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_init(self):
trans = []
trans.append(SubstitutionTransformation({"Fe":"Mn"}))
tsc = PoscarTransmuter.from_filenames([os.path.join(test_dir, "POSCAR"), os.path.join(test_dir, "POSCAR")], trans)
self.assertEqual(len(tsc), 2)
expected_ans = set(["Mn", "O", "P"])
for s in tsc:
els = set([el.symbol for el in s.final_structure.composition.elements])
self.assertEqual(expected_ans, els)
def test_init(self):
trans = []
trans.append(SubstitutionTransformation({"Fe": "Mn"}))
tsc = PoscarTransmuter.from_filenames(
[os.path.join(self.TEST_FILES_DIR, "POSCAR"), os.path.join(self.TEST_FILES_DIR, "POSCAR")], trans
)
self.assertEqual(len(tsc), 2)
expected_ans = set(["Mn", "O", "P"])
for s in tsc:
els = set([el.symbol for el in s.final_structure.composition.elements])
self.assertEqual(expected_ans, els)
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_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+":.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+"})])
tsc.append_transformation(t, extend_collection=True)
self.assertEqual(len(tsc), 8)
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
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"])
