def test_add_site_property(self):
self.modifier.add_site_property("charge", [4.1, -2, -2, -2, -2])
s = self.modifier.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[1].charge, -2)
#test adding multiple properties.
mod2 = MoleculeEditor(s)
mod2.add_site_property("magmom", [3, 2, 2, 2, 2])
s = mod2.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[0].magmom, 3)
def setUp(self):
coords = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
mol = Molecule(["C", "H", "H", "H", "H"], coords)
self.modifier = MoleculeEditor(mol)
class MoleculeEditorTest(unittest.TestCase):
def setUp(self):
coords = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
mol = Molecule(["C", "H", "H", "H", "H"], coords)
self.modifier = MoleculeEditor(mol)
def test_translate_sites(self):
self.modifier.translate_sites([0, 1], [0.5, 0.5, 0.5])
self.assertTrue(np.array_equal(self.modifier.modified_structure
.cart_coords[0],
np.array([0.5, 0.5, 0.5])))
def test_append_site(self):
self.modifier.append_site("Si", [0, 0.5, 0])
self.assertEqual(self.modifier.modified_structure.formula, "Si1 H4 C1",
"Wrong formula!")
self.assertRaises(ValueError, self.modifier.append_site, Element("Si"),
np.array([0, 0.5, 0]))
def test_modified_structure(self):
self.modifier.insert_site(1, "Si", [0, 0.25, 0])
self.assertEqual(self.modifier.modified_structure.formula, "Si1 H4 C1",
"Wrong formula!")
self.modifier.delete_site(0)
self.assertEqual(self.modifier.modified_structure.formula, "Si1 H4",
"Wrong formula!")
self.modifier.replace_site(0, "Ge")
self.assertEqual(self.modifier.modified_structure.formula, "Ge1 H4",
"Wrong formula!")
self.modifier.append_site("Si", [0, 0.75, 0])
self.modifier.replace_species({Element("Si"): Element("Ge")})
self.assertEqual(self.modifier.modified_structure.formula, "Ge2 H4",
"Wrong formula!")
self.modifier.replace_species({Element("Ge"): {Element("Ge"): 0.5,
Element("Si"): 0.5}})
self.assertEqual(self.modifier.modified_structure.formula,
"Si1 Ge1 H4", "Wrong formula!")
#this should change the .5Si .5Ge sites to .75Si .25Ge
self.modifier.replace_species({Element("Ge"): {Element("Ge"): 0.5,
Element("Si"): 0.5}})
self.assertEqual(self.modifier.modified_structure.formula,
"Si1.5 Ge0.5 H4", "Wrong formula!")
d = 0.1
pre_perturbation_sites = self.modifier.modified_structure.sites
self.modifier.perturb_structure(distance=d)
post_perturbation_sites = self.modifier.modified_structure.sites
for i, x in enumerate(pre_perturbation_sites):
self.assertAlmostEqual(x.distance(post_perturbation_sites[i]), d,
3, "Bad perturbation distance")
def test_add_site_property(self):
self.modifier.add_site_property("charge", [4.1, -2, -2, -2, -2])
s = self.modifier.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[1].charge, -2)
#test adding multiple properties.
mod2 = MoleculeEditor(s)
mod2.add_site_property("magmom", [3, 2, 2, 2, 2])
s = mod2.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[0].magmom, 3)