def test_find_in_coord_list(self):
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
test_coord = [0.1, 0.1, 0.1]
self.assertFalse(find_in_coord_list(coords, test_coord))
self.assertEqual(find_in_coord_list(coords, test_coord, atol=0.15)[0],
0)
self.assertFalse(find_in_coord_list([0.99, 0.99, 0.99], test_coord,
atol=0.15))
coords = [[0, 0, 0], [0.5, 0.5, 0.5], [0.1, 0.1, 0.1]]
self.assertArrayEqual(find_in_coord_list(coords, test_coord,
atol=0.15), [0, 2])
def is_valid_op(self, symmop):
"""
Check if a particular symmetry operation is a valid symmetry operation
for a molecule, i.e., the operation maps all atoms to another
equivalent atom.
Args:
symmop:
Symmetry op to test.
"""
coords = self.centered_mol.cart_coords
for site in self.centered_mol:
coord = symmop.operate(site.coords)
ind = find_in_coord_list(coords, coord, self.tol)
if not (len(ind) == 1 and
self.centered_mol[ind[0]].species_and_occu
== site.species_and_occu):
return False
return True
def is_valid_op(self, symmop):
"""
Check if a particular symmetry operation is a valid symmetry operation
for a molecule, i.e., the operation maps all atoms to another
equivalent atom.
Args:
symmop:
Symmetry op to test.
"""
coords = self.centered_mol.cart_coords
for site in self.centered_mol:
coord = symmop.operate(site.coords)
ind = find_in_coord_list(coords, coord, self.tol)
if not (len(ind) == 1
and self.centered_mol[ind[0]].species_and_occu
== site.species_and_occu):
return False
return True
