def _distribute_2(self, disps, forces, first_atom_num, second_atom_num,
reduced_site_sym):
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
reduced_site_sym,
self._symprec)
sym_cart = None
rot_atom_map = None
for i, sym in enumerate(reduced_site_sym):
if disps[rot_map_syms[i, second_atom_num]] is not None:
sym_cart = similarity_transformation(self._lattice, sym)
rot_atom_map = rot_map_syms[i, :]
break
assert sym_cart is not None, "Something is wrong."
forces[second_atom_num] = []
disps[second_atom_num] = []
for i in range(self._num_atom):
forces_2 = [
np.dot(f[rot_atom_map], sym_cart.T)
for f in forces[rot_atom_map[second_atom_num]][rot_atom_map[i]]
]
disps_2 = [[
d3[0], np.dot(sym_cart, d3[1]),
np.dot(sym_cart, d3[2])
] for d3 in disps[rot_atom_map[second_atom_num]][rot_atom_map[i]]]
forces[second_atom_num].append(forces_2)
disps[second_atom_num].append(disps_2)
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy"):
lattice = supercell.get_cell().T
site_sym_cart = [similarity_transformation(lattice, sym)
for sym in site_symmetry]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import anharmonic._phono3py as phono3c
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
phono3c.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(inv_U, _get_rotated_fc2s(
i, j, delta_fc2s, rot_map_syms, site_sym_cart)).reshape(3, 3, 3)
def _distribute_3(self,
disps_3,
forces_3,
second_atom_num,
third_atom_num,
reduced_bond_sym):
positions = self._positions.copy() - self._positions[second_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
reduced_bond_sym,
self._symprec)
sym_cart = None
rot_atom_map = None
for i, sym in enumerate(reduced_bond_sym):
if disps_3[rot_map_syms[i, third_atom_num]] is not None:
sym_cart = similarity_transformation(self._lattice, sym)
rot_atom_map = rot_map_syms[i, :]
break
assert sym_cart is not None, "Something is wrong."
forces = [np.dot(f[rot_atom_map], sym_cart.T)
for f in forces_3[rot_atom_map[third_atom_num]]]
disps = [[d3[0], d3[1], np.dot(sym_cart, d3[2])]
for d3 in disps_3[rot_atom_map[third_atom_num]]]
disps_3[third_atom_num] = disps
forces_3[third_atom_num] = forces
def _distribute_displacements_and_forces(self,
set_of_disps,
sets_of_forces,
first_atom_num,
disp1,
unique_second_atom_nums):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
direction = np.dot(np.linalg.inv(self._lattice), disp1)
reduced_site_sym = get_reduced_site_symmetry(
site_symmetry, direction, self._symprec)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
reduced_site_sym,
self._symprec)
disp_pairs = []
for second_atom_num in range(self._num_atom):
if set_of_disps[second_atom_num] is None:
(sets_of_forces_atom2,
set_of_disps_atom2) = self._copy_dataset_2nd(
second_atom_num,
set_of_disps,
sets_of_forces,
unique_second_atom_nums,
reduced_site_sym,
rot_map_syms)
disp_pairs.append(
[[disp1, d] for d in set_of_disps_atom2])
sets_of_forces[second_atom_num] = sets_of_forces_atom2
else:
disp_pairs.append(
[[disp1, d] for d in set_of_disps[second_atom_num]])
return disp_pairs, sets_of_forces
def _distribute_2(self,
disps,
forces,
first_atom_num,
second_atom_num,
reduced_site_sym):
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
reduced_site_sym,
self._symprec)
sym_cart = None
rot_atom_map = None
for i, sym in enumerate(reduced_site_sym):
if disps[rot_map_syms[i, second_atom_num]] is not None:
sym_cart = similarity_transformation(self._lattice, sym)
rot_atom_map = rot_map_syms[i, :]
break
assert sym_cart is not None, "Something is wrong."
