Add atomic index column to atom tables

[herbertludowieg]

Is your feature request related to a problem? Please describe.
In a geometry optimization the atom index does not seem to be a good way to keep track of the atomic indices within each frame. As such, I propose that we add a new column to keep track of the atomic index within each frame.

Describe the solution you'd like
Would have to change every parse_atom method to include this new column.

Describe alternatives you've considered
Using the set column, however, for the ADF parser this is changed to be used for generating the MO's so it would be more work to change the reference to those columns.