def __init__(self,
fc2,
fc3,
supercell,
primitive,
supercell_extra=None,
nac_params=None,
nac_q_direction=None,
ion_clamped=False,
factor=VaspToTHz,
symprec=1e-5):
self._fc2 = fc2
self._fc3 = fc3
self._scell = supercell
if supercell_extra is not None:
self._scell_extra = supercell_extra
else:
self._scell_extra = supercell
self._pcell = primitive
self._ion_clamped = ion_clamped
self._factor = factor
self._symprec = symprec
if nac_params is None:
self._dm = DynamicalMatrix(self._scell_extra,
self._pcell,
self._fc2,
symprec=self._symprec)
else:
self._dm = DynamicalMatrixNAC(self._scell_extra,
self._pcell,
self._fc2,
symprec=self._symprec)
self._dm.set_nac_params(nac_params)
self._nac_q_direction = nac_q_direction
self._shortest_vectors, self._multiplicity = get_smallest_vectors(
self._scell, self._pcell, self._symprec)
self._shortest_vectors_extra, self._multiplicity_extra = get_smallest_vectors(
self._scell_extra, self._pcell, self._symprec)
if self._ion_clamped:
num_atom_prim = self._pcell.get_number_of_atoms()
self._X = np.zeros((num_atom_prim, 3, 3, 3), dtype=float)
else:
self._X = self._get_X()
self._dPhidu = self._get_dPhidu()
self._gruneisen_parameters = None
self._frequencies = None
self._qpoints = None
self._mesh = None
self._band_paths = None
self._band_distances = None
self._run_mode = None
self._weights = None
def _run_c(self, g_zero=None):
import anharmonic._phono3py as phono3c
num_band = self._primitive.get_number_of_atoms() * 3
svecs, multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
masses = np.array(self._primitive.get_masses(), dtype='double')
p2s = self._primitive.get_primitive_to_supercell_map()
s2p = self._primitive.get_supercell_to_primitive_map()
if g_zero is None:
_g_zero = np.zeros(self._interaction_strength.shape,
dtype='byte', order='C')
else:
_g_zero = g_zero
phono3c.interaction(self._interaction_strength,
_g_zero,
self._frequencies,
self._eigenvectors,
self._triplets_at_q,
self._grid_address,
self._mesh,
self._fc3,
svecs,
multiplicity,
masses,
p2s,
s2p,
self._band_indices,
self._symmetrize_fc3_q,
self._cutoff_frequency)
self._interaction_strength *= self._unit_conversion
def _run_c(self):
import anharmonic._phono3py as phono3c
self.set_phonon(self._triplets_at_q.ravel())
num_band = self._primitive.get_number_of_atoms() * 3
svecs, multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
masses = np.array(self._primitive.get_masses(), dtype='double')
p2s = self._primitive.get_primitive_to_supercell_map()
s2p = self._primitive.get_supercell_to_primitive_map()
phono3c.interaction(self._interaction_strength,
self._frequencies,
self._eigenvectors,
self._triplets_at_q,
self._grid_address,
self._mesh,
self._fc3,
svecs,
multiplicity,
masses,
p2s,
s2p,
self._band_indices,
self._symmetrize_fc3_q,
self._cutoff_frequency)
self._interaction_strength *= self._unit_conversion
def _run_c(self):
import anharmonic._phono3py as phono3c
self.set_phonon(self._triplets_at_q.ravel())
num_band = self._primitive.get_number_of_atoms() * 3
svecs, multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
masses = np.array(self._primitive.get_masses(), dtype='double')
p2s = self._primitive.get_primitive_to_supercell_map()
s2p = self._primitive.get_supercell_to_primitive_map()
