def test_by_label( self ):
s0, s1 = Mock( spec=SymmetryOperation ), Mock( spec=SymmetryOperation )
s0.label = 'A'
s1.label = 'B'
sg = SymmetryGroup( symmetry_operations=[ s0, s1 ] )
self.assertEqual( sg.by_label( 'A' ), s0 )
self.assertEqual( sg.by_label( 'B' ), s1 )
def test_by_label(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
s0.label = 'A'
s1.label = 'B'
sg = SymmetryGroup(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 = SymmetryGroup( 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_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 = SymmetryGroup(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 = SymmetryGroup.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 __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 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 = SymmetryGroup.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 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 = SymmetryGroup.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 = SymmetryGroup.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'))
class ConfigurationSpace:
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
dim = len(objects)
self.objects = objects
if symmetry_group:
for so in symmetry_group.symmetry_operations:
if so.matrix.shape[0] != dim:
raise ValueError
self.symmetry_group = symmetry_group
else:
self.symmetry_group = SymmetryGroup(symmetry_operations=[
SymmetryOperation(np.identity(dim, dtype=int), label='E')
])
def __repr__(self):
to_return = "ConfigurationSpace\n"
to_return += self.objects.__repr__() + "\n"
to_return += "\n".join(self.symmetry_group.__repr__().split("\n")[1:])
return to_return
def unique_configurations(self, site_distribution, verbose=False):
"""
Find the symmetry inequivalent configurations for a given population of objects.
Args:
site_distribution (dict): A dictionary that defines the number of each object
to be arranged in this system.
e.g. for a system with four sites, with two occupied (denoted `1`)
and two unoccupied (denoted `0`)::
{ 1 : 2, 2 : 1 }
verbose (opt:default=False): Print verbose output.
Returns:
unique_configurations (list): A list of :any:`Configuration` objects, for each symmetry
inequivalent configuration.
"""
if verbose:
print('total number of sites: ' +
str(sum(site_distribution.values())))
print('using {:d} symmetry operations: '.format(
len(self.symmetry_group.symmetry_operations)))
permutations = []
working = True
seen = set()
unique_configurations = []
s = flatten_list([[key] * site_distribution[key]
for key in site_distribution])
for new_permutation in unique_permutations(s):
if permutation_as_config_number(new_permutation) not in seen:
config = Configuration.from_tuple(new_permutation)
numeric_equivalents = set(
config.numeric_equivalents(
self.symmetry_group.symmetry_operations))
config.count = len(numeric_equivalents)
[seen.add(i) for i in numeric_equivalents]
unique_configurations.append(config)
if verbose:
print("found {:d}, screened {:d}".format(
len(unique_configurations), len(seen)))
if verbose:
print('unique configurations: ' + str(len(unique_configurations)))
return (unique_configurations)
class ConfigurationSpace:
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 __repr__( self ):
to_return = "ConfigurationSpace\n"
to_return += self.objects.__repr__() + "\n"
to_return += "\n".join( self.symmetry_group.__repr__().split("\n")[1:] )
return to_return
def enumerate_configurations( self, generator, verbose=False ):
"""
Find all symmetry inequivalent configurations within the set produced by
`generator`.
Args:
generator (:obj:`generator`): Generator object, that yields the configurations
to search through.
verbose (opt:default=False): Print verbose output.
Returns:
unique_configurations (list): A list of :any:`Configuration` objects, for each symmetry
inequivalent configuration.
"""
working = True
seen = set()
unique_configurations = []
using_tqdm = hasattr( generator, 'postfix' )
for new_permutation in generator:
if permutation_as_config_number( new_permutation ) not in seen:
config = Configuration.from_tuple( new_permutation )
numeric_equivalents = set( config.numeric_equivalents( self.symmetry_group.symmetry_operations ) )
config.count = len( numeric_equivalents )
[ seen.add( i ) for i in numeric_equivalents ]
unique_configurations.append( config )
if using_tqdm:
generator.set_postfix( found=len(unique_configurations) )
if verbose:
print( 'unique configurations: {} / {}'.format( len( unique_configurations ), len( seen ) ) )
return( unique_configurations )
def unique_configurations( self, site_distribution, verbose=False, show_progress=False ):
"""
Find the symmetry inequivalent configurations for a given population of objects.
Args:
site_distribution (dict): A dictionary that defines the number of each object
to be arranged in this system.
e.g. for a system with four sites, with two occupied (denoted `1`)
and two unoccupied (denoted `0`)::
{ 1: 2, 0: 2 }
verbose (opt:default=False): Print verbose output.
show_progress (opt:default=False): Show a progress bar.
Setting to `True` gives a simple progress bar.
Setting to `"notebook"` gives a Jupyter notebook compatible progress bar.
Returns:
unique_configurations (list): A list of :any:`Configuration` objects, for each symmetry
inequivalent configuration.
"""
s = flatten_list( [ [ key ] * site_distribution[ key ] for key in site_distribution ] )
total_permutations = number_of_unique_permutations( s )
if verbose:
print( 'total number of sites: ' + str( sum( site_distribution.values() ) ) )
print( 'using {:d} symmetry operations.'.format( len( self.symmetry_group.symmetry_operations ) ) )
print( 'evaluating {:d} unique permutations.'.format( total_permutations ) )
generator = unique_permutations( s )
if show_progress:
if show_progress=='notebook':
generator = tqdm_notebook( generator, total=total_permutations, unit=' permutations' )
else:
generator = tqdm( generator, total=total_permutations, unit=' permutations' )
return self.enumerate_configurations( generator, verbose=verbose )
def unique_colourings( self, colours, verbose=False ):
"""
Find the symmetry inequivalent colourings for a given number of 'colours'.
Args:
colours (list): A list of each object that may be arranged zero or more times in this system.
verbose (opt:default=False): Print verbose output.
Returns:
unique_colours (list): A list of :any:`Configuration` objects, for each symmetry
inequivalent colouring.
"""
generator = colourings_generator( colours, self.dim )
return self.enumerate_configurations( generator, verbose=verbose )
def test_append( self ):
s0, s1 = Mock( spec=SymmetryOperation ), Mock( spec=SymmetryOperation )
sg = SymmetryGroup( symmetry_operations=[ s0, s1 ] )
s2 = Mock( spec=SymmetryOperation)
sg.append( s2 )
self.assertEqual( sg.symmetry_operations, [ s0, s1, s2 ] )
def test_labels(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
s0.label = 'A'
s1.label = 'B'
sg = SymmetryGroup(symmetry_operations=[s0, s1])
self.assertEqual(sg.labels, ['A', 'B'])
def test_symmetry_group_is_initialised(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
sg = SymmetryGroup(symmetry_operations=[s0, s1])
self.assertEqual(sg.symmetry_operations[0], s0)
self.assertEqual(sg.symmetry_operations[1], s1)
def test_append(self):
s0, s1 = Mock(spec=SymmetryOperation), Mock(spec=SymmetryOperation)
sg = SymmetryGroup(symmetry_operations=[s0, s1])
s2 = Mock(spec=SymmetryOperation)
sg.append(s2)
self.assertEqual(sg.symmetry_operations, [s0, s1, s2])