I've installed and can run LAMMPS on macOS as desdribed in Okay, I've installed LAMMPS I: My first try of an example gives different & incorrect output and I'm looking forward to my first Xene experience! I've found https://lammpstutorials.github.io/tutorials/04-Graphene.html which begins:
Graphene sheet - First, a graphene sheet will be generated using VMD-topotool. The sheet will be deformed using applied displacement.
and that section begins:
Generation of the system The initial configuration (atoms positions, bonds, angles, etc.) is generated using VMD. Open VMD, and go to Extensions, Modeling, Nanotube Builder. A window named Carbon Nanostructures opens, and from this window it is possible to generate a sheet of graphene or BN, as well as a nanotube. For now tutorial, we are going to generate a 4 nm per 4 nm sheet of graphene. Simply change the values of "Edge length along x" and "Edge length along y" to 4, and click on "Generate Sheet(s)". You shoud see this:
However, at least from where I live I can not even get the following links to work:
and in any event I'll be building my own honeycomb structure to include buckling and defects. So I'd like to ask:
Question: I'd like to make a small graphene flake for a LAMMPS simulation using my Python script (not someone else's program), but how?
I was hoping on reverse-engineering the output file from the VMD-toptool and generating a new one from my python script but now I have nothing to go on. I'm assuming it's a text file with atomic positions on a honeycomb lattice but not sure what else needs to be in it.
update 1: this tutorial looks promising
update 2: potentially very helpful!