phono3c.interaction(self._interaction_strength,
self._frequencies,
self._eigenvectors,
self._triplets_at_q,
self._grid_address,
self._mesh,
self._fc3,
svecs,
multiplicity,
masses,
p2s,
s2p,
self._band_indices,
self._symmetrize_fc3_q,
self._cutoff_frequency)
def _calculate_fc4_normal_c(self):
import anharmonic._phono4py as phono4c
svecs, multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
p2s = self._primitive.get_primitive_to_supercell_map()
s2p = self._primitive.get_supercell_to_primitive_map()
gp = self._grid_point
self._set_phonon_c([gp])
self._set_phonon_c(self._quartets_at_q)
phono4c.fc4_normal_for_frequency_shift(
self._fc4_normal,
self._frequencies,
self._eigenvectors,
gp,
self._quartets_at_q,
self._grid_address,
self._mesh,
np.double(self._fc4),
svecs,
multiplicity,
self._masses,
p2s,
s2p,
self._band_indices,
self._cutoff_frequency)
def _run_c(self, g_zero=None):
import anharmonic._phono3py as phono3c
num_band = self._primitive.get_number_of_atoms() * 3
svecs, multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
masses = np.array(self._primitive.get_masses(), dtype='double')
p2s = self._primitive.get_primitive_to_supercell_map()
s2p = self._primitive.get_supercell_to_primitive_map()
if g_zero is None:
_g_zero = np.zeros(self._interaction_strength.shape,
dtype='byte',
order='C')
else:
_g_zero = g_zero
phono3c.interaction(self._interaction_strength, _g_zero,
self._frequencies, self._eigenvectors,
self._triplets_at_q, self._grid_address,
self._mesh, self._fc3, svecs, multiplicity, masses,
p2s, s2p, self._band_indices,
self._symmetrize_fc3_q, self._cutoff_frequency)
self._interaction_strength *= self._unit_conversion
def __init__(self, primitive, supercell, frequencies=None, eigenvectors=None, symprec=1e-5):
self._primitive = primitive
self._supercell = supercell
supercell_matrix = np.linalg.inv(self._primitive.get_primitive_matrix())
supercell_matrix = np.rint(supercell_matrix).astype("intc")
self._commensurate_points = get_commensurate_points(supercell_matrix)
(self._shortest_vectors, self._multiplicity) = get_smallest_vectors(supercell, primitive, symprec)
self._dynmat = None
n = self._supercell.get_number_of_atoms()
self._force_constants = np.zeros((n, n, 3, 3), dtype="double")
if frequencies is not None and eigenvectors is not None:
self.set_dynamical_matrices(frequencies, eigenvectors)
def __init__(self, fc4, supercell, primitive, mesh, symprec=1e-5):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._mesh = mesh
self._symprec = symprec
num_satom = supercell.get_number_of_atoms()
self._p2s_map = np.intc(primitive.get_primitive_to_supercell_map())
self._s2p_map = np.intc(primitive.get_supercell_to_primitive_map())
(self._smallest_vectors,
self._multiplicity) = get_smallest_vectors(supercell, primitive,
symprec)
self._quartet = None
self._fc4_reciprocal = None
def __init__(self, fc3, supercell, primitive, mesh, symprec=1e-5):
self._fc3 = fc3
self._supercell = supercell
self._primitive = primitive
self._mesh = mesh
self._symprec = symprec
num_satom = supercell.get_number_of_atoms()
self._p2s_map = primitive.get_primitive_to_supercell_map()
self._s2p_map = primitive.get_supercell_to_primitive_map()
# Reduce supercell atom index to primitive index
(self._smallest_vectors,
