def apply_transformation(self, structure):
editor = StructureEditor(structure)
for i, sp in enumerate(self._species):
editor.insert_site(i, sp, self._coords[i],
coords_are_cartesian=self._cartesian,
validate_proximity=self._validate_proximity)
return editor.modified_structure.get_sorted_structure()
def test_init(self):
fitter = StructureFitter(self.b, self.a)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
#Now to try with rotated structure
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False, np.array([0, 0, 1]))
editor = StructureEditor(self.a)
editor.apply_operation(op)
fitter = StructureFitter(self.b, editor.modified_structure)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
#test with a supercell
mod = SupercellMaker(self.a, scaling_matrix=[[2, 0, 0], [0, 1, 0], [0, 0, 1]])
a_super = mod.modified_structure
fitter = StructureFitter(self.b, a_super)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
# Test with a structure with a translated point
editor = StructureEditor(self.a)
site = self.a[0]
editor.delete_site(0)
trans = np.random.randint(0, 1000, 3)
editor.insert_site(0, site.species_and_occu, site.frac_coords + trans, False, False)
fitter = StructureFitter(self.b, editor.modified_structure)
self.assertTrue(fitter.mapping_op != None, "No fit found for translation {}!".format(trans))
parser = CifParser(os.path.join(test_dir, "FePO4a.cif"))
a = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, "FePO4b.cif"))
b = parser.get_structures()[0]
fitter = StructureFitter(b, a)
self.assertTrue(fitter.mapping_op != None, "No fit found!")
class StructureEditorTest(unittest.TestCase):
def setUp(self):
self.si = Element("Si")
self.fe = Element("Fe")
self.ge = Element("Ge")
coords = list()
coords.append(np.array([0, 0, 0]))
coords.append(np.array([0.75, 0.5, 0.75]))
lattice = Lattice.cubic(10)
s = Structure(lattice, [self.si, self.fe], coords)
self.modifier = StructureEditor(s)
def test_translate_sites(self):
self.modifier.translate_sites([0, 1], [0.5, 0.5, 0.5], frac_coords=True)
self.assertTrue(np.array_equal(self.modifier.modified_structure.frac_coords[0], np.array([ 0.5, 0.5, 0.5])))
self.modifier.translate_sites([0], [0.5, 0.5, 0.5], frac_coords=False)
self.assertTrue(np.array_equal(self.modifier.modified_structure.cart_coords[0], np.array([ 5.5, 5.5, 5.5])))
def test_append_site(self):
self.modifier.append_site(self.si, [0, 0.5, 0])
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2", "Wrong formula!")
self.assertRaises(ValueError, self.modifier.append_site, self.si, np.array([0, 0.5, 0]))
def test_modified_structure(self):
self.modifier.insert_site(1, self.si, [0, 0.25, 0])
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2", "Wrong formula!")
self.modifier.delete_site(0)
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1", "Wrong formula!")
self.modifier.replace_site(0, self.ge)
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge1", "Wrong formula!")
self.modifier.append_site(self.si, [0, 0.75, 0])
self.modifier.replace_species({self.si: self.ge})
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge2", "Wrong formula!")
self.modifier.replace_species({self.ge: {self.ge:0.5, self.si:0.5}})
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1 Ge1", "Wrong formula!")
#this should change the .5Si .5Ge sites to .75Si .25Ge
self.modifier.replace_species({self.ge: {self.ge:0.5, self.si:0.5}})
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1.5 Ge0.5", "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, 5])
s = self.modifier.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[1].charge, 5)
#test adding multiple properties.
mod2 = StructureEditor(s)
mod2.add_site_property("magmom", [3, 2])
s = mod2.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[0].magmom, 3)
class StructureEditorTest(unittest.TestCase):
def setUp(self):
self.si = Element("Si")
self.fe = Element("Fe")
self.ge = Element("Ge")
coords = list()
coords.append(np.array([0, 0, 0]))
coords.append(np.array([0.75, 0.5, 0.75]))
lattice = Lattice.cubic(10)
s = Structure(lattice, ["Si", "Fe"], coords)
self.modifier = StructureEditor(s)
def test_to_unit_cell(self):
self.modifier.append_site(self.fe, [1.75, 0.5, 0.75],
validate_proximity=False)
self.modifier.to_unit_cell()
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1",
"Wrong formula!")
def test_to_unit_cell(self):
self.modifier.apply_strain(0.01)
self.assertEqual(self.modifier.modified_structure.lattice.abc,
(10.1, 10.1, 10.1))
def test_translate_sites(self):
self.modifier.translate_sites([0, 1], [0.5, 0.5, 0.5],
frac_coords=True)
self.assertTrue(np.array_equal(self.modifier.modified_structure
.frac_coords[0],
np.array([0.5, 0.5, 0.5])))
self.modifier.translate_sites([0], [0.5, 0.5, 0.5], frac_coords=False)
self.assertTrue(np.array_equal(self.modifier.modified_structure
.cart_coords[0],
np.array([5.5, 5.5, 5.5])))
def test_append_site(self):
self.modifier.append_site(self.si, [0, 0.5, 0])
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2",
"Wrong formula!")
self.assertRaises(ValueError, self.modifier.append_site, self.si,
np.array([0, 0.5, 0]))
def test_modified_structure(self):
self.modifier.insert_site(1, self.si, [0, 0.25, 0])
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2",
"Wrong formula!")
self.modifier.delete_site(0)
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1",
"Wrong formula!")
self.modifier.replace_site(0, self.ge)
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge1",
"Wrong formula!")
self.modifier.append_site(self.si, [0, 0.75, 0])
self.modifier.replace_species({self.si: self.ge})
self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge2",
"Wrong formula!")
self.modifier.replace_species({self.ge: {self.ge: 0.5, self.si: 0.5}})
self.assertEqual(self.modifier.modified_structure.formula,
"Fe1 Si1 Ge1", "Wrong formula!")
#this should change the .5Si .5Ge sites to .75Si .25Ge
self.modifier.replace_species({self.ge: {self.ge: 0.5, self.si: 0.5}})
self.assertEqual(self.modifier.modified_structure.formula,
"Fe1 Si1.5 Ge0.5", "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, 5])
s = self.modifier.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[1].charge, 5)
#test adding multiple properties.
mod2 = StructureEditor(s)
mod2.add_site_property("magmom", [3, 2])
s = mod2.modified_structure
self.assertEqual(s[0].charge, 4.1)
self.assertEqual(s[0].magmom, 3)
def test_add_oxidation_states(self):
si = Element("Si")
fe = Element("Fe")
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice.cubic(10)
s = Structure(lattice, [si, fe], coords)
oxidation_states = {"Fe": 2, "Si": -4}
mod = StructureEditor(s)
mod.add_oxidation_state_by_element(oxidation_states)
mod_s = mod.modified_structure
for site in mod_s:
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, mod.add_oxidation_state_by_element,
oxidation_states)
mod.add_oxidation_state_by_site([2, -4])
mod_s = mod.modified_structure
self.assertEqual(mod_s[0].specie.oxi_state, 2)
self.assertRaises(ValueError, mod.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)
mod = StructureEditor(s_specie)
mod.remove_oxidation_states()
mod_s = mod.modified_structure
self.assertEqual(s_elem, mod_s, "Oxidation state remover failed")
