Comapring KC-n and KC-z

[Anikeya Aditya]

Dear Twister Team,

I read your paper cited as "J. Phys. Chem. C 2019, 123, 9770−9778" and wondered if I could compare KC-n vs KC-z forcefields for a bilayer MoS2 in LAMMPS. I especially wanted to see how it affects the forces on individual atoms. I found the KC-z forcefield and how to set it up in lammps from the TWISTER code. Where can I find the method to set up the full KC-n forcefield? Does it require another forcefield file?

With regards,

Anikeya Aditya

[Indrajit Maity]

Hi Anikeya,

I don't think we have released the KC-n source code for LAMMPS. @Mit originally wrote the code, and I am not sure if he has the time to clean it up for public release.

Best wishes,

Indrajit

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[Anikeya Aditya]

Dear Indrajit,

Thank you for your response.

Can you please explain how to use mpi4py to run the twister code? I am trying to create structures at a very low twist, <0.3 degree, and it is taking a very long time in serial mode. Using MPI4PY might help, but I cannot understand if I have to edit the code somewhere or how to execute it.

With regards,

Anikeya Aditya

[Indrajit Maity]

Hi Anikeya,

Instead of running the command:

python3 path-to-src/get_angle.py get_ang.inp

Try using:

mpirun -np 4 python3 path-to-src/get_angle.py get_ang.inp

You can adjust the number of processors as needed. Once you have MPI for Python installed, you should find mpirun/mpiexec in your /usr/local/bin.

Best wishes,
Indrajit

[Anikeya Aditya]

Dear Indrajit,

Thank you very much for the quick response.

One last thing, I use the homo.sh to generate the structures using the hex table index. So in homo.sh, there are multiple Python files being executed, as shown in the figure below. Can I use mpirun with all of them?

I am not using lammps relaxation and only need lammps input structure so will using it with "python 3 path/twister.py twist.inp" and "python3 tolammps.py" be enough.

With regards,

Anikeya Aditya

[Indrajit Maity]

Hi Anikeya,

Unfortunately, the mpi support is available for get_ang and not for the homo.sh.

One suggestion could be to submit it as a job in a local supercomputer (to avoid crashes while running on your laptop). 

Best wishes,

Indrajit 

[Anikeya Aditya]

Thank you very much for the quick response. 

I see, so to confirm only get_ang.py can use mpi and other scripts like twister.py toqe.py and tolammps.py run serially?

With regards,

Anikeya Aditya

On Wed, Sep 4, 2024 at 1:33 PM Indrajit Maity <indrajit...@gmail.com> wrote:

Hi Anikeya,

Unfortunately, the mpi support is available for get_ang and not for the homo.sh.

One suggestion could be to submit it as a job in a local supercomputer (to avoid crashes while running on your laptop). 

Best wishes,

Indrajit 

On Wed, 4 Sep 2024, 22:25 Anikeya Aditya, <aad...@usc.edu> wrote:

Dear Indrajit,

Thank you very much for the quick response.

One last thing, I use the homo.sh to generate the structures using the hex table index. So in homo.sh, there are multiple Python files being executed, as shown in the figure below. Can I use mpirun with all of them?

I am not using lammps relaxation and only need lammps input structure so will using it with "python 3 path/twister.py twist.inp" and "python3 tolammps.py" be enough.

With regards,

Anikeya Aditya

On Wed, Sep 4, 2024 at 6:45 AM Indrajit Maity <indrajit...@gmail.com> wrote:

Hi Anikeya,

Instead of running the command:

python3 path-to-src/get_angle.py get_ang.inp

Try using:

mpirun -np 4 python3 path-to-src/get_angle.py get_ang.inp

You can adjust the number of processors as needed. Once you have MPI for Python installed, you should find mpirun/mpiexec in your /usr/local/bin.

Best wishes,
Indrajit

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