def test_configuration_is_initialised_with_config_number(self):
mock_sites = [Mock(spec=Site) for i in range(4)]
for m, s in zip(mock_sites, ['A', 'B', 'C', 'D']):
m.species_string = s
mock_structure = Mock(spec=Structure)
mock_structure.sites = mock_sites
mock_polyhedra = [Mock(spec=CoordinationPolyhedron) for i in range(2)]
mock_atoms = [Mock(spec=Atom) for i in range(4)]
for i, m in enumerate(mock_atoms):
m.index = i
mock_polyhedra[0].central_atom = mock_atoms[0]
mock_polyhedra[0].vertices = [mock_atoms[1]]
mock_polyhedra[1].central_atom = mock_atoms[2]
mock_polyhedra[1].vertices = [mock_atoms[3]]
mock_recipe = Mock(spec=PolyhedraRecipe)
mock_recipe.find_polyhedra = Mock(return_value=mock_polyhedra)
with patch('polyhedral_analysis.configuration.Atom') as mock_Atom:
mock_Atom.side_effect = mock_atoms
configuration = Configuration(structure=mock_structure,
recipes=[mock_recipe])
self.assertEqual(configuration.polyhedra, mock_polyhedra)
self.assertEqual(configuration.structure, mock_structure)
self.assertEqual(configuration.config_number, None)
self.assertEqual(configuration.central_atoms,
[mock_atoms[0], mock_atoms[2]])
self.assertEqual(configuration.coordination_atoms,
[mock_atoms[1], mock_atoms[3]])
self.assertEqual(configuration.atoms, mock_atoms)
config_number = 123
with patch('polyhedral_analysis.configuration.Atom') as mock_Atom:
mock_Atom.side_effect = mock_atoms
configuration = Configuration(structure=mock_structure,
recipes=[mock_recipe],
config_number=config_number)
self.assertEqual(configuration.config_number, config_number)
class TestConfiguration(unittest.TestCase):
def setUp(self):
mock_sites = [Mock(spec=Site) for i in range(4)]
for m, s in zip(mock_sites, ['A', 'B', 'C', 'D']):
m.species_string = s
mock_structure = Mock(spec=Structure)
mock_structure.sites = mock_sites
mock_polyhedra = [Mock(spec=CoordinationPolyhedron) for i in range(2)]
mock_atoms = [Mock(spec=Atom) for i in range(4)]
for i, m in enumerate(mock_atoms):
m.index = i
mock_polyhedra[0].central_atom = mock_atoms[0]
mock_polyhedra[0].vertices = [mock_atoms[1]]
mock_polyhedra[1].central_atom = mock_atoms[2]
mock_polyhedra[1].vertices = [mock_atoms[3]]
mock_recipe = Mock(spec=PolyhedraRecipe)
mock_recipe.find_polyhedra = Mock(return_value=mock_polyhedra)
with patch('polyhedral_analysis.configuration.Atom') as mock_Atom:
mock_Atom.side_effect = mock_atoms
self.configuration = Configuration(structure=mock_structure,
recipes=[mock_recipe])
self.mock_atoms = mock_atoms
def test_coordination_atom_by_index(self):
self.assertEqual(self.configuration.coordination_atom_by_index(3),
self.mock_atoms[3])
def test_coordination_atom_by_index_returns_none_if_missing(self):
self.assertEqual(self.configuration.coordination_atom_by_index(2),
None)
def setUp(self):
mock_sites = [Mock(spec=Site) for i in range(4)]
for m, s in zip(mock_sites, ['A', 'B', 'C', 'D']):
m.species_string = s
mock_structure = Mock(spec=Structure)
mock_structure.sites = mock_sites
mock_polyhedra = [Mock(spec=CoordinationPolyhedron) for i in range(2)]
mock_atoms = [Mock(spec=Atom) for i in range(4)]
for i, m in enumerate(mock_atoms):
m.index = i
mock_polyhedra[0].central_atom = mock_atoms[0]
mock_polyhedra[0].vertices = [mock_atoms[1]]
mock_polyhedra[1].central_atom = mock_atoms[2]
mock_polyhedra[1].vertices = [mock_atoms[3]]
mock_recipe = Mock(spec=PolyhedraRecipe)
mock_recipe.find_polyhedra = Mock(return_value=mock_polyhedra)
with patch('polyhedral_analysis.configuration.Atom') as mock_Atom:
mock_Atom.side_effect = mock_atoms
self.configuration = Configuration(structure=mock_structure,
recipes=[mock_recipe])
self.mock_atoms = mock_atoms
def _get_configuration(cls, args: Dict[str, Any]) -> Configuration:
return Configuration(structure=args['structure'],
recipes=args['recipes'])