displacements)
def get_displacement_directions(self):
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_supercells_with_displacements(self):
return self._supercells_with_displacements
def set_post_process(self,
primitive_matrix=np.eye(3, dtype=float),
sets_of_forces=None,
set_of_forces_objects=None,
force_constants=None,
is_nac=False,
calculate_full_force_constants=False,
force_constants_decimals=None,
dynamical_matrix_decimals=None):
"""
Set forces or force constants to prepare phonon calculations.
The order of 'sets_of_forces' has to correspond to that of
'displacements' that should be already stored.
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
sets_of_forces:
[[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # first supercell
[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # second supercell
... ]
set_of_forces_objects:
[FORCES_object, FORCES_object, FORCES_object, ...]
"""
self._is_nac = is_nac
# Primitive cell
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
self._primitive = Primitive(
self._supercell, np.dot(inv_supercell_matrix, primitive_matrix),
self._symprec)
# Set set of FORCES objects or force constants
if sets_of_forces is not None:
self.set_forces(sets_of_forces)
elif set_of_forces_objects is not None:
self.set_force_sets(set_of_forces_objects)
elif force_constants is not None:
self.set_force_constants(force_constants)
# Calculate force cosntants from forces (full or symmetry reduced)
if self._set_of_forces_objects is not None:
if calculate_full_force_constants:
self.set_force_constants_from_forces(
distributed_atom_list=None,
force_constants_decimals=force_constants_decimals)
else:
p2s_map = self._primitive.get_primitive_to_supercell_map()
self.set_force_constants_from_forces(
distributed_atom_list=p2s_map,
force_constants_decimals=force_constants_decimals)
if self._force_constants is None:
print "In set_post_process, sets_of_forces or force_constants"
print "has to be set."
return False
# Dynamical Matrix
self.set_dynamical_matrix(decimals=dynamical_matrix_decimals)
def set_nac_params(self, nac_params, method='wang'):
if self._is_nac:
self._dynamical_matrix.set_nac_params(nac_params, method)
def set_dynamical_matrix(self, decimals=None):
if self._is_nac:
self._dynamical_matrix = \
DynamicalMatrixNAC(self._supercell,
self._primitive,
self._force_constants,
decimals=decimals,
symprec=self._symprec)
else:
self._dynamical_matrix = \
DynamicalMatrix(self._supercell,
self._primitive,
self._force_constants,
decimals=decimals,
symprec=self._symprec)
def get_dynamical_matrix(self):
return self._dynamical_matrix
dynamical_matrix = property(get_dynamical_matrix)
def set_forces(self, sets_of_forces):
forces = []
for i, disp in enumerate(self._displacements):
forces.append(Forces(disp[0], disp[1:4], sets_of_forces[i]))
self._set_of_forces_objects = forces
def set_force_constants_from_forces(self,
distributed_atom_list=None,
force_constants_decimals=None):
self._force_constants = get_force_constants(
self._set_of_forces_objects,
self._symmetry,
self._supercell,
atom_list=distributed_atom_list,
decimals=force_constants_decimals)
def set_force_constants_zero_with_radius(self, cutoff_radius):
cutoff_force_constants(self._force_constants,
self._supercell,
cutoff_radius,
symprec=self._symprec)
def set_force_constants(self, force_constants):
self._force_constants = force_constants
def set_force_sets(self, sets_of_forces_objects):
self._set_of_forces_objects = sets_of_forces_objects
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
def get_force_constants(self):
return self._force_constants
force_constants = property(get_force_constants)
def get_rotational_condition_of_fc(self):
return rotational_invariance(self._force_constants, self._supercell,
self._primitive, self._symprec)
def get_dynamical_matrix_at_q(self, q):
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamical_matrix()
# Frequency at a q-point
def get_frequencies(self, q):
"""
Calculate phonon frequencies at q
q: q-vector in reduced coordinates of primitive cell
"""
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm).real:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor
# Frequency and eigenvector at a q-point
def get_frequencies_with_eigenvectors(self, q):
"""
Calculate phonon frequencies and eigenvectors at q
q: q-vector in reduced coordinates of primitive cell
"""
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
eigvals, eigenvectors = np.linalg.eigh(dm)
frequencies = []
for eig in eigvals:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor, eigenvectors
## This expression may not be supported in old python versions.
# frequencies = np.array(
# [np.sqrt(x) if x > 0 else -np.sqrt(-x) for x in eigvals])
# return frequencies * self._factor, eigenvectors
# Band structure
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
self._primitive,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor)
def get_band_structure(self):
band = self._band_structure
return (band.get_qpoints(), band.get_distances(),
band.get_frequencies(), band.get_eigenvectors())
def plot_band_structure(self, symbols=None):
return self._band_structure.plot_band(symbols)
def write_yaml_band_structure(self):
self._band_structure.write_yaml()
# Mesh sampling
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_symmetry=True,
is_band_connection=False,
is_eigenvectors=False,
is_gamma_center=False):
self._mesh = Mesh(self._dynamical_matrix,
self._primitive,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_symmetry,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
is_gamma_center=is_gamma_center,
group_velocity=self._group_velocity,
factor=self._factor,
symprec=self._symprec)
def get_mesh(self):
return (self._mesh.get_qpoints(), self._mesh.get_weights(),
self._mesh.get_frequencies(), self._mesh.get_eigenvectors())
def write_yaml_mesh(self):
self._mesh.write_yaml()
def write_hdf5_mesh(self):
self._mesh.write_hdf5()
# Thermal property
def set_thermal_properties(self,
t_step=10,
t_max=1000,
t_min=0,
is_projection=False,
cutoff_frequency=None):
if self._mesh == None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
tp = ThermalProperties(self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors(),
is_projection=is_projection,
cutoff_frequency=cutoff_frequency)
tp.set_thermal_properties(t_step, t_max, t_min)
self._thermal_properties = tp
def get_thermal_properties(self):
temps, fe, entropy, cv = \
self._thermal_properties.get_thermal_properties()
return temps, fe, entropy, cv
def plot_thermal_properties(self):
return self._thermal_properties.plot_thermal_properties()
def write_yaml_thermal_properties(self,
filename='thermal_properties.yaml'):
self._thermal_properties.write_yaml(filename=filename)
# Partial DOS
def set_partial_DOS(self,
sigma=None,
omega_min=None,
omega_max=None,
omega_pitch=None,
tetrahedron_method=False):
if self._mesh == None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self._mesh.get_eigenvectors() == None:
print "Eigenvectors have to be calculated."
sys.exit(1)
pdos = PartialDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
pdos.set_draw_area(omega_min, omega_max, omega_pitch)
pdos.calculate()
self._pdos = pdos
def get_partial_DOS(self):
"""
Retern omegas and partial_dos.
The first element is omegas and the second is partial_dos.
omegas: [freq1, freq2, ...]
partial_dos:
[[elem1-freq1, elem1-freq2, ...],
[elem2-freq1, elem2-freq2, ...],
...]
where
elem1: atom1-x compornent
elem2: atom1-y compornent
elem3: atom1-z compornent
elem4: atom2-x compornent
...
"""
return self._pdos.get_partial_dos()
def plot_partial_DOS(self, pdos_indices=None, legend=None):
return self._pdos.plot_pdos(indices=pdos_indices, legend=legend)
def write_partial_DOS(self):
self._pdos.write()
# Total DOS
def set_total_DOS(self,
sigma=None,
omega_min=None,
omega_max=None,
omega_pitch=None,
tetrahedron_method=False):
if self._mesh == None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
total_dos = TotalDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(omega_min, omega_max, omega_pitch)
total_dos.calculate()
self._total_dos = total_dos
def get_total_DOS(self):
"""
Retern omegas and total dos.
The first element is omegas and the second is total dos.
omegas: [freq1, freq2, ...]
total_dos: [dos1, dos2, ...]
"""
return self._total_dos.get_dos()
def set_Debye_frequency(self, freq_max_fit=None):
self._total_dos.set_Debye_frequency(
self._primitive.get_number_of_atoms(), freq_max_fit)
def get_Debye_frequency(self):
return self._total_dos.get_Debye_frequency()
def plot_total_DOS(self):
return self._total_dos.plot_dos()
def write_total_DOS(self):
self._total_dos.write()
# Thermal displacement
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
direction=None,
cutoff_eigenvalue=None):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
direction:
Projection direction in reduced coordinates
"""
if self._mesh == None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
td.set_temperature_range(t_min, t_max, t_step)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
# td.run()
td.run_mesh()
self._thermal_displacements = td
def get_thermal_displacements(self):
if self._thermal_displacements is not None:
return self._thermal_displacements.get_thermal_displacements()
def plot_thermal_displacements(self, is_legend=False):
return self._thermal_displacements.plot(is_legend)
def write_yaml_thermal_displacements(self):
self._thermal_displacements.write_yaml()
def write_hdf5_thermal_displacements(self):
self._thermal_displacements.write_hdf5()
# Thermal displacement matrices
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_eigenvalue=None):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
direction:
Projection direction in reduced coordinates
"""
if self._mesh == None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
tdm.set_temperature_range(t_min, t_max, t_step)
# tdm.run()
tdm.run_mesh()
self._thermal_displacement_matrices = tdm
def get_thermal_displacement_matrices(self):
if self._thermal_displacement_matrices is not None:
return self._thermal_displacement_matrices.get_thermal_displacement_matrices(
)
def write_yaml_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_yaml()
def write_hdf5_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_hdf5()
# Thermal displacement
def set_thermal_distances(self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_eigenvalue=None):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [[1, 2], [1, 4]]
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
"""
td = ThermalDistances(self._mesh.get_frequencies(),
self._mesh.get_eigenvectors(),
self._supercell,
self._primitive,
self._mesh.get_qpoints(),
symprec=self._symprec,
cutoff_eigenvalue=cutoff_eigenvalue)
td.set_temperature_range(t_min, t_max, t_step)
# td.run(atom_pairs)
td.run_mesh(atom_pairs)
self._thermal_distances = td
def write_yaml_thermal_distances(self):
self._thermal_distances.write_yaml()
def write_hdf5_thermal_distances(self):
self._thermal_distances.write_hdf5()
# Q-points mode
def write_yaml_qpoints(self,
q_points,
nac_q_direction=None,
is_eigenvectors=False,
write_dynamical_matrices=False,
factor=VaspToTHz):
write_yaml_qpoints(q_points,
self._primitive,
self._dynamical_matrix,
nac_q_direction=nac_q_direction,
is_eigenvectors=is_eigenvectors,
group_velocity=self._group_velocity,
write_dynamical_matrices=write_dynamical_matrices,
factor=self._factor)
# Animation
def write_animation(self,
q_point=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None,
filename=None):
if q_point == None:
animation = Animation([0, 0, 0],
self._dynamical_matrix,
self._primitive,
shift=shift)
else:
animation = Animation(q_point,
self._dynamical_matrix,
self._primitive,
shift=shift)
if anime_type == 'v_sim':
if amplitude:
amplitude_ = amplitude
else:
amplitude_ = 1.0
if filename:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor,
filename=filename)
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type == 'arc' or anime_type == 'xyz' or anime_type == 'jmol'
or anime_type == 'poscar'):
if band_index == None or amplitude == None or num_div == None:
print "Parameters are not correctly set for animation."
sys.exit(1)
if anime_type == 'arc' or anime_type == None:
if filename:
animation.write_arc(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_arc(band_index, amplitude, num_div)
if anime_type == 'xyz':
if filename:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor,
filename=filename)
else:
animation.write_xyz(band_index, amplitude, num_div,
self._factor)
if anime_type == 'jmol':
if filename:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor,
filename=filename)
else:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor)
if anime_type == 'poscar':
if filename:
animation.write_POSCAR(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_POSCAR(band_index, amplitude, num_div)
# Modulation
def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
self._modulation = Modulation(self._dynamical_matrix,
self._primitive,
dimension=dimension,
phonon_modes=phonon_modes,
delta_q=delta_q,
derivative_order=derivative_order,
nac_q_direction=nac_q_direction,
factor=self._factor)
self._modulation.run()
def get_modulations(self):
"""Returns cells with modulations as Atoms objects"""
return self._modulation.get_modulations()
def get_delta_modulations(self):
"""Return modulations relative to equilibrium supercell
(modulations, supercell)
modulations: Atomic modulations of supercell in Cartesian coordinates
supercell: Supercell as an Atoms object.
"""
return self._modulation.get_delta_modulations()
def write_modulations(self):
"""Create MPOSCAR's"""
self._modulation.write()
def write_yaml_modulations(self):
self._modulation.write_yaml()
# Characters of irreducible representations
def set_irreps(self, q, degeneracy_tolerance=1e-4):
self._irreps = IrReps(self._dynamical_matrix,
q,
factor=self._factor,
symprec=self._symprec,
degeneracy_tolerance=degeneracy_tolerance,
log_level=self._log_level)
return self._irreps.run()
def get_irreps(self):
return self._irreps
def show_irreps(self, show_irreps=False):
self._irreps.show(show_irreps=show_irreps)
def write_yaml_irreps(self, show_irreps=False):
self._irreps.write_yaml(show_irreps=show_irreps)
# Group velocity
def set_group_velocity(self, q_points=None, q_length=1e-4):
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_points=q_points,
symmetry=self._symmetry,
q_length=q_length,
frequency_factor_to_THz=self._factor)
def get_group_velocity(self, q_point):
self._group_velocity.set_q_points([q_point])
return self._group_velocity.get_group_velocity()[0]
def _set_supercell(self):
self._supercell = get_supercell(self._unitcell, self._supercell_matrix,
self._symprec)
def _set_symmetry(self):
self._symmetry = Symmetry(self._supercell, self._symprec,
self._is_symmetry)
def _set_supercells_with_displacements(self):
supercells = []
for disp in self._displacements:
positions = self._supercell.get_positions()
positions[disp[0]] += disp[1:4]
supercells.append(
Atoms(numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),
magmoms=self._supercell.get_magnetic_moments(),
positions=positions,
cell=self._supercell.get_cell(),
pbc=True))
self._supercells_with_displacements = supercells
class Phonopy:
def __init__(self,
unitcell,
supercell_matrix,
primitive_matrix=None,
nac_params=None,
distance=0.01,
factor=VaspToTHz,
is_auto_displacements=True,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=1e-5,
is_symmetry=True,
log_level=0):
self._symprec = symprec
self._factor = factor
self._is_symmetry = is_symmetry
self._log_level = log_level
# Create supercell and primitive cell
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
# Set supercell and primitive symmetry
self._symmetry = None
self._primitive_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
# set_displacements (used only in preprocess)
self._displacement_dataset = None
self._displacements = None
self._displacement_directions = None
self._supercells_with_displacements = None
if is_auto_displacements:
self.generate_displacements(distance=distance)
# set_force_constants or set_forces
self._force_constants = None
self._force_constants_decimals = force_constants_decimals
# set_dynamical_matrix
self._dynamical_matrix = None
self._nac_params = nac_params
self._dynamical_matrix_decimals = dynamical_matrix_decimals
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_tetrahedron_method
self._tetrahedron_method = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
def set_post_process(self,
primitive_matrix=None,
sets_of_forces=None,
displacement_dataset=None,
force_constants=None,
is_nac=None):
print
print ("********************************** Warning"
"**********************************")
print "set_post_process will be obsolete."
print (" produce_force_constants is used instead of set_post_process"
" for producing")
print (" force constants from forces.")
if primitive_matrix is not None:
print (" primitive_matrix has to be given at Phonopy::__init__"
" object creation.")
print ("******************************************"
"**********************************")
print
if primitive_matrix is not None:
self._primitive_matrix = primitive_matrix
self._build_primitive_cell()
self._search_primitive_symmetry()
if sets_of_forces is not None:
self.set_forces(sets_of_forces)
elif displacement_dataset is not None:
self._displacement_dataset = displacement_dataset
elif force_constants is not None:
self.set_force_constants(force_constants)
if self._displacement_dataset is not None:
self.produce_force_constants()
def set_masses(self, masses):
p_masses = np.array(masses)
self._primitive.set_masses(p_masses)
p2p_map = self._primitive.get_primitive_to_primitive_map()
s_masses = p_masses[[p2p_map[x] for x in
self._primitive.get_supercell_to_primitive_map()]]
self._supercell.set_masses(s_masses)
u2s_map = self._supercell.get_unitcell_to_supercell_map()
u_masses = s_masses[u2s_map]
self._unitcell.set_masses(u_masses)
def get_primitive(self):
return self._primitive
primitive = property(get_primitive)
def get_unitcell(self):
return self._unitcell
unitcell = property(get_unitcell)
def get_supercell(self):
return self._supercell
supercell = property(get_supercell)
def set_supercell(self, supercell):
self._supercell = supercell
def get_symmetry(self):
"""return symmetry of supercell"""
return self._symmetry
symmetry = property(get_symmetry)
def get_primitive_symmetry(self):
"""return symmetry of primitive cell"""
return self._primitive_symmetry
def get_unit_conversion_factor(self):
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def produce_force_constants(self,
forces=None,
calculate_full_force_constants=True,
computation_algorithm="svd"):
if forces is not None:
self.set_forces(forces)
if calculate_full_force_constants:
self._run_force_constants_from_forces(
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
else:
p2s_map = self._primitive.get_primitive_to_supercell_map()
self._run_force_constants_from_forces(
distributed_atom_list=p2s_map,
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
def set_nac_params(self, nac_params=None, method=None):
if method is not None:
print "set_nac_params:"
print " Keyword argument of \"method\" is not more supported."
self._nac_params = nac_params
def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacements automatically
displacemsts: List of displacements in Cartesian coordinates.
