def test_operate_on(self):
matrix = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]])
so = SymmetryOperation(matrix)
configuration = Configuration([1, 2, 3])
so.operate_on(configuration)
np.testing.assert_array_equal(
so.operate_on(configuration).vector, np.array([2, 3, 1]))
def test_mul(self):
matrix_a = np.array([[0, 1], [1, 0]])
matrix_b = np.array([[1, 0], [0, 1]])
so_a = SymmetryOperation(matrix_a)
so_b = SymmetryOperation(matrix_b)
np.testing.assert_array_equal((so_a * so_b).matrix,
np.array([[0, 1], [1, 0]]))
def test_similarity_transform( self ):
matrix_a = np.array( [ [ 0, 1, 0 ], [ 0, 0, 1 ], [ 1, 0, 0 ] ] )
matrix_b = np.array( [ [ 1, 0, 0 ], [ 0, 0, 1 ], [ 0, 1, 0 ] ] )
matrix_c = np.linalg.inv( matrix_a )
so_a = SymmetryOperation( matrix_a )
so_b = SymmetryOperation( matrix_b )
np.testing.assert_array_equal( so_a.similarity_transform( so_b ).matrix, matrix_c )
def test_similarity_transform(self):
matrix_a = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]])
matrix_b = np.array([[1, 0, 0], [0, 0, 1], [0, 1, 0]])
matrix_c = np.linalg.inv(matrix_a)
so_a = SymmetryOperation(matrix_a)
so_b = SymmetryOperation(matrix_b)
np.testing.assert_array_equal(
so_a.similarity_transform(so_b).matrix, matrix_c)
def test_similarity_transform_with_label( self ):
matrix_a = np.array( [ [ 0, 1, 0 ], [ 0, 0, 1 ], [ 1, 0, 0 ] ] )
matrix_b = np.array( [ [ 1, 0, 0 ], [ 0, 0, 1 ], [ 0, 1, 0 ] ] )
matrix_c = np.linalg.inv( matrix_a )
so_a = SymmetryOperation( matrix_a )
so_b = SymmetryOperation( matrix_b )
label = 'foo'
np.testing.assert_array_equal( so_a.similarity_transform( so_b, label=label ).label, label )
def test_similarity_transform_with_label(self):
matrix_a = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]])
matrix_b = np.array([[1, 0, 0], [0, 0, 1], [0, 1, 0]])
matrix_c = np.linalg.inv(matrix_a)
so_a = SymmetryOperation(matrix_a)
so_b = SymmetryOperation(matrix_b)
label = 'foo'
np.testing.assert_array_equal(
so_a.similarity_transform(so_b, label=label).label, label)
def test_from_vector_with_label(self):
vector = [2, 3, 1]
label = 'A'
so = SymmetryOperation.from_vector(vector, label=label)
np.testing.assert_array_equal(
so.matrix, np.array([[0, 0, 1], [1, 0, 0], [0, 1, 0]]))
self.assertEqual(so.label, label)
def read_from_file_with_labels(cls, filename):
"""
Create a :any:`SymmetryGroup` object from a file, with labelled symmetry operations.
The file format should be a series of numerical mappings representing each symmetry operation, prepended with a string that will be used as a label.
e.g. for a pair of equivalent sites::
# example input file to define the spacegroup for a pair of equivalent sites
E 1 2
C2 2 1
Args:
filename (str): Name of the file to be read in.
Returns:
spacegroup (SymmetryGroup)
"""
data = np.genfromtxt(filename, dtype=str)
labels = [row[0] for row in data]
vectors = [[float(s) for s in row[1:]] for row in data]
symmetry_operations = [
SymmetryOperation.from_vector(v) for v in vectors
]
[so.set_label(l) for (l, so) in zip(labels, symmetry_operations)]
return (cls(symmetry_operations=symmetry_operations))
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 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 point_group_from_molecule( molecule, subset=None, atol=1e-5 ):
"""
Generates a ``PointGroup`` object from a `pymatgen` ``Molecule``.
Args:
molecule (pymatgen ``Molecule``): molecule to be used to define the :any:`PointGroup`.
