Graphene from Atomsk to LAMMPS, Material Studio

LAMMPS LAMMPS Beginners
1

Hello everyone.
I want to create graphene layers and then cut an atomic system, using a 3-D shape defined in an STL file by using Atomsk (follow this tutorial Atomsk - Tutorial - Using 3-D Models in STL format). Then I import this atomic system into LAMMPS but the file only consists of atomic position information without bond information.
Could you help how to cut an atomic system of graphene layers, using a 3-D shape defined in an STL file by Atomsk and then import into LAMMPS, or Material Studio?

Thank you very much.

2

Not having any bonds is not a problem, if you would be using a (manybody) potential where the bonds are implicit, e.g. Tersoff, Stillinger-Weber, AIREBO, ReaxFF and thus must not be present.