forces[second_atom_num] = []
disps[second_atom_num] = []
for i in range(self._num_atom):
forces_2 = [
np.dot(f[rot_atom_map], sym_cart.T)
for f in forces[rot_atom_map[second_atom_num]][rot_atom_map[i]]]
disps_2 = [
[d3[0], np.dot(sym_cart, d3[1]), np.dot(sym_cart, d3[2])]
for d3 in disps[rot_atom_map[second_atom_num]][rot_atom_map[i]]]
forces[second_atom_num].append(forces_2)
disps[second_atom_num].append(disps_2)
def _solve_fc4(fc4,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc3s,
symprec):
lattice = supercell.get_cell().T
site_sym_cart = np.double([similarity_transformation(lattice, sym)
for sym in site_symmetry])
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
inv_U = np.linalg.pinv(rot_disps)
for (i, j, k) in list(np.ndindex(num_atom, num_atom, num_atom)):
fc4[first_atom_num, i, j, k] = np.dot(
inv_U, _rotate_delta_fc3s(
i, j, k, delta_fc3s, rot_map_syms, site_sym_cart)
).reshape(3, 3, 3, 3)
def _distribute_displacements_and_forces(self, set_of_disps,
sets_of_forces, first_atom_num,
disp1, unique_second_atom_nums):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
direction = np.dot(np.linalg.inv(self._lattice), disp1)
reduced_site_sym = get_reduced_site_symmetry(site_symmetry, direction,
self._symprec)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(self._lattice, positions,
reduced_site_sym,
self._symprec)
disp_pairs = []
for second_atom_num in range(self._num_atom):
if set_of_disps[second_atom_num] is None:
(sets_of_forces_atom2,
set_of_disps_atom2) = self._copy_dataset_2nd(
second_atom_num, set_of_disps, sets_of_forces,
unique_second_atom_nums, reduced_site_sym, rot_map_syms)
disp_pairs.append([[disp1, d] for d in set_of_disps_atom2])
sets_of_forces[second_atom_num] = sets_of_forces_atom2
else:
disp_pairs.append([[disp1, d]
for d in set_of_disps[second_atom_num]])
return disp_pairs, sets_of_forces
def _distribute_3(self, disps_3, forces_3, second_atom_num, third_atom_num,
reduced_bond_sym):
positions = self._positions.copy() - self._positions[second_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
reduced_bond_sym,
self._symprec)
sym_cart = None
rot_atom_map = None
for i, sym in enumerate(reduced_bond_sym):
if disps_3[rot_map_syms[i, third_atom_num]] is not None:
sym_cart = similarity_transformation(self._lattice, sym)
rot_atom_map = rot_map_syms[i, :]
break
assert sym_cart is not None, "Something is wrong."
forces = [
np.dot(f[rot_atom_map], sym_cart.T)
for f in forces_3[rot_atom_map[third_atom_num]]
]
disps = [[d3[0], d3[1], np.dot(sym_cart, d3[2])]
for d3 in disps_3[rot_atom_map[third_atom_num]]]
disps_3[third_atom_num] = disps
forces_3[third_atom_num] = forces
def _fit(self, first_atom_num, disp_triplets, sets_of_forces):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
self._symprec)
site_syms_cart = np.array([similarity_transformation(self._lattice, sym)
for sym in site_symmetry],
dtype='double')
(disp_triplets_rearranged,
num_triplets) = self._create_displacement_triplets_for_c(disp_triplets)
max_num_disp = np.amax(num_triplets[:, :, :, 1])
for second_atom_num in range(self._num_atom):
print second_atom_num + 1
rot_disps_set = []
for third_atom_num in range(self._num_atom):
try:
import anharmonic._forcefit as forcefit
rot_disps_set.append(self._create_displacement_matrix_c(
second_atom_num,
third_atom_num,
disp_triplets_rearranged,
num_triplets,
site_syms_cart,
rot_map_syms,
max_num_disp))
except ImportError:
rot_disps_set.append(self._create_displacement_matrix(
second_atom_num,
third_atom_num,
disp_triplets,
site_syms_cart,
rot_map_syms))
print third_atom_num + 1, rot_disps_set[third_atom_num].shape
inv_disps_set = self._invert_displacements(rot_disps_set)