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:`PointGroup` 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 )
mappings = unique_symmetry_operations_as_vectors_from_structure( molecule, subset=subset, atol=atol )
symmetry_operations = [ SymmetryOperation.from_vector( m ) for m in mappings ]
return PointGroup( symmetry_operations=symmetry_operations )
def read_from_file( cls, filename ):
"""
Create a :any:`SymmetryGroup` object from a file.
The file format should be a series of numerical mappings representing each symmetry operation.
e.g. for a pair of equivalent sites::
# example input file to define the spacegroup for a pair of equivalent sites
1 2
2 1
Args:
filename (str): Name of the file to be read in.
Returns:
spacegroup (SymmetryGroup)
"""
data = np.loadtxt( filename, dtype=int )
symmetry_operations = [ SymmetryOperation.from_vector( row.tolist() ) for row in data ]
return( cls( symmetry_operations = symmetry_operations ) )
def __init__( self, objects, symmetry_group=None ):
"""
Create a :any:`ConfigurationSpace` object.
Args:
objects (list): The set of objects that define the vector space of this configuration space.
symmetry_group (:any:`SymmetryGroup`): The set of symmetry operations describing the symmetries of this configuration space.
Returns:
None
"""
# Check that all properties have compatible dimensions
self.dim = len( objects )
self.objects = objects
if symmetry_group:
for so in symmetry_group.symmetry_operations:
if so.matrix.shape[0] != self.dim:
raise ValueError
self.symmetry_group = symmetry_group
else:
self.symmetry_group = SymmetryGroup( symmetry_operations=[ SymmetryOperation( np.identity( self.dim, dtype=int ), label='E' ) ] )
def point_group_from_molecule(molecule, subset=None, atol=1e-5):
"""
Generates a ``PointGroup`` object from a `pymatgen` ``Molecule``.
Args:
molecule (pymatgen ``Molecule``): molecule to be used to define the :any:`PointGroup`.
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:`PointGroup` 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)
mappings = unique_symmetry_operations_as_vectors_from_structure(
molecule, subset=subset, atol=atol)
symmetry_operations = [SymmetryOperation.from_vector(m) for m in mappings]
return PointGroup(symmetry_operations=symmetry_operations)
def read_from_file(cls, filename):
"""
Create a :any:`SymmetryGroup` object from a file.
The file format should be a series of numerical mappings representing each symmetry operation.
e.g. for a pair of equivalent sites::
# example input file to define the spacegroup for a pair of equivalent sites
1 2
2 1
Args:
filename (str): Name of the file to be read in.
Returns:
spacegroup (SymmetryGroup)
"""
data = np.loadtxt(filename, dtype=int)
symmetry_operations = [
SymmetryOperation.from_vector(row.tolist()) for row in data
]
return (cls(symmetry_operations=symmetry_operations))
def read_from_file_with_labels( cls, filename ):
"""
Create a :any:`SymmetryGroup` object from a file, with labelled symmetry operations.
The file format should be a series of numerical mappings representing each symmetry operation, prepended with a string that will be used as a label.
e.g. for a pair of equivalent sites::
# example input file to define the spacegroup for a pair of equivalent sites
E 1 2
C2 2 1
Args:
filename (str): Name of the file to be read in.
