Change behaviour of comgroup

The comgroup option now applies to all three dimensions instead of only the one that is analysed in the PlanarBase class. Additionally, some tests and code cleanup at the relevant places was performed.

This is only preliminary work, besides the above mentioned changes the center of mass calculation that is consistent with periodic boundary conditions is put into a separate function and thoroughly tested. Later, this will be the basis for other geometries.

Note: This introduces a wrap into the single_frame function. This is because we are at the moment not able to guarantee that modules behave correctly if molecules are far beyond the box edges.