def test_as_from_dict(self):
trans = DopingTransformation("Al3+", min_length=5, alio_tol=1, codopant=False, max_structures_per_enum=1)
d = trans.as_dict()
# Check json encodability
s = json.dumps(d)
trans = DopingTransformation.from_dict(d)
self.assertEqual(str(trans.dopant), "Al3+")
self.assertEqual(trans.max_structures_per_enum, 1)
def test_as_from_dict(self):
trans = DopingTransformation("Al3+", min_length=5, alio_tol=1, codopant=False, max_structures_per_enum=1)
d = trans.as_dict()
# Check json encodability
s = json.dumps(d)
trans = DopingTransformation.from_dict(d)
self.assertEqual(str(trans.dopant), "Al3+")
self.assertEqual(trans.max_structures_per_enum, 1)
def test_apply_transformation(self):
structure = PymatgenTest.get_structure("LiFePO4")
t = DopingTransformation("Ca2+", min_length=10)
ss = t.apply_transformation(structure, 100)
self.assertEqual(len(ss), 1)
t = DopingTransformation("Al3+", min_length=15, ionic_radius_tol=0.1)
ss = t.apply_transformation(structure, 100)
self.assertEqual(len(ss), 0)
# Aliovalent doping with vacancies
for dopant, nstructures in [("Al3+", 4), ("N3-", 420), ("Cl-", 16)]:
t = DopingTransformation(dopant, min_length=4, alio_tol=1,
max_structures_per_enum=1000)
ss = t.apply_transformation(structure, 1000)
self.assertEqual(len(ss), nstructures)
for d in ss:
self.assertEqual(d["structure"].charge, 0)
# Aliovalent doping with codopant
for dopant, nstructures in [("Al3+", 3), ("N3-", 60), ("Cl-", 60)]:
t = DopingTransformation(dopant, min_length=4, alio_tol=1,
codopant=True,
max_structures_per_enum=1000)
ss = t.apply_transformation(structure, 1000)
self.assertEqual(len(ss), nstructures)
if __name__ == '__main__':
for d in ss:
self.assertEqual(d["structure"].charge, 0)
# Make sure compensation is done with lowest oxi state
structure = PymatgenTest.get_structure("SrTiO3")
t = DopingTransformation("Nb5+", min_length=5, alio_tol=1,
max_structures_per_enum=1000,
allowed_doping_species=["Ti4+"])
ss = t.apply_transformation(structure, 1000)
self.assertEqual(len(ss), 3)
for d in ss:
self.assertEqual(d["structure"].formula, "Sr7 Ti6 Nb2 O24")
def test_apply_transformation(self):
structure = PymatgenTest.get_structure("LiFePO4")
a = SpacegroupAnalyzer(structure, 0.1)
structure = a.get_refined_structure()
t = DopingTransformation("Ca2+", min_length=10)
ss = t.apply_transformation(structure, 100)
self.assertEqual(len(ss), 1)
t = DopingTransformation("Al3+", min_length=15, ionic_radius_tol=0.1)
ss = t.apply_transformation(structure, 100)
self.assertEqual(len(ss), 0)
# Aliovalent doping with vacancies
for dopant, nstructures in [("Al3+", 2), ("N3-", 235), ("Cl-", 8)]:
t = DopingTransformation(dopant, min_length=4, alio_tol=1,
max_structures_per_enum=1000)
ss = t.apply_transformation(structure, 1000)
self.assertEqual(len(ss), nstructures)
for d in ss:
self.assertEqual(d["structure"].charge, 0)
# Aliovalent doping with codopant
for dopant, nstructures in [("Al3+", 3), ("N3-", 37), ("Cl-", 37)]:
t = DopingTransformation(dopant, min_length=4, alio_tol=1,
codopant=True,
max_structures_per_enum=1000)
ss = t.apply_transformation(structure, 1000)
self.assertEqual(len(ss), nstructures)
for d in ss:
self.assertEqual(d["structure"].charge, 0)
# Make sure compensation is done with lowest oxi state
structure = PymatgenTest.get_structure("SrTiO3")
t = DopingTransformation("Nb5+", min_length=5, alio_tol=1,
max_structures_per_enum=1000,
allowed_doping_species=["Ti4+"])
ss = t.apply_transformation(structure, 1000)
self.assertEqual(len(ss), 3)
for d in ss:
self.assertEqual(d["structure"].formula, "Sr7 Ti6 Nb2 O24")
