I'm just starting to use lammps to do a damped MD simulation to find the energy minimum for a large 2d layer with about 1k atoms. The system is a big triangular superlattice and is not periodic. I see that in order to name all the interactions in the system there is a lot of redundancy in the input file.
For example, I have to specify the interaction between the 1st atom and each of the other atoms, though there may be no interaction between 1st and 1000 th atom at all, I still have to put many zeros in the input file. This causes a ~10GB input file.
I was wondering how I can cut this redundancy and only specify the interaction that is meaningful in the input file.