def test_unique_colourings( self ):
object_list = [ 1, 1, 2 ]
configuration_space = ConfigurationSpace( objects=object_list )
mock_configuration = Mock( spec=Configuration )
mock_configuration.dim = 3
configuration_space.enumerate_configurations = Mock( return_value=[ mock_configuration ] )
with patch( 'bsym.configuration_space.colourings_generator' ) as mock_colourings_generator:
mock_colourings_generator.return_values = [ [ 1, 1, 2 ], [ 1, 2, 1 ], [ 2, 1, 1 ] ]
colourings = configuration_space.unique_colourings( colours=[ 1, 2 ] )
mock_colourings_generator.assert_called_with( [1, 2], mock_configuration.dim )
configuration_space.enumerate_configurations.assert_called_with(
mock_colourings_generator(), verbose=False )
self.assertEqual( colourings, [ mock_configuration ] )
def test_unique_configurations( self ):
object_list = [ 1, 1, 2 ]
configuration_space = ConfigurationSpace( objects=object_list )
site_distribution = { 1:2, 2:1 }
mock_configuration = Mock( spec=Configuration )
configuration_space.enumerate_configurations = Mock( return_value=[ mock_configuration ] )
with patch( 'bsym.configuration_space.flatten_list' ) as mock_flatten_list:
mock_flatten_list.return_value = [ 1, 1, 2 ]
with patch( 'bsym.configuration_space.unique_permutations' ) as mock_unique_permutations:
mock_unique_permutations.return_value = [ [ 1, 1, 2 ], [ 1, 2, 1 ], [ 2, 1, 1 ] ]
configurations = configuration_space.unique_configurations( site_distribution )
mock_unique_permutations.assert_called_with( [ 1, 1, 2 ] )
mock_flatten_list.assert_called_with( [ [1, 1 ], [ 2 ] ] )
configuration_space.enumerate_configurations.assert_called_with(
mock_unique_permutations(), verbose=False )
self.assertEqual( configurations, [ mock_configuration ] )
def test_configuration_space_initialised_with_no_symmetry_group_creates_sym_op_with_ints(
self):
object_list = ['A', 'B']
configuration_space = ConfigurationSpace(objects=object_list)
self.assertEqual(
issubclass(
configuration_space.symmetry_group.symmetry_operations[0].
matrix.dtype.type, np.integer), True)
def test_configuration_space_initialisation_raises_valueerror_if_dimensions_are_inconsistent( self ):
mock_symmetry_group = Mock( spec=SymmetryGroup )
mock_symmetry_operations = [ Mock( spec=SymmetryOperation ), Mock( spec=SymmetryOperation ) ]
mock_symmetry_operations[0].matrix = np.array( np.zeros( (3,3) ) )
mock_symmetry_operations[1].matrix = np.array( np.zeros( (3,3) ) )
mock_symmetry_group.symmetry_operations = mock_symmetry_operations
object_list = [ 'A', 'B' ]
with self.assertRaises( ValueError ):
ConfigurationSpace( symmetry_group=mock_symmetry_group, objects=object_list )
def test_configuration_space_initialised_with_no_symmetry_group(self):
object_list = ['A', 'B']
configuration_space = ConfigurationSpace(objects=object_list)
self.assertEqual(configuration_space.symmetry_group.size, 1)
self.assertEqual(
configuration_space.symmetry_group.symmetry_operations[0].label,
'E')
np.testing.assert_array_equal(
configuration_space.symmetry_group.symmetry_operations[0].matrix,
np.matrix([[1, 0], [0, 1]]))
def test_configuration_space_is_initialised( self ):
mock_symmetry_group = Mock( spec=SymmetryGroup )
mock_symmetry_operations = [ Mock( spec=SymmetryOperation ), Mock( spec=SymmetryOperation ) ]
mock_symmetry_operations[0].matrix = np.array( np.zeros( (3,3) ) )
mock_symmetry_operations[1].matrix = np.array( np.zeros( (3,3) ) )
mock_symmetry_group.symmetry_operations = mock_symmetry_operations
object_list = [ 'A', 'B', 'C' ]
configuration_space = ConfigurationSpace( symmetry_group=mock_symmetry_group, objects=object_list )
self.assertEqual( configuration_space.symmetry_group, mock_symmetry_group )
self.assertEqual( configuration_space.objects, object_list )
def configuration_space_from_molecule(molecule, subset=None, atol=1e-5):
"""
Generate a ``ConfigurationSpace`` object from a `pymatgen` ``Molecule``.
Args:
molecule (pymatgen ``Molecule``): molecule to be used to define the :any:`ConfigurationSpace`.
subset (Optional [list]): list of atom indices to be used for generating the configuration space.
atol (Optional [float]): tolerance factor for the ``pymatgen`` `coordinate mapping`_ under each symmetry operation.
Returns:
a new :any:`ConfigurationSpace` instance.
.. _coordinate mapping:
http://pymatgen.org/pymatgen.util.coord_utils.html#pymatgen.util.coord_utils.coord_list_mapping
"""
molecule = Molecule(molecule.species,
molecule.cart_coords - molecule.center_of_mass)
point_group = point_group_from_molecule(molecule, subset=subset, atol=atol)
if subset is None:
subset = list(range(1, len(molecule) + 1))
config_space = ConfigurationSpace(objects=subset,
symmetry_group=point_group)
return config_space
def configuration_space_from_structure(structure, subset=None, atol=1e-5):
"""
Generate a ``ConfigurationSpace`` object from a `pymatgen` ``Structure``.
Args:
structure (pymatgen ``Structure``): structure to be used to define the :any:`ConfigurationSpace`.
subset (Optional [list]): list of atom indices to be used for generating the configuration space.
atol (Optional [float]): tolerance factor for the ``pymatgen`` `coordinate mapping`_ under each symmetry operation.
Returns:
a new :any:`ConfigurationSpace` instance.
.. _coordinate mapping:
http://pymatgen.org/pymatgen.util.coord_utils.html#pymatgen.util.coord_utils.coord_list_mapping_pbc
"""
space_group = space_group_from_structure(structure,
subset=subset,
atol=atol)
if subset is None:
subset = list(range(1, len(structure) + 1))
config_space = ConfigurationSpace(objects=subset,
symmetry_group=space_group)
return config_space