self._multiplicity) = get_smallest_vectors(supercell, primitive,
symprec)
self._fc3_reciprocal = None
def _calculate_fc4_normal_c(self):
import anharmonic._phono4py as phono4c
svecs, multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
p2s = np.intc(self._primitive.get_primitive_to_supercell_map())
s2p = np.intc(self._primitive.get_supercell_to_primitive_map())
gp = self._grid_point
self._set_phonon_c([gp])
self._set_phonon_c(self._quartets_at_q)
phono4c.fc4_normal_for_frequency_shift(
self._fc4_normal, self._frequencies, self._eigenvectors, gp,
self._quartets_at_q, self._grid_address, self._mesh,
np.double(self._fc4), svecs, multiplicity, self._masses, p2s, s2p,
self._band_indices, self._cutoff_frequency)
def __init__(
self, supercell, primitive, velocities, symmetry=None, symprec=1e-5 # in m/s either real or reciprocal
):
if symmetry is not None:
symprec = symmetry.get_symmetry_tolerance()
self._point_group_opts = symmetry.get_pointgroup_operations()
else:
self._point_group_opts = None
self._supercell = supercell
self._primitive = primitive
self._velocities = velocities
(self._shortest_vectors, self._multiplicity) = get_smallest_vectors(supercell, primitive, symprec)
self._qpoints = None
self._weights = None
self._velocities_q = None # [timestep, p_atom, qpoitns, 3]
def __init__(self,
primitive,
supercell,
frequencies=None,
eigenvectors=None,
symprec=1e-5):
self._primitive = primitive
self._supercell = supercell
self._commensurate_points = get_commensurate_points(
primitive, supercell)
(self._shortest_vectors,
self._multiplicity) = get_smallest_vectors(supercell, primitive,
symprec)
self._dynmat = None
n = self._supercell.get_number_of_atoms()
self._force_constants = np.zeros((n, n, 3, 3), dtype='double')
if frequencies is not None and eigenvectors is not None:
self.set_dynamical_matrices(frequencies, eigenvectors)
def __init__(self, fc3, supercell, primitive, mesh, symprec=1e-5):
self._fc3 = fc3
self._supercell = supercell
self._primitive = primitive
self._mesh = mesh
self._symprec = symprec
num_satom = supercell.get_number_of_atoms()
self._p2s_map = primitive.get_primitive_to_supercell_map()
self._s2p_map = primitive.get_supercell_to_primitive_map()
# Reduce supercell atom index to primitive index
try:
(self._smallest_vectors,
self._multiplicity) = primitive.get_smallest_vectors()
except AttributeError:
from phonopy.harmonic.dynamical_matrix import get_smallest_vectors
(self._smallest_vectors,
self._multiplicity) = get_smallest_vectors(
supercell, primitive, symprec)
self._fc3_reciprocal = None
def _generate_force_constants_site(self):
"""
natoms_supercell: The number of atoms in the supercell.
natoms_primitive: The number of atoms in the primitive cell.
"""
supercell = self._supercell_average
primitive = self._primitive_average
natoms_supercell = supercell.get_number_of_atoms()
p2s_map = primitive.get_primitive_to_supercell_map()
smallest_vectors, multiplicity = get_smallest_vectors(
supercell, primitive, symprec=self._symprec)
natoms_primitive = primitive.get_number_of_atoms()
relative_positions_site = [[] for _ in range(natoms_primitive)]
force_constants_site = [[] for _ in range(natoms_primitive)]
for index, i in enumerate(p2s_map):
for j in range(natoms_supercell):
if i == j:
continue
nsites = multiplicity[j][i]
