amep.pbc

Periodic Boundary Conditions

The AMEP module amep.pbc contains methods that apply periodic boundary condictions and calculate distances and difference vectors considering periodic boundaries.

Functions

distance_matrix(coords, box_boundary[, ...])	Calculates the distance matrix.
distance_matrix_parallel(coords, box_boundary)	Calculates the distance matrix.
distances(coords[, other_coords])	Returns a 1D array of all pairwise distances.
find_pairs(coords, box_boundary[, ids, ...])	Identifies pairs of particles based on the pairwise distance.
fold(coords, box_boundary)	Applies periodic boundary conditions to the given coordinates, i.e. folds the coordinates back into the box if they are not inside the box.
kdtree(coords, box_boundary[, pbc])	Creates a scipy.spatial._kdtree.KDTree object with and without considering periodic boundary conditions.
mirror_points(coords, box_boundary[, width, ...])	Returns the points and their first periodic mirrors.
pbc_diff(v1, v2, box_boundary[, pbc])	Calculates the difference vector(s) between v1 and v2 considering periodic boundary conditions.
pbc_diff_rect(v1, v2, box_boundary)	Calculate the difference of two vectors, considering periodic boundary conditions within a rectangular box.
pbc_points(coords, box_boundary[, ...])	Returns the points and their first periodic images.