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_undo_and_redo_last_change(self):
trans = [
SubstitutionTransformation({"Li": "Na"}),
SubstitutionTransformation({"Fe": "Mn"})
]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
#Make sure that this works with filters.
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_to_from_dict(self):
species1 = ["Si5+", "Mg2+"]
f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
d = f1.as_dict()
self.assertIsInstance(ContainsSpecieFilter.from_dict(d),
ContainsSpecieFilter)
def test_filtering(self):
coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.25]]
lattice = Lattice([[3.0, 0.0, 0.0], [1.0, 3.0, 0.00],
[0.00, -2.0, 3.0]])
s = Structure(
lattice,
[
{
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
},
{
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
},
{
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
},
{
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
},
],
coords,
)
species1 = [Species("Si", 5), Species("Mg", 2)]
f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
self.assertFalse(f1.test(s), "Incorrect filter")
f2 = ContainsSpecieFilter(species1, strict_compare=False, AND=False)
self.assertTrue(f2.test(s), "Incorrect filter")
species2 = [Species("Si", 4), Species("Mg", 2)]
f3 = ContainsSpecieFilter(species2, strict_compare=True, AND=False)
self.assertTrue(f3.test(s), "Incorrect filter")
f4 = ContainsSpecieFilter(species2, strict_compare=False, AND=False)
self.assertTrue(f4.test(s), "Incorrect filter")
species3 = [Species("Si", 5), Species("O", -2)]
f5 = ContainsSpecieFilter(species3, strict_compare=True, AND=True)
self.assertFalse(f5.test(s), "Incorrect filter")
f6 = ContainsSpecieFilter(species3, strict_compare=False, AND=True)
self.assertTrue(f6.test(s), "Incorrect filter")
species4 = [Species("Si", 4), Species("Mg", 2)]
f7 = ContainsSpecieFilter(species4, strict_compare=True, AND=True)
self.assertFalse(f7.test(s), "Incorrect filter")
f8 = ContainsSpecieFilter(species4, strict_compare=False, AND=True)
self.assertFalse(f8.test(s), "Incorrect filter")
def test_to_from_dict(self):
species1 = ['Si5+', 'Mg2+']
f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
d = f1.as_dict()
self.assertIsInstance(ContainsSpecieFilter.from_dict(d),
ContainsSpecieFilter)
def test_filtering(self):
coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.25]]
lattice = Lattice([[3.0, 0.0, 0.0],
[1.0, 3.0, 0.00],
[0.00, -2.0, 3.0]])
s = Structure(lattice,
[{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25}], coords)
species1 = [Specie('Si', 5), Specie('Mg', 2)]
f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
self.assertFalse(f1.test(s), 'Incorrect filter')
f2 = ContainsSpecieFilter(species1, strict_compare=False, AND=False)
self.assertTrue(f2.test(s), 'Incorrect filter')
species2 = [Specie('Si', 4), Specie('Mg', 2)]
f3 = ContainsSpecieFilter(species2, strict_compare=True, AND=False)
self.assertTrue(f3.test(s), 'Incorrect filter')
f4 = ContainsSpecieFilter(species2, strict_compare=False, AND=False)
self.assertTrue(f4.test(s), 'Incorrect filter')
species3 = [Specie('Si', 5), Specie('O', -2)]
f5 = ContainsSpecieFilter(species3, strict_compare=True, AND=True)
self.assertFalse(f5.test(s), 'Incorrect filter')
f6 = ContainsSpecieFilter(species3, strict_compare=False, AND=True)
self.assertTrue(f6.test(s), 'Incorrect filter')
species4 = [Specie('Si', 4), Specie('Mg', 2)]
f7 = ContainsSpecieFilter(species4, strict_compare=True, AND=True)
self.assertFalse(f7.test(s), 'Incorrect filter')
f8 = ContainsSpecieFilter(species4, strict_compare=False, AND=True)
self.assertFalse(f8.test(s), 'Incorrect filter')
def test_to_from_dict(self):
species1 = ["Si5+", "Mg2+"]
f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
d = f1.to_dict
self.assertIsInstance(ContainsSpecieFilter.from_dict(d), ContainsSpecieFilter)
def test_filtering(self):
coords = list()
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([[3.0, 0.0, 0.0], [1.0, 3.0, 0.00], [0.00, -2.0, 3.0]])
s = Structure(
lattice,
[
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
],
coords,
)
species1 = [Specie("Si", 5), Specie("Mg", 2)]
f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
self.assertFalse(f1.test(s), "Incorrect filter")
f2 = ContainsSpecieFilter(species1, strict_compare=False, AND=False)
self.assertTrue(f2.test(s), "Incorrect filter")
species2 = [Specie("Si", 4), Specie("Mg", 2)]
f3 = ContainsSpecieFilter(species2, strict_compare=True, AND=False)
self.assertTrue(f3.test(s), "Incorrect filter")
f4 = ContainsSpecieFilter(species2, strict_compare=False, AND=False)
self.assertTrue(f4.test(s), "Incorrect filter")
species3 = [Specie("Si", 5), Specie("O", -2)]
f5 = ContainsSpecieFilter(species3, strict_compare=True, AND=True)
self.assertFalse(f5.test(s), "Incorrect filter")
f6 = ContainsSpecieFilter(species3, strict_compare=False, AND=True)
self.assertTrue(f6.test(s), "Incorrect filter")
species4 = [Specie("Si", 4), Specie("Mg", 2)]
f7 = ContainsSpecieFilter(species4, strict_compare=True, AND=True)
self.assertFalse(f7.test(s), "Incorrect filter")
f8 = ContainsSpecieFilter(species4, strict_compare=False, AND=True)
self.assertFalse(f8.test(s), "Incorrect filter")
def test_append_filter(self):
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_to_from_dict(self):
species1 = ['Si5+', 'Mg2+']
f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
d = f1.to_dict
self.assertIsInstance(ContainsSpecieFilter.from_dict(d),
ContainsSpecieFilter)