Does my misuse of fix npt cause the obvious oscillation of graphene during barostat?

Hello everyone,

I started to simulate graphene and try to equilibrate the sheet with fix npt command. But I found that during the barostat the sheet oscillated a lot and it looks like a ripple on the graphene.

The boundary condition is p p s. I used airebo potential. The fix npt command is used to control the pressure at the periodic boundaries to be zero. And some key commands I used are listed as the following. Please find the input file in the attachments.

 pair\_style airebo 3\.0
 pair\_coeff \* \* CH\.airebo C

 neighbor 2\.0 nsq

 min\_style cg
 minimize 0 0 100000 100000

 fix npt\_relax all npt temp 300 300 0\.05 x 0 0 0\.5 y 0 0 0\.5 drag 0\.2

I can understand that at finite temperature the atoms moves around their lattice positions. But the max magnitude of oscillation along the z axis is about 5.5 angstrom in my simulation and it seems a bit high. I also changed the temperature of my simulation, at 10 Kelvin the magnitude is lower with about 2 angstrom. I feel weird that the magnitude also related to the size of the graphene. If I use a bigger sheet which contains about 4 times the number of atoms with total 80000 atoms, the max magnitude increased to about 9.5 angtrom at 300 Kelvin and 4 angtrom at 10 K. Please find the pictures of the oscillation in the attachments.

I checked the docs and tried to change some values in the commands, but the results are similar. The result is OK if I use these command to equilibrate bulk materials. I am not sure whether the oscillation of the graphene sheet is reasonable under the barostat? Do I misuse some commands or parameters? This looks like a very basic question but I am kind of getting stuck with this for weeks. Please guide me if you have any suggestions.

Many thanks in advance!

With My Best Regards,


in.equil (553 Bytes)




The easiest way to answer the question in the head is to run with a fix nvt instead and see if the oscillations persist. They could very well be a “feature” and not a “bug”. I do not know enough about graphene sheets to assess whether or not this behavior is expected. A literature search would be appropriate for that.

Dear Stefan,

Thanks very much for your reply! Following your advice, I have run the simulation with fix nvt as well as with fix nve. At both cases, the oscillation still exists. Nevertheless, the magnitude of the oscillation is smaller.

I have read several papers about graphene, but maybe it is a point too basic to mention about, I have not seen any words in the papers about this problem. And usually top view of the graphene sheet is shown, it also seems hard to find a clue in the figures. But I think I followed the method, which are described in the papers, to relax the graphene.

I am afraid maybe some bad use of the LAMMPS commands or values in my input file caused the oscillation. So I post my question on the mail list with the hope that maybe some users with experiences of simulation of graphene with LAMMPS may give a hand to me. If all the commands in my input file is good, maybe it is a reasonable “feature” as you said. But I am not very sure whether the magnitude is too large.

My Best,