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Re: [lammps-users] Save redundancy in the input file
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Re: [lammps-users] Save redundancy in the input file


From: Lijie Tu <lt374@...827...>
Date: Fri, 27 Oct 2017 13:03:33 -0400

The superlattice (~1k atoms) we model is not periodic and each atom has a uniquely different environment so we have to give a different type to each atom. 

For a similar but much smaller system(~12 atom types), we can build a reasonable potential file. The only obstacle of scaling this file to ~1k atoms is that we need to specify all unnecessary zeros in the end of the file that look like:

# zero terms
Se1 Se1 Se1    0.000   1.000   1.000   1.000   1.000   1.000   1.000   1.000  4  0   0.000
Se1 Se1 W1     0.000   1.000   1.000   1.000   1.000   1.000   1.000   1.000  4  0   0.000
Se1 Se1 Se2    0.000   1.000   1.000   1.000   1.000   1.000   1.000   1.000  4  0   0.000
Se1 Se1 Se3    0.000   1.000   1.000   1.000   1.000   1.000   1.000   1.000  4  0   0.000
Se1 Se1 W2     0.000   1.000   1.000   1.000   1.000   1.000   1.000   1.000  4  0   0.000
......

Is there any way getting around adding zero terms? or do we have to hack the source code?

I have attached the potential file, input file in this email. 

They come from this paper:  https://arxiv.org/abs/1704.03147 

Also the input files can be downloaded at:  http://jiangjinwu.org/sw

Thanks,
Lijie


On Wed, Oct 25, 2017 at 6:14 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Wed, Oct 25, 2017 at 5:11 PM, Lijie Tu <lt374@...12...827...> wrote:
> Hi all,
>
> I'm just starting to use lammps to do a damped MD simulation to find the
> energy minimum for a large 2d layer with about 1k atoms. The system is a big
> triangular superlattice and is not periodic. I see that in order to name all
> the interactions in the system there is a lot of redundancy in the input
> file.
>
> For example, I have to specify the interaction between the 1st atom and each
> of the other atoms, though there may be no interaction between 1st and 1000
> th atom at all, I still have to put many zeros in the input file. This
> causes a ~10GB input file.
>
> I was wondering how I can cut this redundancy and only specify the
> interaction that is meaningful in the input file.

you don't explain, why you have to specify all interactions
explicitly, i.e. give each atom a different type.
in a typical simple input all atoms would have the same atom type and
then only one set of parameters needs to be specified.
more complex systems have a few atom types, even for complex
biomolecular systems, there are rarely more than 50 atom types,
and there all mixed terms can be inferred from the interactions of
those 20-50 atom types with itself through applying a mixing rule.

axel.

>
> Thanks,
> Lijie
>
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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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