def get_matched_structure_mapping(base: Structure, inserted: Structure,
sm: StructureMatcher):
"""
Get the mapping from the inserted structure onto the base structure,
assuming that the inserted structure sans the working ion is some kind
of SC of the base.
Args:
base: host structure, smaller cell
inserted: bigger cell
sm: StructureMatcher instance
Returns:
sc_m : supercell matrix to apply to s1 to get s2
total-t : translation to apply on s1 * sc_m to get s2
"""
s1, s2 = sm._process_species([base, inserted])
fu, _ = sm._get_supercell_size(s1, s2)
try:
val, dist, sc_m, total_t, mapping = sm._strict_match(s1,
s2,
fu=fu,
s1_supercell=True)
except TypeError:
return None
sc = s1 * sc_m
sc.lattice = Lattice.from_parameters(*sc.lattice.abc,
*sc.lattice.angles,
vesta=True) # type: ignore
return sc_m, total_t
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu', 'Ag'], [[0] * 3] * 5)
s2 = Structure(l2, ['Cu', 'Cu', 'Ag'], [[0] * 3] * 3)
sm = StructureMatcher(supercell_size='volume')
self.assertEqual(sm._get_supercell_size(s1, s2), (1, True))
self.assertEqual(sm._get_supercell_size(s2, s1), (1, True))
sm = StructureMatcher(supercell_size='num_sites')
self.assertEqual(sm._get_supercell_size(s1, s2), (2, False))
self.assertEqual(sm._get_supercell_size(s2, s1), (2, True))
sm = StructureMatcher(supercell_size='Ag')
self.assertEqual(sm._get_supercell_size(s1, s2), (2, False))
self.assertEqual(sm._get_supercell_size(s2, s1), (2, True))
sm = StructureMatcher(supercell_size='wfieoh')
self.assertRaises(ValueError, sm._get_supercell_size, s1, s2)
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ["Mg", "Cu", "Ag", "Cu", "Ag"], [[0] * 3] * 5)
s2 = Structure(l2, ["Cu", "Cu", "Ag"], [[0] * 3] * 3)
sm = StructureMatcher(supercell_size="volume")
self.assertEqual(sm._get_supercell_size(s1, s2), (1, True))
self.assertEqual(sm._get_supercell_size(s2, s1), (1, True))
sm = StructureMatcher(supercell_size="num_sites")
self.assertEqual(sm._get_supercell_size(s1, s2), (2, False))
self.assertEqual(sm._get_supercell_size(s2, s1), (2, True))
sm = StructureMatcher(supercell_size="Ag")
self.assertEqual(sm._get_supercell_size(s1, s2), (2, False))
self.assertEqual(sm._get_supercell_size(s2, s1), (2, True))
sm = StructureMatcher(supercell_size="wfieoh")
self.assertRaises(ValueError, sm._get_supercell_size, s1, s2)
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu', 'Ag'], [[0] * 3] * 5)
s2 = Structure(l2, ['Cu', 'Cu', 'Ag'], [[0] * 3] * 3)
sm = StructureMatcher(supercell_size='volume')
self.assertEqual(sm._get_supercell_size(s1, s2),
(1, True))
self.assertEqual(sm._get_supercell_size(s2, s1),
(1, True))
sm = StructureMatcher(supercell_size='num_sites')
self.assertEqual(sm._get_supercell_size(s1, s2),
(2, False))
self.assertEqual(sm._get_supercell_size(s2, s1),
(2, True))
sm = StructureMatcher(supercell_size='Ag')
self.assertEqual(sm._get_supercell_size(s1, s2),
(2, False))
self.assertEqual(sm._get_supercell_size(s2, s1),
(2, True))
sm = StructureMatcher(supercell_size='wfieoh')
self.assertRaises(ValueError, sm._get_supercell_size, s1, s2)
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu', 'Ag'], [[0]*3]*5)
s2 = Structure(l2, ['Cu', 'Cu', 'Ag'], [[0]*3]*3)
sm = StructureMatcher(supercell_size='volume')
result = sm._get_supercell_size(s1, s2)
self.assertEqual(result[0], 1)
self.assertEqual(result[1], True)
result = sm._get_supercell_size(s2, s1)
self.assertEqual(result[0], 1)
self.assertEqual(result[1], True)
sm = StructureMatcher(supercell_size='num_sites')
result = sm._get_supercell_size(s1, s2)
self.assertEqual(result[0], 2)
self.assertEqual(result[1], False)
result = sm._get_supercell_size(s2, s1)
self.assertEqual(result[0], 2)
self.assertEqual(result[1], True)
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu', 'Ag'], [[0]*3]*5)
s2 = Structure(l2, ['Cu', 'Cu', 'Ag'], [[0]*3]*3)
sm = StructureMatcher(supercell_size='volume')
result = sm._get_supercell_size(s1, s2)
self.assertEqual(result[0], 1)
self.assertEqual(result[1], True)
result = sm._get_supercell_size(s2, s1)
self.assertEqual(result[0], 1)
self.assertEqual(result[1], True)
sm = StructureMatcher(supercell_size='num_sites')
result = sm._get_supercell_size(s1, s2)
self.assertEqual(result[0], 2)
self.assertEqual(result[1], False)
result = sm._get_supercell_size(s2, s1)
self.assertEqual(result[0], 2)
self.assertEqual(result[1], True)