for third_atom_num in range(self._num_atom):
rot_forces = self._create_force_matrix(
second_atom_num,
third_atom_num,
sets_of_forces,
site_syms_cart,
rot_map_syms)
fc = self._solve(inv_disps_set[third_atom_num], rot_forces)
# For elements with index exchange symmetry
fc2 = fc[:, 7:10, :].reshape((self._num_atom, 3, 3))
fc3 = fc[:, 46:55, :].reshape((self._num_atom, 3, 3, 3))
fc4 = fc[:, 172:199, :].reshape((self._num_atom, 3, 3, 3, 3))
self._fc2[third_atom_num] = fc2
self._fc3[second_atom_num, third_atom_num] = fc3
self._fc4[first_atom_num, second_atom_num, third_atom_num] = fc4
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy",
verbose=False):
if verbose:
text = "Solving fc3[ %d, x, x ] with " % (first_atom_num + 1)
if len(displacements_first) > 1:
text += "displacements:"
else:
text += "a displacement:"
print(text)
for i, v in enumerate(displacements_first):
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
sys.stdout.flush()
if verbose > 2:
print(" Site symmetry:")
for i, v in enumerate(site_symmetry):
print(" [%2d %2d %2d] #%2d" % tuple(list(v[0]) + [i + 1]))
print(" [%2d %2d %2d]" % tuple(v[1]))
print(" [%2d %2d %2d]\n" % tuple(v[2]))
sys.stdout.flush()
lattice = supercell.get_cell().T
site_sym_cart = [
similarity_transformation(lattice, sym) for sym in site_symmetry
]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import phonopy._lapackepy as lapackepy
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
lapackepy.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(
inv_U,
_get_rotated_fc2s(i, j, delta_fc2s, rot_map_syms,
site_sym_cart)).reshape(3, 3, 3)
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy",
verbose=False):
if verbose:
text = "Solving fc3[ %d, x, x ] with " % (first_atom_num + 1)
if len(displacements_first) > 1:
text += "displacements:"
else:
text += "a displacement:"
print(text)
for i, v in enumerate(displacements_first):
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
sys.stdout.flush()
if verbose > 2:
print(" Site symmetry:")
for i, v in enumerate(site_symmetry):
print(" [%2d %2d %2d] #%2d" % tuple(list(v[0])+[i + 1]))
print(" [%2d %2d %2d]" % tuple(v[1]))
print(" [%2d %2d %2d]\n" % tuple(v[2]))
sys.stdout.flush()
lattice = supercell.get_cell().T
site_sym_cart = [similarity_transformation(lattice, sym)
for sym in site_symmetry]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import phonopy._lapackepy as lapackepy
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
lapackepy.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(inv_U, _get_rotated_fc2s(
i, j, delta_fc2s, rot_map_syms, site_sym_cart)).reshape(3, 3, 3)
def _fit(self, first_atom_num, disp_triplets, sets_of_forces):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(self._lattice, positions,
site_symmetry,
self._symprec)
site_syms_cart = np.array([
similarity_transformation(self._lattice, sym)
for sym in site_symmetry
],
dtype='double')
(disp_triplets_rearranged, num_triplets
) = self._create_displacement_triplets_for_c(disp_triplets)
max_num_disp = np.amax(num_triplets[:, :, :, 1])
for second_atom_num in range(self._num_atom):
print second_atom_num + 1
rot_disps_set = []
for third_atom_num in range(self._num_atom):
try:
import anharmonic._forcefit as forcefit
rot_disps_set.append(
self._create_displacement_matrix_c(
second_atom_num, third_atom_num,
disp_triplets_rearranged, num_triplets,
site_syms_cart, rot_map_syms, max_num_disp))
except ImportError:
rot_disps_set.append(
self._create_displacement_matrix(
second_atom_num, third_atom_num, disp_triplets,
site_syms_cart, rot_map_syms))
print third_atom_num + 1, rot_disps_set[third_atom_num].shape