[[0, 0.01, 0.00, 0.00], ...]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[0, 1, 0, 0],
[7, 1, 0, 1], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
displacement_directions = get_least_displacements(
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
log_level=self._log_level)
displacement_dataset = direction_to_displacement(
displacement_directions,
distance,
self._supercell)
self.set_displacement_dataset(displacement_dataset)
def set_displacements(self, displacements):
print
print ("********************************** Warning"
"**********************************")
print "set_displacements is obsolete. Do nothing."
print ("******************************************"
"**********************************")
print
def get_displacements(self):
return self._displacements
displacements = property(get_displacements)
def get_displacement_directions(self):
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_displacement_dataset(self):
return self._displacement_dataset
def get_supercells_with_displacements(self):
if self._displacement_dataset is None:
return None
else:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_dynamical_matrix(self):
return self._dynamical_matrix
dynamical_matrix = property(get_dynamical_matrix)
def set_forces(self, sets_of_forces):
"""
sets_of_forces:
[[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # first supercell
[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # second supercell
... ]
"""
for disp, forces in zip(
self._displacement_dataset['first_atoms'], sets_of_forces):
disp['forces'] = forces
def set_force_constants_zero_with_radius(self, cutoff_radius):
cutoff_force_constants(self._force_constants,
self._supercell,
cutoff_radius,
symprec=self._symprec)
def set_force_constants(self, force_constants):
self._force_constants = force_constants
def set_force_sets(self, force_sets):
print
print ("********************************** Warning"
"**********************************")
print "set_force_sets will be obsolete."
print (" The method name is changed to set_displacement_dataset.")
print ("******************************************"
"**********************************")
print
self.set_displacement_dataset(force_sets)
def set_displacement_dataset(self, displacement_dataset):
"""
displacement_dataset:
{'natom': number_of_atoms_in_supercell,
'first_atoms': [
{'number': atom index of displaced atom,
'displacement': displacement in Cartesian coordinates,
'direction': displacement direction with respect to axes
'forces': forces on atoms in supercell},
{...}, ...]}
"""
self._displacement_dataset = displacement_dataset
self._displacements = []
self._displacement_directions = []
for disp in self._displacement_dataset['first_atoms']:
x = disp['displacement']
self._displacements.append([disp['number'], x[0], x[1], x[2]])
if 'direction' in disp:
y = disp['direction']
self._displacement_directions.append(
[disp['number'], y[0], y[1], y[2]])
if not self._displacement_directions:
self._displacement_directions = None
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
def symmetrize_force_constants_by_space_group(self):
rotations = self._symmetry.get_symmetry_operations()['rotations']
translations = self._symmetry.get_symmetry_operations()['translations']
set_tensor_symmetry(self._force_constants,
self._supercell.get_cell().T,
self._supercell.get_scaled_positions(),
rotations,
translations,
self._symprec)
def get_force_constants(self):
return self._force_constants
force_constants = property(get_force_constants)
def get_rotational_condition_of_fc(self):
return rotational_invariance(self._force_constants,
self._supercell,
self._primitive,
self._symprec)
def set_dynamical_matrix(self):
self._set_dynamical_matrix()
def get_dynamical_matrix_at_q(self, q):
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamical_matrix()
def get_frequencies(self, q):
"""
Calculate phonon frequencies at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm).real:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor
def get_frequencies_with_eigenvectors(self, q):
"""
Calculate phonon frequencies and eigenvectors at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
eigvals, eigenvectors = np.linalg.eigh(dm)
frequencies = []
for eig in eigvals:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor, eigenvectors
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
self._set_dynamical_matrix()
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor)
def get_band_structure(self):
band = self._band_structure
return (band.get_qpoints(),
band.get_distances(),
band.get_frequencies(),
band.get_eigenvectors())
def plot_band_structure(self, symbols=None):
return self._band_structure.plot_band(symbols)
def write_yaml_band_structure(self):
self._band_structure.write_yaml()
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False):
self._set_dynamical_matrix()
self._mesh = Mesh(
self._dynamical_matrix,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_mesh_symmetry,
is_eigenvectors=is_eigenvectors,
is_gamma_center=is_gamma_center,
group_velocity=self._group_velocity,
rotations=self._primitive_symmetry.get_pointgroup_operations(),
factor=self._factor)
def get_mesh(self):
return (self._mesh.get_qpoints(),
self._mesh.get_weights(),
self._mesh.get_frequencies(),
self._mesh.get_eigenvectors())
def write_yaml_mesh(self):
self._mesh.write_yaml()
def set_thermal_properties(self,
t_step=10,
t_max=1000,
t_min=0,
is_projection=False,
band_indices=None,
cutoff_frequency=None):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
return False
else:
tp = ThermalProperties(self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors(),
is_projection=is_projection,
band_indices=band_indices,
cutoff_frequency=cutoff_frequency)
tp.set_thermal_properties(t_step=t_step,
t_max=t_max,
t_min=t_min)
self._thermal_properties = tp
def get_thermal_properties(self):
temps, fe, entropy, cv = \
self._thermal_properties.get_thermal_properties()
return temps, fe, entropy, cv
def plot_thermal_properties(self):
return self._thermal_properties.plot_thermal_properties()
def write_yaml_thermal_properties(self, filename='thermal_properties.yaml'):
self._thermal_properties.write_yaml(filename=filename)
def set_partial_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False,
direction=None):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if direction is not None:
direction_cart = np.dot(direction, self._primitive.get_cell())
else:
direction_cart = None
pdos = PartialDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method,
direction=direction_cart)
pdos.set_draw_area(freq_min, freq_max, freq_pitch)
pdos.run()
self._pdos = pdos
def get_partial_DOS(self):
"""
Retern frequencies and partial_dos.
The first element is freqs and the second is partial_dos.
frequencies: [freq1, freq2, ...]
partial_dos:
[[atom1-freq1, atom1-freq2, ...],
[atom2-freq1, atom2-freq2, ...],
...]
"""
return self._pdos.get_partial_dos()
def plot_partial_DOS(self, pdos_indices=None, legend=None):
return self._pdos.plot_pdos(indices=pdos_indices,
legend=legend)
def write_partial_DOS(self):
self._pdos.write()
def set_total_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
total_dos = TotalDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(freq_min, freq_max, freq_pitch)
total_dos.run()
self._total_dos = total_dos
def get_total_DOS(self):
"""
Retern frequencies and total dos.
The first element is freqs and the second is total dos.
frequencies: [freq1, freq2, ...]
total_dos: [dos1, dos2, ...]
"""
return self._total_dos.get_dos()
def set_Debye_frequency(self, freq_max_fit=None):
self._total_dos.set_Debye_frequency(
self._primitive.get_number_of_atoms(),
freq_max_fit=freq_max_fit)
def get_Debye_frequency(self):
return self._total_dos.get_Debye_frequency()
def plot_total_DOS(self):
return self._total_dos.plot_dos()
def write_total_DOS(self):
self._total_dos.write()
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
direction=None,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
td.run()
self._thermal_displacements = td
def get_thermal_displacements(self):
if self._thermal_displacements is not None:
return self._thermal_displacements.get_thermal_displacements()
def plot_thermal_displacements(self, is_legend=False):
return self._thermal_displacements.plot(is_legend)
def write_yaml_thermal_displacements(self):
self._thermal_displacements.write_yaml()
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
tdm.set_temperature_range(t_min, t_max, t_step)
tdm.run()
self._thermal_displacement_matrices = tdm
def get_thermal_displacement_matrices(self):
if self._thermal_displacement_matrices is not None:
return self._thermal_displacement_matrices.get_thermal_displacement_matrices()
def write_yaml_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_yaml()
def set_thermal_distances(self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [[1, 2], [1, 4]]
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
"""
td = ThermalDistances(self._mesh.get_frequencies(),
self._mesh.get_eigenvectors(),
self._supercell,
self._primitive,
self._mesh.get_qpoints(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
td.run(atom_pairs)
self._thermal_distances = td
def write_yaml_thermal_distances(self):
self._thermal_distances.write_yaml()
def set_qpoints_phonon(self,
q_points,
nac_q_direction=None,
is_eigenvectors=False,
write_dynamical_matrices=False,
factor=VaspToTHz):
self._set_dynamical_matrix()
self._qpoints_phonon = QpointsPhonon(
q_points,
self._dynamical_matrix,
nac_q_direction=nac_q_direction,
is_eigenvectors=is_eigenvectors,
group_velocity=self._group_velocity,
write_dynamical_matrices=write_dynamical_matrices,
factor=self._factor)
def get_qpoints_phonon(self):
return (self._qpoints_phonon.get_frequencies(),
self._qpoints_phonon.get_eigenvectors())
def write_yaml_qpoints_phonon(self):
self._qpoints_phonon.write_yaml()
def write_animation(self,
q_point=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None,
filename=None):
self._set_dynamical_matrix()
if q_point is None:
animation = Animation([0, 0, 0],
self._dynamical_matrix,
shift=shift)
else:
animation = Animation(q_point,
self._dynamical_matrix,
shift=shift)
if anime_type == 'v_sim':
if amplitude:
amplitude_ = amplitude
else:
amplitude_ = 1.0
if filename:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor,
filename=filename)
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type == 'arc' or
anime_type == 'xyz' or
anime_type == 'jmol' or
anime_type == 'poscar'):
if band_index is None or amplitude is None or num_div is None:
print "Parameters are not correctly set for animation."
sys.exit(1)
if anime_type == 'arc' or anime_type is None:
if filename:
animation.write_arc(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_arc(band_index,
amplitude,
num_div)
if anime_type == 'xyz':
if filename:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor,
filename=filename)
else:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor)
if anime_type == 'jmol':
if filename:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor,
filename=filename)
else:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor)
if anime_type == 'poscar':
if filename:
animation.write_POSCAR(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_POSCAR(band_index,
amplitude,
num_div)
def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
self._set_dynamical_matrix()
self._modulation = Modulation(self._dynamical_matrix,
dimension,
phonon_modes,
delta_q=delta_q,
derivative_order=derivative_order,
nac_q_direction=nac_q_direction,
factor=self._factor)
self._modulation.run()
def get_modulations(self):
"""Returns cells with modulations as Atoms objects"""
return self._modulation.get_modulations()
def get_delta_modulations(self):
"""Return modulations relative to equilibrium supercell
(modulations, supercell)
modulations: Atomic modulations of supercell in Cartesian coordinates
supercell: Supercell as an Atoms object.
"""
return self._modulation.get_delta_modulations()
def write_modulations(self):
"""Create MPOSCAR's"""
self._modulation.write()
def write_yaml_modulations(self):
self._modulation.write_yaml()
def set_irreps(self,
q,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=1e-4):
self._set_dynamical_matrix()
self._irreps = IrReps(
self._dynamical_matrix,
q,
is_little_cogroup=is_little_cogroup,
nac_q_direction=nac_q_direction,
factor=self._factor,
symprec=self._symprec,
degeneracy_tolerance=degeneracy_tolerance,
log_level=self._log_level)
return self._irreps.run()
def get_irreps(self):
return self._irreps
def show_irreps(self, show_irreps=False):
self._irreps.show(show_irreps=show_irreps)
def write_yaml_irreps(self, show_irreps=False):
self._irreps.write_yaml(show_irreps=show_irreps)
def set_group_velocity(self, q_length=None):
self._set_dynamical_matrix()
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
def get_group_velocity(self):
return self._group_velocity.get_group_velocity()
def get_group_velocity_at_q(self, q_point):
if self._group_velocity is None:
self.set_group_velocity()
self._group_velocity.set_q_points([q_point])
return self._group_velocity.get_group_velocity()[0]
def _run_force_constants_from_forces(self,
distributed_atom_list=None,
decimals=None,
computation_algorithm="svd"):
if self._displacement_dataset is not None:
self._force_constants = get_fc2(
self._supercell,
self._symmetry,
self._displacement_dataset,
atom_list=distributed_atom_list,
decimals=decimals,
computation_algorithm=computation_algorithm)
def _set_dynamical_matrix(self):
if self._nac_params is None:
self._dynamical_matrix = DynamicalMatrix(
self._supercell,
self._primitive,
self._force_constants,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
else:
self._dynamical_matrix = DynamicalMatrixNAC(
self._supercell,
self._primitive,
self._force_constants,
nac_params=self._nac_params,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
def _search_symmetry(self):
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive,
self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) !=
len(self._primitive_symmetry.get_pointgroup_operations())):
print ("Warning: point group symmetries of supercell and primitive"
"cell are different.")
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
def _build_supercells_with_displacements(self):
supercells = []
for disp in self._displacement_dataset['first_atoms']:
positions = self._supercell.get_positions()
positions[disp['number']] += disp['displacement']
supercells.append(Atoms(
numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),
magmoms=self._supercell.get_magnetic_moments(),
positions=positions,
cell=self._supercell.get_cell(),
pbc=True))
self._supercells_with_displacements = supercells
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
if self._primitive_matrix is None:
trans_mat = inv_supercell_matrix
else:
trans_mat = np.dot(inv_supercell_matrix, self._primitive_matrix)
self._primitive = get_primitive(
self._supercell, trans_mat, self._symprec)
num_satom = self._supercell.get_number_of_atoms()
num_patom = self._primitive.get_number_of_atoms()
if abs(num_satom * np.linalg.det(trans_mat) - num_patom) < 0.1:
return True
else:
return False
def __init__(
self,
interaction,
symmetry,
grid_points=None,
temperatures=None,
sigmas=None,
sigma_cutoff=None,
is_isotope=False,
mass_variances=None,
mesh_divisors=None,
coarse_mesh_shifts=None,
boundary_mfp=None, # in micrometre
is_kappa_star=True,
gv_delta_q=None, # finite difference for group veolocity
is_full_pp=False,
log_level=0):
if sigmas is None:
self._sigmas = []
else:
self._sigmas = sigmas
self._sigma_cutoff = sigma_cutoff
self._pp = interaction
self._is_full_pp = is_full_pp
self._collision = None # has to be set derived class
if temperatures is None:
self._temperatures = None
else:
self._temperatures = np.array(temperatures, dtype='double')
self._is_kappa_star = is_kappa_star
self._gv_delta_q = gv_delta_q
self._log_level = log_level
self._primitive = self._pp.get_primitive()
self._dm = self._pp.get_dynamical_matrix()
self._frequency_factor_to_THz = self._pp.get_frequency_factor_to_THz()
self._cutoff_frequency = self._pp.get_cutoff_frequency()
self._boundary_mfp = boundary_mfp
self._symmetry = symmetry
if not self._is_kappa_star:
self._point_operations = np.array([np.eye(3, dtype='intc')],
dtype='intc')
else:
self._point_operations = symmetry.get_reciprocal_operations()
rec_lat = np.linalg.inv(self._primitive.get_cell())
self._rotations_cartesian = np.array([
similarity_transformation(rec_lat, r)
for r in self._point_operations
],
dtype='double')
self._grid_points = None
self._grid_weights = None
self._grid_address = None
self._ir_grid_points = None
self._ir_grid_weights = None
self._read_gamma = False
self._read_gamma_iso = False
self._kappa = None
self._mode_kappa = None
self._frequencies = None
self._cv = None
self._gv = None
self._gv_sum2 = None
self._gamma = None
self._gamma_iso = None
self._num_sampling_grid_points = 0
self._mesh = None
self._mesh_divisors = None
self._coarse_mesh = None
self._coarse_mesh_shifts = None
self._set_mesh_numbers(mesh_divisors=mesh_divisors,
coarse_mesh_shifts=coarse_mesh_shifts)
volume = self._primitive.get_volume()
self._conversion_factor = unit_to_WmK / volume
self._isotope = None
self._mass_variances = None
self._is_isotope = is_isotope
if mass_variances is not None:
self._is_isotope = True
if self._is_isotope:
self._set_isotope(mass_variances)
self._grid_point_count = None
self._set_grid_properties(grid_points)
self._gv_obj = GroupVelocity(
self._dm,
q_length=self._gv_delta_q,
symmetry=self._symmetry,
frequency_factor_to_THz=self._frequency_factor_to_THz,
log_level=self._log_level)
# gv_delta_q may be changed.
self._gv_delta_q = self._gv_obj.get_q_length()
class Phonopy(object):
def __init__(self,
unitcell,
supercell_matrix,
primitive_matrix=None,
nac_params=None,
distance=None,
factor=VaspToTHz,
is_auto_displacements=None,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=1e-5,
is_symmetry=True,
use_lapack_solver=False,
log_level=0):
if is_auto_displacements is not None:
print("Warning: \'is_auto_displacements\' argument is obsolete.")
