Help with heating simulation of moire mos2 structure

[Anikeya Aditya]

Dear Twister team,

Thank you for developing the excellent code. I have been using it to see how different rotations in mos2 look. 

I wanted to heat the system to room temperature (300K) to see how it affects the moire pattern. But the system is not stable. I am using the force fields provided in the code(tmd.sw MoS.KC) and attaching the lammps input file and a video of the heating simulation. Please tell me if I am not using the forcefield correctly or if there is something wrong with the input file.

I would greatly appreciate your help.

With warm regards,

Anikeya Aditya

Graduate Student

CACS, USC

[Mit Naik]

Hi Anikeya,

Can you provide your input atom positions as well? Does the structural minimization at 0K look okay?

Best,

Mit

[Indrajit Maity]

Hi Anikeya,

I took a quick look at your input script. Sorry for the super late response.

 As Mit pointed out, a lammps.dat file would be easy to debug. However, based on the input file that you provided, I suspect the following could happen:

1) I see you are using tmd.sw files provided by Jiang et al. Normally, this requires to recompilation of lammps with some modifications which are discussed here: path-to-FFRelaxation/mos2/near_0/relax/without_python/README

If you follow this you should be able to recompile lammps with a modified pair_sw.cpp provided in the same folder and run the calculations as you have been doing.

Alternatively, if you don't want to do any reinstallation or modification of lammps yourself:

You could use the most recent version of lammps and replace the following two lines:

pair_style hybrid/overlay sw sw kolmogorov/crespi/z 14.0 kolmogorov/crespi/z 14.0 kolmogorov/crespi/z 14.0 kolmogorov/crespi/z 14.0 lj/cut 10.0     by

pair_style hybrid/overlay sw/mod sw/mod kolmogorov/crespi/z 14.0 kolmogorov/crespi/z 14.0 kolmogorov/crespi/z 14.0 kolmogorov/crespi/z 14.0 lj/cut 10.0

and

pair_coeff * * sw 1 tmd.sw Mo S S NULL NULL NULL
pair_coeff * * sw 2 tmd.sw NULL NULL NULL Mo S S

by

pair_coeff * * sw/mod 1 tmd.sw Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw NULL NULL NULL Mo S S

I will try to update the README file and the source code example for the latter option accordingly soon (through GitHub). Hope this helps.

Best regards,

Indrajit

--
You received this message because you are subscribed to the Google Groups "Twister Help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to twister-help...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/twister-help/460d88a8-7242-4cf8-8948-3b4f7d12b70dn%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Anikeya Aditya]

Dear Mit and Indrajit,

Sorry for getting back to you late.

I had compiled lammps with user misc and interlayer, but I had not done the pair_sw.cpp part. So I tried the alternative approach, and it is working. The system does not blow up on heating. Would you still recommend recompiling the lammps with modified pair_sw.cpp file or continue using the alternative methods?

How should I modify the lammps input file for bilayer graphene for a similar simulation?

I use the twister package to create the structures, then relax them in lammps using CG relax method to get minimum energy structure.

I am attaching files from the successful MoS2 simulation here.

lammps.in_nvt_heat --> input script for heating to 300K in nvt ensemble

lammps.in_cg --> input script for cg relax of generated structure

dump.300k-2.nvt --> dump file for last step of nvt run where the structure is at 300K

lammps.dat_min --> relaxed structure from cg relax

lammps.data --> structure generated by twister

Here are my graphene bilayer input files and output structures. I think they are fine but I would like your opinion if the input script(especially the forcefield setup) is correct.

lammps.in_graphene _cg --> input script for relaxing graphene bilayer in cg

lammps.in_graphene_nvt_heat --> heating relaxed str to 300K in nvt

lammps.dat_min_graphene --> relaxed str after cg relax

dump.300K-2.nvt_graphene --> structure after heating to 300 K

Waiting for your reply

with warm regards

Anikeya Aditya

[Indrajit Maity]

Hi Anikeya,

"I had compiled lammps with user misc and interlayer, but I had not done the pair_sw.cpp part. So I tried the alternative approach, and it is working. The system does not blow up on heating. Would you still recommend recompiling the lammps with modified pair_sw.cpp file or continue using the alternative methods?"

I will suggest sticking to the new lammps (and it doesn't require the modification of the original pair_sw file).

How should I modify the lammps input file for bilayer graphene for a similar simulation?

Should be fairly straightforward since your simulations of twisted bilayer MoS2 are already working. You need the intralayer and interlayer interaction files. Also, the files look good to me.

Best regards,

Indrajit

To view this discussion on the web visit https://groups.google.com/d/msgid/twister-help/7155f2fe-2cc8-47ec-9279-15614d7d5706n%40googlegroups.com.