WIP: More consistent Atom class

Open username-removed-71312 requested to merge new-atom-class into master

Atom class will now instantiate an internal Atoms of length 1 if it does not refer to another Atoms object.

This guarantees that it will behave the same always.

This also fixes one or more errors related to writing back into Atom objects (momenta).

Fixes: #3, #23

Edited by username-removed-71312