Corrections to make everything 3N-dim vectors.

Positions, velocities, and masses should be 3N-dimensional, even in these
toy models.
Added convert_to_3Ndim function.

This will lead to a better way of doing switch between toy dynamics and
atomic systems.
Finished incorporating convert_to_3Ndim

Much cleaner. Now the internals of toy_dynamics use the natural arrays of
size ndof, while Snapshots etc see 3N atoms.
Fixes so langevin_integrator_check works.

Required a few more fixes and some undoing for the way we handle the 3xN-dim
vectors vs the ndofs-dim vectors.