uf3.data.composition.ChemicalSystem

class ChemicalSystem(element_list: Collection[str], degree: int = 2)

Bases: object

Handler class for managing quantities related to elements, composition, and element-element interactions.

Parameters

• element_list (list) – set of elements in chemical system e.g. [‘Ne’, ‘Xe’] or [10, 54]

• degree (int) – handle N-body interactions e.g. 2 to fit pair potentials.

Methods

from_config	Instantiate from configuration dictionary
get_composition_tuple	Extract composition vector from ase.Atoms object.
get_interaction_hashes	Compute integer hashes for element-element interactions.
get_interactions_list	Return flattened list of interactions from interactions map.
get_interactions_map	Compute interactions map from combinations of elements with replacement.

Attributes

degree
element_list
numbers
interactions
interactions_map
interaction_hashes

static from_config(config: Dict[Any, Any])

Instantiate from configuration dictionary

get_composition_tuple(geometry: ase.atoms.Atoms) → numpy.ndarray

Extract composition vector from ase.Atoms object.

Parameters

geometry (ase.Atoms) –

Returns

vector of frequency of

each element in self.element_list.

Return type

composition_vector

get_interaction_hashes() → Dict[int, numpy.ndarray]

Compute integer hashes for element-element interactions.

Returns

mapping of interaction tuples to integer

hashes based on element numbers, sorted by electronegativity.

Return type

interaction_hashes

get_interactions_list() → List[Tuple[str]]

Return flattened list of interactions from interactions map.

Returns

list of tuples of element symbols,

in order of degree. e.g. for unary system, [“W”, (“W”, “W”), (“W”, “W”, “W”)]

Return type

interactions_list

get_interactions_map() → Dict[int, Collection[Tuple[str]]]

Compute interactions map from combinations of elements with replacement.

Returns

tuples of element symbols, grouped by degree

up to self.degree, e.g. two-body (2) and three-body (3).

Return type

interactions_map