Atomic clusters

The main information on the nodes and linkers in chic is exposed by the AtomicCluster class:

class chic.atomic_cluster.AtomicCluster[source]

Represents a cluster of atoms in a structure.

property graph

Getter for _graph attribute.

property bead_ids

Getter for bead_ids attribute. These are the unique IDs assigned to the beads for the cluster.

property beads_frac_coords

Getter for beads_frac_coords attribute. These are the fractional coordinates of the beads.

property beads_images

Getter for beads_images attribute. These are the images of the beads.

property atom_to_bead_index

Getter for atom_to_bead_index attribute. This is a dictionary mapping the atom indices to the beads indices.

property internal_bead_bonds

Getter for internal_bead_bonds attribute. This is a list of tuples representing the bonds between beads in the cluster.

property site_indices: List[int]

list of site indices in the cluster.

Type:

return

property species: List[str]

list of species in the cluster.

Type:

return

property cart_coords: ndarray

cartesian coordinates of the cluster.

Type:

return

property coordination_number: int

coordination number of the cluster, i.e. the number of external edges.

Type:

return

property skip: bool

Getter for skip attribute.

get_indices_by_species(species: str) → List[int][source]

Get the indices of the sites in the cluster with a given species.

get_cart_coords_by_species(species: str) → ndarray[source]

Get the cartesian coordinates of the sites in the cluster with a given species.

assign_beads(bead_ids: List[int], beads_frac_coords: ndarray, beads_images: ndarray, atom_to_bead_index: Dict[int, List[int]], internal_bead_bonds: List[Tuple[int, int]])[source]

Assign beads to the cluster.

Parameters:

  • bead_ids – list of bead IDs.

  • beads_frac_coords – fractional coordinates of the beads.

  • beads_images – images of the beads.

  • atom_to_bead_index – dictionary mapping the atom indices to the beads indices.

  • internal_bead_bonds – list of tuples representing the bonds between beads in the cluster.

get_centroid(skip_elements: List[str] | None = None) → ndarray[source]

Compute the centroid of the cluster.

Parameters:

skip_elements – the elements to skip when computing the centroid.

find_rings(including: List[str] | None = None, strong_rings: bool = False, connective_including: bool = False)[source]

Find all rings in the cluster.

Parameters:

  • including – list of elements to include in the rings. If None, all rings will be returned irrespective of the elements included.

  • connective_including – whether or not the connecting elements specified in “including” must also be the elements that connect to other building units.

  • strong_rings – whether to make sure the rings cannot be decomposed into smaller rings.

to_molecule() → Molecule[source]

Convert the AtomicCluster to a pymatgen Molecule object.

Note, this has a lot of shared functionality, but loses the site indexing that I want to keep uniform across all representations.

get_image_by_site_index(site_index: int) → ndarray[source]

Exctract the periodic image for a given site index.

visualise()[source]

Visualise the cluster using crystal toolkit.

classmethod with_updated_coordinates_and_images(instance, new_cart_coords: ndarray, new_images: ndarray)[source]

Create a copy of an existing AtomicCluster instance with updated cartesian coordinates and images. Also set edges_external to None.

Parameters:

  • instance – An instance of AtomicCluster to be copied.

  • new_cart_coords – Updated cartesian coordinates.

  • new_images – Updated images.

Returns:

New AtomicCluster instance with updated attributes.