def test_site_index_mapping_two(self):
a = 6.19399
lattice = Lattice.from_parameters(a, a, a, 90, 90, 90)
coords1 = np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])
coords2 = np.array([[0.4, 0.6, 0.4], [0.1, 0.1, 0.1]])
sites1 = [
PeriodicSite(species='Na', coords=c, lattice=lattice)
for c in coords1
]
sites2 = [
PeriodicSite(species='Na', coords=c, lattice=lattice)
for c in coords2
]
structure1 = Structure.from_sites(sites1)
structure2 = Structure.from_sites(sites2)
mapping = site_index_mapping(structure1, structure2)
np.testing.assert_array_equal(mapping, np.array([1, 0]))
mapping = site_index_mapping(structure1, structure2)
np.testing.assert_array_equal(mapping, np.array([1, 0]))
def test_site_index_mapping_with_one_to_one_mapping_raises_ValueError_one(
self):
a = 6.19399
lattice = Lattice.from_parameters(a, a, a, 90, 90, 90)
coords1 = np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])
coords2 = np.array([[0.4, 0.6, 0.4], [0.1, 0.1, 0.1]])
species2 = ['Na', 'Cl']
sites1 = [
PeriodicSite(species='Na', coords=c, lattice=lattice)
for c in coords1
]
sites2 = [
PeriodicSite(species=s, coords=c, lattice=lattice)
for s, c in zip(species2, coords2)
]
structure1 = Structure.from_sites(sites1)
structure2 = Structure.from_sites(sites2)
with self.assertRaises(ValueError):
site_index_mapping(structure1, structure2, species2='Na')
def test_site_index_mapping_with_species_1_as_string(self):
a = 6.19399
lattice = Lattice.from_parameters(a, a, a, 90, 90, 90)
coords1 = np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])
coords2 = np.array([[0.4, 0.6, 0.4], [0.1, 0.1, 0.1]])
species1 = ['Na', 'Cl']
sites1 = [
PeriodicSite(species=s, coords=c, lattice=lattice)
for s, c in zip(species1, coords1)
]
sites2 = [
PeriodicSite(species='Na', coords=c, lattice=lattice)
for c in coords2
]
structure1 = Structure.from_sites(sites1)
structure2 = Structure.from_sites(sites2)
mapping = site_index_mapping(structure1, structure2, species1='Na')
np.testing.assert_array_equal(mapping, np.array([1]))
def test_site_index_mapping_with_return_mapping_distances(self):
a = 6.19399
lattice = Lattice.from_parameters(a, a, a, 90, 90, 90)
coords1 = np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])
coords2 = np.array([[0.1, 0.1, 0.1], [0.4, 0.6, 0.4]])
sites1 = [
PeriodicSite(species='Na', coords=c, lattice=lattice)
for c in coords1
]
sites2 = [
PeriodicSite(species='Na', coords=c, lattice=lattice)
for c in coords2
]
structure1 = Structure.from_sites(sites1)
structure2 = Structure.from_sites(sites2)
mapping, distances = site_index_mapping(structure1,
structure2,
return_mapping_distances=True)
np.testing.assert_array_equal(mapping, np.array([0, 1]))
expected_distance = np.sqrt(3 * ((0.1 * a)**2))
np.testing.assert_array_almost_equal(
distances, np.array([expected_distance, expected_distance]))