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SBC Class

Class for performing Symmetry-based clustering (SBC).

You can apply this class for partitioning a larger material into grains, a heterostructure into it's component etc. The clustering is based on finding periodically repeating motifs, and as such it is not suitable for e.g. finding molecules. Any atoms that do not have enough periodic repetitions will be returned as isolated clusters.

get_clusters​

def get_clusters(system,
                 angle_tol=20,
                 max_cell_size=6,
                 pos_tol=0.7,
                 merge_threshold=0.5,
                 merge_radius=1,
                 bond_threshold=0.65,
                 overlap_threshold=-0.1,
                 radii="covalent",
                 seed=7)

Used to detect and return structurally separate clusters within the given system.

Arguments:

  • system ase.Atoms - The structure to partition.

  • angle_tol float - angle_tol parameter for PeriodicFinder

  • max_cell_size float - max_cell_size parameter for PeriodicFinder.get_region

  • pos_tol float - pos_tol parameter for PeriodicFinder.get_region

  • merge_threshold float - A threshold for merging two clusters together. Give as a fraction of shared atoms. Value of 1 would mean that clusters are never merged, value of 0 means that they are merged always when at least one atom is shared.

  • merge_radius float - Radius for finding nearby atoms when deciding which cluster is closest. The atomic radii are subtracted from distances. Given in angstroms.

  • bond_threshold(float) - Used to control the connectivity threshold for defining a chemical connection between atoms. Controls e.g. what types of unit cells are accepted and how outliers are removed from clusters.

  • overlap_threshold(float) - Used to exclude non-physical cells by checking overlap of atoms. Overlap between two atoms is calculated by subtracting atomic radii from the distance between the atoms.

  • radii(str|np.ndarray) - The radii to use for atoms. Use either a preset or a custom list of atomic radii for each atom. The available presets are:

    • covalent: Covalent radii from DOI:10.1039/B801115J
    • vdw: van Der Waals radii from DOI:10.1039/C3DT50599E
    • vdw_covalent: preferably van Der Waals radii, covalent if vdw not defined.

  • seed(int) - The seed that is used for random number generation.

Returns:

A list of Clusters.