Revised ligand::evaluate() and ligand::compose_result() to use one 3x3 matrix only
Renamed orientations_q to q, origins to o, and axes to a
Renamed coordinates to c and derivatives to d
Renamed forces to gf and torques to gt
Renamed conf to x
Removed intra-molecular free energy variable f
Renamed c0, c1 and c2 to x0, x1 and x2
Replaced {uniform_11(rng), ...} by make_array()