Returns:
spacegroup (SymmetryGroup)
"""
data = np.genfromtxt( filename, dtype=str )
labels = [ row[0] for row in data ]
vectors = [ [ float(s) for s in row[1:] ] for row in data ]
symmetry_operations = [ SymmetryOperation.from_vector( v ) for v in vectors ]
[ so.set_label( l ) for (l, so) in zip( labels, symmetry_operations ) ]
return( cls( symmetry_operations=symmetry_operations ) )
def test_mul_raises_TypeError_with_invalid_type( self ):
so = SymmetryOperation.from_vector( [ 2, 3, 1 ] )
with self.assertRaises( TypeError ):
new_conf = so * 'foo'
def test_repr( self ):
matrix = np.array( [ [ 1, 0 ], [ 0, 1 ] ] )
so = SymmetryOperation( matrix, label='L' )
this_repr = so.__repr__()
self.assertNotEqual( this_repr.find( 'L' ), 0 )
self.assertNotEqual( this_repr.find( "[[1, 0],\n[0, 1]]" ), 0 )
def test_se_label( self ):
matrix = np.array( [ [ 1, 0 ], [ 0, 1 ] ] )
so = SymmetryOperation( matrix )
so.set_label( 'new_label' )
self.assertEqual( so.label, 'new_label' )
def test_as_vector( self ):
matrix = np.array( [ [ 0, 0, 1 ], [ 1, 0, 0 ], [ 0, 1, 0 ] ] )
so = SymmetryOperation( matrix )
self.assertEqual( so.as_vector(), [ 2, 3, 1 ] )
def test_operate_on_raises_TypeError_with_invalid_type( self ):
matrix = np.array( [ [ 0, 1, 0 ], [ 0, 0, 1 ], [ 1, 0, 0 ] ] )
so = SymmetryOperation( matrix )
with self.assertRaises( TypeError ):
so.operate_on( 'foo' )
def test_pprint(self):
matrix = np.matrix([[1, 0], [0, 1]])
so = SymmetryOperation(matrix)
with patch('sys.stdout', new=io.StringIO()) as mock_stdout:
so.pprint()
self.assertEqual(mock_stdout.getvalue(), '--- : 1 2\n')
def test_from_vector(self):
vector = [2, 3, 1]
so = SymmetryOperation.from_vector(vector)
np.testing.assert_array_equal(
so.matrix, np.array([[0, 0, 1], [1, 0, 0], [0, 1, 0]]))
def test_invert(self):
matrix_a = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]])
matrix_b = np.array([[0, 0, 1], [1, 0, 0], [0, 1, 0]])
so = SymmetryOperation(matrix_a)
np.testing.assert_array_equal(so.invert().matrix, matrix_b)
def test_invert_sets_label(self):
matrix_a = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]])
so = SymmetryOperation(matrix_a).invert(label='A')
self.assertEqual(so.label, 'A')
def test_mul_raises_TypeError_with_invalid_type(self):
so = SymmetryOperation.from_vector([2, 3, 1])
with self.assertRaises(TypeError):
new_conf = so * 'foo'
def test_mul_with_configuration(self):
so = SymmetryOperation.from_vector([2, 3, 1])
conf = Configuration([1, 2, 3])
new_conf = so * conf
self.assertEqual(type(new_conf), Configuration)
self.assertEqual(new_conf.matches(Configuration([3, 1, 2])), True)
def test_as_vector(self):
matrix = np.array([[0, 0, 1], [1, 0, 0], [0, 1, 0]])
so = SymmetryOperation(matrix)
self.assertEqual(so.as_vector(), [2, 3, 1])
def test_from_vector( self ):
vector = [ 2, 3, 1 ]
so = SymmetryOperation.from_vector( vector )
np.testing.assert_array_equal( so.matrix, np.array( [ [ 0, 0, 1 ], [ 1, 0, 0 ], [ 0, 1, 0 ] ] ) )
def test_character(self):
matrix = np.array([[1, 0], [0, 1]])
so = SymmetryOperation(matrix)
self.assertEqual(so.character(), 2)
def test_symmetry_operation_raises_valueerror_for_nonsquare_matrix(self):
array = np.array([[1, 0, 0], [0, 0, 1]])
with self.assertRaises(ValueError):
SymmetryOperation(array)
def test_symmetry_operation_is_initialised_with_label(self):
matrix = np.array([[1, 0], [0, 1]])
label = 'E'
so = SymmetryOperation(matrix, label=label)
self.assertEqual(so.label, label)
def test_symmetry_operation_is_initialised_from_an_array(self):
array = np.array([[1, 0], [0, 1]])
so = SymmetryOperation(array)
np.testing.assert_array_equal(so.matrix, np.array(array))
