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

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1

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,

Liu

in.equil (553 Bytes)

initial_top_view.png

300K_side_view.png

10K_side_view.png

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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.

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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,

Liu