Feels like I have been actively abusing the mailing list lately, apologise in advance…
I am trying to add my own classes (atoms, forces, bonds etc) and it came across my mind whether I need to worry about MPI implementation at all? Or should the base code of LAMMPS handle the MPI communicator for me?
Depends on what you want to add. Parallelisms of many low-level parts are handled by high-level codes so most of the time you don’t need to worry about parallelism. But it is a good practice to identify the existing class that most resembles your modification and examine what additional measures have been taken to consider parallelism.