bsym.configuration

class bsym.configuration.Configuration(vector: list[int] | ndarray[tuple[int, ...], dtype[int64]])[source]

Bases: object

A Configuration describes a specific arrangement of objects in the vector space of possible positions. Objects are represented by integers, with indistinguishable objects denoted by identical integers. Internally, the configuration is stored as a numpy.int8 array.

count

If symmetry-inequivalent configurations have been generated for a configuration space, this records the number of configurations equivalent to this one. Value at initialisation is None.

Type:: int

lowest_numeric_representation

If the numeric representations for the set of equivalent configurations are calculated, this can be used to store the lowest valued numeric representation, for use as a simple hash.

Type:: int

Example

>>> Configuration([1, 1, 0])
Configuration([1, 1, 0])

static array_to_bytes(arr: ndarray) → bytes[source]

Convert configuration array to bytes.

Assumes array is already int8. Used for transformations.

Parameters:: arr – Configuration as int8 numpy array.
Returns:: Byte representation for hashing.
Return type:: bytes

as_bytes() → bytes[source]: Get byte representation of this configuration.

property as_number: int

A numeric representation of this configuration.

Examples

>>> c = Configuration([1, 2, 0])
>>> c.as_number
120

classmethod from_dict(d: dict) → Configuration[source]

Create Configuration from dictionary.

Parameters:: d – Dictionary with ‘vector’ key containing configuration values.
Returns:: New Configuration instance.

classmethod from_tuple(configuration_tuple)[source]

Create a Configuration from a tuple.

Configurations are stored as int8 arrays, supporting species labels 0-255.

Parameters:: configuration_tuple – Tuple of configuration values (0-255).
Returns:: New configuration object.
Return type:: Configuration

get_byte_equivalents(symmetry_group) → set[bytes][source]: Get byte representations of all symmetry-equivalent configurations.

has_equivalent_in_list(the_list: list[Configuration], symmetry_operations: list[SymmetryOperation]) → bool[source]

Test whether this configuration is equivalent by symmetry to one or more in a list of configurations.

Parameters:

list (list(bsym.Configuration)) – A list of Configuration instances.
symmetry_operations (list(bsym.SymmetryOperation)) – A list of SymmetryOperation objects.

Returns:

True | False

Return type:

(bool)

is_equivalent_to(test_configuration: Configuration, symmetry_operations: list[SymmetryOperation]) → bool[source]

Test whether this configuration is equivalent to another configuration under one or more of a set of symmetry operations.

Parameters:

test_configuration (Configuration) – The configuration to compare against.
symmetry_operations (list(SymmetryOperation) – A list of SymmetryOperation objects.

Returns:

True | False

Return type:

(bool)

is_in_list(the_list: list[Configuration]) → bool[source]

Test whether this configuration is in a list of configurations.

Parameters:: list (list(bsym.Comfiguration)) – A list of Configuration instances.
Returns:: True | False
Return type:: (bool)

map_objects(objects: list) → dict[int, Any][source]

Returns a dict of objects sorted according to this configuration.

Parameters:: [list] (objects) – A list of objects.
Returns:: A dictionary of sorted objects.
Return type:: sorted_objects [dict]

matches(test_configuration: Configuration) → bool[source]

Test whether this configuration is equal to another configuration.

Parameters:: test_configuration (Configuration) – The configuration to compare against.
Returns:: True | False.
Return type:: (bool)

numeric_equivalents(symmetry_operations: list[SymmetryOperation]) → list[int][source]

Returns a list of all symmetry equivalent configurations generated by a set of symmetry operations with each configuration given in numeric representation.

Parameters:: symmetry_operations (list) – A list of SymmetryOperation instances.
Returns:: A list of numbers representing each equivalent configuration.
Return type:: (list(int))

position(label: int) → list[int][source]

Returns the vector indices where elements are equal to label.

Parameters:: label (int) – The label used to select the vector positions.
Returns:: A list of all positions that match label.
Return type:: (list)

pprint() → None[source]

set_lowest_numeric_representation(symmetry_operations: list[SymmetryOperation]) → None[source]

Sets self.lowest_numeric_representation to the lowest value numeric representation of this configuration when permutated under a set of symmetry operations.

Parameters:: symmetry_operations (list) – A list of SymmetryOperation instances.
Returns:: None

to_dict() → dict[source]

Convert to JSON-serialisable dictionary.

Returns:: Dictionary with ‘vector’ key containing the configuration as a list.

tolist() → list[int][source]

Returns the configuration data as a list.

Parameters:: None
Returns:: (List)

static tuple_to_bytes(tup: tuple) → bytes[source]

Convert configuration tuple to bytes.

Used for initial permutation checking in enumerate_configurations.

Parameters:: tup – Configuration as tuple.
Returns:: Byte representation for hashing.
Return type:: bytes

bsym.configuration.as_number(a: list[int] | ndarray[tuple[int, ...], dtype[int64]]) → int[source]

bsym.configuration.load_configurations(filename: str) → list[Configuration][source]

Load configurations from a JSON file.

Parameters:: filename – Path to input file.
Returns:: List of Configuration objects.

bsym.configuration.save_configurations(configurations: list[Configuration], filename: str) → None[source]

Save configurations to a JSON file.

Parameters:

configurations – List of Configuration objects to save.
filename – Path to output file.