Unfold the traj before calculating the MSD.
Instead of the complex periodic in time boundary condition
Implicit sum over all sites and time origin
less verbose and estimate time left after reading
Mv all pos of a given atom in a single array. Decrease io
Print site label for which one computes MSD. Give idea of advance
Print estimation of remaining time, plus cleanup
Unfold correctly: add length to every timestep after crossing, not the single one