if is_auto_displacements is False:
print("Sets of displacements are not created as default.")
else:
print("Use \'generate_displacements\' method explicitly to "
"create sets of displacements.")
if distance is not None:
print("Warning: \'distance\' keyword argument is obsolete at "
"Phonopy instantiation.")
print("Specify \'distance\' keyword argument when calling "
"\'generate_displacements\'")
print("method (See the Phonopy API document).")
self._symprec = symprec
self._factor = factor
self._is_symmetry = is_symmetry
self._use_lapack_solver = use_lapack_solver
self._log_level = log_level
# Create supercell and primitive cell
self._unitcell = Atoms(atoms=unitcell)
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
# Set supercell and primitive symmetry
self._symmetry = None
self._primitive_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
# set_displacements (used only in preprocess)
self._displacement_dataset = None
self._displacements = None
self._displacement_directions = None
self._supercells_with_displacements = None
# set_force_constants or set_forces
self._force_constants = None
self._force_constants_decimals = force_constants_decimals
# set_dynamical_matrix
self._dynamical_matrix = None
self._nac_params = nac_params
self._dynamical_matrix_decimals = dynamical_matrix_decimals
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_tetrahedron_method
self._tetrahedron_method = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
def get_version(self):
return __version__
def get_primitive(self):
return self._primitive
primitive = property(get_primitive)
def get_unitcell(self):
return self._unitcell
unitcell = property(get_unitcell)
def get_supercell(self):
return self._supercell
supercell = property(get_supercell)
def get_symmetry(self):
"""return symmetry of supercell"""
return self._symmetry
symmetry = property(get_symmetry)
def get_primitive_symmetry(self):
"""return symmetry of primitive cell"""
return self._primitive_symmetry
def get_supercell_matrix(self):
return self._supercell_matrix
def get_primitive_matrix(self):
return self._primitive_matrix
def get_unit_conversion_factor(self):
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def get_displacement_dataset(self):
return self._displacement_dataset
def get_displacements(self):
return self._displacements
displacements = property(get_displacements)
def get_displacement_directions(self):
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_supercells_with_displacements(self):
if self._displacement_dataset is None:
return None
else:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_force_constants(self):
return self._force_constants
force_constants = property(get_force_constants)
def get_rotational_condition_of_fc(self):
return rotational_invariance(self._force_constants,
self._supercell,
self._primitive,
self._symprec)
def get_nac_params(self):
return self._nac_params
def get_dynamical_matrix(self):
return self._dynamical_matrix
dynamical_matrix = property(get_dynamical_matrix)
def set_unitcell(self, unitcell):
self._unitcell = unitcell
self._build_supercell()
self._build_primitive_cell()
self._search_symmetry()
self._search_primitive_symmetry()
self._displacement_dataset = None
def set_masses(self, masses):
p_masses = np.array(masses)
self._primitive.set_masses(p_masses)
p2p_map = self._primitive.get_primitive_to_primitive_map()
s_masses = p_masses[[p2p_map[x] for x in
self._primitive.get_supercell_to_primitive_map()]]
self._supercell.set_masses(s_masses)
u2s_map = self._supercell.get_unitcell_to_supercell_map()
u_masses = s_masses[u2s_map]
self._unitcell.set_masses(u_masses)
self._set_dynamical_matrix()
def set_nac_params(self, nac_params=None):
self._nac_params = nac_params
self._set_dynamical_matrix()
def set_displacement_dataset(self, displacement_dataset):
"""
displacement_dataset:
{'natom': number_of_atoms_in_supercell,
'first_atoms': [
{'number': atom index of displaced atom,
'displacement': displacement in Cartesian coordinates,
'direction': displacement direction with respect to axes
'forces': forces on atoms in supercell},
{...}, ...]}
"""
self._displacement_dataset = displacement_dataset
self._displacements = []
self._displacement_directions = []
for disp in self._displacement_dataset['first_atoms']:
x = disp['displacement']
self._displacements.append([disp['number'], x[0], x[1], x[2]])
if 'direction' in disp:
y = disp['direction']
self._displacement_directions.append(
[disp['number'], y[0], y[1], y[2]])
if not self._displacement_directions:
self._displacement_directions = None
def set_forces(self, sets_of_forces):
"""
sets_of_forces:
[[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # first supercell
[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # second supercell
... ]
"""
for disp, forces in zip(
self._displacement_dataset['first_atoms'], sets_of_forces):
disp['forces'] = forces
def set_force_constants(self, force_constants):
self._force_constants = force_constants
self._set_dynamical_matrix()
def set_force_constants_zero_with_radius(self, cutoff_radius):
cutoff_force_constants(self._force_constants,
self._supercell,
cutoff_radius,
symprec=self._symprec)
self._set_dynamical_matrix()
def set_dynamical_matrix(self):
self._set_dynamical_matrix()
def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacements automatically
displacemsts: List of displacements in Cartesian coordinates.
[[0, 0.01, 0.00, 0.00], ...]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[0, 1, 0, 0],
[7, 1, 0, 1], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
displacement_directions = get_least_displacements(
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
log_level=self._log_level)
displacement_dataset = direction_to_displacement(
displacement_directions,
distance,
self._supercell)
self.set_displacement_dataset(displacement_dataset)
def produce_force_constants(self,
forces=None,
calculate_full_force_constants=True,
computation_algorithm="svd"):
if forces is not None:
self.set_forces(forces)
# A primitive check if 'forces' key is in displacement_dataset.
for disp in self._displacement_dataset['first_atoms']:
if 'forces' not in disp:
return False
if calculate_full_force_constants:
self._run_force_constants_from_forces(
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
else:
p2s_map = self._primitive.get_primitive_to_supercell_map()
self._run_force_constants_from_forces(
distributed_atom_list=p2s_map,
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
self._set_dynamical_matrix()
return True
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
self._set_dynamical_matrix()
def symmetrize_force_constants_by_space_group(self):
from phonopy.harmonic.force_constants import (set_tensor_symmetry,
set_tensor_symmetry_PJ)
set_tensor_symmetry_PJ(self._force_constants,
self._supercell.get_cell().T,
self._supercell.get_scaled_positions(),
self._symmetry)
self._set_dynamical_matrix()
#####################
# Phonon properties #
#####################
# Single q-point
def get_dynamical_matrix_at_q(self, q):
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return None
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamical_matrix()
def get_frequencies(self, q):
"""
Calculate phonon frequencies at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return None
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm).real:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor
def get_frequencies_with_eigenvectors(self, q):
"""
Calculate phonon frequencies and eigenvectors at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return None
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
eigvals, eigenvectors = np.linalg.eigh(dm)
frequencies = []
for eig in eigvals:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor, eigenvectors
# Band structure
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._band_structure = None
return False
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor)
return True
def get_band_structure(self):
band = self._band_structure
return (band.get_qpoints(),
band.get_distances(),
band.get_frequencies(),
band.get_eigenvectors())
def plot_band_structure(self, labels=None):
import matplotlib.pyplot as plt
if labels:
from matplotlib import rc
rc('text', usetex=True)
self._band_structure.plot(plt, labels=labels)
return plt
def write_yaml_band_structure(self,
labels=None,
comment=None,
filename="band.yaml"):
self._band_structure.write_yaml(labels=labels,
comment=comment,
filename=filename)
# Sampling mesh
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._mesh = None
return False
self._mesh = Mesh(
self._dynamical_matrix,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_mesh_symmetry,
is_eigenvectors=is_eigenvectors,
is_gamma_center=is_gamma_center,
group_velocity=self._group_velocity,
rotations=self._primitive_symmetry.get_pointgroup_operations(),
factor=self._factor,
use_lapack_solver=self._use_lapack_solver)
return True
def get_mesh(self):
if self._mesh is None:
return None
else:
return (self._mesh.get_qpoints(),
self._mesh.get_weights(),
self._mesh.get_frequencies(),
self._mesh.get_eigenvectors())
def get_mesh_grid_info(self):
if self._mesh is None:
return None
else:
return (self._mesh.get_grid_address(),
self._mesh.get_ir_grid_points(),
self._mesh.get_grid_mapping_table())
def write_hdf5_mesh(self):
self._mesh.write_hdf5()
def write_yaml_mesh(self):
self._mesh.write_yaml()
# Plot band structure and DOS (PDOS) together
def plot_band_structure_and_dos(self, pdos_indices=None, labels=None):
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
if labels:
from matplotlib import rc
rc('text', usetex=True)
plt.figure(figsize=(10, 6))
gs = gridspec.GridSpec(1, 2, width_ratios=[3, 1])
ax1 = plt.subplot(gs[0, 0])
self._band_structure.plot(plt, labels=labels)
ax2 = plt.subplot(gs[0, 1], sharey=ax1)
plt.subplots_adjust(wspace=0.03)
plt.setp(ax2.get_yticklabels(), visible=False)
if pdos_indices is None:
self._total_dos.plot(plt,
ylabel="",
draw_grid=False,
flip_xy=True)
else:
self._pdos.plot(plt,
indices=pdos_indices,
ylabel="",
draw_grid=False,
flip_xy=True)
return plt
# DOS
def set_total_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False):
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before DOS calculation.")
self._total_dos = None
return False
total_dos = TotalDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(freq_min, freq_max, freq_pitch)
total_dos.run()
self._total_dos = total_dos
return True
def get_total_DOS(self):
"""
Retern frequencies and total dos.
The first element is freqs and the second is total dos.
frequencies: [freq1, freq2, ...]
total_dos: [dos1, dos2, ...]
"""
return self._total_dos.get_dos()
def set_Debye_frequency(self, freq_max_fit=None):
self._total_dos.set_Debye_frequency(
self._primitive.get_number_of_atoms(),
freq_max_fit=freq_max_fit)
def get_Debye_frequency(self):
return self._total_dos.get_Debye_frequency()
def plot_total_DOS(self):
import matplotlib.pyplot as plt
self._total_dos.plot(plt)
return plt
def write_total_DOS(self):
self._total_dos.write()
# PDOS
def set_partial_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False,
direction=None,
xyz_projection=False):
self._pdos = None
if self._mesh is None:
print("Warning: \'set_mesh\' has to be called before "
"PDOS calculation.")
return False
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
num_grid = np.prod(self._mesh.get_mesh_numbers())
if num_grid != len(self._mesh.get_ir_grid_points()):
print("Warning: \'set_mesh\' has to be called with "
"is_mesh_symmetry=False.")
return False
if direction is not None:
direction_cart = np.dot(direction, self._primitive.get_cell())
else:
direction_cart = None
self._pdos = PartialDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method,
direction=direction_cart,
xyz_projection=xyz_projection)
self._pdos.set_draw_area(freq_min, freq_max, freq_pitch)
self._pdos.run()
return True
def get_partial_DOS(self):
"""
Retern frequencies and partial_dos.
The first element is freqs and the second is partial_dos.
frequencies: [freq1, freq2, ...]
partial_dos:
[[atom1-freq1, atom1-freq2, ...],
[atom2-freq1, atom2-freq2, ...],
...]
"""
return self._pdos.get_partial_dos()
def plot_partial_DOS(self, pdos_indices=None, legend=None):
import matplotlib.pyplot as plt
self._pdos.plot(plt,
indices=pdos_indices,
legend=legend)
return plt
def write_partial_DOS(self):
self._pdos.write()
# Thermal property
def set_thermal_properties(self,
t_step=10,
t_max=1000,
t_min=0,
temperatures=None,
is_projection=False,
band_indices=None,
cutoff_frequency=None):
if self._mesh is None:
print("Warning: set_mesh has to be done before "
"set_thermal_properties")
return False
else:
tp = ThermalProperties(self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors(),
is_projection=is_projection,
band_indices=band_indices,
cutoff_frequency=cutoff_frequency)
if temperatures is None:
tp.set_temperature_range(t_step=t_step,
t_max=t_max,
t_min=t_min)
else:
tp.set_temperatures(temperatures)
tp.run()
self._thermal_properties = tp
def get_thermal_properties(self):
temps, fe, entropy, cv = \
self._thermal_properties.get_thermal_properties()
return temps, fe, entropy, cv
def plot_thermal_properties(self):
import matplotlib.pyplot as plt
self._thermal_properties.plot(plt)
return plt
def write_yaml_thermal_properties(self, filename='thermal_properties.yaml'):
self._thermal_properties.write_yaml(filename=filename)
# Thermal displacement
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
temperatures=None,
direction=None,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
self._thermal_displacements = None
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before \'set_thermal_displacements\'.")
return False
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(mesh_nums) != len(eigvecs):
print("Warning: Sampling mesh must not be symmetrized.")
return False
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
if temperatures is None:
td.set_temperature_range(t_min, t_max, t_step)
else:
td.set_temperatures(temperatures)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
td.run()
self._thermal_displacements = td
return True
def get_thermal_displacements(self):
if self._thermal_displacements is not None:
return self._thermal_displacements.get_thermal_displacements()
def plot_thermal_displacements(self, is_legend=False):
import matplotlib.pyplot as plt
self._thermal_displacements.plot(plt, is_legend=is_legend)
return plt
def write_yaml_thermal_displacements(self):
self._thermal_displacements.write_yaml()
# Thermal displacement matrix
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None,
t_cif=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
self._thermal_displacement_matrices = None
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before \'set_thermal_displacement_matrices\'.")
return False
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(mesh_nums) != len(eigvecs):
print("Warning: Sampling mesh must not be symmetrized.")
return False
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency,
lattice=self._primitive.get_cell().T)
if t_cif is None:
tdm.set_temperature_range(t_min, t_max, t_step)
else:
tdm.set_temperatures([t_cif])
tdm.run()
self._thermal_displacement_matrices = tdm
return True
def get_thermal_displacement_matrices(self):
tdm = self._thermal_displacement_matrices
if tdm is not None:
return tdm.get_thermal_displacement_matrices()
def write_yaml_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_yaml()
def write_thermal_displacement_matrix_to_cif(self,
temperature_index):
self._thermal_displacement_matrices.write_cif(self._primitive,
temperature_index)
# Mean square distance between a pair of atoms
def set_thermal_distances(self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [[1, 2], [1, 4]]
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
"""
td = ThermalDistances(self._mesh.get_frequencies(),
self._mesh.get_eigenvectors(),
self._supercell,
self._primitive,
self._mesh.get_qpoints(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
td.run(atom_pairs)
self._thermal_distances = td
def write_yaml_thermal_distances(self):
self._thermal_distances.write_yaml()
# Sampling at q-points
def set_qpoints_phonon(self,
q_points,
nac_q_direction=None,
is_eigenvectors=False,
write_dynamical_matrices=False):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._qpoints_phonon = None
return False
self._qpoints_phonon = QpointsPhonon(
np.reshape(q_points, (-1, 3)),
self._dynamical_matrix,
nac_q_direction=nac_q_direction,
is_eigenvectors=is_eigenvectors,
group_velocity=self._group_velocity,
write_dynamical_matrices=write_dynamical_matrices,
factor=self._factor)
return True
def get_qpoints_phonon(self):
return (self._qpoints_phonon.get_frequencies(),
self._qpoints_phonon.get_eigenvectors())
def write_hdf5_qpoints_phonon(self):
self._qpoints_phonon.write_hdf5()
def write_yaml_qpoints_phonon(self):
self._qpoints_phonon.write_yaml()
# Normal mode animation
def write_animation(self,
q_point=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None,
filename=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return False
if q_point is None:
animation = Animation([0, 0, 0],
self._dynamical_matrix,
shift=shift)
else:
animation = Animation(q_point,
self._dynamical_matrix,
shift=shift)
if anime_type == 'v_sim':
if amplitude:
amplitude_ = amplitude
else:
amplitude_ = 1.0
if filename:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor,
filename=filename)
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type == 'arc' or
anime_type == 'xyz' or
anime_type == 'jmol' or
anime_type == 'poscar'):
if band_index is None or amplitude is None or num_div is None:
print("Warning: Parameters are not correctly set for "
"animation.")
return False
if anime_type == 'arc' or anime_type is None:
if filename:
animation.write_arc(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_arc(band_index,
amplitude,
num_div)
if anime_type == 'xyz':
if filename:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor,
filename=filename)
else:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor)
if anime_type == 'jmol':
if filename:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor,
filename=filename)
else:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor)
if anime_type == 'poscar':
if filename:
animation.write_POSCAR(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_POSCAR(band_index,
amplitude,
num_div)
return True
# Atomic modulation of normal mode
def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._modulation = None
return False
self._modulation = Modulation(self._dynamical_matrix,
dimension,
phonon_modes,
delta_q=delta_q,
derivative_order=derivative_order,
nac_q_direction=nac_q_direction,
factor=self._factor)
self._modulation.run()
return True
def get_modulated_supercells(self):
"""Returns cells with modulations as Atoms objects"""
return self._modulation.get_modulated_supercells()
def get_modulations_and_supercell(self):
"""Return modulations and supercell
(modulations, supercell)
modulations: Atomic modulations of supercell in Cartesian coordinates
supercell: Supercell as an Atoms object.