inv_disps_set = self._invert_displacements(rot_disps_set)
for third_atom_num in range(self._num_atom):
rot_forces = self._create_force_matrix(second_atom_num,
third_atom_num,
sets_of_forces,
site_syms_cart,
rot_map_syms)
fc = self._solve(inv_disps_set[third_atom_num], rot_forces)
# For elements with index exchange symmetry
fc2 = fc[:, 7:10, :].reshape((self._num_atom, 3, 3))
fc3 = fc[:, 46:55, :].reshape((self._num_atom, 3, 3, 3))
fc4 = fc[:, 172:199, :].reshape((self._num_atom, 3, 3, 3, 3))
self._fc2[third_atom_num] = fc2
self._fc3[second_atom_num, third_atom_num] = fc3
self._fc4[first_atom_num, second_atom_num,
third_atom_num] = fc4
def _get_matrices(self, first_atom_num):
disps = []
sets_of_forces = []
for dataset_1st in self._dataset["first_atoms"]:
if first_atom_num != dataset_1st["number"]:
continue
disps.append(dataset_1st["displacement"])
sets_of_forces.append(dataset_1st["forces"])
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry, self._symprec)
site_sym_cart = [similarity_transformation(self._lattice, sym) for sym in site_symmetry]
rot_disps = self._create_displacement_matrix(disps, site_sym_cart)
rot_forces = self._create_force_matrix(sets_of_forces, site_sym_cart, rot_map_syms)
return rot_disps, rot_forces
def _fit(self, first_atom_num, disp_pairs, sets_of_forces):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry,
self._symprec)
for second_atom_num in range(self._num_atom):
rot_atom_map = rot_map_syms[:, second_atom_num]
rot_disps = self._create_displacement_matrix(
disp_pairs, site_symmetry, rot_atom_map)
rot_forces = self._create_force_matrix(sets_of_forces,
site_symmetry, rot_atom_map,
rot_map_syms)
fc = self._solve(rot_disps, rot_forces)
fc2 = fc[:, 1:4, :].reshape((self._num_atom, 3, 3))
fc3 = fc[:, 7:16, :].reshape((self._num_atom, 3, 3, 3))
self._fc3[first_atom_num, second_atom_num] = fc3
def _fit(self, first_atom_num, disp_pairs, sets_of_forces):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
self._symprec)
for second_atom_num in range(self._num_atom):
rot_atom_map = rot_map_syms[:, second_atom_num]
rot_disps = self._create_displacement_matrix(disp_pairs,
site_symmetry,
rot_atom_map)
rot_forces = self._create_force_matrix(sets_of_forces,
site_symmetry,
rot_atom_map,
rot_map_syms)
fc = self._solve(rot_disps, rot_forces)
fc2 = fc[:, 1:4, :].reshape((self._num_atom, 3, 3))
fc3 = fc[:, 7:16, :].reshape((self._num_atom, 3, 3, 3))
self._fc3[first_atom_num, second_atom_num] = fc3
def _fit(self, first_atom_num, disp_pairs, sets_of_forces):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry,
self._symprec)
for second_atom_num in range(self._num_atom):
rot_atom_map = rot_map_syms[:, second_atom_num]
rot_disps = self._create_displacement_matrix(
disp_pairs, site_symmetry, rot_atom_map)
rot_forces = self._create_force_matrix(sets_of_forces,
site_symmetry, rot_atom_map,
rot_map_syms)
fc = self._solve(rot_disps, rot_forces)
fc2 = fc[:, 1:4, :].reshape((self._num_atom, 3, 3))
fc2_2 = fc[:, 5:8, :].reshape((self._num_atom, 3, 3))
fc3 = fc[:, 7:16, :].reshape((self._num_atom, 3, 3, 3))
fc3_21 = fc[:, 16:25, :].reshape((self._num_atom, 3, 3, 3))
for i, j in list(np.ndindex(3, 3)):
self._fc3[first_atom_num, second_atom_num, :, i,
j, :] = (fc3[:, i, j, :] + fc3_21[:, j, i, :]) / 2
def _get_matrices(self, first_atom_num):
disps = []
sets_of_forces = []
for dataset_1st in self._dataset['first_atoms']:
if first_atom_num != dataset_1st['number']:
continue
disps.append(dataset_1st['displacement'])
sets_of_forces.append(dataset_1st['forces'])
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = (self._positions.copy() - self._positions[first_atom_num])
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry,
