def get_equivalent_smallest_vectors(atom_number_supercell,
atom_number_primitive, supercell, symprec):
s_pos = supercell.get_scaled_positions()
svecs, multi = get_smallest_vectors(supercell.get_cell(),
[s_pos[atom_number_supercell]],
[s_pos[atom_number_primitive]],
symprec=symprec)
return svecs[0, 0]
def get_smallest_vector_of_atom_pair(atom_number_supercell,
atom_number_primitive,
supercell: PhonopyAtoms, symprec):
"""Return smallest vectors of an atom pair in supercell."""
s_pos = supercell.scaled_positions
svecs, _ = get_smallest_vectors(
supercell.cell,
[s_pos[atom_number_supercell]],
[s_pos[atom_number_primitive]],
store_dense_svecs=True,
symprec=symprec,
)
return svecs[0]
def cutoff_force_constants(force_constants,
supercell,
primitive,
cutoff_radius,
symprec=1e-5):
fc_shape = force_constants.shape
if fc_shape[0] == fc_shape[1]:
svecs, _ = get_smallest_vectors(supercell.get_cell(),
supercell.get_scaled_positions(),
supercell.get_scaled_positions(),
symprec=symprec)
min_distances = np.sqrt(np.sum(
np.dot(svecs[:, :, 0, :], supercell.get_cell()) ** 2, axis=-1))
else:
svecs, _ = primitive.get_smallest_vectors()
min_distances = np.sqrt(np.sum(
np.dot(svecs[:, :, 0, :], primitive.get_cell()) ** 2, axis=-1))
for i in range(fc_shape[0]):
for j in range(fc_shape[1]):
if min_distances[j, i] > cutoff_radius:
force_constants[i, j] = 0.0
def cutoff_force_constants(force_constants,
supercell,
primitive,
cutoff_radius,
symprec=1e-5):
"""Set zero to force constants outside of cutoff distance.
Note
----
`force_constants` is overwritten.
"""
fc_shape = force_constants.shape
if fc_shape[0] == fc_shape[1]:
svecs, multi = get_smallest_vectors(
supercell.cell,
supercell.scaled_positions,
supercell.scaled_positions,
symprec=symprec,
store_dense_svecs=primitive.store_dense_svecs,
)
lattice = supercell.cell
else:
svecs, multi = primitive.get_smallest_vectors()
lattice = primitive.cell
if primitive.store_dense_svecs:
_svecs = svecs[multi[:, :, 1]]
else:
_svecs = svecs[:, :, 0, :]
min_distances = np.sqrt(np.sum(np.dot(_svecs, lattice)**2, axis=-1))
for i in range(fc_shape[0]):
for j in range(fc_shape[1]):
if min_distances[j, i] > cutoff_radius:
force_constants[i, j] = 0.0