Make inner size of passive volume box three-dimensional

With this, the parameter inner_size of the passive model BoxModel reaches out to a new dimension!

Up to now, this parameter was 2D and the subtracted volume would extend the original volume in z, leaving the box open along z.

I made this parameter 3D, such that now one gets an actual box, see attached image.

Note: It is now no longer possible to leave one side open - I'll make a remark on this in the discussion though.