def _get_fc3_one_atom(fc3, supercell, disp_dataset, fc2, first_atom_num,
site_symmetry, translational_symmetry_type,
is_permutation_symmetry, symprec, verbose):
displacements_first = []
delta_fc2s = []
for dataset_first_atom in disp_dataset['first_atoms']:
if first_atom_num != dataset_first_atom['number']:
continue
displacements_first.append(dataset_first_atom['displacement'])
if 'delta_fc2' in dataset_first_atom:
delta_fc2s.append(dataset_first_atom['delta_fc2'])
else:
direction = np.dot(dataset_first_atom['displacement'],
np.linalg.inv(supercell.get_cell()))
reduced_site_sym = get_reduced_site_symmetry(
site_symmetry, direction, symprec)
delta_fc2s.append(
get_delta_fc2(dataset_first_atom['second_atoms'],
dataset_first_atom['number'], fc2, supercell,
reduced_site_sym, translational_symmetry_type,
is_permutation_symmetry, symprec))
solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
verbose=verbose)
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 _get_fc3_done(supercell, disp_dataset, symmetry):
num_atom = supercell.get_number_of_atoms()
fc3_done = np.zeros((num_atom, num_atom, num_atom), 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 = []
for rot_pos in (np.dot(positions, rot.T) + trans):
diffs = positions - rot_pos
diffs -= np.rint(diffs)
diffs = np.dot(diffs, lattice.T)
dists = np.sqrt(np.sum(diffs**2, axis=1))
atom_indices.append((np.where(dists < symprec))[0][0])
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 second_atoms['included']:
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)
second_atom_nums = []
for red_rot in reduced_site_sym:
for i in least_second_atom_nums:
second_atom_nums.append(
_get_atom_by_symmetry(lattice, positions_shifted, red_rot,
np.zeros(3, dtype='double'), i,
symprec))
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 _get_fc3_least_atoms(supercell,
primitive,
disp_dataset,
fc2,
symmetry,
is_compact_fc=False,
verbose=True):
symprec = symmetry.get_symmetry_tolerance()
num_satom = supercell.get_number_of_atoms()
unique_first_atom_nums = np.unique(
[x['number'] for x in disp_dataset['first_atoms']])
if is_compact_fc:
num_patom = primitive.get_number_of_atoms()
s2p_map = primitive.get_supercell_to_primitive_map()
p2p_map = primitive.get_primitive_to_primitive_map()
first_atom_nums = []
for i in unique_first_atom_nums:
if i != s2p_map[i]:
print("Something wrong in disp_fc3.yaml")
raise RuntimeError
else:
first_atom_nums.append(i)
fc3 = np.zeros((num_patom, num_satom, num_satom, 3, 3, 3),
dtype='double',
order='C')
else:
first_atom_nums = unique_first_atom_nums
fc3 = np.zeros((num_satom, num_satom, num_satom, 3, 3, 3),
dtype='double',
order='C')
for first_atom_num in first_atom_nums:
site_symmetry = symmetry.get_site_symmetry(first_atom_num)
displacements_first = []
delta_fc2s = []
for dataset_first_atom in disp_dataset['first_atoms']:
if first_atom_num != dataset_first_atom['number']:
continue
displacements_first.append(dataset_first_atom['displacement'])
if 'delta_fc2' in dataset_first_atom:
delta_fc2s.append(dataset_first_atom['delta_fc2'])
else:
direction = np.dot(dataset_first_atom['displacement'],
np.linalg.inv(supercell.get_cell()))
reduced_site_sym = get_reduced_site_symmetry(
site_symmetry, direction, symprec)
delta_fc2s.append(
get_delta_fc2(dataset_first_atom['second_atoms'],
dataset_first_atom['number'], fc2, supercell,
reduced_site_sym, symprec))
fc3_first = solve_fc3(first_atom_num,
supercell,
site_symmetry,
displacements_first,
np.array(delta_fc2s, dtype='double', order='C'),
symprec,
verbose=verbose)
if is_compact_fc:
fc3[p2p_map[s2p_map[first_atom_num]]] = fc3_first
else:
fc3[first_atom_num] = fc3_first
return fc3
def _get_fc3_done(supercell: PhonopyAtoms, disp_dataset, symmetry: Symmetry,
array_shape):
num_atom = len(supercell)
fc3_done = np.zeros(array_shape, dtype="byte")
symprec = symmetry.tolerance
lattice = supercell.cell.T
positions = supercell.scaled_positions
rotations = symmetry.symmetry_operations["rotations"]
translations = symmetry.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.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_smallest_vector_of_atom_pair(
first_atom_num, second_atoms["number"], supercell, symprec)
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 _get_fc3_least_atoms(supercell,
primitive,
disp_dataset,
fc2,
symmetry,
is_compact_fc=False,
verbose=True):
symprec = symmetry.tolerance
num_satom = len(supercell)
unique_first_atom_nums = np.unique(
[x["number"] for x in disp_dataset["first_atoms"]])
if is_compact_fc:
num_patom = primitive.get_number_of_atoms()
s2p_map = primitive.s2p_map
p2p_map = primitive.p2p_map
first_atom_nums = []
for i in unique_first_atom_nums:
if i != s2p_map[i]:
print("Something wrong in disp_fc3.yaml")
raise RuntimeError
else:
first_atom_nums.append(i)
fc3 = np.zeros((num_patom, num_satom, num_satom, 3, 3, 3),
dtype="double",
order="C")
else:
first_atom_nums = unique_first_atom_nums
fc3 = np.zeros((num_satom, num_satom, num_satom, 3, 3, 3),
dtype="double",
order="C")
for first_atom_num in first_atom_nums:
site_symmetry = symmetry.get_site_symmetry(first_atom_num)
displacements_first = []
delta_fc2s = []
for dataset_first_atom in disp_dataset["first_atoms"]:
if first_atom_num != dataset_first_atom["number"]:
continue
displacements_first.append(dataset_first_atom["displacement"])
if "delta_fc2" in dataset_first_atom:
delta_fc2s.append(dataset_first_atom["delta_fc2"])
else:
direction = np.dot(
dataset_first_atom["displacement"],
np.linalg.inv(supercell.cell),
)
reduced_site_sym = get_reduced_site_symmetry(
site_symmetry, direction, symprec)
delta_fc2s.append(
_get_delta_fc2(
dataset_first_atom["second_atoms"],
dataset_first_atom["number"],
dataset_first_atom["forces"],
fc2,
supercell,
reduced_site_sym,
symprec,
))
fc3_first = _solve_fc3(
first_atom_num,
supercell,
site_symmetry,
displacements_first,
np.array(delta_fc2s, dtype="double", order="C"),
symprec,
verbose=verbose,
)
if is_compact_fc:
fc3[p2p_map[s2p_map[first_atom_num]]] = fc3_first
else:
fc3[first_atom_num] = fc3_first
return fc3
