def _determine_inversion(self, permlist):
x = np.array(self.atom_positions)
xi = -x
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, xi):
if exact.check_match(x, xi, rot, invert):
self.inversion = exact._last_checked_rotation
return
def _determine_inversion(self, permlist):
x = np.array(self.atom_positions)
xi = -x
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, xi):
if exact.check_match(x, xi, rot, invert):
self.inversion = exact._last_checked_rotation
return
def _determine_rotational_symmetry(self, permlist):
x = np.array(self.atom_positions)
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, x):
if exact.check_match(x, x, rot, invert):
rot = exact._last_checked_rotation
exists = False
for rot2 in self.symmetries:
if np.linalg.norm(rot2 - rot) < 1e-6:
exists = True
break
if not exists:
self.symmetries.append(rot)
def _determine_rotational_symmetry(self, permlist):
x = np.array(self.atom_positions)
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, x):
if exact.check_match(x, x, rot, invert):
rot = exact._last_checked_rotation
exists=False
for rot2 in self.symmetries:
if np.linalg.norm(rot2 - rot) < 1e-6:
exists=True
break
if not exists:
self.symmetries.append(rot)
def get_compare_exact(self, **kwargs):
permlist = [range(self.natoms)]
return ExactMatchAtomicCluster(permlist=permlist, **kwargs)
def get_compare_exact(self, **kwargs):
"""this function quickly determines whether two clusters are identical
given translational, rotational and permutational symmeties
"""
permlist = self.get_permlist()
return ExactMatchAtomicCluster(permlist=permlist, **kwargs)
def get_compare_exact(self, **kwargs):
permlist = self.get_permlist()
return ExactMatchAtomicCluster(permlist=permlist, **kwargs)