def test_distance(self):
index = 456
site = Mock(spec=Site)
label = 'foo'
other_atom = Atom(index=index, site=site, label=label)
self.atom.site.distance = Mock(return_value=2.3)
self.assertEqual(self.atom.distance(other_atom), 2.3)
def __init__(self,
structure: Structure,
recipes: List[PolyhedraRecipe]) -> None:
"""
A Configuration object describes a single atomic geometry.
Args:
structure (pymatgen.Structure): A pymatgen Structure object for this configuration.
recipes (list(PolyhedraRecipe): A list of PolyhedraRecipe objects used to construct
polyhedra for this configuration.
Attributes:
atoms (list(Atom)): A list of atoms that make up this configuration.
polyhedra (list(CoordinationPolyhedron)): A list of polyhedra, generated using
the PolyhedraRecipe definitions passed in as the `recipes` list.
central_atoms (list(Atom)): A list of atoms that define the centres of the
coordination polyhedra.
coordination_atoms (list(Atom)): A list of atoms that define the vertices of
the coordination polyhedra.
"""
self.atoms = [Atom(index=i,
site=site,
label=site.species_string)
for i, site in enumerate(structure.sites)]
self.polyhedra: List[CoordinationPolyhedron] = []
for recipe in recipes:
self.polyhedra.extend(recipe.find_polyhedra(self.atoms, structure))
self.central_atoms = sorted(list(set(
[p.central_atom for p in self.polyhedra])),
key=lambda x: x.index)
self.coordination_atoms = sorted(list(set(flatten(
[p.vertices for p in self.polyhedra]))),
key=lambda x: x.index)
def test___eq___when_false(self):
index = 456
site = Mock(spec=Site)
label = 'foo'
site.frac_coords = np.array([1.0, 2.0, 3.0])
site.coords = np.array([10.0, 11.0, 12.0])
site.lattice = Mock(spec=Lattice)
other_atom = Atom(index=index, site=site, label=label)
self.assertNotEqual(self.atom, other_atom)
def test___lt__(self):
index = 456
site = MagicMock(spec=Site)
label = 'bar'
self.frac_coords = np.array([2.0, 3.0, 4.0])
site.coords = np.array([20.0, 21.0, 22.0])
site.lattice = Mock(spec=Lattice)
other_atom = Atom(index=index, site=site, label=label)
self.assertTrue(self.atom < other_atom)
def setUp(self):
index = 123
site = Mock(spec=Site)
label = 'foo'
site.frac_coords = np.array([1.0, 2.0, 3.0])
site.coords = np.array([10.0, 11.0, 12.0])
site.lattice = Mock(spec=Lattice)
self.site = site
self.atom = Atom(index=index, site=site, label=label)
def test_atom_is_initialised_without_label( self ):
index = 123
site = Mock( spec=Site )
atom = Atom( index=index, site=site )
self.assertEqual( atom.index, index )
self.assertEqual( atom.site, site )
self.assertEqual( atom.label, None )
self.assertEqual( atom.in_polyhedra, [] )
self.assertEqual( atom.neighbours, None )
def test_atom_is_initialised_without_label(self):
index = 123
site = Mock(spec=Site)
site.species_string = 'bar'
atom = Atom(index=index, site=site)
self.assertEqual(atom.index, index)
self.assertEqual(atom.site, site)
self.assertEqual(atom.label, 'bar')
self.assertEqual(atom.in_polyhedra, [])
self.assertEqual(atom.neighbours, {})
def test_atom_is_initialised(self):
index = 123
site = Mock(spec=Site)
label = 'foo'
atom = Atom(index=index, site=site, label=label)
self.assertEqual(atom.index, index)
self.assertEqual(atom.site, site)
self.assertEqual(atom.label, label)
self.assertEqual(atom.in_polyhedra, [])
self.assertEqual(atom.neighbours, {})