dscribe.utils.geometry module

Copyright 2019 DScribe developers

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

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dscribe.utils.geometry.get_adjacency_list(adjacency_matrix)[source]

Used to transform an adjacency matrix into an adjacency list. The adjacency list provides much faster access to the neighbours of a node.

Parameters

adjacency_matrix (scipy.sparse.spmatrix) – The adjacency matrix from which the adjacency list is constructed from. Any of the scipy sparse matrix classes.

Returns

A list of neighbouring indices. The list of neighbouring indices for atom at index i is given by accessing the ith element of this list.

Return type

list

dscribe.utils.geometry.get_adjacency_matrix(radius, pos1, pos2=None, output_type='coo_matrix')[source]

Calculates a sparse adjacency matrix by only considering distances within a certain cutoff. Uses a k-d tree to reach O(n log(N)) time complexity.

Parameters

  • radius (float) – The cutoff radius within which distances are calculated. Distances outside this radius are not included.

  • pos1 (np.ndarray) – A list of N-dimensional positions.

  • pos2 (np.ndarray) – A list of N-dimensional positions. If not provided, is assumed to be the same as pos1.

  • output_type (str) – Which container to use for output data. Options: “dok_matrix”, “coo_matrix”, “dict”, or “ndarray”. Default: “dok_matrix”.

Returns

Symmetric sparse 2D matrix containing the pairwise distances.

Return type

dok_matrix | np.array | coo_matrix | dict

dscribe.utils.geometry.get_extended_system(system, radial_cutoff, centers=None, return_cell_indices=False)[source]

Used to create a periodically extended system. If centers are not specified, simply takes returns the original system multiplied by an integer amount of times in each direction to cover the radial cutoff. If centers are provided, returns the exact atoms that are within the given radial cutoff from the given centers.

Parameters

  • original_system (ase.Atoms) – The original periodic system to duplicate.

  • radial_cutoff (float) – The radial cutoff to use in constructing the extended system.

  • centers (np.ndarray) – Array of xyz-coordinates from which the distance is calculated. If provided, these centers are used to calculate the exact distance and only atoms within the radial cutoff from these centers are returned.

  • return_cell_indices (boolean) – Whether to return an array of cell indices for each atom in the extended system.

Returns

If return_cell_indices is False, returns the new extended system. Else returns a tuple containing the new extended system as the first entry and the index of the periodically repeated cell for each atom as the second entry.

Return type

ase.Atoms | tuple