class StructureTest(PymatgenTest):
def setUp(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"], coords)
def test_non_hash(self):
self.assertRaises(TypeError, dict, [(self.structure, 1)])
def test_append_insert_remove_replace(self):
s = self.structure
s.insert(1, "O", [0.5, 0.5, 0.5])
self.assertEqual(s.formula, "Si2 O1")
self.assertTrue(s.ntypesp == 2)
self.assertTrue(s.symbol_set == ("Si", "O"))
self.assertTrue(s.indices_from_symbol("Si") == (0,2))
self.assertTrue(s.indices_from_symbol("O") == (1,))
s.remove(2)
self.assertEqual(s.formula, "Si1 O1")
self.assertTrue(s.indices_from_symbol("Si") == (0,))
self.assertTrue(s.indices_from_symbol("O") == (1,))
s.append("N", [0.25, 0.25, 0.25])
self.assertEqual(s.formula, "Si1 N1 O1")
self.assertTrue(s.ntypesp == 3)
self.assertTrue(s.symbol_set == ("Si", "O", "N"))
self.assertTrue(s.indices_from_symbol("Si") == (0,))
self.assertTrue(s.indices_from_symbol("O") == (1,))
self.assertTrue(s.indices_from_symbol("N") == (2,))
s.replace(0, "Ge")
self.assertEqual(s.formula, "Ge1 N1 O1")
self.assertTrue(s.symbol_set == ("Ge", "O", "N"))
s.replace_species({"Ge": "Si"})
self.assertEqual(s.formula, "Si1 N1 O1")
self.assertTrue(s.ntypesp == 3)
s.replace_species({"Si": {"Ge": 0.5, "Si": 0.5}})
self.assertEqual(s.formula, "Si0.5 Ge0.5 N1 O1")
#this should change the .5Si .5Ge sites to .75Si .25Ge
s.replace_species({"Ge": {"Ge": 0.5, "Si": 0.5}})
self.assertEqual(s.formula, "Si0.75 Ge0.25 N1 O1")
# In this case, s.ntypesp is ambiguous.
# for the time being, we raise AttributeError.
with self.assertRaises(AttributeError):
s.ntypesp
s.remove_species(["Si"])
self.assertEqual(s.formula, "Ge0.25 N1 O1")
s.remove_sites([1, 2])
self.assertEqual(s.formula, "Ge0.25")
def test_add_site_property(self):
s = self.structure
s.add_site_property("charge", [4.1, -5])
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[1].charge, -5)
s.add_site_property("magmom", [3, 2])
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[0].magmom, 3)
def test_perturb(self):
d = 0.1
pre_perturbation_sites = self.structure.sites[:]
self.structure.perturb(distance=d)
post_perturbation_sites = self.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_oxidation_states(self):
oxidation_states = {"Si": -4}
self.structure.add_oxidation_state_by_element(oxidation_states)
for site in self.structure:
for k in site.species_and_occu.keys():
self.assertEqual(k.oxi_state, oxidation_states[k.symbol],
"Wrong oxidation state assigned!")
