New version of output files

[YHordijk]

It would be good to have a new version of the output files. The current output files are limited in that they only contain the information requested. For many properties, such as geometrical parameters, it would be better to calculate them in a post-processing analysis/plotting script. For example, if the xyz-coordinates for each step were included we could calculate bond-distances/angles/dihedrals on the fly. We can also store things like orbital energies/overlaps.