def test_apply_transformation(self):
enum_trans = EnumerateStructureTransformation(refine_structure=True)
enum_trans2 = EnumerateStructureTransformation(refine_structure=True,
sort_criteria="nsites")
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
struct = p.structure
expected_ans = [1, 3, 1]
for i, frac in enumerate([0.25, 0.5, 0.75]):
trans = SubstitutionTransformation({'Fe': {'Fe': frac}})
s = trans.apply_transformation(struct)
oxitrans = OxidationStateDecorationTransformation(
{'Li': 1, 'Fe': 2, 'P': 5, 'O': -2})
s = oxitrans.apply_transformation(s)
alls = enum_trans.apply_transformation(s, 100)
self.assertEqual(len(alls), expected_ans[i])
self.assertIsInstance(trans.apply_transformation(s), Structure)
for ss in alls:
self.assertIn("energy", ss)
alls = enum_trans2.apply_transformation(s, 100)
self.assertEqual(len(alls), expected_ans[i])
self.assertIsInstance(trans.apply_transformation(s), Structure)
for ss in alls:
self.assertIn("num_sites", ss)
# make sure it works for non-oxidation state decorated structure
trans = SubstitutionTransformation({'Fe': {'Fe': 0.5}})
s = trans.apply_transformation(struct)
alls = enum_trans.apply_transformation(s, 100)
self.assertEqual(len(alls), 3)
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertNotIn("energy", s)
def test_apply_transformation(self):
enum_trans = EnumerateStructureTransformation(refine_structure=True)
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
struct = p.structure
expected_ans = [1, 3, 1]
for i, frac in enumerate([0.25, 0.5, 0.75]):
trans = SubstitutionTransformation({'Fe': {'Fe': frac}})
s = trans.apply_transformation(struct)
oxitrans = OxidationStateDecorationTransformation({'Li': 1,
'Fe': 2,
'P': 5,
'O': -2})
s = oxitrans.apply_transformation(s)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), expected_ans[i])
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertIn("energy", s)
#make sure it works for non-oxidation state decorated structure
trans = SubstitutionTransformation({'Fe': {'Fe': 0.5}})
s = trans.apply_transformation(struct)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), 3)
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertNotIn("energy", s)
def test_apply_transformations_best_first(self):
p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR,
"POSCAR.LiFePO4"),
check_for_POTCAR=False)
t1 = OxidationStateDecorationTransformation({
"Li": 1,
"Fe": 2,
"P": 5,
"O": -2
})
s = t1.apply_transformation(p.structure)
t = PartialRemoveSpecieTransformation(
"Li+", 0.5, PartialRemoveSpecieTransformation.ALGO_BEST_FIRST)
self.assertEqual(len(t.apply_transformation(s)), 26)
def test_apply_transformation(self):
t = OxidationStateDecorationTransformation({"Li": 1, "O": -2})
coords = []
coords.append([0, 0, 0])
coords.append([0.75, 0.75, 0.75])
coords.append([0.5, 0.5, 0.5])
coords.append([0.25, 0.25, 0.25])
lattice = Lattice([
[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603],
])
struct = Structure(lattice, ["Li", "Li", "O", "O"], coords)
s = t.apply_transformation(struct)
self.assertEqual(s[0].species_string, "Li+")
self.assertEqual(s[2].species_string, "O2-")
d = t.as_dict()
self.assertEqual(
type(OxidationStateDecorationTransformation.from_dict(d)),
OxidationStateDecorationTransformation,
)