def test_is_in_list_fails(self):
configuration_list = [
Configuration([0, 1, 0]),
Configuration([1, 0, 0])
]
self.configuration.matches = Mock(return_value=False)
self.assertEqual(self.configuration.is_in_list(configuration_list),
False)
def test_is_equivalent_to_if_not_equivalent(self):
test_configuration = Configuration([0, 1, 0])
symmetry_operations = [Mock(spec=SymmetryOperation)]
symmetry_operations[0].operate_on = Mock(
return_value=Configuration([0, 0, 1]))
self.assertEqual(
self.configuration.is_equivalent_to(test_configuration,
symmetry_operations), False)
def test_has_equivalent_in_list_fails(self):
configuration_list = [
Configuration([0, 1, 0]),
Configuration([1, 0, 0])
]
symmetry_operations = [Mock(spec=SymmetryOperation)]
self.configuration.is_equivalent_to = Mock(return_value=False)
self.assertEqual(
self.configuration.has_equivalent_in_list(configuration_list,
symmetry_operations),
False)
def operate_on(self, configuration):
"""
Return the Configuration generated by appliying this symmetry operation
Args:
configuration (Configuration): the configuration / occupation vector to operate on
Returns:
(Configuration): the new configuration obtained by operating on configuration with this symmetry operation.
"""
if not isinstance(configuration, Configuration):
raise TypeError
return Configuration(self.matrix.dot(configuration.vector))
def unique_configurations_from_sites( site_distribution, spacegroup, verbose=False ):
number_of_sites = sum( site_distribution.values() )
if verbose:
print( 'total number of sites: ' + str( number_of_sites ) )
print( 'found {:d} inequivalent symmetry operations: '.format( len( spacegroup.symmetry_operations ) ) )
permutations = []
working = True
seen = set()
unique_configurations = []
count = 0
s = flatten_list( [ [ key ] * site_distribution[ key ] for key in site_distribution ] )
while working:
working, new_permutation = next_permutationS( s )
count += 1
config = Configuration.from_tuple( new_permutation )
config_id = int( ''.join( map( str, new_permutation ) ) )
if config_id not in seen:
[ seen.add( i ) for i in config.numeric_equivalents( spacegroup.symmetry_operations ) ]
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 )
def setUp(self):
self.configuration = Configuration([1, 0, 0])
class TestConfiguration(unittest.TestCase):
def setUp(self):
self.configuration = Configuration([1, 0, 0])
def test_matches_returns_true_for_a_match(self):
self.assertEqual(self.configuration.matches(self.configuration), True)
def test_matches_returns_false_for_a_non_match(self):
other_configuration = Configuration([0, 0, 1])
self.assertEqual(self.configuration.matches(other_configuration),
False)
def test_matches_raises_TypeError_for_invalid_type(self):
other_configuration = 'foo'
with self.assertRaises(TypeError):
self.configuration.matches(other_configuration)
def test_is_equivalent_to_if_equivalent(self):
test_configuration = Configuration([0, 1, 0])
symmetry_operations = [Mock(spec=SymmetryOperation)]
symmetry_operations[0].operate_on = Mock(
return_value=test_configuration)
self.assertEqual(
self.configuration.is_equivalent_to(test_configuration,
symmetry_operations), True)
def test_is_equivalent_to_if_not_equivalent(self):
test_configuration = Configuration([0, 1, 0])
symmetry_operations = [Mock(spec=SymmetryOperation)]
symmetry_operations[0].operate_on = Mock(
return_value=Configuration([0, 0, 1]))
self.assertEqual(
self.configuration.is_equivalent_to(test_configuration,
symmetry_operations), False)
def test_is_in_list(self):
configuration_list = [
Configuration([0, 1, 0]),
Configuration([1, 0, 0])
]
self.configuration.matches = Mock(return_value=True)
self.assertEqual(self.configuration.is_in_list(configuration_list),
True)
def test_is_in_list_fails(self):
configuration_list = [
Configuration([0, 1, 0]),
Configuration([1, 0, 0])
]
self.configuration.matches = Mock(return_value=False)
self.assertEqual(self.configuration.is_in_list(configuration_list),
