Further refactoring of the geometry and simulation box

Description

Further refactoring of the geometry and simulation box. The lattice vectors are now part of the geometry and are initialized along with it. This allows to simplify the code, as we can now transform the reduced coordinates read from the input file into Cartesian coordinates while initializing the geometry.

Also, many routines where previously in the simul_box module instead of the geometry because they required the lattice vectors. This is now changed, which allows to simplify many things.

In a subsequent merge request I'll make the lattice vectors in the simulation box private. I didn't want to do it here as this merge request is already quite large.

Closes #257 (closed)