"""
return self._modulation.get_modulations_and_supercell()
def write_modulations(self):
"""Create MPOSCAR's"""
self._modulation.write()
def write_yaml_modulations(self):
self._modulation.write_yaml()
# Irreducible representation
def set_irreps(self,
q,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=1e-4):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._irreps = None
return None
self._irreps = IrReps(
self._dynamical_matrix,
q,
is_little_cogroup=is_little_cogroup,
nac_q_direction=nac_q_direction,
factor=self._factor,
symprec=self._symprec,
degeneracy_tolerance=degeneracy_tolerance,
log_level=self._log_level)
return self._irreps.run()
def get_irreps(self):
return self._irreps
def show_irreps(self, show_irreps=False):
self._irreps.show(show_irreps=show_irreps)
def write_yaml_irreps(self, show_irreps=False):
self._irreps.write_yaml(show_irreps=show_irreps)
# Group velocity
def set_group_velocity(self, q_length=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._group_velocity = None
return False
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
return True
def get_group_velocity(self):
return self._group_velocity.get_group_velocity()
def get_group_velocity_at_q(self, q_point):
if self._group_velocity is None:
self.set_group_velocity()
self._group_velocity.set_q_points([q_point])
return self._group_velocity.get_group_velocity()[0]
# Moment
def set_moment(self,
order=1,
is_projection=False,
freq_min=None,
freq_max=None):
if self._mesh is None:
print("Warning: set_mesh has to be done before set_moment")
return False
else:
if is_projection:
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
moment = PhononMoment(
self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors())
else:
moment = PhononMoment(
self._mesh.get_frequencies(),
weights=self._mesh.get_weights())
if freq_min is not None or freq_max is not None:
moment.set_frequency_range(freq_min=freq_min,
freq_max=freq_max)
moment.run(order=order)
self._moment = moment.get_moment()
return True
def get_moment(self):
return self._moment
#################
# Local methods #
#################
def _run_force_constants_from_forces(self,
distributed_atom_list=None,
decimals=None,
computation_algorithm="svd"):
if self._displacement_dataset is not None:
self._force_constants = get_fc2(
self._supercell,
self._symmetry,
self._displacement_dataset,
atom_list=distributed_atom_list,
decimals=decimals,
computation_algorithm=computation_algorithm)
def _set_dynamical_matrix(self):
self._dynamical_matrix = None
if (self._supercell is None or self._primitive is None):
print("Bug: Supercell or primitive is not created.")
return False
elif self._force_constants is None:
print("Warning: Force constants are not prepared.")
return False
elif self._primitive.get_masses() is None:
print("Warning: Atomic masses are not correctly set.")
return False
else:
if self._nac_params is None:
self._dynamical_matrix = DynamicalMatrix(
self._supercell,
self._primitive,
self._force_constants,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
else:
self._dynamical_matrix = DynamicalMatrixNAC(
self._supercell,
self._primitive,
self._force_constants,
nac_params=self._nac_params,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
return True
def _search_symmetry(self):
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive,
self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) !=
len(self._primitive_symmetry.get_pointgroup_operations())):
print("Warning: Point group symmetries of supercell and primitive"
"cell are different.")
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
def _build_supercells_with_displacements(self):
supercells = []
for disp in self._displacement_dataset['first_atoms']:
positions = self._supercell.get_positions()
positions[disp['number']] += disp['displacement']
supercells.append(Atoms(
numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),
magmoms=self._supercell.get_magnetic_moments(),
positions=positions,
cell=self._supercell.get_cell(),
pbc=True))
self._supercells_with_displacements = supercells
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
if self._primitive_matrix is None:
trans_mat = inv_supercell_matrix
else:
trans_mat = np.dot(inv_supercell_matrix, self._primitive_matrix)
self._primitive = get_primitive(
self._supercell, trans_mat, self._symprec)
num_satom = self._supercell.get_number_of_atoms()
num_patom = self._primitive.get_number_of_atoms()
if abs(num_satom * np.linalg.det(trans_mat) - num_patom) < 0.1:
return True
else:
return False
class Collision():
def __init__(
self,
interaction,
sigmas=np.array([0.1]),
temperatures=None,
lang="C",
is_tetrahedron_method=False,
mass_variances=None,
length=None,
gv_delta_q=None,
is_adaptive_sigma=False,
is_group_velocity=False, # Use gv to determine smearing factor
write=False,
read=False,
cutoff_frequency=1e-4): #unit: THz
self._pp = interaction
self._sigmas = sigmas
self._temperatures = temperatures
self._mesh = self._pp.get_mesh_numbers()
self._is_nosym = self._pp._is_nosym
if interaction._is_nosym:
self._point_operations = np.array(
[[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype="intc")
else:
self._point_operations = self._pp.get_point_group_operations()
self._kpoint_operations = self._pp._kpoint_operations
self._is_dispersed = self._pp.get_is_dispersed()
self._cutoff_frequency = cutoff_frequency
self._grid_point = None
self._grid_point_triplets = None
self._triplet_weights = None
self._is_thm = is_tetrahedron_method
self._lang = lang
self._frequencies_all = None
self._eigenvectors_all = None
self._band_indices = None
self._fc3_normal_squared = None
self._occupations_all = None
self._sigma = None
self._temperature = None
self._isigma = None
self._itemp = None
self._is_group_velocity = is_group_velocity
self._write_col = write
self._read_col = read
self._is_adaptive_sigma = is_adaptive_sigma
self._is_on_iteration = False
self._asigma = None
self._gamma_all = None
self._irr_mapping_indices = None
self._collision_in = None
self._collision_out = None
self._collision_in_all = None
self._is_read_error = None
self._unit_conversion = np.pi / 4 * (
(Hbar * EV)**3 # Hbar * EV : hbar
* EV**2 / Angstrom**6 / (2 * np.pi * THz)**3 / AMU**3 /
(Hbar * EV)**2 / (2 * np.pi * THz)**2 / np.prod(self._mesh))
self._init_grids_properties()
self._length = length
self._gv_delta_q = gv_delta_q
if is_group_velocity or self._length is not None:
self._init_group_velocity()
if mass_variances is not None:
self._collision_iso = \
CollisionIso(self._mesh,
self._pp._primitive,
mass_variances,
self._band_indices,
self._sigma)
self._collision_iso.set_dynamical_matrix(
dynamical_matrix=self._pp.get_dynamical_matrix())
else:
self._collision_iso = None
def _init_group_velocity(self):
self._group_velocity = GroupVelocity(
self._pp.get_dynamical_matrix(),
symmetry=self._pp._symmetry,
q_length=self._gv_delta_q,
frequency_factor_to_THz=self._pp.get_frequency_factor_to_THz())
num_grids_all, num_band = self._pp._frequencies.shape
self._gv_all = np.zeros((num_grids_all, num_band, 3), dtype="double")
self._gv_done_all = np.zeros(num_grids_all, dtype="bool")
def _init_grids_properties(self):
num_grids_all, num_band = self._pp._frequencies.shape
num_temp = len(self._temperatures)
num_sigma = len(self._sigmas)
self._occupations_all = np.zeros((num_grids_all, num_temp, num_band),
dtype="double")
self._collision_out_all = np.zeros(
(num_sigma, num_grids_all, num_temp, num_band), dtype="double")
self._gamma_all = np.zeros_like(self._collision_out_all)
self._n_done = np.zeros((num_grids_all, num_temp), dtype="bool")
def set_grid(self, grid_point):
if grid_point is None:
self._grid_point = None
else:
self._pp.set_grid_point(grid_point)
(self._grid_point_triplets,
self._triplet_weights) = self._pp.get_triplets_at_q()
self._grid_point = self._grid_point_triplets[0, 0]
self._grid_address = self._pp.get_grid_address()
self._qpoint = self._grid_address[self._grid_point] / np.double(
self._mesh)
kpg_index = get_kgp_index_at_grid(self._grid_address[grid_point],
self._mesh,
self._kpoint_operations)
self._inv_rot_sum = self._kpoint_operations[kpg_index].sum(axis=0)
self._kpg_at_q_index = kpg_index
self._fc3_normal_squared = None
if self._collision_iso is not None:
grid_points2 = self.get_grid_point_triplets()[:, 1].astype(
"intc").copy()
weights2 = self.get_triplets_weights()
self._collision_iso.set_grid_point(grid_point,
grid_points2=grid_points2,
weights2=weights2)
def set_pp_grid_points_all(self, grid_points):
self._pp.set_grid_points(grid_points)
def set_grids(self, grid_points):
self._pp._grid_points = grid_points
self._collision_done = None
if self._pp._unique_triplets == None:
self._pp.set_grid_points(grid_points)
if not self._is_dispersed:
bi = self._pp._band_indices
nband = 3 * self._pp._primitive.get_number_of_atoms()
luniq = len(self._pp._unique_triplets)
try:
self._collision_in_all = np.zeros((luniq, 3, len(bi), nband),
dtype="double")
except MemoryError:
print "A memory error occurs in allocating the whole collision array"
print "--disperse is recommended as a possible solution"
sys.exit(1)
self._collision_done = np.zeros(luniq, dtype="bool")
def get_occupation(self):
return self._occupations_all
def get_grid_point_triplets(self):
return self._grid_point_triplets
def get_triplets_weights(self):
return self._triplet_weights
def get_collision_out(self):
if self._cutoff_frequency is None:
return self._collision_out
else: # Averaging imag-self-energies by degenerate bands
deg_sets = self._degeneracy_all[self._grid_point]
cout = np.zeros_like(self._collision_out)
for i, dset in enumerate(deg_sets):
cout[i] = np.average(
self._collision_out[np.where(deg_sets == dset)])
return cout
def get_collision_in(self):
return self._collision_in
def read_collision_all(self, log_level=0, is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
is_error = read_collision_all_from_hdf5(
self._collision_in_all,
self._mesh,
self._sigma,
self._temperature,
is_adaptive_sigma=is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
if is_error:
self.set_write_collision(True)
else:
if self._is_adaptive_sigma and (not self._is_on_iteration):
self._collision_done[:] = False
else:
self._collision_done[:] = True
def read_collision_at_grid(self,
grid,
log_level=0,
is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
is_error = read_collision_at_grid_from_hdf5(
self._collision_in,
self._mesh,
grid,
self._sigma,
self._temperature,
is_adaptive_sigma=is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
self._is_read_error = is_error
if self._is_read_error:
self.set_read_collision(False)
self.set_write_collision(True)
def write_collision_at_grid(self,
grid,
log_level=0,
is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
write_collision_to_hdf5_at_grid(self._collision_in,
self._mesh,
grid,
self._sigma,
self._temperature,
is_adaptive_sigma=is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
if self._is_read_error: # Condition: read argument is invoked
self.set_read_collision(True)
self.set_write_collision(False)
def write_collision_all(self, log_level=0, is_adaptive_sigma=None):
if is_adaptive_sigma == None:
is_adaptive_sigma = self._is_adaptive_sigma
if self._write_col:
write_collision_to_hdf5_all(self._collision_in_all,
self._mesh,
self._sigma,
self._temperature,
is_adaptive_sigma=is_adaptive_sigma,
log_level=log_level,
is_nosym=self._pp._is_nosym)
def set_temperature(self, temperature):
for i, t in enumerate(self._temperatures):
if temperature == t:
self._itemp = i
break
self._temperature = temperature
def set_is_adaptive_sigma(self, is_adaptive_sigma=False):
self._is_adaptive_sigma = is_adaptive_sigma
def set_is_on_iteration(self, is_on_iteration=True):
self._is_on_iteration = is_on_iteration
def set_sigma(self, sigma):
for i, s in enumerate(self._sigmas):
if s == sigma:
self._isigma = i
break
self._sigma = sigma
if self._sigma is None:
self._is_thm = True
@total_time.timeit
def set_asigma(self, gamma_prev=None, gamma_pprev=None):
if self._is_dispersed:
if not self._read_col:
triplets = self._grid_point_triplets
elif self._is_adaptive_sigma or self._is_group_velocity:
return
else:
triplets = self._triplets_reduced
if self._is_adaptive_sigma:
if gamma_prev is not None:
if gamma_pprev is not None:
gamma_all = (self._gamma_all[self._isigma, :, self._itemp]
+ gamma_prev + gamma_pprev) / 3
else:
gamma_all = (self._gamma_all[self._isigma, :, self._itemp]
+ gamma_prev) / 2
else:
gamma_all = self._gamma_all[self._isigma, :, self._itemp]
triplet_gammas = gamma_all[triplets]
gt = (triplet_gammas * 2 * np.pi)**2 / (
2 * np.log(2)) # 2pi comes from the definition of gamma
self._asigma = np.sqrt(gt[:, 0, :, np.newaxis, np.newaxis] +
gt[:, 1, np.newaxis, :, np.newaxis] +
gt[:, 2, np.newaxis, np.newaxis, :])
elif self._is_group_velocity:
self._set_group_velocity(grid_points=np.unique(triplets))
triplet1, triplet2 = triplets[:, 1], triplets[:, 2]
gv1, gv2 = self._gv_all[triplet1], self._gv_all[triplet2]
reciprocal_lattice = np.linalg.inv(self._pp._primitive.get_cell())
num_band = len(self._band_indices)
gvs = gv1[:, :, np.newaxis] - gv2[:, np.newaxis, :]
normalized_gvs = np.dot(gvs, reciprocal_lattice) / np.array(
self._mesh)
sigmas = np.sqrt(np.sum(normalized_gvs**2, axis=-1) / 12)
self._asigma = np.repeat(sigmas[:, np.newaxis],
repeats=num_band,
axis=1)
else:
if self._read_col:
nband = self._pp._primitive.get_number_of_atoms() * 3
self._asigma = np.zeros((0, nband, nband, nband),
dtype="double")
def _set_group_velocity(self, grid_points):
undone_grid_points = np.extract(self._gv_done_all[grid_points] == 0,
grid_points)
qpoints = [
self._grid_address[gp] / np.double(self._mesh)
for gp in undone_grid_points
]
if len(qpoints) != 0:
self._group_velocity.set_q_points(q_points=qpoints)
self._gv_all[
undone_grid_points] = self._group_velocity.get_group_velocity(
)
self._gv_done_all[undone_grid_points] = True
def set_write_collision(self, is_write_col):
self._write_col = is_write_col
def set_read_collision(self, is_read_col):
self._read_col = is_read_col
def get_write_collision(self):
return self._write_col
def get_read_collision(self):
return self._read_col
def get_is_dispersed(self):
return self._is_dispersed
def get_collision_out_all(self):
return self._collision_out_all
@total_time.timeit
def run_interaction_at_grid_point(self, g_skip=None):
self.set_phonons_triplets()
if self._read_col and ((not self._is_adaptive_sigma)
or self._is_on_iteration):
nband = self._pp._primitive.get_number_of_atoms() * 3
self._fc3_normal_squared = np.zeros((0, nband, nband, nband),
dtype="double")
self._fc3_normal_squared_reduced = np.zeros(
(0, nband, nband, nband), dtype="double")
else:
self._pp.run(g_skip=g_skip, lang=self._lang)
self._fc3_normal_squared = self._pp.get_interaction_strength()
self._fc3_normal_squared_reduced = self._fc3_normal_squared[
self._undone_triplet_index]
if self._collision_iso:
self._collision_iso.set_frequencies(
frequencies=self._frequencies_all,
eigenvectors=self._eigenvectors_all,
phonons_done=self._pp._phonon_done,
degeneracies=self._degeneracy_all)
def set_phonons_triplets(self):
self._pp.set_phonons(lang=self._lang)
(self._frequencies_all,
self._eigenvectors_all) = self._pp.get_phonons()[:2]
self._degeneracy_all = self._pp.get_degeneracy()
self._band_indices = self._pp.get_band_indices()
def reduce_triplets(self):
num_triplets = len(self._pp.get_triplets_at_q()[0])
num_band0 = len(self._band_indices)
num_band = self._pp._primitive.get_number_of_atoms() * 3
self._collision_out = None
self._collision_in = np.zeros((num_triplets, num_band0, num_band),
dtype="double")
self._triplets_mapping = self._pp.get_triplets_mapping_at_grid()
self.extract_undone_triplets()
self._collision_in_reduced = np.zeros(
(len(self._undone_uniq_index), 3, num_band0, num_band),
dtype="double")
self._triplets_reduced = self._pp.get_triplets_at_q()[0][
self._undone_triplet_index]
assert (self._pp._phonon_done[self._triplets_reduced] == True).all()
self._frequencies_reduced = self._frequencies_all[
self._triplets_reduced]
# self.set_grid_points_occupation()
self._occu_reduced = self._occupations_all[self._triplets_reduced,
self._itemp]
def set_grid_points_occupation(self, grid_points=None):
if grid_points is None:
grid_points = self._grid_point_triplets
uniq_grids = np.unique(grid_points)
for g in uniq_grids:
if not self._n_done[g, self._itemp]:
n = occupation(self._frequencies_all[g], self._temperature)
n[np.where(
self._frequencies_all[g] < self._cutoff_frequency)] = 0
self._occupations_all[g, self._itemp] = n
self._n_done[g, self._itemp] = True
if self._collision_iso is not None:
self._collision_iso.set_occupation(
occupations=self._occupations_all[:, self._itemp],
occupations_done=self._n_done[:, self._itemp])
def set_grid_points_group_velocity(self, grid_points=None):
if grid_points is None:
grid_points = self._grid_point_triplets
uniq_grids = np.unique(grid_points)
def extract_undone_triplets(self):
unique_map, index = np.unique(self._triplets_mapping,
return_index=True)
if self._is_dispersed:
self._undone_uniq_index = unique_map
self._undone_triplet_index = index
else:
self._undone_uniq_index = np.extract(
self._collision_done[unique_map] == False, unique_map)
self._undone_triplet_index = np.extract(
self._collision_done[unique_map] == False, index)
def broadcast_collision_out(self):
grid_map = self._pp.get_grid_mapping()
bz_to_pp_map = self._pp.get_bz_to_pp_map()
bz_to_irred_map = grid_map[bz_to_pp_map]
equiv_pos = np.where(bz_to_irred_map == self._grid_point)
cm_out = self.get_collision_out()
self._collision_out_all[self._isigma, equiv_pos, self._itemp] = cm_out
n = self.get_occupation()[self._grid_point, self._itemp]
nn1 = n * (n + 1)
is_pass = self._frequencies_all[
self._grid_point] < self._cutoff_frequency
self._gamma_all[self._isigma, equiv_pos, self._itemp] = \
cm_out * np.where(is_pass, 0, 1 / nn1) / 2.