False)
def test_has_equivalent_in_list(self):
configuration_list = [
Configuration([0, 1, 0]),
Configuration([1, 0, 0])
]
symmetry_operations = [Mock(spec=SymmetryOperation)]
self.configuration.is_equivalent_to = Mock(return_value=True)
self.assertEqual(
self.configuration.has_equivalent_in_list(configuration_list,
symmetry_operations),
True)
def test_has_equivalent_in_list_fails(self):
configuration_list = [
Configuration([0, 1, 0]),
Configuration([1, 0, 0])
]
symmetry_operations = [Mock(spec=SymmetryOperation)]
self.configuration.is_equivalent_to = Mock(return_value=False)
self.assertEqual(
self.configuration.has_equivalent_in_list(configuration_list,
symmetry_operations),
False)
def test_set_lowest_numeric_representation(self):
symmetry_operations = [
Mock(spec=SymmetryOperation),
Mock(spec=SymmetryOperation)
]
c1, c2 = Mock(spec=Configuration), Mock(spec=Configuration)
c1.as_number = 4
c2.as_number = 2
symmetry_operations[0].operate_on = Mock(return_value=c1)
symmetry_operations[1].operate_on = Mock(return_value=c2)
self.configuration.set_lowest_numeric_representation(
symmetry_operations)
self.assertEqual(self.configuration.lowest_numeric_representation, 2)
def test_numeric_equivalents(self):
symmetry_operations = [
Mock(spec=SymmetryOperation),
Mock(spec=SymmetryOperation)
]
c1, c2 = Mock(spec=Configuration), Mock(spec=Configuration)
c1.as_number = 4
c2.as_number = 2
symmetry_operations[0].operate_on = Mock(return_value=c1)
symmetry_operations[1].operate_on = Mock(return_value=c2)
self.assertEqual(
self.configuration.numeric_equivalents(symmetry_operations),
[4, 2])
def test_as_number(self):
with patch('bsym.configuration.Configuration.tolist') as mock_tolist:
mock_tolist.side_effect = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
self.assertEqual(Configuration([1, 0, 0]).as_number, 100)
self.assertEqual(Configuration([0, 1, 0]).as_number, 10)
self.assertEqual(Configuration([0, 0, 1]).as_number, 1)
def test_from_tuple(self):
np.testing.assert_array_equal(
Configuration.from_tuple((1, 1, 0)).vector,
Configuration([1, 1, 0]).vector)
def test_tolist(self):
self.assertEqual(self.configuration.tolist(), [1, 0, 0])
def test_position(self):
self.assertEqual(self.configuration.position(0), [1, 2])
def test_map_objects(self):
self.assertEqual(self.configuration.map_objects(['A', 'B', 'C']), {
1: ['A'],
0: ['B', 'C']
})
def test_map_objects_with_incompatible_object_list_raises_ValueError(self):
with self.assertRaises(ValueError):
self.configuration.map_objects(['A', 'B'])
def test_matches_returns_false_for_a_non_match(self):
other_configuration = Configuration([0, 0, 1])
self.assertEqual(self.configuration.matches(other_configuration),
False)
def test_from_tuple(self):
np.testing.assert_array_equal(
Configuration.from_tuple((1, 1, 0)).vector,
Configuration([1, 1, 0]).vector)
def test_as_number(self):
with patch('bsym.configuration.Configuration.tolist') as mock_tolist:
mock_tolist.side_effect = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
self.assertEqual(Configuration([1, 0, 0]).as_number, 100)
self.assertEqual(Configuration([0, 1, 0]).as_number, 10)
self.assertEqual(Configuration([0, 0, 1]).as_number, 1)
def test_from_tuple( self ):
np.testing.assert_array_equal( Configuration.from_tuple( ( 1, 1, 0 ) ).vector,
Configuration( [ 1, 1, 0 ] ).vector )
def setUp( self ):
self.configuration = Configuration( [ 1, 0, 0 ] )
class TestConfiguration( unittest.TestCase ):
def setUp( self ):
self.configuration = Configuration( [ 1, 0, 0 ] )
def test_matches_returns_true_for_a_match( self ):
self.assertEqual( self.configuration.matches( self.configuration ), True )
def test_matches_returns_false_for_a_non_match( self ):
other_configuration = Configuration( [0, 0, 1] )
self.assertEqual( self.configuration.matches( other_configuration ), False )
def test_matches_raises_TypeError_for_invalid_type( self ):
other_configuration = 'foo'