# TODO(ikeda):
# "get_fc_tmp" should be renamed.
# Finally, force_constants_pair format will change,
# and this part should also change.
# Instead, new variable fora the correspondence between
# the symbols and the order should be given.
# TODO(ikeda):
# relative_positions should be a "numpy.array".
# TODO(ikeda):
# Check what happen if we exchange "i" and "j".
# Maybe we should take the correspondence to the enlarged
# force constants.
fc_tmp = get_fc_tmp(i, j, self._force_constants_pair, nsites)
for k in range(nsites):
relative_positions_site[index].append(
smallest_vectors[j][i][k])
force_constants_site[index].append(fc_tmp)
self._relative_positions_site = relative_positions_site
self._force_constants_site = force_constants_site
def __init__(self,
fc4,
supercell,
primitive,
mesh,
symprec=1e-5):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._mesh = mesh
self._symprec = symprec
num_satom = supercell.get_number_of_atoms()
self._p2s_map = np.intc(primitive.get_primitive_to_supercell_map())
self._s2p_map = np.intc(primitive.get_supercell_to_primitive_map())
(self._smallest_vectors,
self._multiplicity) = get_smallest_vectors(supercell,
primitive,
symprec)
self._quartet = None
self._fc4_reciprocal = None
def __init__(self,
fc3,
supercell,
primitive,
mesh,
symprec=1e-5,
atom_triplet_cut=None):
self._fc3 = fc3
self._supercell = supercell
self._primitive = primitive
self._mesh = mesh
self._symprec = symprec
self._atc = atom_triplet_cut # atom_triplet cut (dtype=bool)
num_satom = supercell.get_number_of_atoms()
self._p2s_map = np.intc(primitive.get_primitive_to_supercell_map())
self._s2p_map = np.intc(primitive.get_supercell_to_primitive_map())
# Reduce supercell atom index to primitive index
(self._smallest_vectors,
self._multiplicity) = get_smallest_vectors(supercell, primitive,
symprec)
self._fc3_reciprocal = None
def __init__(self,
fc3,
supercell,
primitive,
mesh,
symprec=1e-5):
self._fc3 = fc3
self._supercell = supercell
self._primitive = primitive
self._mesh = mesh
self._symprec = symprec
num_satom = supercell.get_number_of_atoms()
self._p2s_map = np.intc(primitive.get_primitive_to_supercell_map())
self._s2p_map = np.intc(primitive.get_supercell_to_primitive_map())
# Reduce supercell atom index to primitive index
(self._smallest_vectors,
self._multiplicity) = get_smallest_vectors(supercell,
primitive,
symprec)
self._fc3_reciprocal = None
def __init__(self,
supercell,
primitive,
velocities, # in m/s either real or reciprocal
symmetry=None,
symprec=1e-5):
if symmetry is not None:
symprec = symmetry.get_symmetry_tolerance()
self._point_group_opts = symmetry.get_pointgroup_operations()
else:
self._point_group_opts = None
self._supercell = supercell
self._primitive = primitive
self._velocities = velocities
(self._shortest_vectors,
self._multiplicity) = get_smallest_vectors(supercell,
primitive,
symprec)
self._qpoints = None
self._weights = None
self._velocities_q = None # [timestep, p_atom, qpoitns, 3]
def __init__(self,
fc3,
supercell,
primitive,
mesh,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_nosym=False,
symmetrize_fc3_q=False,
symprec=1e-3,
triplet_cut_super = None,
triplet_cut_prim = None,
cutoff_frequency=None,
cutoff_hfrequency=None,
cutoff_delta = None,
is_triplets_dispersed=False,
is_read_amplitude=False,
is_write_amplitude = False,
is_triplets_permute=True,
lapack_zheev_uplo='L'):
self._fc3 = fc3
self._supercell = supercell
self._primitive = primitive
self._mesh = np.intc(mesh)
num_band = primitive.get_number_of_atoms() * 3
if band_indices is None:
self._band_indices = np.arange(num_band, dtype='intc')
else:
self._band_indices = band_indices.astype("intc")
self._frequency_factor_to_THz = frequency_factor_to_THz
self._symprec = symprec
self._is_tripelts_permute=is_triplets_permute
natom_super = supercell.get_number_of_atoms()
natom_prim = primitive.get_number_of_atoms()
if triplet_cut_super is None:
self._triplet_cut_super=np.zeros((natom_super, natom_super, natom_super), dtype='bool')
else:
self._triplet_cut_super=triplet_cut_super
if triplet_cut_prim is None:
self._triplet_cut_prim=np.zeros((natom_prim, natom_prim, natom_prim), dtype='bool')
else:
self._triplet_cut_prim=triplet_cut_prim
if cutoff_delta is None:
self._cutoff_delta = 1000.0
else:
self._cutoff_delta = cutoff_delta
if cutoff_frequency is None:
self._cutoff_frequency = 0
else:
self._cutoff_frequency = cutoff_frequency
if cutoff_hfrequency is None:
self._cutoff_hfrequency = 10000.0 # THz
elif symmetrize_fc3_q:
print "Warning: symmetryze_fc3_q and cutoff_hfrequency are not compatible"
self._cutoff_hfrequency = 10000.0
else:
self._cutoff_hfrequency = cutoff_hfrequency
self._is_nosym = is_nosym
self._symmetrize_fc3_q = symmetrize_fc3_q
self._lapack_zheev_uplo = lapack_zheev_uplo
self._symmetry = Symmetry(primitive, symprec=symprec)
if self._is_nosym:
self._point_group_operations = np.array([np.eye(3)],dtype="intc")
self._kpoint_operations = get_kpoint_group(self._mesh, self._point_group_operations, is_time_reversal=False)
else:
self._point_group_operations = self._symmetry.get_pointgroup_operations()
self._kpoint_operations = get_kpoint_group(self._mesh, self._point_group_operations)
if self.is_nosym():
grid_mapping = np.arange(np.prod(self._mesh))
grid_mapping_rots = np.zeros(len(grid_mapping), dtype="intc")
else:
grid_mapping, grid_mapping_rots = get_mappings(self._mesh,
self.get_point_group_operations(),
qpoints=np.array([0,0,0],dtype="double"))
self._svecs, self._multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
self._grid_mapping = grid_mapping
self._grid_mapping_rot = grid_mapping_rots
self._is_read_amplitude = is_read_amplitude
self._is_write_amplitude = is_write_amplitude
self._grid_point = None
self._triplets_at_q = None
self._weights_at_q = None
self._grid_address = None
self._interaction_strength = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._degenerates = None
self._grid_points = None
self._dm = None
self._nac_q_direction = None
self._triplets = None
self._triplets_mappings = None
self._triplets_sequence = None
self._unique_triplets = None
self._amplitude_all = None
self._is_dispersed = is_triplets_dispersed
self._allocate_phonon()
def __init__(self,
supercell,
primitive,
mesh,
symmetry,
fc3=None,
band_indices=None,
constant_averaged_interaction=None,
frequency_factor_to_THz=VaspToTHz,
unit_conversion=None,
is_mesh_symmetry=True,
symmetrize_fc3_q=False,
cutoff_frequency=None,
lapack_zheev_uplo='L'):
self._fc3 = fc3
self._supercell = supercell
self._primitive = primitive
self._mesh = np.array(mesh, dtype='intc')
self._symmetry = symmetry
self._band_indices = None
self._set_band_indices(band_indices)
self._constant_averaged_interaction = constant_averaged_interaction
self._frequency_factor_to_THz = frequency_factor_to_THz
# Unit to eV^2
if unit_conversion is None:
num_grid = np.prod(self._mesh)
self._unit_conversion = ((Hbar * EV) ** 3 / 36 / 8
* EV ** 2 / Angstrom ** 6
/ (2 * np.pi * THz) ** 3
/ AMU ** 3 / num_grid
/ EV ** 2)
else:
self._unit_conversion = unit_conversion
if cutoff_frequency is None:
self._cutoff_frequency = 0
else:
self._cutoff_frequency = cutoff_frequency
self._is_mesh_symmetry = is_mesh_symmetry
self._symmetrize_fc3_q = symmetrize_fc3_q
self._lapack_zheev_uplo = lapack_zheev_uplo
self._symprec = symmetry.get_symmetry_tolerance()
self._grid_point = None
self._triplets_at_q = None
self._weights_at_q = None
self._triplets_map_at_q = None
self._ir_map_at_q = None
self._grid_address = None
self._bz_map = None
self._interaction_strength = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._dm = None
self._nac_q_direction = None
self._band_index_count = 0
try:
svecs, multiplicity = self._primitive.get_smallest_vectors()
except AttributeError:
from phonopy.harmonic.dynamical_matrix import get_smallest_vectors
svecs, multiplicity = get_smallest_vectors(self._supercell,
self._primitive,
self._symprec)
self._smallest_vectors = svecs
self._multiplicity = multiplicity
self._masses = np.array(self._primitive.get_masses(), dtype='double')
self._p2s = self._primitive.get_primitive_to_supercell_map()
self._s2p = self._primitive.get_supercell_to_primitive_map()
self._allocate_phonon()