oxidation_states = {"Fe": 2}
self.assertRaises(ValueError,
self.structure.add_oxidation_state_by_element,
oxidation_states)
self.structure.add_oxidation_state_by_site([2, -4])
self.assertEqual(self.structure[0].specie.oxi_state, 2)
self.assertRaises(ValueError,
self.structure.add_oxidation_state_by_site,
[1])
def test_remove_oxidation_states(self):
co_elem = Element("Co")
o_elem = Element("O")
co_specie = Specie("Co", 2)
o_specie = Specie("O", -2)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice.cubic(10)
s_elem = Structure(lattice, [co_elem, o_elem], coords)
s_specie = Structure(lattice, [co_specie, o_specie], coords)
s_specie.remove_oxidation_states()
self.assertEqual(s_elem, s_specie, "Oxidation state remover "
"failed")
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.structure.apply_operation(op)
self.assertArrayAlmostEqual(
self.structure.lattice.matrix,
[[0.000000, 3.840198, 0.000000],
[-3.325710, 1.920099, 0.000000],
[2.217138, -0.000000, 3.135509]], 5)
def test_apply_strain(self):
self.structure.apply_strain(0.01)
self.assertAlmostEqual(
self.structure.lattice.abc,
(3.8785999130369997, 3.878600984287687, 3.8785999130549516))
def test_translate_sites(self):
self.structure.translate_sites([0, 1], [0.5, 0.5, 0.5],
frac_coords=True)
self.assertArrayEqual(self.structure.frac_coords[0],
[0.5, 0.5, 0.5])
self.structure.translate_sites([0], [0.5, 0.5, 0.5],
frac_coords=False)
self.assertArrayAlmostEqual(self.structure.cart_coords[0],
[3.38014845, 1.05428585, 2.06775453])
def test_make_supercell(self):
self.structure.make_supercell([2, 1, 1])
self.assertEqual(self.structure.formula, "Si4")
self.structure.make_supercell([[1, 0, 0], [2, 1, 0], [0, 0, 1]])
self.assertEqual(self.structure.formula, "Si4")
self.structure.make_supercell(2)
self.assertEqual(self.structure.formula, "Si32")
self.assertArrayAlmostEqual(self.structure.lattice.abc,
[15.360792, 35.195996, 7.680396], 5)
def test_to_from_dict(self):
d = self.structure.to_dict
s2 = Structure.from_dict(d)
self.assertEqual(type(s2), Structure)
class StructureTest(PymatgenTest):
def setUp(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"], coords)
def test_non_hash(self):
self.assertRaises(TypeError, dict, [(self.structure, 1)])
def test_append_insert_remove_replace(self):
s = self.structure
s.insert(1, "O", [0.5, 0.5, 0.5])
self.assertEqual(s.formula, "Si2 O1")
self.assertTrue(s.ntypesp == 2)
self.assertTrue(s.symbol_set == ("Si", "O"))
self.assertTrue(s.indices_from_symbol("Si") == (0, 2))
self.assertTrue(s.indices_from_symbol("O") == (1, ))
s.remove(2)
self.assertEqual(s.formula, "Si1 O1")
self.assertTrue(s.indices_from_symbol("Si") == (0, ))
self.assertTrue(s.indices_from_symbol("O") == (1, ))
s.append("N", [0.25, 0.25, 0.25])
self.assertEqual(s.formula, "Si1 N1 O1")
self.assertTrue(s.ntypesp == 3)
self.assertTrue(s.symbol_set == ("Si", "O", "N"))
self.assertTrue(s.indices_from_symbol("Si") == (0, ))
self.assertTrue(s.indices_from_symbol("O") == (1, ))
self.assertTrue(s.indices_from_symbol("N") == (2, ))
s.replace(0, "Ge")
self.assertEqual(s.formula, "Ge1 N1 O1")
self.assertTrue(s.symbol_set == ("Ge", "O", "N"))
s.replace_species({"Ge": "Si"})
self.assertEqual(s.formula, "Si1 N1 O1")
self.assertTrue(s.ntypesp == 3)
s.replace_species({"Si": {"Ge": 0.5, "Si": 0.5}})
self.assertEqual(s.formula, "Si0.5 Ge0.5 N1 O1")
#this should change the .5Si .5Ge sites to .75Si .25Ge
s.replace_species({"Ge": {"Ge": 0.5, "Si": 0.5}})
self.assertEqual(s.formula, "Si0.75 Ge0.25 N1 O1")
# In this case, s.ntypesp is ambiguous.
# for the time being, we raise AttributeError.
with self.assertRaises(AttributeError):
s.ntypesp
s.remove_species(["Si"])
self.assertEqual(s.formula, "Ge0.25 N1 O1")
s.remove_sites([1, 2])
self.assertEqual(s.formula, "Ge0.25")
def test_add_site_property(self):
s = self.structure
s.add_site_property("charge", [4.1, -5])
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[1].charge, -5)
s.add_site_property("magmom", [3, 2])
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[0].magmom, 3)
def test_perturb(self):
d = 0.1
pre_perturbation_sites = self.structure.sites[:]
self.structure.perturb(distance=d)
post_perturbation_sites = self.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_oxidation_states(self):
oxidation_states = {"Si": -4}
self.structure.add_oxidation_state_by_element(oxidation_states)
for site in self.structure:
for k in site.species_and_occu.keys():
self.assertEqual(k.oxi_state, oxidation_states[k.symbol],
"Wrong oxidation state assigned!")
