def test_equality(self):
""" Test that AtomicStructure is equal to itself but not others """
self.assertEqual(self.structure, self.structure)
self.assertEqual(self.structure, deepcopy(self.structure))
self.assertNotEqual(self.structure, self.substructure)
# Special case: make structures from Crystals
c1 = Crystal.from_database("vo2-m1")
c2 = deepcopy(c1)
s1 = AtomicStructure(atoms=c1)
s2 = AtomicStructure(atoms=c2.atoms)
self.assertEqual(s1, s2)
def test_equality(structure):
""" Test that AtomicStructure is equal to itself but not others """
substructure = next(iter(structure.substructures))
assert structure == structure
assert structure == deepcopy(structure)
assert structure != substructure
# Special case: make structures from Crystals
c1 = Crystal.from_database("vo2-m1")
c2 = deepcopy(c1)
s1 = AtomicStructure(atoms=c1)
s2 = AtomicStructure(atoms=c2.atoms)
assert s1 == s2
def test_addition(structure):
""" Test the addition of two different AtomicStructures works as expected. """
new_struct = AtomicStructure(
atoms=[Atom("U", [0, 1, 0])],
substructures=[
AtomicStructure(atoms=[Atom("Ag", [0.5, 0, 0]), Atom("Ag", [1, 0.3, 1])])
],
)
addition = structure + new_struct
assert len(new_struct) + len(structure) == len(addition)
assert len(new_struct.atoms) + len(structure.atoms) == len(addition.atoms)
assert len(new_struct.substructures) + len(structure.substructures) == len(
addition.substructures
)
def test_chemical_composition_add_to_unity(self):
""" Test that AtomicStructure.chemical_composition always adds up to 1 """
# Faster to create a large atomic structure from a Crystal object
# Testing for 10 crystal structures only
for name in islice(Crystal.builtins, 10):
with self.subTest("Chemical composition: " + name):
structure = AtomicStructure(atoms=Crystal.from_database(name))
self.assertAlmostEqual(sum(structure.chemical_composition.values()), 1)
def test_substructure_preservation(self):
""" Test that initializing a crystal with substructures preserves the substructures """
atoms = [Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])]
substructures = [AtomicStructure(atoms=[Atom("U", [0, 0, 0])])]
c = Crystal(unitcell=atoms + substructures, lattice_vectors=np.eye(3))
self.assertEqual(len(c), 3)
self.assertIn(substructures[0], c.substructures)
def test_substructure_preservation():
"""Test that initializing a crystal with substructures preserves the substructures"""
atoms = [Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])]
substructures = [AtomicStructure(atoms=[Atom("U", [0, 0, 0])])]
c = Crystal(unitcell=atoms + substructures, lattice_vectors=np.eye(3))
assert len(c) == 3
assert substructures[0] in c.substructures
def test_chemical_formula_hill_notation(structure):
""" Test that the Hill notation, where elements are alphabetically ordered except C and H, which are first. """
structure = AtomicStructure(
atoms=[
Atom("Ag", [0, 1, 0]),
Atom("C", [0, 0, 0]),
Atom("H", [0, 1, 0]),
Atom("U", [1, 1, 1]),
]
)
assert structure.chemical_formula == "C H Ag U"
def test_addition(self):
""" Test the addition of two different AtomicStructures works as expected. """
new_struct = AtomicStructure(
atoms=[Atom("U", [0, 1, 0])],
substructures=[
AtomicStructure(
atoms=[Atom("Ag", [0.5, 0, 0]), Atom("Ag", [1, 0.3, 1])]
)
],
)
addition = self.structure + new_struct
self.assertEqual(len(new_struct) + len(self.structure), len(addition))
self.assertEqual(
len(new_struct.atoms) + len(self.structure.atoms), len(addition.atoms)
)
self.assertEqual(
len(new_struct.substructures) + len(self.structure.substructures),
len(addition.substructures),
)
def test_truthiness(structure):
""" Test that empty AtomicStructures are falsey, and truthy otherwise. """
empty_structure = AtomicStructure()
assert not empty_structure
assert structure
def test_addition_trivial(structure):
""" Test that the addition of two AtomicStructures, one being empty, works as expected """
addition = structure + AtomicStructure()
assert addition == structure