def run(self):
if self._is_dispersed and self._read_col:
self.read_collision_at_grid(self._grid_point)
if self._lang == "C":
self.run_c()
else:
self.run_py()
if self._is_dispersed and self._write_col:
self.write_collision_at_grid(self._grid_point)
# self._collision_in *= self._unit_conversion # unit in THz
summation = np.sum(self._collision_in, axis=-1)
self._collision_out = np.dot(self._triplet_weights, summation) / 2.0
# Set the diagonal part in A_in as 0
# bz_to_pp = self._pp._bz_to_pp_map
# triplets = bz_to_pp[self.get_grid_point_triplets()]
# diag_pos = np.where(triplets[:, 1] == triplets[0,0])[0][0]
# self._collision_out += self._collision_in[diag_pos].diagonal()
# np.fill_diagonal(self._collision_in[diag_pos], 0)
# Set the diagonal part in A_in as 0
if self._collision_iso is not None:
self._collision_iso.run()
self._collision_out += self._collision_iso._collision_out
self._collision_in += self._collision_iso._collision_in
if self._length is not None:
self._collision_out += self.get_boundary_scattering_strength()
self.broadcast_collision_out()
@total_time.timeit
def get_boundary_scattering_strength(self):
self._set_group_velocity(grid_points=[self._grid_point])
bnd_collision_unit = 100. / 1e-6 / THz / (
2 * np.pi) # unit in THz, unit of length is micron
gv = self._gv_all[self._grid_point]
dm = self._pp.get_dynamical_matrix()
gv1 = get_group_velocity(
self._qpoint,
dm,
symmetry=self._pp._symmetry,
q_length=self._gv_delta_q,
frequency_factor_to_THz=self._pp.get_frequency_factor_to_THz())
gv_average = np.sqrt(np.sum(gv**2, axis=-1))
n = self._occupations_all[self._grid_point, self._itemp]
cout_bnd = gv_average / self._length * n * (n + 1)
return cout_bnd * bnd_collision_unit
def run_py(self):
for i, triplet in enumerate(self._grid_point_triplets):
occu = occupation(self._frequencies_all[triplet],
self._temperature)
freq = self._frequencies_all[triplet]
for (j, k, l) in np.ndindex(self._fc3_normal_squared.shape[1:]):
if self._asigma:
sigma = self._asigma[i, j, k, l]
else:
sigma = self._sigma
f0 = freq[0, j]
f1 = freq[1, k]
f2 = freq[2, l]
if (f0 < self._cutoff_frequency or f1 < self._cutoff_frequency
or f2 < self._cutoff_frequency):
continue
n0 = occu[0, j]
n1 = occu[1, k]
n2 = occu[2, l]
delta1 = gaussian(f0 + f1 - f2, sigma)
delta2 = gaussian(f0 + f2 - f1, sigma)
delta3 = gaussian(f0 - f1 - f2, sigma)
self._collision_in[
i, j, k] += self._fc3_normal_squared[i, j, k, l] * (
(n0 + 1) * n1 * n2 * delta3 +
(n1 + 1) * n0 * n2 * delta2 +
(n2 + 1) * n0 * n1 * delta1)
self._collision_in *= self._unit_conversion
def set_integration_weights(self, cutoff_g=1e-8):
f_points = self._frequencies_all[self._grid_point][self._band_indices]
is_read_g = False
is_write_g = False
if not self._is_adaptive_sigma and len(self._temperatures) > 1:
if self._pp.get_is_read_amplitude(
) or self._pp.get_is_write_amplitude():
if self._itemp == 0:
is_write_g = True
is_read_g = False
else:
is_write_g = False
is_read_g = True
if self._asigma is not None:
sigma_object = self._asigma
cutoff_g = np.where(self._asigma > 0, cutoff_g / self._asigma, 0)
if self._is_dispersed and not self._read_col:
cutoff_g = cutoff_g[self._undone_triplet_index]
else:
sigma_object = self._sigma
if sigma_object is not None:
cutoff_g = cutoff_g / self._sigma
if self._is_dispersed:
if is_read_g:
self._g = read_integration_weight_from_hdf5_at_grid(
self._mesh, self._sigma, self._grid_point)
elif not self._read_col:
self._g = get_triplets_integration_weights(
self._pp,
np.array(f_points, dtype='double'),
sigma_object,
band_indices=self._band_indices,
triplets=self._grid_point_triplets,
is_triplet_symmetry=self._pp._symmetrize_fc3_q)
# when all the integration weights are smaller than the cutoff value
# the interaction strength will not be calculated
if is_write_g:
write_integration_weight_to_hdf5_at_grid(
self._mesh, self._sigma, self._grid_point, self._g)
self._g_skip = np.array(
self._g[:,
self._undone_triplet_index].sum(axis=0) < cutoff_g,
dtype="bool")
else:
self._g_skip = None
else:
if is_read_g:
self._g = read_integration_weight_from_hdf5_at_grid(
self._mesh, self._sigma, self._grid_point)
else:
self._g = get_triplets_integration_weights(
self._pp,
np.array(f_points, dtype='double'),
sigma_object,
band_indices=self._band_indices,
triplets=self._triplets_reduced,
is_triplet_symmetry=self._pp._symmetrize_fc3_q)
if is_write_g:
write_integration_weight_to_hdf5_at_grid(
self._mesh, self._sigma, self._grid_point, self._g)
if self._pp.get_triplets_done().all(
): #when the interaction strengths are all done
self._g_skip = None
else:
self._g_skip = np.array(
np.abs(self._g).sum(axis=0) < cutoff_g, dtype="bool")
def get_integration_weights(self):
return self._g
def get_interaction_skip(self):
return self._g_skip
@total_time.timeit
def run_c(self):
import anharmonic._phono3py as phono3c
freq = self._frequencies_all[self._grid_point_triplets]
if self._is_dispersed:
if not self._read_col:
phono3c.collision(self._collision_in,
self._fc3_normal_squared.copy(), freq.copy(),
self._g.copy(), self._temperature,
self._cutoff_frequency)
phono3c.collision_degeneracy(
self._collision_in, self._degeneracy_all.astype('intc'),
self._grid_point_triplets.astype("intc"), False)
self._collision_in *= self._unit_conversion # unit in THz
else:
phono3c.collision_all_permute(
self._collision_in_reduced,
self._fc3_normal_squared_reduced.copy(),
self._occu_reduced.copy(), self._frequencies_reduced.copy(),
self._g.copy(), self._cutoff_frequency)
self._collision_in_reduced *= self._unit_conversion # unit in THz
phono3c.collision_degeneracy(
self._collision_in_reduced,
self._degeneracy_all.astype('intc'),
self._triplets_reduced.astype('intc').copy(), True)
self._collision_in_all[
self._undone_uniq_index] = self._collision_in_reduced[:]
self._collision_done[self._undone_uniq_index] = True
phono3c.collision_from_reduced(
self._collision_in, self._collision_in_all,
self._pp.get_triplets_mapping_at_grid().astype("intc"),
self._pp.get_triplets_sequence_at_grid().astype("byte"))
# #############debugging############################
# f_points = self._frequencies_all[self._grid_point][self._band_indices]
# if self._asigma is not None:
# sigma_object = self._asigma
# else:
# sigma_object = self._sigma
# self._g = get_triplets_integration_weights(
# self._pp,
# np.array(f_points, dtype='double'),
# sigma_object,
# triplets = self._grid_point_triplets)
# collision_in = np.zeros_like(self._collision_in)
#
# phono3c.collision(collision_in,
# self._fc3_normal_squared.copy(),
# freq.copy(),
# self._g.copy(),
# self._temperature,
# self._cutoff_frequency)
# grid_points2 = self._grid_point_triplets[:, 1]
# phono3c.collision_degeneracy_grid(collision_in,
# self._degeneracy_all.astype('intc'),
# grid_points2.astype('intc').copy(),
# self._grid_point)
# collision_in *= self._unit_conversion # unit in THz
# diff = np.abs(collision_in - self._collision_in)
# if len(diff)>0:
# print diff.max()
# tt, bb0, bb1 = np.unravel_index(diff.argmax(), diff.shape)
# grid0, grid1, grid2 = self._grid_point_triplets[tt]
# n0 = self._occupations_all[grid0, self._itemp, bb0]
# n1 = self._occupations_all[grid1, self._itemp, bb1]
# n2 = self._occupations_all[grid2, self._itemp]
# g0 = self._g[0, tt, bb0, bb1]
# g1 = self._g[1, tt, bb0, bb1]
# g2 = self._g[2, tt, bb0, bb1]
# ng = n0 * n1 * (n2 + 1) * g2 + n0 * (n1 + 1) * n2 * g1 + (n0 + 1) * n1 * n2 * g0
# nga = ng * self._fc3_normal_squared[tt, bb0, bb1] * self._unit_conversion
# print
@total_time.timeit
def calculate_collision(self, grid_point, sigma=None, temperature=None):
"On behalf of the limited memory, each time only one temperature and one sigma is calculated"
if sigma is not None:
self.set_sigma(sigma)
if temperature is not None:
self.set_temperature(temperature)
self.set_grid(grid_point)
self.set_phonons_triplets()
self.set_grid_points_occupation()
self.reduce_triplets()
self.set_asigma()
self.set_integration_weights()
self.run_interaction_at_grid_point(g_skip=self._g_skip)
self.run()
class Phonopy:
def __init__(self,
unitcell,
supercell_matrix,
distance=0.01,
factor=VaspToTHz,
is_auto_displacements=True,
symprec=1e-5,
is_symmetry=True,
log_level=0):
self._symprec = symprec
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._factor = factor
self._is_symmetry = is_symmetry
self._log_level = log_level
self._supercell = None
self._set_supercell()
self._symmetry = None
self._set_symmetry()
# set_displacements (used only in preprocess)
self._displacements = None
self._displacement_directions = None
self._supercells_with_displacements = None
if is_auto_displacements:
self.generate_displacements(distance)
# set_post_process
self._primitive = None
self._dynamical_matrix = None
self._is_nac = False
# set_force_constants or set_forces
self._set_of_forces_objects = None
self._force_constants = None
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
def get_primitive(self):
return self._primitive
primitive = property(get_primitive)
def set_primitive(self, primitive):
self._primitive = primitive
def get_unitcell(self):
return self._unitcell
unitcell = property(get_unitcell)
def get_supercell(self):
return self._supercell
supercell = property(get_supercell)
def set_supercell(self, supercell):
self._supercell = supercell
def get_symmetry(self):
return self._symmetry
symmetry = property(get_symmetry)
def get_unit_conversion_factor(self):
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacements automatically
displacements:
List of displacements in Cartesian coordinates.
See 'set_displacements'
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[0, 1, 0, 0],
[7, 1, 0, 1], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
lattice = self._supercell.get_cell()
self._displacements = []
self._displacement_directions = \
get_least_displacements(self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
log_level=self._log_level)
for disp in self._displacement_directions:
atom_num = disp[0]
disp_cartesian = np.dot(disp[1:], lattice)
disp_cartesian *= distance / np.linalg.norm(disp_cartesian)
self._displacements.append([atom_num,
disp_cartesian[0],
disp_cartesian[1],
disp_cartesian[2]])
self._set_supercells_with_displacements()
def set_displacements(self, displacements):
"""Set displacements manually
displacemsts: List of disctionaries
[[0, 0.01, 0.00, 0.00], ...]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
"""
self._displacements = displacements
self._set_supercells_with_displacements()
def get_displacements(self):
return self._displacements
displacements = property(get_displacements)
def get_displacement_directions(self):
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_supercells_with_displacements(self):
return self._supercells_with_displacements
def set_post_process(self,
primitive_matrix=np.eye(3, dtype=float),
sets_of_forces=None,
set_of_forces_objects=None,
force_constants=None,
is_nac=False,
calculate_full_force_constants=False,
force_constants_decimals=None,
dynamical_matrix_decimals=None):
"""
Set forces or force constants to prepare phonon calculations.
The order of 'sets_of_forces' has to correspond to that of
'displacements' that should be already stored.
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
sets_of_forces:
[[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # first supercell
[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # second supercell
... ]
set_of_forces_objects:
[FORCES_object, FORCES_object, FORCES_object, ...]
