Changed the order in which we read the lattice vectors and the simulation box. For this to work, a few changes are done to the input:
 a) LatticeParameters is now mandatory for periodic systems (even for mixed periodicity).
 b) The length of the lattice vectors is used as the default length for the simulation box along the **non-periodic** dimensions.
 c) It is now possible to set LSize along with LatticeParameters. In that case the length of the resulting box along periodic dimensions must be the same as the length of the corresponding lattice vectors, but this allows to override the length of the non-periodic dimensions that is given by the lattice vectors.
 d) For a cylinder parallel along the axis, the Xlength variable is now ignored. Instead, the length of the cylinder is determined by the length of the lattice vector.