assert addition is not structure
def structure():
substructure = AtomicStructure(atoms=[Atom("U", [0, 0, 0])])
return AtomicStructure(
atoms=[Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])],
substructures=[substructure],
)
def test_chemical_composition_add_to_unity(name):
""" Test that AtomicStructure.chemical_composition always adds up to 1 """
# Faster to create a large atomic structure from a Crystal object
# Testing for 10 crystal structures only
structure = AtomicStructure(atoms=Crystal.from_database(name))
assert round(abs(sum(structure.chemical_composition.values()) - 1), 7) == 0
def test_truthiness(self):
""" Test that empty AtomicStructures are falsey, and truthy otherwise. """
empty_structure = AtomicStructure()
self.assertFalse(empty_structure)
self.assertTrue(self.structure)
def test_addition_trivial(self):
""" Test that the addition of two AtomicStructures, one being empty, works as expected """
addition = self.structure + AtomicStructure()
self.assertEqual(addition, self.structure)
self.assertIsNot(addition, self.structure)
def setUp(self):
self.substructure = AtomicStructure(atoms=[Atom("U", [0, 0, 0])])
self.structure = AtomicStructure(
atoms=[Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])],
substructures=[self.substructure],
)
class TestAtomicStructure(unittest.TestCase):
def setUp(self):
self.substructure = AtomicStructure(atoms=[Atom("U", [0, 0, 0])])
self.structure = AtomicStructure(
atoms=[Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])],
substructures=[self.substructure],
)
def test_iteration(self):
""" Test iteration of AtomicStructure yields from orphan atoms and substructure atoms alike """
elements = [atm.element for atm in self.structure]
self.assertTrue(len(elements), 3)
def test_addition_trivial(self):
""" Test that the addition of two AtomicStructures, one being empty, works as expected """
addition = self.structure + AtomicStructure()
self.assertEqual(addition, self.structure)
self.assertIsNot(addition, self.structure)
def test_addition_uniqueness(self):
""" Test that the addition of two AtomicStructures, works as expected regarding unique atoms """
self.assertEqual(self.structure + self.structure, self.structure)
def test_addition(self):
""" Test the addition of two different AtomicStructures works as expected. """
new_struct = AtomicStructure(
atoms=[Atom("U", [0, 1, 0])],
substructures=[
AtomicStructure(
atoms=[Atom("Ag", [0.5, 0, 0]), Atom("Ag", [1, 0.3, 1])]
)
],
)
addition = self.structure + new_struct
self.assertEqual(len(new_struct) + len(self.structure), len(addition))
self.assertEqual(
len(new_struct.atoms) + len(self.structure.atoms), len(addition.atoms)
)
self.assertEqual(
len(new_struct.substructures) + len(self.structure.substructures),
len(addition.substructures),
)
def test_addition_subclasses(self):
""" Test that the addition of two subclass of AtomicStructures is preserved under addition. """
class NewAtomicStructure(AtomicStructure):
pass
addition = NewAtomicStructure() + NewAtomicStructure()
self.assertIs(type(addition), NewAtomicStructure)
def test_truthiness(self):
""" Test that empty AtomicStructures are falsey, and truthy otherwise. """
empty_structure = AtomicStructure()
self.assertFalse(empty_structure)
self.assertTrue(self.structure)
def test_trivial_transformation(self):
""" Test that the identity transformation of an AtomicStructure works as expected. """
transformed = self.structure.transform(np.eye(3))
# transformed structure should be different, but equal, to original structure
self.assertIsNot(transformed, self.structure)
self.assertEqual(transformed, self.structure)
def test_transformations_inversions(self):
""" Test that symmetry operations work as expected when inverted. """
operator = np.random.random(size=(3, 3))
inv_op = np.linalg.inv(operator)
transformed1 = self.structure.transform(operator)
transformed2 = transformed1.transform(inv_op)
