structuretoolkit.analyse.neighbors.get_neighborhood

structuretoolkit.analyse.neighbors.get_neighborhood#

structuretoolkit.analyse.neighbors.get_neighborhood(structure: Atoms, positions: ndarray, num_neighbors: int = 12, cutoff_radius: float = inf, width_buffer: float = 1.2, mode: str = 'filled', norm_order: int = 2)[source]#
Parameters:

  • structure

  • position – Position in a box whose neighborhood information is analysed

  • num_neighbors (int) – Number of nearest neighbors

  • cutoff_radius (float) – Upper bound of the distance to which the search is to be done

  • width_buffer (float) – Width of the layer to be added to account for pbc.

  • mode (str) – Representation of per-atom quantities (distances etc.). Choose from ‘filled’, ‘ragged’ and ‘flattened’.

  • norm_order (int) – Norm to use for the neighborhood search and shell recognition. The definition follows the conventional Lp norm (cf. https://en.wikipedia.org/wiki/Lp_space). This is an feature and for anything other than norm_order=2, there is no guarantee that this works flawlessly.

Returns:

Neighbors instances with the neighbor

indices, distances and vectors

Return type:

structuretoolkit.analyse.neighbors.Tree