Extract common logics to helper functions

[GardevoirX]

Currently we have compute metatomic, fix metatomic, and pair metatomic. And they share a lot of common parts. This PR aims at extracting them and put them into files like metatomic_systems and metatomic_types to ensure that in the future development these shared code won't be out of sync

One thing I am not sure is that this part exists in both compute and fix, but not in pair

    auto mincut = mta_data->max_cutoff + neighbor->skin;
    if (comm->get_comm_cutoff() < mincut) {
        if (comm->me == 0) {
            error->warning(FLERR,
                "Increasing communication cutoff to {:.8} for fix metatomic",
                mincut
            );
        }
        comm->cutghostuser = mincut;
    }

idk if this should also be in pair

[Luthaf]

One thing I am not sure is that this part exists in both compute and fix, but not in pair

No, the pairs code already properly handle this in LAMMPS.