def test_find_in_coord_list_pbc(self):
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
test_coord = [0.1, 0.1, 0.1]
self.assertEqual(
coord.find_in_coord_list_pbc(coords, test_coord).size, 0)
self.assertEqual(
coord.find_in_coord_list_pbc(coords, test_coord, atol=0.15)[0], 0)
test_coord = [0.99, 0.99, 0.99]
self.assertEqual(
coord.find_in_coord_list_pbc(coords, test_coord, atol=0.02)[0], 0)
test_coord = [-0.499, -0.499, -0.499]
self.assertEqual(
coord.find_in_coord_list_pbc(coords, test_coord, atol=0.01)[0], 1)
def test_subset(self):
sm = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=False,
allow_subset=True)
l = Lattice.orthorhombic(10, 20, 30)
s1 = Structure(l, ['Si', 'Si', 'Ag'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Ag'], [[0, 0.1, 0], [-.7, .5, .4]])
result = sm.get_s2_like_s1(s1, s2)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0, 0, 0.1])), 1)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0.7, 0.4, 0.5])),
1)
#test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Si'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Si'], [[0, 0.1, 0], [-.7, .5, .4]])
result = sm.get_s2_like_s1(s1, s2)
mindists = np.min(s1.lattice.get_all_distances(s1.frac_coords,
result.frac_coords),
axis=0)
self.assertLess(np.max(mindists), 1e-6)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0, 0, 0.1])), 1)
self.assertEqual(
len(find_in_coord_list_pbc(result.frac_coords, [0.7, 0.4, 0.5])),
1)
#test with not enough sites in s1
#test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Cl'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Si'], [[0, 0.1, 0], [-.7, .5, .4]])
self.assertEqual(sm.get_s2_like_s1(s1, s2), None)
def test_subset(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=False,
allow_subset=True)
l = Lattice.orthorhombic(10, 20, 30)
s1 = Structure(l, ['Si', 'Si', 'Ag'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Ag'],
[[0, 0.1, 0], [-.7, .5, .4]])
result = sm.get_s2_like_s1(s1, s2)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0, 0, 0.1])), 1)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0.7, 0.4, 0.5])), 1)
# test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Si'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Si'],
[[0, 0.1, 0], [-.7, .5, .4]])
result = sm.get_s2_like_s1(s1, s2)
mindists = np.min(s1.lattice.get_all_distances(
s1.frac_coords, result.frac_coords), axis=0)
self.assertLess(np.max(mindists), 1e-6)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0, 0, 0.1])), 1)
self.assertEqual(len(find_in_coord_list_pbc(result.frac_coords,
[0.7, 0.4, 0.5])), 1)
# test with not enough sites in s1
# test with fewer species in s2
s1 = Structure(l, ['Si', 'Ag', 'Cl'],
[[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]])
s2 = Structure(l, ['Si', 'Si'],
[[0, 0.1, 0], [-.7, .5, .4]])
self.assertEqual(sm.get_s2_like_s1(s1, s2), None)
def get_matching_coord(coord):
keys = list(coord_to_species.keys())
coords = np.array(keys)
for op in self.symmetry_operations:
c = op.operate(coord)
inds = find_in_coord_list_pbc(coords,
c,
atol=self._site_tolerance)
# cant use if inds, because python is dumb and np.array([0]) evaluates
# to False
if len(inds):
return keys[inds[0]]
return False