with self.assertRaises( TypeError ):
self.configuration.matches( other_configuration )
def test_is_equivalent_to_if_equivalent( self ):
test_configuration = Configuration( [0, 1, 0] )
symmetry_operations = [ Mock( spec=SymmetryOperation ) ]
symmetry_operations[0].operate_on = Mock( return_value=test_configuration )
self.assertEqual( self.configuration.is_equivalent_to( test_configuration, symmetry_operations ), True )
def test_is_equivalent_to_if_not_equivalent( self ):
test_configuration = Configuration( [ 0, 1, 0 ] )
symmetry_operations = [ Mock( spec=SymmetryOperation ) ]
symmetry_operations[0].operate_on = Mock( return_value=Configuration( [ 0, 0, 1 ] ) )
self.assertEqual( self.configuration.is_equivalent_to( test_configuration, symmetry_operations ), False )
def test_is_in_list( self ):
configuration_list = [ Configuration( [ 0, 1, 0 ] ),
Configuration( [ 1, 0, 0 ] ) ]
self.configuration.matches = Mock( return_value=True )
self.assertEqual( self.configuration.is_in_list( configuration_list ), True )
def test_is_in_list_fails( self ):
configuration_list = [ Configuration( [ 0, 1, 0 ] ),
Configuration( [ 1, 0, 0 ] ) ]
self.configuration.matches = Mock( return_value=False )
self.assertEqual( self.configuration.is_in_list( configuration_list ), False )
def test_has_equivalent_in_list( self ):
configuration_list = [ Configuration( [ 0, 1, 0 ] ),
Configuration( [ 1, 0, 0 ] ) ]
symmetry_operations = [ Mock( spec=SymmetryOperation ) ]
self.configuration.is_equivalent_to = Mock( return_value=True )
self.assertEqual( self.configuration.has_equivalent_in_list( configuration_list, symmetry_operations ), True )
def test_has_equivalent_in_list_fails( self ):
configuration_list = [ Configuration( [ 0, 1, 0 ] ),
Configuration( [ 1, 0, 0 ] ) ]
symmetry_operations = [ Mock( spec=SymmetryOperation ) ]
self.configuration.is_equivalent_to = Mock( return_value=False )
self.assertEqual( self.configuration.has_equivalent_in_list( configuration_list, symmetry_operations ), False )
def test_set_lowest_numeric_representation( self ):
symmetry_operations = [ Mock( spec=SymmetryOperation ), Mock( spec=SymmetryOperation ) ]
c1, c2 = Mock( spec=Configuration ), Mock( spec=Configuration )
c1.as_number = 4
c2.as_number = 2
symmetry_operations[0].operate_on = Mock( return_value = c1 )
symmetry_operations[1].operate_on = Mock( return_value = c2 )
self.configuration.set_lowest_numeric_representation( symmetry_operations )
self.assertEqual( self.configuration.lowest_numeric_representation, 2 )
def test_numeric_equivalents( self ):
symmetry_operations = [ Mock( spec=SymmetryOperation ), Mock( spec=SymmetryOperation ) ]
c1, c2 = Mock( spec=Configuration ), Mock( spec=Configuration )
c1.as_number = 4
c2.as_number = 2
symmetry_operations[0].operate_on = Mock( return_value = c1 )
symmetry_operations[1].operate_on = Mock( return_value = c2 )
self.assertEqual( self.configuration.numeric_equivalents( symmetry_operations ), [ 4, 2 ] )
def test_as_number( self ):
with patch( 'bsym.configuration.Configuration.tolist' ) as mock_tolist:
mock_tolist.side_effect = [ [ 1, 0, 0 ], [ 0, 1, 0 ], [ 0, 0, 1 ] ]
self.assertEqual( Configuration( [ 1, 0, 0 ] ).as_number, 100 )
self.assertEqual( Configuration( [ 0, 1, 0 ] ).as_number, 10 )
self.assertEqual( Configuration( [ 0, 0, 1 ] ).as_number, 1 )
def test_from_tuple( self ):
np.testing.assert_array_equal( Configuration.from_tuple( ( 1, 1, 0 ) ).vector,
Configuration( [ 1, 1, 0 ] ).vector )
def test_tolist( self ):
self.assertEqual( self.configuration.tolist(), [ 1, 0, 0 ] )
def test_position( self ):
self.assertEqual( self.configuration.position( 0 ), [ 1, 2 ] )
def test_map_objects( self ):
self.assertEqual( self.configuration.map_objects( [ 'A', 'B', 'C' ] ), { 1: [ 'A' ], 0: [ 'B', 'C' ] } )
def test_map_objects_with_incompatible_object_list_raises_ValueError( self ):
with self.assertRaises( ValueError ):
self.configuration.map_objects( [ 'A', 'B' ] )