oxidation_states = {"Fe": 2}
self.assertRaises(ValueError,
self.structure.add_oxidation_state_by_element,
oxidation_states)
self.structure.add_oxidation_state_by_site([2, -4])
self.assertEqual(self.structure[0].specie.oxi_state, 2)
self.assertRaises(ValueError,
self.structure.add_oxidation_state_by_site, [1])
def test_remove_oxidation_states(self):
co_elem = Element("Co")
o_elem = Element("O")
co_specie = Specie("Co", 2)
o_specie = Specie("O", -2)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice.cubic(10)
s_elem = Structure(lattice, [co_elem, o_elem], coords)
s_specie = Structure(lattice, [co_specie, o_specie], coords)
s_specie.remove_oxidation_states()
self.assertEqual(s_elem, s_specie, "Oxidation state remover " "failed")
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.structure.apply_operation(op)
self.assertArrayAlmostEqual(
self.structure.lattice.matrix,
[[0.000000, 3.840198, 0.000000], [-3.325710, 1.920099, 0.000000],
[2.217138, -0.000000, 3.135509]], 5)
def test_apply_strain(self):
initial_coord = self.structure[1].coords
self.structure.apply_strain(0.01)
self.assertAlmostEqual(
self.structure.lattice.abc,
(3.8785999130369997, 3.878600984287687, 3.8785999130549516))
self.assertArrayAlmostEqual(self.structure[1].coords,
initial_coord * 1.01)
def test_scale_lattice(self):
initial_coord = self.structure[1].coords
self.structure.scale_lattice(self.structure.volume * 1.01**3)
self.assertArrayAlmostEqual(
self.structure.lattice.abc,
(3.8785999130369997, 3.878600984287687, 3.8785999130549516))
self.assertArrayAlmostEqual(self.structure[1].coords,
initial_coord * 1.01)
def test_translate_sites(self):
self.structure.translate_sites([0, 1], [0.5, 0.5, 0.5],
frac_coords=True)
self.assertArrayEqual(self.structure.frac_coords[0], [0.5, 0.5, 0.5])
self.structure.translate_sites([0], [0.5, 0.5, 0.5], frac_coords=False)
self.assertArrayAlmostEqual(self.structure.cart_coords[0],
[3.38014845, 1.05428585, 2.06775453])
self.structure.translate_sites([0], [0.5, 0.5, 0.5],
frac_coords=True,
to_unit_cell=False)
self.assertArrayAlmostEqual(self.structure.frac_coords[0],
[1.00187517, 1.25665291, 1.15946374])
def test_make_supercell(self):
self.structure.make_supercell([2, 1, 1])
self.assertEqual(self.structure.formula, "Si4")
self.structure.make_supercell([[1, 0, 0], [2, 1, 0], [0, 0, 1]])
self.assertEqual(self.structure.formula, "Si4")
self.structure.make_supercell(2)
self.assertEqual(self.structure.formula, "Si32")
self.assertArrayAlmostEqual(self.structure.lattice.abc,
[15.360792, 35.195996, 7.680396], 5)
def test_disordered_supercell_primitive_cell(self):
l = Lattice.cubic(2)
f = [[0.5, 0.5, 0.5]]
sp = [{'Si': 0.54738}]
s = Structure(l, sp, f)
#this supercell often breaks things
s.make_supercell([[0, -1, 1], [-1, 1, 0], [1, 1, 1]])
self.assertEqual(len(s.get_primitive_structure()), 1)
def test_another_supercell(self):
#this is included b/c for some reason the old algo was failing on it
s = self.structure.copy()
s.make_supercell([[0, 2, 2], [2, 0, 2], [2, 2, 0]])
self.assertEqual(s.formula, "Si32")
s = self.structure.copy()
s.make_supercell([[0, 2, 0], [1, 0, 0], [0, 0, 1]])
self.assertEqual(s.formula, "Si4")
def test_to_from_dict(self):
d = self.structure.to_dict
s2 = Structure.from_dict(d)
self.assertEqual(type(s2), Structure)