"""
self._is_nac = is_nac
# Primitive cell
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
self._primitive = Primitive(
self._supercell,
np.dot(inv_supercell_matrix, primitive_matrix),
self._symprec)
# Set set of FORCES objects or force constants
if sets_of_forces is not None:
self.set_forces(sets_of_forces)
elif set_of_forces_objects is not None:
self.set_force_sets(set_of_forces_objects)
elif force_constants is not None:
self.set_force_constants(force_constants)
# Calculate force cosntants from forces (full or symmetry reduced)
if self._set_of_forces_objects is not None:
if calculate_full_force_constants:
self.set_force_constants_from_forces(
distributed_atom_list=None,
force_constants_decimals=force_constants_decimals)
else:
p2s_map = self._primitive.get_primitive_to_supercell_map()
self.set_force_constants_from_forces(
distributed_atom_list=p2s_map,
force_constants_decimals=force_constants_decimals)
if self._force_constants is None:
print "In set_post_process, sets_of_forces or force_constants"
print "has to be set."
return False
# Dynamical Matrix
self.set_dynamical_matrix(decimals=dynamical_matrix_decimals)
def set_nac_params(self, nac_params, method='wang'):
if self._is_nac:
self._dynamical_matrix.set_nac_params(nac_params, method)
def set_dynamical_matrix(self, decimals=None):
if self._is_nac:
self._dynamical_matrix = \
DynamicalMatrixNAC(self._supercell,
self._primitive,
self._force_constants,
decimals=decimals,
symprec=self._symprec)
else:
self._dynamical_matrix = \
DynamicalMatrix(self._supercell,
self._primitive,
self._force_constants,
decimals=decimals,
symprec=self._symprec)
def get_dynamical_matrix(self):
return self._dynamical_matrix
dynamical_matrix = property(get_dynamical_matrix)
def set_forces(self, sets_of_forces):
forces = []
for i, disp in enumerate(self._displacements):
forces.append(Forces(disp[0],
disp[1:4],
sets_of_forces[i]))
self._set_of_forces_objects = forces
def set_force_constants_from_forces(self,
distributed_atom_list=None,
force_constants_decimals=None):
self._force_constants = get_force_constants(
self._set_of_forces_objects,
self._symmetry,
self._supercell,
atom_list=distributed_atom_list,
decimals=force_constants_decimals)
def set_force_constants_zero_with_radius(self,
cutoff_radius):
cutoff_force_constants(self._force_constants,
self._supercell,
cutoff_radius,
symprec=self._symprec)
def set_force_constants(self, force_constants):
self._force_constants = force_constants
def set_force_sets(self, sets_of_forces_objects):
self._set_of_forces_objects = sets_of_forces_objects
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
def get_force_constants(self):
return self._force_constants
force_constants = property(get_force_constants)
def get_rotational_condition_of_fc(self):
return rotational_invariance(self._force_constants,
self._supercell,
self._primitive,
self._symprec)
def get_dynamical_matrix_at_q(self, q):
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamical_matrix()
# Frequency at a q-point
def get_frequencies(self, q):
"""
Calculate phonon frequencies at q
q: q-vector in reduced coordinates of primitive cell
"""
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm).real:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor
# Frequency and eigenvector at a q-point
def get_frequencies_with_eigenvectors(self, q):
"""
Calculate phonon frequencies and eigenvectors at q
q: q-vector in reduced coordinates of primitive cell
"""
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
eigvals, eigenvectors = np.linalg.eigh(dm)
frequencies = []
for eig in eigvals:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor, eigenvectors
## This expression may not be supported in old python versions.
# frequencies = np.array(
# [np.sqrt(x) if x > 0 else -np.sqrt(-x) for x in eigvals])
# return frequencies * self._factor, eigenvectors
# Band structure
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
self._primitive,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor)
def get_band_structure(self):
band = self._band_structure
return (band.get_qpoints(),
band.get_distances(),
band.get_frequencies(),
band.get_eigenvectors())
def plot_band_structure(self, symbols=None):
return self._band_structure.plot_band(symbols)
def write_yaml_band_structure(self):
self._band_structure.write_yaml()
# Mesh sampling
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_symmetry=True,
is_band_connection=False,
is_eigenvectors=False,
is_gamma_center=False):
self._mesh = Mesh(self._dynamical_matrix,
self._primitive,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_symmetry,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
is_gamma_center=is_gamma_center,
group_velocity=self._group_velocity,
factor=self._factor,
symprec=self._symprec)
def get_mesh(self):
return (self._mesh.get_qpoints(),
self._mesh.get_weights(),
self._mesh.get_frequencies(),
self._mesh.get_eigenvectors())
def write_yaml_mesh(self):
self._mesh.write_yaml()
def write_hdf5_mesh(self):
self._mesh.write_hdf5()
# Thermal property
def set_thermal_properties(self,
t_step=10,
t_max=1000,
t_min=0,
is_projection=False,
cutoff_frequency=None):
if self._mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
tp = ThermalProperties(self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors(),
is_projection=is_projection,
cutoff_frequency=cutoff_frequency)
tp.set_thermal_properties(t_step, t_max, t_min)
self._thermal_properties = tp
def get_thermal_properties(self):
temps, fe, entropy, cv = \
self._thermal_properties.get_thermal_properties()
return temps, fe, entropy, cv
def plot_thermal_properties(self):
return self._thermal_properties.plot_thermal_properties()
def write_yaml_thermal_properties(self, filename='thermal_properties.yaml'):
self._thermal_properties.write_yaml(filename=filename)
# Partial DOS
def set_partial_DOS(self,
sigma=None,
omega_min=None,
omega_max=None,
omega_pitch=None,
tetrahedron_method=False):
if self._mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self._mesh.get_eigenvectors() == None:
print "Eigenvectors have to be calculated."
sys.exit(1)
pdos = PartialDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
pdos.set_draw_area(omega_min,
omega_max,
omega_pitch)
pdos.calculate()
self._pdos = pdos
def get_partial_DOS(self):
"""
Retern omegas and partial_dos.
The first element is omegas and the second is partial_dos.
omegas: [freq1, freq2, ...]
partial_dos:
[[elem1-freq1, elem1-freq2, ...],
[elem2-freq1, elem2-freq2, ...],
...]
where
elem1: atom1-x compornent
elem2: atom1-y compornent
elem3: atom1-z compornent
elem4: atom2-x compornent
...
"""
return self._pdos.get_partial_dos()
def plot_partial_DOS(self, pdos_indices=None, legend=None):
return self._pdos.plot_pdos(indices=pdos_indices,
legend=legend)
def write_partial_DOS(self):
self._pdos.write()
# Total DOS
def set_total_DOS(self,
sigma=None,
omega_min=None,
omega_max=None,
omega_pitch=None,
tetrahedron_method=False):
if self._mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
total_dos = TotalDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(omega_min,
omega_max,
omega_pitch)
total_dos.calculate()
self._total_dos = total_dos
def get_total_DOS(self):
"""
Retern omegas and total dos.
The first element is omegas and the second is total dos.
omegas: [freq1, freq2, ...]
total_dos: [dos1, dos2, ...]
"""
return self._total_dos.get_dos()
def set_Debye_frequency(self, freq_max_fit=None):
self._total_dos.set_Debye_frequency(
self._primitive.get_number_of_atoms(), freq_max_fit)
def get_Debye_frequency(self):
return self._total_dos.get_Debye_frequency()
def plot_total_DOS(self):
return self._total_dos.plot_dos()
def write_total_DOS(self):
self._total_dos.write()
# Thermal displacement
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
direction=None,
cutoff_eigenvalue=None):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
direction:
Projection direction in reduced coordinates
"""
if self._mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
td.set_temperature_range(t_min, t_max, t_step)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
# td.run()
td.run_mesh()
self._thermal_displacements = td
def get_thermal_displacements(self):
if self._thermal_displacements is not None:
return self._thermal_displacements.get_thermal_displacements()
def plot_thermal_displacements(self, is_legend=False):
return self._thermal_displacements.plot(is_legend)
def write_yaml_thermal_displacements(self):
self._thermal_displacements.write_yaml()
def write_hdf5_thermal_displacements(self):
self._thermal_displacements.write_hdf5()
# Thermal displacement matrices
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_eigenvalue=None):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
direction:
Projection direction in reduced coordinates
"""
if self._mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
tdm.set_temperature_range(t_min, t_max, t_step)
# tdm.run()
tdm.run_mesh()
self._thermal_displacement_matrices = tdm
def get_thermal_displacement_matrices(self):
if self._thermal_displacement_matrices is not None:
return self._thermal_displacement_matrices.get_thermal_displacement_matrices()
def write_yaml_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_yaml()
def write_hdf5_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_hdf5()
# Thermal displacement
def set_thermal_distances(self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_eigenvalue=None):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [[1, 2], [1, 4]]
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
"""
td = ThermalDistances(self._mesh.get_frequencies(),
self._mesh.get_eigenvectors(),
self._supercell,
self._primitive,
self._mesh.get_qpoints(),
symprec=self._symprec,
cutoff_eigenvalue=cutoff_eigenvalue)
td.set_temperature_range(t_min, t_max, t_step)
# td.run(atom_pairs)
td.run_mesh(atom_pairs)
self._thermal_distances = td
def write_yaml_thermal_distances(self):
self._thermal_distances.write_yaml()
def write_hdf5_thermal_distances(self):
self._thermal_distances.write_hdf5()
# Q-points mode
def write_yaml_qpoints(self,
q_points,
nac_q_direction=None,
is_eigenvectors=False,
write_dynamical_matrices=False,
factor=VaspToTHz):
write_yaml_qpoints(q_points,
self._primitive,
self._dynamical_matrix,
nac_q_direction=nac_q_direction,
is_eigenvectors=is_eigenvectors,
group_velocity=self._group_velocity,
write_dynamical_matrices=write_dynamical_matrices,
factor=self._factor)
# Animation
def write_animation(self,
q_point=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None,
filename=None):
if q_point==None:
animation = Animation([0, 0, 0],
self._dynamical_matrix,
self._primitive,
shift=shift)
else:
animation = Animation(q_point,
self._dynamical_matrix,
self._primitive,
shift=shift)
if anime_type=='v_sim':
if amplitude:
amplitude_ = amplitude
else:
amplitude_ = 1.0
if filename:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor,
filename=filename)
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type=='arc' or
anime_type=='xyz' or
anime_type=='jmol' or
anime_type=='poscar'):
if band_index==None or amplitude==None or num_div==None:
print "Parameters are not correctly set for animation."
sys.exit(1)
if anime_type=='arc' or anime_type==None:
if filename:
animation.write_arc(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_arc(band_index,
amplitude,
num_div)
if anime_type=='xyz':
if filename:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor,
filename=filename)
else:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor)
if anime_type=='jmol':
if filename:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor,
filename=filename)
else:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor)
if anime_type=='poscar':
if filename:
animation.write_POSCAR(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_POSCAR(band_index,
amplitude,
num_div)
# Modulation
def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
self._modulation = Modulation(self._dynamical_matrix,
self._primitive,
dimension=dimension,
phonon_modes=phonon_modes,
delta_q= delta_q,
derivative_order=derivative_order,
nac_q_direction=nac_q_direction,
factor=self._factor)
self._modulation.run()
def get_modulations(self):
"""Returns cells with modulations as Atoms objects"""
return self._modulation.get_modulations()
def get_delta_modulations(self):
"""Return modulations relative to equilibrium supercell
(modulations, supercell)
modulations: Atomic modulations of supercell in Cartesian coordinates
supercell: Supercell as an Atoms object.
"""
return self._modulation.get_delta_modulations()
def write_modulations(self):
"""Create MPOSCAR's"""
self._modulation.write()
def write_yaml_modulations(self):
self._modulation.write_yaml()
# Characters of irreducible representations
def set_irreps(self, q, degeneracy_tolerance=1e-4):
self._irreps = IrReps(
self._dynamical_matrix,
q,
factor=self._factor,
symprec=self._symprec,
degeneracy_tolerance=degeneracy_tolerance,
log_level=self._log_level)
return self._irreps.run()
def get_irreps(self):
return self._irreps
def show_irreps(self, show_irreps=False):
self._irreps.show(show_irreps=show_irreps)
def write_yaml_irreps(self, show_irreps=False):
self._irreps.write_yaml(show_irreps=show_irreps)
# Group velocity
def set_group_velocity(self,
q_points=None,
q_length=1e-4):
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_points=q_points,
symmetry=self._symmetry,
q_length=q_length,
frequency_factor_to_THz=self._factor)
def get_group_velocity(self, q_point):
self._group_velocity.set_q_points([q_point])
return self._group_velocity.get_group_velocity()[0]
def _set_supercell(self):
self._supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
def _set_symmetry(self):
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
def _set_supercells_with_displacements(self):
supercells = []
for disp in self._displacements:
positions = self._supercell.get_positions()
positions[disp[0]] += disp[1:4]
supercells.append(Atoms(
numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),
magmoms=self._supercell.get_magnetic_moments(),
positions=positions,
cell=self._supercell.get_cell(),
pbc=True))
self._supercells_with_displacements = supercells
class Phonopy(object):
def __init__(self,
unitcell,
supercell_matrix,
primitive_matrix=None,
nac_params=None,
distance=None,
factor=VaspToTHz,
is_auto_displacements=None,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=1e-5,
is_symmetry=True,
use_lapack_solver=False,
log_level=0):
if is_auto_displacements is not None:
print("Warning: \'is_auto_displacements\' argument is obsolete.")
if is_auto_displacements is False:
print("Sets of displacements are not created as default.")
else:
print("Use \'generate_displacements\' method explicitly to "
"create sets of displacements.")
if distance is not None:
print("Warning: \'distance\' keyword argument is obsolete at "
"Phonopy instantiation.")
print("Specify \'distance\' keyword argument when calling "
"\'generate_displacements\'")
print("method (See the Phonopy API document).")
self._symprec = symprec
self._factor = factor
self._is_symmetry = is_symmetry
self._use_lapack_solver = use_lapack_solver
self._log_level = log_level
# Create supercell and primitive cell
self._unitcell = Atoms(atoms=unitcell)
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
# Set supercell and primitive symmetry
self._symmetry = None
self._primitive_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
# set_displacements (used only in preprocess)
self._displacement_dataset = None
self._displacements = None
self._displacement_directions = None
self._supercells_with_displacements = None
# set_force_constants or set_forces
self._force_constants = None
self._force_constants_decimals = force_constants_decimals
# set_dynamical_matrix
self._dynamical_matrix = None
self._nac_params = nac_params
self._dynamical_matrix_decimals = dynamical_matrix_decimals
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_tetrahedron_method
self._tetrahedron_method = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
def get_version(self):
return __version__
def get_primitive(self):
return self._primitive
primitive = property(get_primitive)
def get_unitcell(self):
return self._unitcell
unitcell = property(get_unitcell)
def get_supercell(self):
return self._supercell
supercell = property(get_supercell)
def get_symmetry(self):
"""return symmetry of supercell"""
return self._symmetry
symmetry = property(get_symmetry)
def get_primitive_symmetry(self):
"""return symmetry of primitive cell"""
return self._primitive_symmetry
def get_supercell_matrix(self):
return self._supercell_matrix
def get_primitive_matrix(self):
return self._primitive_matrix
def get_unit_conversion_factor(self):
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def get_displacement_dataset(self):
return self._displacement_dataset
def get_displacements(self):
return self._displacements
displacements = property(get_displacements)
def get_displacement_directions(self):
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_supercells_with_displacements(self):
if self._displacement_dataset is None:
return None
else:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_force_constants(self):
return self._force_constants
force_constants = property(get_force_constants)
def get_rotational_condition_of_fc(self):
return rotational_invariance(self._force_constants,
self._supercell,
self._primitive,
self._symprec)
def get_nac_params(self):
return self._nac_params
def get_dynamical_matrix(self):
return self._dynamical_matrix
dynamical_matrix = property(get_dynamical_matrix)
def set_unitcell(self, unitcell):
self._unitcell = unitcell
self._build_supercell()
self._build_primitive_cell()
self._search_symmetry()
self._search_primitive_symmetry()
self._displacement_dataset = None
def set_masses(self, masses):
p_masses = np.array(masses)
self._primitive.set_masses(p_masses)
p2p_map = self._primitive.get_primitive_to_primitive_map()
s_masses = p_masses[[p2p_map[x] for x in
self._primitive.get_supercell_to_primitive_map()]]
self._supercell.set_masses(s_masses)
u2s_map = self._supercell.get_unitcell_to_supercell_map()
u_masses = s_masses[u2s_map]
self._unitcell.set_masses(u_masses)
self._set_dynamical_matrix()
def set_nac_params(self, nac_params=None):
self._nac_params = nac_params
self._set_dynamical_matrix()
def set_displacement_dataset(self, displacement_dataset):
"""
displacement_dataset:
{'natom': number_of_atoms_in_supercell,
'first_atoms': [
{'number': atom index of displaced atom,
'displacement': displacement in Cartesian coordinates,
'direction': displacement direction with respect to axes
'forces': forces on atoms in supercell},
{...}, ...]}
"""
self._displacement_dataset = displacement_dataset
self._displacements = []
self._displacement_directions = []
for disp in self._displacement_dataset['first_atoms']:
x = disp['displacement']
self._displacements.append([disp['number'], x[0], x[1], x[2]])
if 'direction' in disp:
y = disp['direction']
self._displacement_directions.append(
[disp['number'], y[0], y[1], y[2]])
if not self._displacement_directions:
self._displacement_directions = None
def set_forces(self, sets_of_forces):
"""
sets_of_forces:
[[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # first supercell
[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # second supercell
... ]
"""
for disp, forces in zip(
self._displacement_dataset['first_atoms'], sets_of_forces):
disp['forces'] = forces
def set_force_constants(self, force_constants):
self._force_constants = force_constants
self._set_dynamical_matrix()
def set_force_constants_zero_with_radius(self, cutoff_radius):
cutoff_force_constants(self._force_constants,
self._supercell,
cutoff_radius,
symprec=self._symprec)
self._set_dynamical_matrix()
def set_dynamical_matrix(self):
self._set_dynamical_matrix()
def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacements automatically
displacemsts: List of displacements in Cartesian coordinates.
