def _get_fc3_done(supercell, disp_dataset, symmetry, array_shape):
num_atom = supercell.get_number_of_atoms()
fc3_done = np.zeros(array_shape, dtype='byte')
symprec = symmetry.get_symmetry_tolerance()
lattice = supercell.get_cell().T
positions = supercell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
atom_mapping = []
for rot, trans in zip(rotations, translations):
atom_indices = [
_get_atom_by_symmetry(lattice, positions, rot, trans, i, symprec)
for i in range(num_atom)
]
atom_mapping.append(atom_indices)
for dataset_first_atom in disp_dataset['first_atoms']:
first_atom_num = dataset_first_atom['number']
site_symmetry = symmetry.get_site_symmetry(first_atom_num)
direction = np.dot(dataset_first_atom['displacement'],
np.linalg.inv(supercell.get_cell()))
reduced_site_sym = get_reduced_site_symmetry(site_symmetry, direction,
symprec)
least_second_atom_nums = []
for second_atoms in dataset_first_atom['second_atoms']:
if 'included' in second_atoms:
if second_atoms['included']:
least_second_atom_nums.append(second_atoms['number'])
elif 'cutoff_distance' in disp_dataset:
min_vec = get_equivalent_smallest_vectors(
first_atom_num, second_atoms['number'], supercell,
symprec)[0]
min_distance = np.linalg.norm(np.dot(lattice, min_vec))
if 'pair_distance' in second_atoms:
assert (abs(min_distance - second_atoms['pair_distance']) <
1e-4)
if min_distance < disp_dataset['cutoff_distance']:
least_second_atom_nums.append(second_atoms['number'])
positions_shifted = positions - positions[first_atom_num]
least_second_atom_nums = np.unique(least_second_atom_nums)
for red_rot in reduced_site_sym:
second_atom_nums = [
_get_atom_by_symmetry(lattice, positions_shifted, red_rot,
np.zeros(3, dtype='double'), i, symprec)
for i in least_second_atom_nums
]
second_atom_nums = np.unique(second_atom_nums)
for i in range(len(rotations)):
rotated_atom1 = atom_mapping[i][first_atom_num]
for j in second_atom_nums:
fc3_done[rotated_atom1, atom_mapping[i][j]] = 1
return fc3_done
def cutoff_fc3_by_zero(fc3, supercell, cutoff_distance, symprec=1e-5):
num_atom = supercell.get_number_of_atoms()
lattice = supercell.get_cell().T
min_distances = np.zeros((num_atom, num_atom), dtype='double')
for i in range(num_atom): # run in supercell
for j in range(num_atom): # run in primitive
min_distances[i, j] = np.linalg.norm(
np.dot(lattice,
get_equivalent_smallest_vectors(
i, j, supercell, symprec)[0]))
for i, j, k in np.ndindex(num_atom, num_atom, num_atom):
for pair in ((i, j), (j, k), (k, i)):
if min_distances[pair] > cutoff_distance:
fc3[i, j, k] = 0
break