def test_by_label(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
s0.label = 'A'
s1.label = 'B'
sg = SpaceGroup(symmetry_operations=[s0, s1])
self.assertEqual(sg.by_label('A'), s0)
self.assertEqual(sg.by_label('B'), s1)
def test_save_symmetry_operation_vectors_to(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
s0.as_vector.return_value = [1, 2]
s1.as_vector.return_value = [2, 1]
sg = SpaceGroup(symmetry_operations=[s0, s1])
with patch('numpy.savetxt') as mock_savetxt:
sg.save_symmetry_operation_vectors_to('filename')
self.assertEqual(mock_savetxt.call_args[0][0], 'filename')
np.testing.assert_array_equal(mock_savetxt.call_args[0][1],
np.array([[1, 2], [2, 1]]))
def test_read_from_file(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
with patch('numpy.loadtxt') as mock_np_loadtxt:
mock_np_loadtxt.return_value = np.array([[1, 2], [2, 1]])
with patch('bsym.symmetry_operation.SymmetryOperation.from_vector'
) as mock_from_vector:
mock_from_vector.side_effect = [s0, s1]
sg = SpaceGroup.read_from_file('mock_filename')
self.assertEqual(sg.symmetry_operations[0], s0)
self.assertEqual(sg.symmetry_operations[1], s1)
self.assertEqual(mock_from_vector.call_args_list[0],
call([1, 2]))
self.assertEqual(mock_from_vector.call_args_list[1],
call([2, 1]))
def test_read_from_file_with_labels(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
with patch('numpy.genfromtxt') as mock_np_genfromtxt:
mock_np_genfromtxt.return_value = np.array([['E', '1', '2'],
['C2', '2', '1']])
with patch('bsym.symmetry_operation.SymmetryOperation.from_vector'
) as mock_from_vector:
mock_from_vector.side_effect = [s0, s1]
sg = SpaceGroup.read_from_file_with_labels('mock_filename')
self.assertEqual(sg.symmetry_operations[0], s0)
self.assertEqual(sg.symmetry_operations[1], s1)
self.assertEqual(mock_from_vector.call_args_list[0],
call([1, 2]))
self.assertEqual(mock_from_vector.call_args_list[1],
call([2, 1]))
self.assertEqual(s0.set_label.call_args, call('E'))
self.assertEqual(s1.set_label.call_args, call('C2'))
def space_group_from_structure(structure, subset=None, atol=1e-5):
"""
Generates a ``SpaceGroup`` object from a `pymatgen` ``Structure``.
Args:
structure (pymatgen ``Structure``): structure to be used to define the :any:`SpaceGroup`.
subset (Optional [list]): list of atom indices to be used for generating the symmetry operations.
atol (Optional [float]): tolerance factor for the ``pymatgen`` `coordinate mapping`_ under each symmetry operation.
Returns:
a new :any:`SpaceGroup` instance
.. _coordinate mapping:
http://pymatgen.org/pymatgen.util.coord_utils.html#pymatgen.util.coord_utils.coord_list_mapping_pbc
"""
mappings = unique_symmetry_operations_as_vectors_from_structure(
structure, subset=subset, atol=atol)
symmetry_operations = [SymmetryOperation.from_vector(m) for m in mappings]
return SpaceGroup(symmetry_operations=symmetry_operations)
def test_spacegroup_is_initialised(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
sg = SpaceGroup(symmetry_operations=[s0, s1])
self.assertEqual(sg.symmetry_operations[0], s0)
self.assertEqual(sg.symmetry_operations[1], s1)
def test_labels(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
s0.label = 'A'
s1.label = 'B'
sg = SpaceGroup(symmetry_operations=[s0, s1])
self.assertEqual(sg.labels, ['A', 'B'])
def test_append(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
sg = SpaceGroup(symmetry_operations=[s0, s1])
s2 = Mock(spec=SymmetryOperation)
sg.append(s2)
self.assertEqual(sg.symmetry_operations, [s0, s1, s2])