class StructureTest(unittest.TestCase):
def setUp(self):
self.si = Element("Si")
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
self.lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.struct = Structure(self.lattice, [self.si, self.si], coords)
self.assertEqual(len(self.struct), 2,
"Wrong number of sites in structure!")
self.assertTrue(self.struct.is_ordered)
coords = list()
coords.append([0, 0, 0])
coords.append([0., 0, 0.0000001])
self.assertRaises(StructureError, Structure, self.lattice,
[self.si, self.si], coords, True)
self.propertied_structure = Structure(self.lattice, [self.si, self.si],
coords,
site_properties={'magmom':
[5, -5]})
def test_volume_and_density(self):
self.assertAlmostEqual(self.struct.volume, 40.04, 2, "Volume wrong!")
self.assertAlmostEqual(self.struct.density, 2.33, 2,
"Incorrect density")
def test_specie_init(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = Structure(self.lattice, [{Specie('O', -2):1.0},
{Specie('Mg', 2):0.8}], coords)
self.assertEqual(str(s.composition), 'Mg2+0.8 O2-1')
def test_get_sorted_structure(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = Structure(self.lattice, ["O", "Li"], coords,
site_properties={'charge': [-2, 1]})
sorted_s = s.get_sorted_structure()
self.assertEqual(sorted_s[0].species_and_occu, Composition("Li"))
self.assertEqual(sorted_s[1].species_and_occu, Composition("O"))
self.assertEqual(sorted_s[0].charge, 1)
self.assertEqual(sorted_s[1].charge, -2)
def test_fractional_occupations(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = Structure(self.lattice, [{Element('O'):1.0}, {Element('Mg'):0.8}],
coords)
self.assertEqual(str(s.composition), 'Mg0.8 O1')
self.assertFalse(s.is_ordered)
def test_get_distance(self):
self.assertAlmostEqual(self.struct.get_distance(0, 1), 2.35, 2,
"Distance calculated wrongly!")
pt = [0.9, 0.9, 0.8]
self.assertAlmostEqual(self.struct[0].distance_from_point(pt),
1.50332963784, 2,
"Distance calculated wrongly!")
def test_to_dict(self):
si = Specie("Si", 4)
mn = Element("Mn")
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = Structure(self.lattice, [{si:0.5, mn:0.5}, {si:0.5}], coords)
self.assertIn("lattice", struct.to_dict)
self.assertIn("sites", struct.to_dict)
d = self.propertied_structure.to_dict
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = Structure(self.lattice, [{Specie('O', -2,
properties={"spin":3}):1.0},
{Specie('Mg', 2,
properties={"spin":2}):0.8}],
coords, site_properties={'magmom': [5, -5]})
d = s.to_dict
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
self.assertEqual(d['sites'][0]['species'][0]['properties']['spin'], 3)
def test_from_dict(self):
d = self.propertied_structure.to_dict
s = Structure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
d = {'lattice': {'a': 3.8401979337, 'volume': 40.044794644251596,
'c': 3.8401979337177736, 'b': 3.840198994344244,
'matrix': [[3.8401979337, 0.0, 0.0],
[1.9200989668, 3.3257101909, 0.0],
[0.0, -2.2171384943, 3.1355090603]],
'alpha': 119.9999908639842, 'beta': 90.0,
'gamma': 60.000009137322195},
'sites': [{'properties': {'magmom': 5}, 'abc': [0.0, 0.0, 0.0],
'occu': 1.0, 'species': [{'occu': 1.0,
'oxidation_state':-2,
'properties': {'spin': 3},
'element': 'O'}],
'label': 'O2-', 'xyz': [0.0, 0.0, 0.0]},
{'properties': {'magmom':-5}, 'abc': [0.75, 0.5, 0.75],
'occu': 0.8, 'species': [{'occu': 0.8,
'oxidation_state': 2,
'properties': {'spin': 2},
'element': 'Mg'}],
'label': 'Mg2+:0.800',
'xyz': [3.8401979336749994, 1.2247250003039056e-06,
2.351631795225]}]}
s = Structure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
self.assertEqual(s[0].specie.spin, 3)
def test_site_properties(self):
site_props = self.propertied_structure.site_properties
self.assertEqual(site_props['magmom'], [5, -5])
self.assertEqual(self.propertied_structure[0].magmom, 5)
self.assertEqual(self.propertied_structure[1].magmom, -5)
def test_copy(self):
new_struct = self.propertied_structure.copy(site_properties={'charge':
[2, 3]})
self.assertEqual(new_struct[0].magmom, 5)
self.assertEqual(new_struct[1].magmom, -5)
self.assertEqual(new_struct[0].charge, 2)
self.assertEqual(new_struct[1].charge, 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0., 0, 0.0000001])
structure = Structure(self.lattice, ["O", "Si"], coords,
site_properties={'magmom': [5, -5]})
new_struct = structure.copy(site_properties={'charge': [2, 3]},
sanitize=True)
self.assertEqual(new_struct[0].magmom, -5)
self.assertEqual(new_struct[1].magmom, 5)
self.assertEqual(new_struct[0].charge, 3)
self.assertEqual(new_struct[1].charge, 2)
self.assertAlmostEqual(new_struct.volume, structure.volume)
def test_interpolate(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = Structure(self.lattice, [self.si, self.si], coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = Structure(self.struct.lattice, [self.si, self.si], coords2)
int_s = struct.interpolate(struct2, 10)
for s in int_s:
self.assertIsNotNone(s, "Interpolation Failed!")
self.assertTrue((int_s[1][1].frac_coords == [0.725, 0.5, 0.725]).all())
badlattice = [[1, 0.00, 0.00], [0, 1, 0.00], [0.00, 0, 1]]
struct2 = Structure(badlattice, [self.si, self.si], coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = Structure(self.struct.lattice, [self.si, Element("Fe")],
coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
def test_get_primitive_structure(self):
coords = [[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5]]
fcc_ag = Structure(Lattice.cubic(4.09), ["Ag"] * 4, coords)
self.assertEqual(len(fcc_ag.get_primitive_structure()), 1)
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
bcc_li = Structure(Lattice.cubic(4.09), ["Li"] * 2, coords)
self.assertEqual(len(bcc_li.get_primitive_structure()), 1)
def test_primitive_structure_volume_check(self):
l = Lattice.tetragonal(10, 30)
coords = [[0.5, 0.8, 0], [0.5, 0.2, 0],
[0.5, 0.8, 0.333], [0.5, 0.5, 0.333],
[0.5, 0.5, 0.666], [0.5, 0.2, 0.666]]
s = Structure(l, ["Ag"] * 6, coords)
sprim = s.get_primitive_structure(tolerance=0.1)
self.assertEqual(len(sprim), 6)
def test_get_all_neighbors_and_get_neighbors(self):
s = self.struct
r = random.uniform(3, 6)
all_nn = s.get_all_neighbors(r)
for i in range(len(s)):
self.assertEqual(len(all_nn[i]), len(s.get_neighbors(s[i], r)))
def test_get_dist_matrix(self):
ans = [[0., 2.3516318],
[2.3516318, 0.]]
self.assertTrue(np.allclose(self.struct.distance_matrix, ans))
