WIP: Add set_atoms to calculator object

The Atoms object assumes the calculator object should have a set_atoms method, however, this was missing from the actual calculator template. I feel like this is a mistake? At least it broke Vasp2, after a change, where I didn't realise the atoms.calc property was relying on the existence of a calc.set_atoms method.

However, it seems like this breaks the EMT calculator, and I can't quite see why? It seems like the initialize is never called, but I don't quite understand why enforcing the set_atoms function would be incorrect. ideas, @askhl?