[[0, 0.01, 0.00, 0.00], ...]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[0, 1, 0, 0],
[7, 1, 0, 1], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
displacement_directions = get_least_displacements(
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
log_level=self._log_level)
displacement_dataset = direction_to_displacement(
displacement_directions,
distance,
self._supercell)
self.set_displacement_dataset(displacement_dataset)
def produce_force_constants(self,
forces=None,
calculate_full_force_constants=True,
computation_algorithm="svd"):
if forces is not None:
self.set_forces(forces)
# A primitive check if 'forces' key is in displacement_dataset.
for disp in self._displacement_dataset['first_atoms']:
if 'forces' not in disp:
return False
if calculate_full_force_constants:
self._run_force_constants_from_forces(
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
else:
p2s_map = self._primitive.get_primitive_to_supercell_map()
self._run_force_constants_from_forces(
distributed_atom_list=p2s_map,
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
self._set_dynamical_matrix()
return True
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
self._set_dynamical_matrix()
def symmetrize_force_constants_by_space_group(self):
from phonopy.harmonic.force_constants import (set_tensor_symmetry,
set_tensor_symmetry_PJ)
set_tensor_symmetry_PJ(self._force_constants,
self._supercell.get_cell().T,
self._supercell.get_scaled_positions(),
self._symmetry)
self._set_dynamical_matrix()
#####################
# Phonon properties #
#####################
# Single q-point
def get_dynamical_matrix_at_q(self, q):
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return None
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamical_matrix()
def get_frequencies(self, q):
"""
Calculate phonon frequencies at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return None
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm).real:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor
def get_frequencies_with_eigenvectors(self, q):
"""
Calculate phonon frequencies and eigenvectors at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return None
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
eigvals, eigenvectors = np.linalg.eigh(dm)
frequencies = []
for eig in eigvals:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor, eigenvectors
# Band structure
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._band_structure = None
return False
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor)
return True
def get_band_structure(self):
band = self._band_structure
return (band.get_qpoints(),
band.get_distances(),
band.get_frequencies(),
band.get_eigenvectors())
def plot_band_structure(self, labels=None):
import matplotlib.pyplot as plt
if labels:
from matplotlib import rc
rc('text', usetex=True)
fig, ax = plt.subplots()
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.xaxis.set_tick_params(which='both', direction='in')
ax.yaxis.set_tick_params(which='both', direction='in')
self._band_structure.plot(plt, labels=labels)
return plt
def write_yaml_band_structure(self,
labels=None,
comment=None,
filename="band.yaml"):
self._band_structure.write_yaml(labels=labels,
comment=comment,
filename=filename)
# Sampling mesh
def run_mesh(self):
if self._mesh is not None:
self._mesh.run()
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False,
run_immediately=True):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._mesh = None
return False
self._mesh = Mesh(
self._dynamical_matrix,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_mesh_symmetry,
is_eigenvectors=is_eigenvectors,
is_gamma_center=is_gamma_center,
group_velocity=self._group_velocity,
rotations=self._primitive_symmetry.get_pointgroup_operations(),
factor=self._factor,
use_lapack_solver=self._use_lapack_solver)
if run_immediately:
self._mesh.run()
return True
def get_mesh(self):
if self._mesh is None:
return None
else:
return (self._mesh.get_qpoints(),
self._mesh.get_weights(),
self._mesh.get_frequencies(),
self._mesh.get_eigenvectors())
def get_mesh_grid_info(self):
if self._mesh is None:
return None
else:
return (self._mesh.get_grid_address(),
self._mesh.get_ir_grid_points(),
self._mesh.get_grid_mapping_table())
def write_hdf5_mesh(self):
self._mesh.write_hdf5()
def write_yaml_mesh(self):
self._mesh.write_yaml()
# Plot band structure and DOS (PDOS) together
def plot_band_structure_and_dos(self, pdos_indices=None, labels=None):
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
if labels:
from matplotlib import rc
rc('text', usetex=True)
plt.figure(figsize=(10, 6))
gs = gridspec.GridSpec(1, 2, width_ratios=[3, 1])
ax1 = plt.subplot(gs[0, 0])
ax1.xaxis.set_ticks_position('both')
ax1.yaxis.set_ticks_position('both')
ax1.xaxis.set_tick_params(which='both', direction='in')
ax1.yaxis.set_tick_params(which='both', direction='in')
self._band_structure.plot(plt, labels=labels)
ax2 = plt.subplot(gs[0, 1], sharey=ax1)
ax2.xaxis.set_ticks_position('both')
ax2.yaxis.set_ticks_position('both')
ax2.xaxis.set_tick_params(which='both', direction='in')
ax2.yaxis.set_tick_params(which='both', direction='in')
plt.subplots_adjust(wspace=0.03)
plt.setp(ax2.get_yticklabels(), visible=False)
if pdos_indices is None:
self._total_dos.plot(plt,
ylabel="",
draw_grid=False,
flip_xy=True)
else:
self._pdos.plot(plt,
indices=pdos_indices,
ylabel="",
draw_grid=False,
flip_xy=True)
ax2.set_xlim((0, None))
return plt
# DOS
def set_total_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False):
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before DOS calculation.")
self._total_dos = None
return False
total_dos = TotalDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(freq_min, freq_max, freq_pitch)
total_dos.run()
self._total_dos = total_dos
return True
def get_total_DOS(self):
"""
Retern frequencies and total dos.
The first element is freqs and the second is total dos.
frequencies: [freq1, freq2, ...]
total_dos: [dos1, dos2, ...]
"""
return self._total_dos.get_dos()
def set_Debye_frequency(self, freq_max_fit=None):
self._total_dos.set_Debye_frequency(
self._primitive.get_number_of_atoms(),
freq_max_fit=freq_max_fit)
def get_Debye_frequency(self):
return self._total_dos.get_Debye_frequency()
def plot_total_DOS(self):
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.xaxis.set_tick_params(which='both', direction='in')
ax.yaxis.set_tick_params(which='both', direction='in')
self._total_dos.plot(plt, draw_grid=False)
ax.set_ylim((0, None))
return plt
def write_total_DOS(self):
self._total_dos.write()
# PDOS
def set_partial_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False,
direction=None,
xyz_projection=False):
self._pdos = None
if self._mesh is None:
print("Warning: \'set_mesh\' has to be called before "
"PDOS calculation.")
return False
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
num_grid = np.prod(self._mesh.get_mesh_numbers())
if num_grid != len(self._mesh.get_ir_grid_points()):
print("Warning: \'set_mesh\' has to be called with "
"is_mesh_symmetry=False.")
return False
if direction is not None:
direction_cart = np.dot(direction, self._primitive.get_cell())
else:
direction_cart = None
self._pdos = PartialDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method,
direction=direction_cart,
xyz_projection=xyz_projection)
self._pdos.set_draw_area(freq_min, freq_max, freq_pitch)
self._pdos.run()
return True
def get_partial_DOS(self):
"""
Retern frequencies and partial_dos.
The first element is freqs and the second is partial_dos.
frequencies: [freq1, freq2, ...]
partial_dos:
[[atom1-freq1, atom1-freq2, ...],
[atom2-freq1, atom2-freq2, ...],
...]
"""
return self._pdos.get_partial_dos()
def plot_partial_DOS(self, pdos_indices=None, legend=None):
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.xaxis.set_tick_params(which='both', direction='in')
ax.yaxis.set_tick_params(which='both', direction='in')
self._pdos.plot(plt,
indices=pdos_indices,
legend=legend,
draw_grid=False)
ax.set_ylim((0, None))
return plt
def write_partial_DOS(self):
self._pdos.write()
# Thermal property
def set_thermal_properties(self,
t_step=10,
t_max=1000,
t_min=0,
temperatures=None,
is_projection=False,
band_indices=None,
cutoff_frequency=None,
pretend_real=False):
if self._mesh is None:
print("Warning: set_mesh has to be done before "
"set_thermal_properties")
return False
else:
tp = ThermalProperties(self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors(),
is_projection=is_projection,
band_indices=band_indices,
cutoff_frequency=cutoff_frequency,
pretend_real=pretend_real)
if temperatures is None:
tp.set_temperature_range(t_step=t_step,
t_max=t_max,
t_min=t_min)
else:
tp.set_temperatures(temperatures)
tp.run()
self._thermal_properties = tp
def get_thermal_properties(self):
temps, fe, entropy, cv = \
self._thermal_properties.get_thermal_properties()
return temps, fe, entropy, cv
def plot_thermal_properties(self):
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.xaxis.set_tick_params(which='both', direction='in')
ax.yaxis.set_tick_params(which='both', direction='in')
self._thermal_properties.plot(plt)
temps, _, _, _ = self._thermal_properties.get_thermal_properties()
ax.set_xlim((0, temps[-1]))
return plt
def write_yaml_thermal_properties(self, filename='thermal_properties.yaml'):
self._thermal_properties.write_yaml(filename=filename)
# Thermal displacement
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
temperatures=None,
direction=None,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
self._thermal_displacements = None
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before \'set_thermal_displacements\'.")
return False
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(mesh_nums) != len(eigvecs):
print("Warning: Sampling mesh must not be symmetrized.")
return False
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
if temperatures is None:
td.set_temperature_range(t_min, t_max, t_step)
else:
td.set_temperatures(temperatures)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
td.run()
self._thermal_displacements = td
return True
def get_thermal_displacements(self):
if self._thermal_displacements is not None:
return self._thermal_displacements.get_thermal_displacements()
def plot_thermal_displacements(self, is_legend=False):
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.xaxis.set_tick_params(which='both', direction='in')
ax.yaxis.set_tick_params(which='both', direction='in')
self._thermal_displacements.plot(plt, is_legend=is_legend)
temps, _ = self._thermal_displacements.get_thermal_displacements()
ax.set_xlim((0, temps[-1]))
return plt
def write_yaml_thermal_displacements(self):
self._thermal_displacements.write_yaml()
# Thermal displacement matrix
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None,
t_cif=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
self._thermal_displacement_matrices = None
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before \'set_thermal_displacement_matrices\'.")
return False
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(mesh_nums) != len(eigvecs):
print("Warning: Sampling mesh must not be symmetrized.")
return False
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency,
lattice=self._primitive.get_cell().T)
if t_cif is None:
tdm.set_temperature_range(t_min, t_max, t_step)
else:
tdm.set_temperatures([t_cif])
tdm.run()
self._thermal_displacement_matrices = tdm
return True
def get_thermal_displacement_matrices(self):
tdm = self._thermal_displacement_matrices
if tdm is not None:
return tdm.get_thermal_displacement_matrices()
def write_yaml_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_yaml()
def write_thermal_displacement_matrix_to_cif(self,
temperature_index):
self._thermal_displacement_matrices.write_cif(self._primitive,
temperature_index)
# Mean square distance between a pair of atoms
def set_thermal_distances(self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [[1, 2], [1, 4]]
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
"""
td = ThermalDistances(self._mesh.get_frequencies(),
self._mesh.get_eigenvectors(),
self._supercell,
self._primitive,
self._mesh.get_qpoints(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
td.run(atom_pairs)
self._thermal_distances = td
def write_yaml_thermal_distances(self):
self._thermal_distances.write_yaml()
# Sampling at q-points
def set_qpoints_phonon(self,
q_points,
nac_q_direction=None,
is_eigenvectors=False,
write_dynamical_matrices=False):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._qpoints_phonon = None
return False
self._qpoints_phonon = QpointsPhonon(
np.reshape(q_points, (-1, 3)),
self._dynamical_matrix,
nac_q_direction=nac_q_direction,
is_eigenvectors=is_eigenvectors,
group_velocity=self._group_velocity,
write_dynamical_matrices=write_dynamical_matrices,
factor=self._factor)
return True
def get_qpoints_phonon(self):
return (self._qpoints_phonon.get_frequencies(),
self._qpoints_phonon.get_eigenvectors())
def write_hdf5_qpoints_phonon(self):
self._qpoints_phonon.write_hdf5()
def write_yaml_qpoints_phonon(self):
self._qpoints_phonon.write_yaml()
# Normal mode animation
def write_animation(self,
q_point=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None,
filename=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
return False
if q_point is None:
animation = Animation([0, 0, 0],
self._dynamical_matrix,
shift=shift)
else:
animation = Animation(q_point,
self._dynamical_matrix,
shift=shift)
if anime_type == 'v_sim':
if amplitude:
amplitude_ = amplitude
else:
amplitude_ = 1.0
if filename:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor,
filename=filename)
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type == 'arc' or
anime_type == 'xyz' or
anime_type == 'jmol' or
anime_type == 'poscar'):
if band_index is None or amplitude is None or num_div is None:
print("Warning: Parameters are not correctly set for "
"animation.")
return False
if anime_type == 'arc' or anime_type is None:
if filename:
animation.write_arc(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_arc(band_index,
amplitude,
num_div)
if anime_type == 'xyz':
if filename:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor,
filename=filename)
else:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor)
if anime_type == 'jmol':
if filename:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor,
filename=filename)
else:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor)
if anime_type == 'poscar':
if filename:
animation.write_POSCAR(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_POSCAR(band_index,
amplitude,
num_div)
return True
# Atomic modulation of normal mode
def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._modulation = None
return False
self._modulation = Modulation(self._dynamical_matrix,
dimension,
phonon_modes,
delta_q=delta_q,
derivative_order=derivative_order,
nac_q_direction=nac_q_direction,
factor=self._factor)
self._modulation.run()
return True
def get_modulated_supercells(self):
"""Returns cells with modulations as Atoms objects"""
return self._modulation.get_modulated_supercells()
def get_modulations_and_supercell(self):
"""Return modulations and supercell
(modulations, supercell)
modulations: Atomic modulations of supercell in Cartesian coordinates
supercell: Supercell as an Atoms object.
"""
return self._modulation.get_modulations_and_supercell()
def write_modulations(self):
"""Create MPOSCAR's"""
self._modulation.write()
def write_yaml_modulations(self):
self._modulation.write_yaml()
# Irreducible representation
def set_irreps(self,
q,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=1e-4):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._irreps = None
return None
self._irreps = IrReps(
self._dynamical_matrix,
q,
is_little_cogroup=is_little_cogroup,
nac_q_direction=nac_q_direction,
factor=self._factor,
symprec=self._symprec,
degeneracy_tolerance=degeneracy_tolerance,
log_level=self._log_level)
return self._irreps.run()
def get_irreps(self):
return self._irreps
def show_irreps(self, show_irreps=False):
self._irreps.show(show_irreps=show_irreps)
def write_yaml_irreps(self, show_irreps=False):
self._irreps.write_yaml(show_irreps=show_irreps)
# Group velocity
def set_group_velocity(self, q_length=None):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._group_velocity = None
return False
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
return True
def get_group_velocity(self):
return self._group_velocity.get_group_velocity()
def get_group_velocity_at_q(self, q_point):
if self._group_velocity is None:
self.set_group_velocity()
self._group_velocity.set_q_points([q_point])
return self._group_velocity.get_group_velocity()[0]
# Moment
def set_moment(self,
order=1,
is_projection=False,
freq_min=None,
freq_max=None):
if self._mesh is None:
print("Warning: set_mesh has to be done before set_moment")
return False
else:
if is_projection:
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
moment = PhononMoment(
self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors())
else:
moment = PhononMoment(
self._mesh.get_frequencies(),
weights=self._mesh.get_weights())
if freq_min is not None or freq_max is not None:
moment.set_frequency_range(freq_min=freq_min,
freq_max=freq_max)
moment.run(order=order)
self._moment = moment.get_moment()
return True
def get_moment(self):
return self._moment
#################
# Local methods #
#################
def _run_force_constants_from_forces(self,
distributed_atom_list=None,
decimals=None,
computation_algorithm="svd"):
if self._displacement_dataset is not None:
self._force_constants = get_fc2(
self._supercell,
self._symmetry,
self._displacement_dataset,
atom_list=distributed_atom_list,
decimals=decimals,
computation_algorithm=computation_algorithm)
def _set_dynamical_matrix(self):
self._dynamical_matrix = None
if (self._supercell is None or self._primitive is None):
print("Bug: Supercell or primitive is not created.")
return False
elif self._force_constants is None:
print("Warning: Force constants are not prepared.")
return False
elif self._primitive.get_masses() is None:
print("Warning: Atomic masses are not correctly set.")
return False
else:
if self._nac_params is None:
self._dynamical_matrix = DynamicalMatrix(
self._supercell,
self._primitive,
self._force_constants,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
else:
self._dynamical_matrix = DynamicalMatrixNAC(
self._supercell,
self._primitive,
self._force_constants,
nac_params=self._nac_params,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
return True
def _search_symmetry(self):
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive,
self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) !=
len(self._primitive_symmetry.get_pointgroup_operations())):
print("Warning: Point group symmetries of supercell and primitive"
"cell are different.")
