Resolve "Remove atoms from base calculator"

Now the configuration manager is responsible for the configuration being sampled.

changes

• added atoms property to configuration manager

• renamed to get_swap_state, get_flip_state. Other name suggestions are welcome.

• let get_swap_state and get_flip_state return the much more usable format indices : List[int], elements: List[int]. This format can go directly to update_occupation(indices, elements)

• add a new method in base_ensemble get_property_change(indices, elements) ->float that takes this input and give you the calculators property difference of new - old state.

Closes #185 (closed)