box

Functions related to simulation boxes and boundary conditions.

Functions

box_volume	Calculate the volume of a (triclinic) box.
diagonal	Calculate the length of the diagonal of an orthogonal box.
make_whole	Make compounds of a MDAnalysis AtomGroup whole that are split across periodic boundaries.
unwrap	Unwrap the atoms of a MDAnalysis AtomGroup out of the primary unit cell, i.e. calculate their coordinates in real space.
unwrap_trj	Unwrap the atoms of a MDAnalysis AtomGroup out of the primary unit cell, i.e. calculate their coordinates in real space.
vdist	Calculate the distance vectors between two position arrays.
volume	Calculate the volume of orthogonal boxes.
wrap	Shift compounds of an MDAnalysis AtomGroup back into the primary unit cell.
wrap_pos	Shift all particle positions into the primary unit cell.