Apply CSVR (Canonical Sampling through Velocity Rescaling) thermostat Based on Bussi, Donadio, Parrinello, J. Chem. Phys. 126, 014101 (2007) This the

* @return the atoms in the constraint as a tuple */

Build a spanning tree of the molecule using BFS Handles disconnected fragments by building a separate tree for each component

* Build a molecule with a UnitCell attached (for crystal tests). * After building a normal molecule, consumes 6 floats for cell parameters. */

compute the RMSD between the two sets of coordinates

Separate the three components, then cast for unsigned char and store.