def test_get_uc_pos():
errors = []
# set up parameters to initiate get_uc_pos
uc_lattice = mg_Li.symm_structure.lattice
isite = [x for x in input_struct_i.sites if x.species_string == "Li"][0]
esite = [x for x in input_struct_e.sites if x.species_string == "Li"][0]
sm = StructureMatcher(ignored_species=[list(mg_Li.m_graph.graph.edges(data=True))[0][2]["hop"].isite.specie.name])
wi_specie = mg_Li.symm_structure[-1].specie
p0, p1, p2 = get_uc_pos(isite, esite, mg_Li.symm_structure, input_struct_i, sm)
# generate correct sites to compare
test_p0 = PeriodicSite(
wi_specie, np.array([2.91418875, 1.02974425, 4.4933425]), uc_lattice, coords_are_cartesian=True
)
test_p1 = PeriodicSite(
wi_specie, np.array([4.82950555, 1.0247028, 4.10369437]), uc_lattice, coords_are_cartesian=True
)
test_p2 = PeriodicSite(
wi_specie, np.array([6.74482475, 1.01967025, 3.7140425]), uc_lattice, coords_are_cartesian=True
)
if not test_p0.__eq__(p0):
errors.append("Initial site does not match")
if not test_p1.__eq__(p1):
errors.append("Middle site does not match")
if not test_p2.__eq__(p2):
errors.append("Ending site does not match")
assert not errors, "errors occured:\n" + "\n".join(errors)
class PeriodicSiteTest(unittest.TestCase):
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", np.array([0.25, 0.35, 0.45]), self.lattice)
self.site2 = PeriodicSite({"Si":0.5}, np.array([0, 0, 0]), self.lattice)
self.assertEquals(self.site2.species_and_occu, {Element('Si'): 0.5}, "Inconsistent site created!")
self.propertied_site = PeriodicSite(Specie("Fe", 2), [0.25, 0.35, 0.45], self.lattice, properties={'magmom':5.1, 'charge':4.2})
def test_properties(self):
"""
Test the properties for a site
"""
self.assertEquals(self.site.a, 0.25)
self.assertEquals(self.site.b, 0.35)
self.assertEquals(self.site.c, 0.45)
self.assertEquals(self.site.x, 2.5)
self.assertEquals(self.site.y, 3.5)
self.assertEquals(self.site.z, 4.5)
self.assertTrue(self.site.is_ordered)
self.assertFalse(self.site2.is_ordered)
self.assertEqual(self.propertied_site.magmom, 5.1)
self.assertEqual(self.propertied_site.charge, 4.2)
def test_distance(self):
other_site = PeriodicSite("Fe", np.array([0, 0, 0]), self.lattice)
self.assertAlmostEquals(self.site.distance(other_site), 6.22494979899, 5)
def test_distance_from_point(self):
self.assertNotAlmostEqual(self.site.distance_from_point(np.array([0.1, 0.1, 0.1])), 6.22494979899, 5)
self.assertAlmostEqual(self.site.distance_from_point(np.array([0.1, 0.1, 0.1])), 6.0564015718906887, 5)
def test_distance_and_image(self):
other_site = PeriodicSite("Fe", np.array([1, 1, 1]), self.lattice)
(distance, image) = self.site.distance_and_image(other_site)
self.assertAlmostEquals(distance, 6.22494979899, 5)
self.assertTrue(([-1, -1, -1] == image).all())
(distance, image) = self.site.distance_and_image(other_site, [1, 0, 0])
self.assertAlmostEquals(distance, 19.461500456028563, 5)
# Test that old and new distance algo give the same ans for "standard lattices"
lattice = Lattice(np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]))
site1 = PeriodicSite("Fe", np.array([0.01, 0.02, 0.03]), lattice)
site2 = PeriodicSite("Fe", np.array([0.99, 0.98, 0.97]), lattice)
self.assertTrue(site1.distance_and_image_old(site2)[0] == site1.distance_and_image(site2)[0])
lattice = Lattice.from_parameters(1, 0.01, 1, 10, 10, 10)
site1 = PeriodicSite("Fe", np.array([0.01, 0.02, 0.03]), lattice)
site2 = PeriodicSite("Fe", np.array([0.99, 0.98, 0.97]), lattice)
self.assertTrue(site1.distance_and_image_old(site2)[0] > site1.distance_and_image(site2)[0])
site2 = PeriodicSite("Fe", np.random.rand(3), lattice)
(dist_old, jimage_old) = site1.distance_and_image_old(site2)
(dist_new, jimage_new) = site1.distance_and_image(site2)
self.assertTrue(dist_old >= dist_new, "New distance algo should always give smaller answers!")
self.assertFalse((dist_old == dist_new) ^ (jimage_old == jimage_new).all(), "If old dist == new dist, the images returned must be the same!")
def test_is_periodic_image(self):
other = PeriodicSite("Fe", np.array([1.25, 2.35, 4.45]), self.lattice)
self.assertTrue(self.site.is_periodic_image(other), "This other site should be a periodic image.")
other = PeriodicSite("Fe", np.array([1.25, 2.35, 4.46]), self.lattice)
self.assertFalse(self.site.is_periodic_image(other), "This other site should not be a periodic image.")
other = PeriodicSite("Fe", np.array([1.25, 2.35, 4.45]), Lattice.rhombohedral(2))
self.assertFalse(self.site.is_periodic_image(other), "Different lattices should result in different periodic sites.")
def test_equality(self):
other_site = PeriodicSite("Fe", np.array([1, 1, 1]), self.lattice)
self.assertTrue(self.site.__eq__(self.site))
self.assertFalse(other_site.__eq__(self.site))
self.assertFalse(self.site.__ne__(self.site))
self.assertTrue(other_site.__ne__(self.site))
def test_to_from_dict(self):
d = self.site2.to_dict
site = PeriodicSite.from_dict(d)
self.assertEqual(site, self.site2)
self.assertNotEqual(site, self.site)
d = self.propertied_site.to_dict
site = Site.from_dict(d)
self.assertEqual(site.magmom, 5.1)
self.assertEqual(site.charge, 4.2)
def test_equality(self):
other_site = PeriodicSite("Fe", np.array([1, 1, 1]), self.lattice)
self.assertTrue(self.site.__eq__(self.site))
self.assertFalse(other_site.__eq__(self.site))
self.assertFalse(self.site.__ne__(self.site))
self.assertTrue(other_site.__ne__(self.site))
