Dear LAMMPS Users,
I am trying to simulate a system which a graphite as the bottom substrate.
We all know the original structure of graphite surface is in shape of rhombus.
However, I want to setup the simulation system as a cubic instead of Triclinic box.
Does anyone have a idea about this？
Do I need change the most initial shape of graphite surface? Or is there any lammps command to realize this?
Thank you very much for any suggestion in advance!
Liyi Bai
Hello Liyi,
You only need to figure out (by drawing the graphene lattice) a small
rectangular unit cell. Here are the coordinates of a possible unit
cell for single-layer graphene:
atom id x y z
atom 1: sqrt(3)/2*1.42 0 0
atom 2: 0 1.42/2 0
atom 3: 0 1.42*3/2 0
atom 4: sqrt(3)*1.42/2 1.42*2 0
Here, I assume that the bond length is 1.42 A. With the unit cell
defined, you can simply make copies of it in the planar directions (x
and y here). If you were considering multi-layer graphene (graphite),
you can do it in a similar way. I think you can do it within a LAMMPS
input script, but I usually suggest my students to do this kind of
work by writing a small piece of code using a computer language (e.g.
matlab or python).
Best,
Bruce
Dear Professor Fan.
Thank you very much for your nice suggestion.
I followed the process as you pointed out and did a short MD simulation.
However, the surface is not perfect combined when PBC applied.
The atoms inside the yellow box is single unit simulation cell.(see following snapshot)
There is no bonds between cells.
Could you point out what’s going on here?
Thank you very much.
Liyi Bai
Bruce Fan <brucenju@…24…> 于2018年12月5日周三 上午5:15写道：
Hello,
I don't know what do you mean exactly. Your box lengths (based on your
figure) look more or less reasonable. The box length in the vertical
direction seems to be a little bit smaller than "the correct value"
but I don't think it will cause problems in MD simulation.
Best,
Bruce