ENH: Fix properties type hint
Pyright does not handle properties defined via property(...) very well. Type hints for properties like Atoms.positions or Atoms.numbers are often missing or inaccurate. Switching to the decorator syntax improves type hinting support.
I’ve also made a few changes:
Reordered some class methods in Atoms to group related functionality together.
Added a new property: velocities.
I'm considering adding more properties, such as charges, which would automatically retrieve values from either initial_charges or _calc.get_charges(). Some existing getter/setter functions, like _get_positions, seem redundant in the presence of the @Property syntax and could potentially be deprecated.
(BTW, is there a method to get free runner time? It's a bit annoying...)