Generalize 'model_system'

[Bernadette-Mohr]

Could we rename, e.g., atom_index or atomic_system to index and system, and isolate calls to specific ase functionalities to appropriate cases?
Would this also make sense for electronic-calculations-specific methods, e.g. Symmetry?

[JFRudzinski]

I propose particle_indices instead of atom_indices in #150

We need to discuss which quantities live in model system versus, e.g., cell