autofragment.core.periodic

Periodic boundary condition utilities.

Functions

all_distances_periodic(positions, lattice)	Calculate all pairwise minimum image distances.
detect_periodic_bonds(system[, distance_cutoffs])	Detect bonds considering periodic boundaries.
get_bond_cutoff(elem1, elem2[, cutoffs])	Get bond cutoff distance for an element pair.
make_supercell(system, repetitions)	Create supercell by repeating unit cell.
minimum_image_distance(pos1, pos2, lattice)	Calculate minimum image distance between two points.
minimum_image_vector(pos1, pos2, lattice)	Get minimum image displacement vector from pos1 to pos2.

Classes

PeriodicGraph(system)

Graph representation for periodic systems.