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
def _build_supercells_with_displacements(self):
supercells = []
for disp in self._displacement_dataset['first_atoms']:
positions = self._supercell.get_positions()
positions[disp['number']] += disp['displacement']
supercells.append(Atoms(
numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),
magmoms=self._supercell.get_magnetic_moments(),
positions=positions,
cell=self._supercell.get_cell(),
pbc=True))
self._supercells_with_displacements = supercells
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
if self._primitive_matrix is None:
trans_mat = inv_supercell_matrix
else:
trans_mat = np.dot(inv_supercell_matrix, self._primitive_matrix)
self._primitive = get_primitive(
self._supercell, trans_mat, self._symprec)
num_satom = self._supercell.get_number_of_atoms()
num_patom = self._primitive.get_number_of_atoms()
if abs(num_satom * np.linalg.det(trans_mat) - num_patom) < 0.1:
return True
else:
return False
class Phonopy:
def __init__(self,
unitcell,
supercell_matrix,
primitive_matrix=None,
nac_params=None,
distance=0.01,
factor=VaspToTHz,
is_auto_displacements=True,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=1e-5,
is_symmetry=True,
log_level=0):
self._symprec = symprec
self._factor = factor
self._is_symmetry = is_symmetry
self._log_level = log_level
# Create supercell and primitive cell
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
# Set supercell and primitive symmetry
self._symmetry = None
self._primitive_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
# set_displacements (used only in preprocess)
self._displacement_dataset = None
self._displacements = None
self._displacement_directions = None
self._supercells_with_displacements = None
if is_auto_displacements:
self.generate_displacements(distance=distance)
# set_force_constants or set_forces
self._force_constants = None
self._force_constants_decimals = force_constants_decimals
# set_dynamical_matrix
self._dynamical_matrix = None
self._nac_params = nac_params
self._dynamical_matrix_decimals = dynamical_matrix_decimals
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_tetrahedron_method
self._tetrahedron_method = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
def set_post_process(self,
primitive_matrix=None,
sets_of_forces=None,
displacement_dataset=None,
force_constants=None,
is_nac=None):
print
print(
"********************************** Warning"
"**********************************")
print "set_post_process will be obsolete."
print(
" produce_force_constants is used instead of set_post_process"
" for producing")
print(" force constants from forces.")
if primitive_matrix is not None:
print(
" primitive_matrix has to be given at Phonopy::__init__"
" object creation.")
print(
"******************************************"
"**********************************")
print
if primitive_matrix is not None:
self._primitive_matrix = primitive_matrix
self._build_primitive_cell()
self._search_primitive_symmetry()
if sets_of_forces is not None:
self.set_forces(sets_of_forces)
elif displacement_dataset is not None:
self._displacement_dataset = displacement_dataset
elif force_constants is not None:
self.set_force_constants(force_constants)
if self._displacement_dataset is not None:
self.produce_force_constants()
def set_masses(self, masses):
p_masses = np.array(masses)
self._primitive.set_masses(p_masses)
p2p_map = self._primitive.get_primitive_to_primitive_map()
s_masses = p_masses[[
p2p_map[x]
for x in self._primitive.get_supercell_to_primitive_map()
]]
self._supercell.set_masses(s_masses)
u2s_map = self._supercell.get_unitcell_to_supercell_map()
u_masses = s_masses[u2s_map]
self._unitcell.set_masses(u_masses)
def get_primitive(self):
return self._primitive
primitive = property(get_primitive)
def get_unitcell(self):
return self._unitcell
unitcell = property(get_unitcell)
def get_supercell(self):
return self._supercell
supercell = property(get_supercell)
def set_supercell(self, supercell):
self._supercell = supercell
def get_symmetry(self):
"""return symmetry of supercell"""
return self._symmetry
symmetry = property(get_symmetry)
def get_primitive_symmetry(self):
"""return symmetry of primitive cell"""
return self._primitive_symmetry
def get_unit_conversion_factor(self):
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def produce_force_constants(self,
forces=None,
calculate_full_force_constants=True,
computation_algorithm="svd"):
if forces is not None:
self.set_forces(forces)
if calculate_full_force_constants:
self._run_force_constants_from_forces(
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
else:
p2s_map = self._primitive.get_primitive_to_supercell_map()
self._run_force_constants_from_forces(
distributed_atom_list=p2s_map,
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
def set_nac_params(self, nac_params=None, method=None):
if method is not None:
print "set_nac_params:"
print " Keyword argument of \"method\" is not more supported."
self._nac_params = nac_params
def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacements automatically
displacemsts: List of displacements in Cartesian coordinates.
[[0, 0.01, 0.00, 0.00], ...]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[0, 1, 0, 0],
[7, 1, 0, 1], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
displacement_directions = get_least_displacements(
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
log_level=self._log_level)
displacement_dataset = direction_to_displacement(
displacement_directions, distance, self._supercell)
self.set_displacement_dataset(displacement_dataset)
def set_displacements(self, displacements):
print
print(
"********************************** Warning"
"**********************************")
print "set_displacements is obsolete. Do nothing."
print(
"******************************************"
"**********************************")
print
def get_displacements(self):
return self._displacements
displacements = property(get_displacements)
def get_displacement_directions(self):
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_displacement_dataset(self):
return self._displacement_dataset
def get_supercells_with_displacements(self):
if self._displacement_dataset is None:
return None
else:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_dynamical_matrix(self):
return self._dynamical_matrix
dynamical_matrix = property(get_dynamical_matrix)
def set_forces(self, sets_of_forces):
"""
sets_of_forces:
[[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # first supercell
[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # second supercell
... ]
"""
for disp, forces in zip(self._displacement_dataset['first_atoms'],
sets_of_forces):
disp['forces'] = forces
def set_force_constants_zero_with_radius(self, cutoff_radius):
cutoff_force_constants(self._force_constants,
self._supercell,
cutoff_radius,
symprec=self._symprec)
def set_force_constants(self, force_constants):
self._force_constants = force_constants
def set_force_sets(self, force_sets):
print
print(
"********************************** Warning"
"**********************************")
print "set_force_sets will be obsolete."
print(" The method name is changed to set_displacement_dataset.")
print(
"******************************************"
"**********************************")
print
self.set_displacement_dataset(force_sets)
def set_displacement_dataset(self, displacement_dataset):
"""
displacement_dataset:
{'natom': number_of_atoms_in_supercell,
'first_atoms': [
{'number': atom index of displaced atom,
'displacement': displacement in Cartesian coordinates,
'direction': displacement direction with respect to axes
'forces': forces on atoms in supercell},
{...}, ...]}
"""
self._displacement_dataset = displacement_dataset
self._displacements = []
self._displacement_directions = []
for disp in self._displacement_dataset['first_atoms']:
x = disp['displacement']
self._displacements.append([disp['number'], x[0], x[1], x[2]])
if 'direction' in disp:
y = disp['direction']
self._displacement_directions.append(
[disp['number'], y[0], y[1], y[2]])
if not self._displacement_directions:
self._displacement_directions = None
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
def symmetrize_force_constants_by_space_group(self):
rotations = self._symmetry.get_symmetry_operations()['rotations']
translations = self._symmetry.get_symmetry_operations()['translations']
set_tensor_symmetry(self._force_constants,
self._supercell.get_cell().T,
self._supercell.get_scaled_positions(), rotations,
translations, self._symprec)
def get_force_constants(self):
return self._force_constants
force_constants = property(get_force_constants)
def get_rotational_condition_of_fc(self):
return rotational_invariance(self._force_constants, self._supercell,
self._primitive, self._symprec)
def set_dynamical_matrix(self):
self._set_dynamical_matrix()
def get_dynamical_matrix_at_q(self, q):
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamical_matrix()
def get_frequencies(self, q):
"""
Calculate phonon frequencies at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm).real:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor
def get_frequencies_with_eigenvectors(self, q):
"""
Calculate phonon frequencies and eigenvectors at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
eigvals, eigenvectors = np.linalg.eigh(dm)
frequencies = []
for eig in eigvals:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor, eigenvectors
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
self._set_dynamical_matrix()
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor)
def get_band_structure(self):
band = self._band_structure
return (band.get_qpoints(), band.get_distances(),
band.get_frequencies(), band.get_eigenvectors())
def plot_band_structure(self, symbols=None):
return self._band_structure.plot_band(symbols)
def write_yaml_band_structure(self):
self._band_structure.write_yaml()
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False):
self._set_dynamical_matrix()
self._mesh = Mesh(
self._dynamical_matrix,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_mesh_symmetry,
is_eigenvectors=is_eigenvectors,
is_gamma_center=is_gamma_center,
group_velocity=self._group_velocity,
rotations=self._primitive_symmetry.get_pointgroup_operations(),
factor=self._factor)
def get_mesh(self):
return (self._mesh.get_qpoints(), self._mesh.get_weights(),
self._mesh.get_frequencies(), self._mesh.get_eigenvectors())
def write_yaml_mesh(self):
self._mesh.write_yaml()
def set_thermal_properties(self,
t_step=10,
t_max=1000,
t_min=0,
is_projection=False,
band_indices=None,
cutoff_frequency=None):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
return False
else:
tp = ThermalProperties(self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors(),
is_projection=is_projection,
band_indices=band_indices,
cutoff_frequency=cutoff_frequency)
tp.set_thermal_properties(t_step=t_step, t_max=t_max, t_min=t_min)
self._thermal_properties = tp
def get_thermal_properties(self):
temps, fe, entropy, cv = \
self._thermal_properties.get_thermal_properties()
return temps, fe, entropy, cv
def plot_thermal_properties(self):
return self._thermal_properties.plot_thermal_properties()
def write_yaml_thermal_properties(self,
filename='thermal_properties.yaml'):
self._thermal_properties.write_yaml(filename=filename)
def set_partial_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False,
direction=None):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if direction is not None:
direction_cart = np.dot(direction, self._primitive.get_cell())
else:
direction_cart = None
pdos = PartialDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method,
direction=direction_cart)
pdos.set_draw_area(freq_min, freq_max, freq_pitch)
pdos.run()
self._pdos = pdos
def get_partial_DOS(self):
"""
Retern frequencies and partial_dos.
The first element is freqs and the second is partial_dos.
frequencies: [freq1, freq2, ...]
partial_dos:
[[atom1-freq1, atom1-freq2, ...],
[atom2-freq1, atom2-freq2, ...],
...]
"""
return self._pdos.get_partial_dos()
def plot_partial_DOS(self, pdos_indices=None, legend=None):
return self._pdos.plot_pdos(indices=pdos_indices, legend=legend)
def write_partial_DOS(self):
self._pdos.write()
def set_total_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
total_dos = TotalDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(freq_min, freq_max, freq_pitch)
total_dos.run()
self._total_dos = total_dos
def get_total_DOS(self):
"""
Retern frequencies and total dos.
The first element is freqs and the second is total dos.
frequencies: [freq1, freq2, ...]
total_dos: [dos1, dos2, ...]
"""
return self._total_dos.get_dos()
def set_Debye_frequency(self, freq_max_fit=None):
self._total_dos.set_Debye_frequency(
self._primitive.get_number_of_atoms(), freq_max_fit=freq_max_fit)
def get_Debye_frequency(self):
return self._total_dos.get_Debye_frequency()
def plot_total_DOS(self):
return self._total_dos.plot_dos()
def write_total_DOS(self):
self._total_dos.write()
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
direction=None,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
td.run()
self._thermal_displacements = td
def get_thermal_displacements(self):
if self._thermal_displacements is not None:
return self._thermal_displacements.get_thermal_displacements()
def plot_thermal_displacements(self, is_legend=False):
return self._thermal_displacements.plot(is_legend)
def write_yaml_thermal_displacements(self):
self._thermal_displacements.write_yaml()
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
tdm.set_temperature_range(t_min, t_max, t_step)
tdm.run()
self._thermal_displacement_matrices = tdm
def get_thermal_displacement_matrices(self):
if self._thermal_displacement_matrices is not None:
return self._thermal_displacement_matrices.get_thermal_displacement_matrices(
)
def write_yaml_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_yaml()
def set_thermal_distances(self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [[1, 2], [1, 4]]
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
"""
td = ThermalDistances(self._mesh.get_frequencies(),
self._mesh.get_eigenvectors(),
self._supercell,
self._primitive,
self._mesh.get_qpoints(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
td.run(atom_pairs)
self._thermal_distances = td
def write_yaml_thermal_distances(self):
self._thermal_distances.write_yaml()
def set_qpoints_phonon(self,
q_points,
nac_q_direction=None,
is_eigenvectors=False,
write_dynamical_matrices=False,
factor=VaspToTHz):
self._set_dynamical_matrix()
self._qpoints_phonon = QpointsPhonon(
q_points,
self._dynamical_matrix,
nac_q_direction=nac_q_direction,
is_eigenvectors=is_eigenvectors,
group_velocity=self._group_velocity,
write_dynamical_matrices=write_dynamical_matrices,
factor=self._factor)
def get_qpoints_phonon(self):
return (self._qpoints_phonon.get_frequencies(),
self._qpoints_phonon.get_eigenvectors())
def write_yaml_qpoints_phonon(self):
self._qpoints_phonon.write_yaml()
def write_animation(self,
q_point=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None,
filename=None):
self._set_dynamical_matrix()
if q_point is None:
animation = Animation([0, 0, 0],
self._dynamical_matrix,
shift=shift)
else:
animation = Animation(q_point, self._dynamical_matrix, shift=shift)
if anime_type == 'v_sim':
if amplitude:
amplitude_ = amplitude
else:
amplitude_ = 1.0
if filename:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor,
filename=filename)
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type == 'arc' or anime_type == 'xyz' or anime_type == 'jmol'
or anime_type == 'poscar'):
if band_index is None or amplitude is None or num_div is None:
print "Parameters are not correctly set for animation."
sys.exit(1)
if anime_type == 'arc' or anime_type is None:
if filename:
animation.write_arc(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_arc(band_index, amplitude, num_div)
if anime_type == 'xyz':
if filename:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor,
filename=filename)
else:
animation.write_xyz(band_index, amplitude, num_div,
self._factor)
if anime_type == 'jmol':
if filename:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor,
filename=filename)
else:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor)
if anime_type == 'poscar':
if filename:
animation.write_POSCAR(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_POSCAR(band_index, amplitude, num_div)
def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
self._set_dynamical_matrix()
self._modulation = Modulation(self._dynamical_matrix,
dimension,
phonon_modes,
delta_q=delta_q,
derivative_order=derivative_order,
nac_q_direction=nac_q_direction,
factor=self._factor)
self._modulation.run()
def get_modulations(self):
"""Returns cells with modulations as Atoms objects"""
return self._modulation.get_modulations()
def get_delta_modulations(self):
"""Return modulations relative to equilibrium supercell
(modulations, supercell)
modulations: Atomic modulations of supercell in Cartesian coordinates
supercell: Supercell as an Atoms object.
"""
return self._modulation.get_delta_modulations()
def write_modulations(self):
"""Create MPOSCAR's"""
self._modulation.write()
def write_yaml_modulations(self):
self._modulation.write_yaml()
def set_irreps(self,
q,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=1e-4):
self._set_dynamical_matrix()
self._irreps = IrReps(self._dynamical_matrix,
q,
is_little_cogroup=is_little_cogroup,
nac_q_direction=nac_q_direction,
factor=self._factor,
symprec=self._symprec,
degeneracy_tolerance=degeneracy_tolerance,
log_level=self._log_level)
return self._irreps.run()
def get_irreps(self):
return self._irreps
def show_irreps(self, show_irreps=False):
self._irreps.show(show_irreps=show_irreps)
def write_yaml_irreps(self, show_irreps=False):
self._irreps.write_yaml(show_irreps=show_irreps)
def set_group_velocity(self, q_length=None):
self._set_dynamical_matrix()
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
def get_group_velocity(self):
return self._group_velocity.get_group_velocity()
def get_group_velocity_at_q(self, q_point):
if self._group_velocity is None:
self.set_group_velocity()
self._group_velocity.set_q_points([q_point])
return self._group_velocity.get_group_velocity()[0]
def _run_force_constants_from_forces(self,
distributed_atom_list=None,
decimals=None,
computation_algorithm="svd"):
if self._displacement_dataset is not None:
self._force_constants = get_fc2(
self._supercell,
self._symmetry,
self._displacement_dataset,
atom_list=distributed_atom_list,
decimals=decimals,
computation_algorithm=computation_algorithm)
def _set_dynamical_matrix(self):
if self._nac_params is None:
self._dynamical_matrix = DynamicalMatrix(
self._supercell,
self._primitive,
self._force_constants,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
else:
self._dynamical_matrix = DynamicalMatrixNAC(
self._supercell,
self._primitive,
self._force_constants,
nac_params=self._nac_params,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
def _search_symmetry(self):
self._symmetry = Symmetry(self._supercell, self._symprec,
self._is_symmetry)
def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive, self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) != len(
self._primitive_symmetry.get_pointgroup_operations())):
print(
"Warning: point group symmetries of supercell and primitive"
"cell are different.")
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell, self._supercell_matrix,
self._symprec)
def _build_supercells_with_displacements(self):
supercells = []
for disp in self._displacement_dataset['first_atoms']:
positions = self._supercell.get_positions()
positions[disp['number']] += disp['displacement']
supercells.append(
Atoms(numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),
magmoms=self._supercell.get_magnetic_moments(),
positions=positions,
cell=self._supercell.get_cell(),
pbc=True))
self._supercells_with_displacements = supercells
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
if self._primitive_matrix is None:
trans_mat = inv_supercell_matrix
else:
trans_mat = np.dot(inv_supercell_matrix, self._primitive_matrix)
self._primitive = get_primitive(self._supercell, trans_mat,
self._symprec)
num_satom = self._supercell.get_number_of_atoms()
num_patom = self._primitive.get_number_of_atoms()
if abs(num_satom * np.linalg.det(trans_mat) - num_patom) < 0.1:
return True
else:
return False
