def test_apply_transformation(self):
tl = [SubstitutionTransformation({"Li+": "Na+"}),
SubstitutionTransformation({"Li+": "K+"})]
t = SuperTransformation(tl)
coords = list()
coords.append([0, 0, 0])
coords.append([0.375, 0.375, 0.375])
coords.append([.5, .5, .5])
coords.append([0.875, 0.875, 0.875])
coords.append([0.125, 0.125, 0.125])
coords.append([0.25, 0.25, 0.25])
coords.append([0.625, 0.625, 0.625])
coords.append([0.75, 0.75, 0.75])
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+", "Li+", "Li+", "Li+", "Li+",
"O2-", "O2-"], coords)
s = t.apply_transformation(struct, return_ranked_list=True)
for s_and_t in s:
self.assertEqual(s_and_t['transformation']
.apply_transformation(struct),
s_and_t['structure'])
def test_apply_transformation(self):
tl = [SubstitutionTransformation({"Li+": "Na+"}),
SubstitutionTransformation({"Li+": "K+"})]
t = SuperTransformation(tl)
coords = list()
coords.append([0, 0, 0])
coords.append([0.375, 0.375, 0.375])
coords.append([.5, .5, .5])
coords.append([0.875, 0.875, 0.875])
coords.append([0.125, 0.125, 0.125])
coords.append([0.25, 0.25, 0.25])
coords.append([0.625, 0.625, 0.625])
coords.append([0.75, 0.75, 0.75])
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+", "Li+", "Li+", "Li+", "Li+",
"O2-", "O2-"], coords)
s = t.apply_transformation(struct, return_ranked_list=True)
for s_and_t in s:
self.assertEqual(s_and_t['transformation']
.apply_transformation(struct),
s_and_t['structure'])
def test_apply_transformation_mult(self):
# Test returning multiple structures from each transformation.
disord = Structure(np.eye(3) * 4.209, [{"Cs+": 0.5, "K+": 0.5}, "Cl-"], [[0, 0, 0], [0.5, 0.5, 0.5]])
disord.make_supercell([2, 2, 1])
tl = [EnumerateStructureTransformation(), OrderDisorderedStructureTransformation()]
t = SuperTransformation(tl, nstructures_per_trans=10)
self.assertEqual(len(t.apply_transformation(disord, return_ranked_list=20)), 8)
t = SuperTransformation(tl)
self.assertEqual(len(t.apply_transformation(disord, return_ranked_list=20)), 2)
def test_transmuter(self):
tsc = PoscarTransmuter.from_filenames(
[os.path.join(self.TEST_FILES_DIR, "POSCAR")])
tsc.append_transformation(RemoveSpeciesTransformation("O"))
self.assertEqual(len(tsc[0].final_structure), 8)
tsc.append_transformation(
SubstitutionTransformation({
"Fe": {
"Fe2+": 0.25,
"Mn3+": 0.75
},
"P": "P5+"
}))
tsc.append_transformation(OrderDisorderedStructureTransformation(),
extend_collection=50)
self.assertEqual(len(tsc), 4)
t = SuperTransformation([
SubstitutionTransformation({"Fe2+": "Mg2+"}),
SubstitutionTransformation({"Fe2+": "Zn2+"}),
SubstitutionTransformation({"Fe2+": "Be2+"}),
])
tsc.append_transformation(t, extend_collection=True)
self.assertEqual(len(tsc), 12)
for x in tsc:
# should be 4 trans + starting structure
self.assertEqual(
len(x),
5,
"something might be wrong with the number of transformations in the history",
)
# test the filter
tsc.apply_filter(
ContainsSpecieFilter(["Zn2+", "Be2+", "Mn4+"],
strict_compare=True,
AND=False))
self.assertEqual(len(tsc), 8)
self.assertEqual(
tsc.transformed_structures[0].as_dict()["history"][-1]["@class"],
"ContainsSpecieFilter",
)
tsc.apply_filter(ContainsSpecieFilter(["Be2+"]))
self.assertEqual(len(tsc), 4)
# Test set_parameter and add_tag.
tsc.set_parameter("para1", "hello")
self.assertEqual(
tsc.transformed_structures[0].as_dict()["other_parameters"]
["para1"],
"hello",
)
tsc.add_tags(["world", "universe"])
self.assertEqual(
tsc.transformed_structures[0].as_dict()["other_parameters"]
["tags"],
["world", "universe"],
)
def test_transmuter(self):
tsc = PoscarTransmuter.from_filenames(
[os.path.join(test_dir, "POSCAR")])
tsc.append_transformation(RemoveSpeciesTransformation('O'))
self.assertEqual(len(tsc[0].final_structure), 8)
tsc.append_transformation(
SubstitutionTransformation({
"Fe": {
"Fe2+": 0.25,
"Mn3+": .75
},
"P": "P5+"
}))
tsc.append_transformation(OrderDisorderedStructureTransformation(),
extend_collection=50)
self.assertEqual(len(tsc), 4)
t = SuperTransformation([
SubstitutionTransformation({"Fe2+": "Mg2+"}),
SubstitutionTransformation({"Fe2+": "Zn2+"}),
SubstitutionTransformation({"Fe2+": "Be2+"})
])
tsc.append_transformation(t, extend_collection=True)
self.assertEqual(len(tsc), 12)
for x in tsc:
self.assertEqual(
len(x), 5,
'something might be wrong with the number of transformations in the history'
) #should be 4 trans + starting structure
#test the filter
tsc.apply_filter(
ContainsSpecieFilter(['Zn2+', 'Be2+', 'Mn4+'],
strict_compare=True,
AND=False))
self.assertEqual(len(tsc), 8)
self.assertEqual(
tsc.get_transformed_structures()[0].as_dict()['history'][-1]
['@class'], 'ContainsSpecieFilter')
tsc.apply_filter(ContainsSpecieFilter(['Be2+']))
self.assertEqual(len(tsc), 4)
#Test set_parameter and add_tag.
tsc.set_parameter("para1", "hello")
self.assertEqual(
tsc.transformed_structures[0].as_dict()['other_parameters']
['para1'], 'hello')
tsc.add_tags(["world", "universe"])
self.assertEqual(
tsc.transformed_structures[0].as_dict()['other_parameters']
['tags'], ["world", "universe"])
def test_apply_transformation_mult(self):
# Test returning multiple structures from each transformation.
disord = Structure(np.eye(3) * 4.209, [{"Cs+": 0.5, "K+": 0.5}, "Cl-"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
disord.make_supercell([2, 2, 1])
tl = [EnumerateStructureTransformation(),
OrderDisorderedStructureTransformation()]
t = SuperTransformation(tl, nstructures_per_trans=10)
self.assertEqual(len(t.apply_transformation(disord,
return_ranked_list=20)), 8)
t = SuperTransformation(tl)
self.assertEqual(len(t.apply_transformation(disord,
return_ranked_list=20)), 2)