# transformed2 structure should be different, but equal, to original structure
self.assertIsNot(transformed2, self.structure)
self.assertEqual(transformed2, self.structure)
def test_transform_subclass(self):
""" Test that the object returned by the transform() method is the
same class as the method caller. """
class NewAtomicStructure(AtomicStructure):
pass
structure = NewAtomicStructure(
atoms=[Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])]
)
transformed = structure.transform(np.eye(3))
self.assertIs(type(transformed), type(structure))
def test_transformations_correctness(self):
""" Test that AtomicStructure.transform() works as expected. """
operator = 2 * np.eye(3)
transformed = self.structure.transform(operator)
expected_atoms = [atm.transform(operator) for atm in self.structure]
for atm in expected_atoms:
self.assertIn(atm, transformed)
def test_itersorted(self):
""" Test that AtomicStructure.itersorted() works as expected """
sorted_from_structure = list(self.structure.itersorted())
sorted_from_list = list(sorted(self.structure, key=lambda a: a.element))
self.assertListEqual(sorted_from_structure, sorted_from_list)
def test_chemical_composition_trivial(self):
""" Test that AtomicStructure.chemical_composition works as expected """
expected = {"U": 1 / 3, "Ag": 2 / 3}
self.assertDictEqual(self.structure.chemical_composition, expected)
def test_chemical_composition_add_to_unity(self):
""" Test that AtomicStructure.chemical_composition always adds up to 1 """
# Faster to create a large atomic structure from a Crystal object
# Testing for 10 crystal structures only
for name in islice(Crystal.builtins, 10):
with self.subTest("Chemical composition: " + name):
structure = AtomicStructure(atoms=Crystal.from_database(name))
self.assertAlmostEqual(sum(structure.chemical_composition.values()), 1)
def test_chemical_formula(self):
""" Test that AtomicStructure.chemical_formula is working as expected. """
self.assertEqual(self.structure.chemical_formula, "Ag2 U")
def test_chemical_formula_hill_notation(self):
""" Test that the Hill notation, where elements are alphabetically ordered except C and H, which are first. """
structure = AtomicStructure(
atoms=[
Atom("Ag", [0, 1, 0]),
Atom("C", [0, 0, 0]),
Atom("H", [0, 1, 0]),
Atom("U", [1, 1, 1]),
]
)
self.assertEqual(structure.chemical_formula, "C H Ag U")
def test_length(self):
""" Test the __len__ methods """
self.assertTrue(len(self.structure), 3)
def test_containership_substructures(self):
""" Test that containership works on substructure and atoms separately """
self.assertIn(self.substructure, self.structure)
self.assertNotIn(self.structure, self.substructure)
def test_containership_atoms(self):
""" Test that atom containership testing is working, even in substructures """
atm = next(iter(self.substructure))
self.assertIn(atm, self.structure)
def test_equality(self):
""" Test that AtomicStructure is equal to itself but not others """
self.assertEqual(self.structure, self.structure)
self.assertEqual(self.structure, deepcopy(self.structure))
self.assertNotEqual(self.structure, self.substructure)
def test_array(self):
""" Test AtomicStructure.__array__ """
arr = np.array(self.structure)
self.assertSequenceEqual(arr.shape, (len(self.structure), 4))
def test_picklable(self):
""" Test that Crystal instances can be pickled, and that the unpickled instance
is identical to the source """
pickled = pickle.dumps(self.structure)
unpickled = pickle.loads(pickled)
self.assertEqual(self.structure, unpickled)
def test_abstract_base_classes(self):
""" Test that AtomicStructure fits with collections.abc module """
for abstract_base_class in (abc.Hashable, abc.Iterable, abc.Sized):
self.assertIsInstance(self.structure, abstract_base_class)
def test_satisfying(self):
""" Test the AtomicStructure.satisfying method """
uranium = self.structure.satisfying(lambda a: a.element == "U")
silver = self.structure.satisfying(lambda a: a.element == "Ag")
self.assertEqual(len(uranium), 1)
self.assertEqual(len(silver), 2)