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_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 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, {})
class TestAtom(unittest.TestCase):
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_frac_coords(self):
np.testing.assert_array_equal(
self.atom.frac_coords, self.site.frac_coords)
def test_coords(self):
np.testing.assert_array_equal(self.atom.coords, self.site.coords)
def test_lattice(self):
self.assertEqual(self.atom.lattice, self.site.lattice)
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 test___lt__raises_TypeError_if_not_passed_Atom(self):
with self.assertRaises(TypeError):
self.atom < 'foo'
def test___eq___when_true(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)
other_atom = Atom(index=index, site=site, label=label)
self.assertEqual(self.atom, other_atom)
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___eq__is_False_if_not_passed_Atom(self):
self.assertNotEqual(self.atom, 'foo')
def test___hash__(self):
self.assertEqual(hash(self.atom), self.atom.index)
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 test_as_dict(self):
self.atom.site.as_dict = Mock(return_value={'key': 'value'})
mock_other_polyhedra = Mock(spec=CoordinationPolyhedron)
mock_other_polyhedra.index = 15
self.atom.in_polyhedra = [mock_other_polyhedra]
expected_dict = {'index': 123,
'site': {'key': 'value'},
'label': 'foo', 'in_polyhedra': [15],
'neighbours': {},
'@module': 'polyhedral_analysis.atom',
'@class': 'Atom'}
self.assertEqual(self.atom.as_dict(), expected_dict)
def test_to_json(self):
self.atom.site.as_dict = Mock(return_value={'key': 'value'})
mock_other_polyhedra = Mock(spec=CoordinationPolyhedron)
mock_other_polyhedra.index = 15
self.atom.in_polyhedra = [mock_other_polyhedra]
expected_dict = {'index': 123,
'site': {'key': 'value'},
'label': 'foo', 'in_polyhedra': [15],
'neighbours': {},
'@module': 'polyhedral_analysis.atom',
'@class': 'Atom'}
self.assertEqual(self.atom.to(), json.dumps(expected_dict))
def test_to_json_file(self):
self.atom.site.as_dict = Mock(return_value={'key': 'value'})
mock_other_polyhedra = Mock(spec=CoordinationPolyhedron)
mock_other_polyhedra.index = 15
self.atom.in_polyhedra = [mock_other_polyhedra]
expected_dict = {'index': 123,
'site': {'key': 'value'},
'label': 'foo', 'in_polyhedra': [15],
'neighbours': {},
'@module': 'polyhedral_analysis.atom',
'@class': 'Atom'}
with patch('polyhedral_analysis.atom.zopen', mock_open(), create=True) as m:
self.atom.to(filename='filename')
m.assert_called_once_with('filename', 'wt')
m().write.assert_called_once_with(json.dumps(expected_dict))
def test_to_json_file_with_fmt_equals_JSON(self):
self.atom.site.as_dict = Mock(return_value={'key': 'value'})
mock_other_polyhedra = Mock(spec=CoordinationPolyhedron)
mock_other_polyhedra.index = 15
self.atom.in_polyhedra = [mock_other_polyhedra]
expected_dict = {'index': 123,
'site': {'key': 'value'},
'label': 'foo', 'in_polyhedra': [15],
'neighbours': {},
'@module': 'polyhedral_analysis.atom',
'@class': 'Atom'}
with patch('polyhedral_analysis.atom.zopen', mock_open(), create=True) as m:
self.atom.to(filename='filename', fmt='JSON')
m.assert_called_once_with('filename', 'wt')
m().write.assert_called_once_with(json.dumps(expected_dict))
def test_to_json_file_with_unknown_fmt_raises_ValueError(self):
self.atom.site.as_dict = Mock(return_value={'key': 'value'})
mock_other_polyhedra = Mock(spec=CoordinationPolyhedron)
mock_other_polyhedra.index = 15
self.atom.in_polyhedra = [mock_other_polyhedra]
with self.assertRaises(ValueError):
self.atom.to(filename='filename', fmt='FOO')