self._symprec)
site_sym_cart = [
similarity_transformation(self._lattice, sym)
for sym in site_symmetry
]
rot_disps = self._create_displacement_matrix(disps, site_sym_cart)
rot_forces = self._create_force_matrix(sets_of_forces, site_sym_cart,
rot_map_syms)
return rot_disps, rot_forces
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy"):
lattice = supercell.get_cell().T
site_sym_cart = [
similarity_transformation(lattice, sym) for sym in site_symmetry
]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import anharmonic._phono3py as phono3c
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
phono3c.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(
inv_U,
_get_rotated_fc2s(i, j, delta_fc2s, rot_map_syms,
site_sym_cart)).reshape(3, 3, 3)
def _fit(self, first_atom_num, disp_pairs, sets_of_forces):
site_symmetry = self._symmetry.get_site_symmetry(first_atom_num)
positions = self._positions.copy() - self._positions[first_atom_num]
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
self._symprec)
for second_atom_num in range(self._num_atom):
rot_atom_map = rot_map_syms[:, second_atom_num]
rot_disps = self._create_displacement_matrix(disp_pairs,
site_symmetry,
rot_atom_map)
rot_forces = self._create_force_matrix(sets_of_forces,
site_symmetry,
rot_atom_map,
rot_map_syms)
fc = self._solve(rot_disps, rot_forces)
fc2 = fc[:, 1:4, :].reshape((self._num_atom, 3, 3))
fc2_2 = fc[:, 5:8, :].reshape((self._num_atom, 3, 3))
fc3 = fc[:, 7:16, :].reshape((self._num_atom, 3, 3, 3))
fc3_21 = fc[:, 16:25, :].reshape((self._num_atom, 3, 3, 3))
for i, j in list(np.ndindex(3, 3)):
self._fc3[first_atom_num, second_atom_num, :, i, j, :] = (
fc3[:, i, j, :] + fc3_21[:, j, i, :]) / 2
def solve_fc3(first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv_solver="numpy",
verbose=False):
logger.debug("solve_fc3")
if pinv_solver == "numpy":
solver = "numpy.linalg.pinv"
else:
try:
import phono3py._lapackepy as lapackepy
solver = "lapacke-dgesvd"
except ImportError:
print("Phono3py C-routine is not compiled correctly.")
solver = "numpy.linalg.pinv"
if verbose:
text = ("Computing fc3[ %d, x, x ] using %s with " %
(first_atom_num + 1, solver))
if len(displacements_first) > 1:
text += "displacements:"
else:
text += "a displacement:"
print(text)
for i, v in enumerate(displacements_first):
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
sys.stdout.flush()
if verbose > 2:
print(" Site symmetry:")
for i, v in enumerate(site_symmetry):
print(" [%2d %2d %2d] #%2d" % tuple(list(v[0]) + [i + 1]))
print(" [%2d %2d %2d]" % tuple(v[1]))
print(" [%2d %2d %2d]\n" % tuple(v[2]))
sys.stdout.flush()
lattice = supercell.get_cell().T
site_sym_cart = np.array(
[similarity_transformation(lattice, sym) for sym in site_symmetry],
dtype='double',
order='C')
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
logger.debug("get_positions_sent_by_rot_inv")
rot_map_syms = get_positions_sent_by_rot_inv(lattice, positions,
site_symmetry, symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
logger.debug("pinv")
if "numpy" in solver:
inv_U = np.array(np.linalg.pinv(rot_disps), dtype='double', order='C')
else:
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double',
order='C')
lapackepy.pinv(inv_U, rot_disps, 1e-13)
fc3 = np.zeros((num_atom, num_atom, 3, 3, 3), dtype='double', order='C')
logger.debug("rotate_delta_fc2s")
try:
import phono3py._phono3py as phono3c
phono3c.rotate_delta_fc2s(fc3, delta_fc2s, inv_U, site_sym_cart,
rot_map_syms)
except ImportError:
for i, j in np.ndindex(num_atom, num_atom):
fc3[i, j] = np.dot(
inv_U,
_get_rotated_fc2s(i, j, delta_fc2s, rot_map_syms,
site_sym_cart)).reshape(3, 3, 3)
return fc3
