uf3.representation.distances

This module provides functions for computing neighbor lists, evaluating pair distances, computing direction cosines for force components, and fitting/evaluating one-dimensional BSplines.

Functions

compute_direction_cosines	Intermediate function for computing derivatives for forces.
derivatives_by_interaction	Identify pair distances within a supercell and derivatives for evaluating forces, subject to lower and upper bounds given by r_min_map and r_max_map, per pair interaction e.g.
distances_by_interaction	Identify pair distances within an entry (or between an entry and its supercell), subject to lower and upper bounds given by r_min_map and r_max_map, per pair interaction e.g.
distances_from_geometry	Identify pair distances within a geometry (or between a geometry and its supercell), subject to r_min < r < r_max.
get_distance_derivatives	Identify pair distances within a supercell, subject to r_min < r < r_max, along with derivatives for evaluating forces.
get_distance_matrix	Get distance matrix from geometry and, optionally, supercell including atoms from adjacent images.
kronecker_delta
kronecker_vectorized
mask_matrix_by_pair_interaction	Generates boolean mask for the distance matrix based on composition
mask_supercell_with_radius	Makes a copy of supercell and deletes atoms that are further than r_max away from any atom in the unit cell geometry.
summarize_distances	Construct histogram of distances per pair interaction across