improved the handling of the internal basis of the molecule

- decremented the numbers of the read-in origin-/axes-atoms in the
  configuration class to account for C++s counting habits
- added the member function set_intbasis() to the molecule class
  to (initially) set the internal basis of the molecule
- modified the function Molecule::clean_up() to use the internal
  basis as a reference
- added the function Molecule::update_geomprops() to recalculate the
  geometric properties of the molecule after the coordinates have
  been changed