def test_symmetry_operation_is_initialised_from_a_list(self):
this_list = [[1, 0], [0, 1]]
so = SymmetryOperation(this_list)
np.testing.assert_array_equal(so.matrix, np.array(this_list))
def test_operate_on( self ):
matrix = np.array( [ [ 0, 1, 0 ], [ 0, 0, 1 ], [ 1, 0, 0 ] ] )
so = SymmetryOperation( matrix )
configuration = Configuration( [ 1, 2, 3 ] )
so.operate_on( configuration )
np.testing.assert_array_equal( so.operate_on( configuration ).vector, np.array( [ 2, 3, 1 ] ) )
def test_operate_on_raises_TypeError_with_invalid_type(self):
matrix = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]])
so = SymmetryOperation(matrix)
with self.assertRaises(TypeError):
so.operate_on('foo')
def test_character( self ):
matrix = np.array( [ [ 1, 0 ], [ 0, 1 ] ] )
so = SymmetryOperation( matrix )
self.assertEqual( so.character(), 2 )
def test_repr(self):
matrix = np.array([[1, 0], [0, 1]])
so = SymmetryOperation(matrix, label='L')
this_repr = so.__repr__()
self.assertNotEqual(this_repr.find('L'), 0)
self.assertNotEqual(this_repr.find("[[1, 0],\n[0, 1]]"), 0)
def test_as_vector_counting_from_zero( self ):
matrix = np.array( [ [ 1, 0 ], [ 0, 1 ] ] )
so = SymmetryOperation( matrix )
self.assertEqual( so.as_vector( count_from_zero=True ), [ 0, 1 ] )
def test_from_vector_counting_from_zero( self ):
vector = [ 1, 2, 0 ]
so = SymmetryOperation.from_vector( vector, count_from_zero=True )
np.testing.assert_array_equal( so.matrix, np.array( [ [ 0, 0, 1 ], [ 1, 0, 0 ], [ 0, 1, 0 ] ] ) )
def test_pprint_with_label( self ):
matrix = np.array( [ [ 1, 0 ], [ 0, 1 ] ] )
so = SymmetryOperation( matrix, label='L' )
with patch( 'sys.stdout', new=io.StringIO() ) as mock_stdout:
so.pprint()
self.assertEqual( mock_stdout.getvalue(), 'L : 1 2\n' )
def test_se_label(self):
matrix = np.array([[1, 0], [0, 1]])
so = SymmetryOperation(matrix)
so.set_label('new_label')
self.assertEqual(so.label, 'new_label')
def test_mul_with_configuration( self ):
so = SymmetryOperation.from_vector( [ 2, 3, 1 ] )
conf = Configuration( [ 1, 2, 3 ] )
new_conf = so * conf
self.assertEqual( type( new_conf ), Configuration )
self.assertEqual( new_conf.matches( Configuration( [ 3, 1, 2 ] ) ), True )
def test_symmetry_operation_is_initialised_from_a_matrix(self):
matrix = np.array([[1, 0], [0, 1]])
so = SymmetryOperation(matrix)
np.testing.assert_array_equal(so.matrix, matrix)
def test_invert( self ):
matrix_a = np.array( [ [ 0, 1, 0 ], [ 0, 0, 1 ], [ 1, 0, 0 ] ] )
matrix_b = np.array( [ [ 0, 0, 1 ], [ 1, 0, 0 ], [ 0, 1, 0 ] ] )
so = SymmetryOperation( matrix_a )
np.testing.assert_array_equal( so.invert().matrix, matrix_b )
def test_pprint_with_label(self):
matrix = np.array([[1, 0], [0, 1]])
so = SymmetryOperation(matrix, label='L')
with patch('sys.stdout', new=io.StringIO()) as mock_stdout:
so.pprint()
self.assertEqual(mock_stdout.getvalue(), 'L : 1 2\n')
def test_from_vector_with_label( self ):
vector = [ 2, 3, 1 ]
label = 'A'
so = SymmetryOperation.from_vector( vector, label=label )
np.testing.assert_array_equal( so.matrix, np.array( [ [ 0, 0, 1 ], [ 1, 0, 0 ], [ 0, 1, 0 ] ] ) )
self.assertEqual( so.label, label )
def test_symmetry_operation_raises_typeerror_for_invalid_type(self):
objects = ['foo', 1, None]
for o in objects:
with self.assertRaises(TypeError):
SymmetryOperation(o)
def test_from_vector_counting_from_zero(self):
vector = [1, 2, 0]
so = SymmetryOperation.from_vector(vector, count_from_zero=True)
np.testing.assert_array_equal(
so.matrix, np.array([[0, 0, 1], [1, 0, 0], [0, 1, 0]]))
def test_as_vector_counting_from_zero(self):
matrix = np.array([[1, 0], [0, 1]])
so = SymmetryOperation(matrix)
self.assertEqual(so.as_vector(count_from_zero=True), [0, 1])
