def distribute_fc3(fc3,
first_disp_atoms,
lattice,
positions,
rotations,
translations,
symprec,
verbose):
num_atom = len(positions)
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
if verbose > 2:
print " [ %d, x, x ] to [ %d, x, x ]" % (i_rot + 1, i + 1)
sys.stdout.flush()
atom_mapping = np.zeros(num_atom, dtype='intc')
for j in range(num_atom):
atom_mapping[j] = get_atom_by_symmetry(positions,
rot,
trans,
j,
symprec)
rot_cart_inv = np.double(
similarity_transformation(lattice, rot).T.copy())
try:
import anharmonic._phono3py as phono3c
phono3c.distribute_fc3(fc3,
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[i_rot, j_rot, k_rot])
def distribute_fc3(fc3,
first_disp_atoms,
lattice,
positions,
rotations,
translations,
symprec,
verbose):
num_atom = len(positions)
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
if verbose > 2:
print " [ %d, x, x ] to [ %d, x, x ]" % (i_rot + 1, i + 1)
sys.stdout.flush()
atom_mapping = np.zeros(num_atom, dtype='intc')
for j in range(num_atom):
atom_mapping[j] = get_atom_by_symmetry(positions,
rot,
trans,
j,
symprec)
rot_cart_inv = np.double(
similarity_transformation(lattice, rot).T.copy())
try:
import anharmonic._phono3py as phono3c
phono3c.distribute_fc3(fc3,
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[i_rot, 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 anharmonic._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
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 anharmonic._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