Allow passing simulation settings via config files

In PR #594, we are introducing a way to pass the `surface_refinement_limits` used for the surface refinement via the config file, by storing it to `sim.world`. We might want to think about allowing for the same thing for all (?) keyword arguments of `calculate_electric_potential!` etc. such that the setting can also be saved to a file.
We might also think about storing the simulation settings used to the `sim.config_dict` (see also #435).