def distribute_fc3(fc3,
first_disp_atoms,
target_atoms,
lattice,
rotations,
permutations,
s2compact,
verbose=False):
"""Distribute fc3
fc3[i, :, :, 0:3, 0:3, 0:3] where i=indices done are distributed to
symmetrically equivalent fc3 elements by tensor rotations.
Search symmetry operation (R, t) that performs
i_target -> i_done
and
atom_mapping[i_target] = i_done
fc3[i_target, j_target, k_target] = R_inv[i_done, j, k]
Parameters
----------
target_atoms: list or ndarray
Supercell atom indices to which fc3 are distributed.
s2compact: ndarray
Maps supercell index to compact index. For full-fc3,
s2compact=np.arange(n_satom).
shape=(n_satom,)
dtype=intc
"""
n_satom = fc3.shape[1]
for i_target in target_atoms:
for i_done in first_disp_atoms:
rot_indices = np.where(permutations[:, i_target] == i_done)[0]
if len(rot_indices) > 0:
atom_mapping = np.array(permutations[rot_indices[0]],
dtype='intc')
rot = rotations[rot_indices[0]]
rot_cart_inv = np.array(similarity_transformation(
lattice, rot).T,
dtype='double',
order='C')
break
if len(rot_indices) == 0:
print("Position or symmetry may be wrong.")
raise RuntimeError
if verbose > 2:
print(" [ %d, x, x ] to [ %d, x, x ]" %
(i_done + 1, i_target + 1))
sys.stdout.flush()
try:
import phono3py._phono3py as phono3c
phono3c.distribute_fc3(fc3, int(s2compact[i_target]),
int(s2compact[i_done]), atom_mapping,
rot_cart_inv)
except ImportError:
print("Phono3py C-routine is not compiled correctly.")
for j in range(n_satom):
j_rot = atom_mapping[j]
for k in range(n_satom):
k_rot = atom_mapping[k]
fc3[i_target, j, k] = third_rank_tensor_rotation(
rot_cart_inv, fc3[i_done, j_rot, k_rot])
def distribute_fc3(fc3_least_atoms,
first_disp_atoms,
lattice,
positions,
rotations,
translations,
symprec,
overwrite=True,
verbose=False):
num_atom = len(positions)
atom_mapping = np.zeros(num_atom, dtype='intc')
if overwrite:
fc3 = fc3_least_atoms
else:
fc3 = np.zeros((num_atom, num_atom, num_atom, 3, 3, 3), dtype='double')
for i in range(num_atom):
# if i in first_disp_atoms:
# continue
for atom_index_done in first_disp_atoms:
rot_num = get_atom_mapping_by_symmetry(positions, i,
atom_index_done, rotations,
translations, symprec)
if rot_num > -1:
i_rot = atom_index_done
rot = rotations[rot_num]
trans = translations[rot_num]
break
if rot_num < 0:
print("Position or symmetry may be wrong.")
raise ValueError
for j in range(num_atom):
atom_mapping[j] = get_atom_by_symmetry(positions, rot, trans, j,
symprec)
rot_cart_inv = np.array(similarity_transformation(lattice, rot).T,
dtype='double',
order='C')
if not (overwrite and i == i_rot):
if verbose > 2:
print(" [ %d, x, x ] to [ %d, x, x ]" % (i_rot + 1, i + 1))
sys.stdout.flush()
try:
import phono3py._phono3py as phono3c
phono3c.distribute_fc3(fc3, fc3_least_atoms, i, atom_mapping,
rot_cart_inv)
except ImportError:
for j in range(num_atom):
j_rot = atom_mapping[j]
for k in range(num_atom):
k_rot = atom_mapping[k]
fc3[i, j, k] = third_rank_tensor_rotation(
rot_cart_inv, fc3_least_atoms[i_rot, j_rot, k_rot])
if not overwrite:
return fc3