def _compute_permutation_c(
positions_a, # scaled positions
positions_b,
lattice, # column vectors
symprec):
"""Version of '_compute_permutation_for_rotation' which just directly
calls the C function, without any conditioning of the data.
Skipping the conditioning step makes this EXTREMELY slow on large
structures.
"""
permutation = np.zeros(shape=(len(positions_a), ), dtype='intc')
def permutation_error():
raise ValueError(
"Input forces are not enough to calculate force constants, "
"or something wrong (e.g. crystal structure does not match).")
try:
import phonopy._phonopy as phonoc
tolerance = symprec
for _ in range(20):
is_found = phonoc.compute_permutation(permutation, lattice,
positions_a, positions_b,
tolerance)
if is_found:
break
else:
tolerance *= 1.05
if tolerance / symprec > 1.5:
import warnings
msg = ("Crystal structure is distorted in a tricky way so that "
"phonopy could not handle the crystal symmetry properly. "
"It is recommended to symmetrize crystal structure well "
"and then re-start phonon calculation from scratch.")
warnings.warn(msg)
if not is_found:
permutation_error()
except ImportError:
for i, pos_b in enumerate(positions_b):
diffs = positions_a - pos_b
diffs -= np.rint(diffs)
diffs = np.dot(diffs, lattice.T)
possible_j = np.nonzero(
np.sqrt(np.sum(diffs**2, axis=1)) < symprec)[0]
if len(possible_j) != 1:
permutation_error()
permutation[i] = possible_j[0]
if -1 in permutation:
permutation_error()
return permutation
def _compute_permutation_c(positions_a, # scaled positions
positions_b,
lattice, # column vectors
symprec):
"""Version of '_compute_permutation_for_rotation' which just directly
calls the C function, without any conditioning of the data.
Skipping the conditioning step makes this EXTREMELY slow on large
structures.
"""
permutation = np.zeros(shape=(len(positions_a),), dtype='intc')
def permutation_error():
raise ValueError("Input forces are not enough to calculate force constants, "
"or something wrong (e.g. crystal structure does not match).")
try:
import phonopy._phonopy as phonoc
is_found = phonoc.compute_permutation(permutation,
lattice,
positions_a,
positions_b,
symprec)
if not is_found:
permutation_error()
except ImportError:
for i, pos_b in enumerate(positions_b):
diffs = positions_a - pos_b
diffs -= np.rint(diffs)
diffs = np.dot(diffs, lattice.T)
possible_j = np.nonzero(
np.sqrt(np.sum(diffs**2, axis=1)) < symprec)[0]
if len(possible_j) != 1:
permutation_error()
permutation[i] = possible_j[0]
if -1 in permutation:
permutation_error()
return permutation
def _compute_permutation_c(
positions_a, # scaled positions
positions_b,
lattice, # column vectors
symprec):
permutation = np.zeros(shape=(len(positions_a), ), dtype='intc')
def permutation_error():
raise ValueError(
"Input forces are not enough to calculate force constants, "
"or something wrong (e.g. crystal structure does not match).")
try:
import phonopy._phonopy as phonoc
is_found = phonoc.compute_permutation(permutation, lattice,
positions_a, positions_b,
symprec)
if not is_found:
permutation_error()
except ImportError:
for i, pos_b in enumerate(positions_b):
diffs = positions_a - pos_b
diffs -= np.rint(diffs)
diffs = np.dot(diffs, lattice.T)
possible_j = np.nonzero(
np.sqrt(np.sum(diffs**2, axis=1)) < symprec)[0]
if len(possible_j) != 1:
permutation_error()
permutation[i] = possible_j[0]
if -1 in permutation:
permutation_error()
return permutation