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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: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 27 Oct 2017 13:28:13 -0400

On Fri, Oct 27, 2017 at 1:03 PM, Lijie Tu <lt374@...827...> wrote:
> 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.

no, you don't. how many atom types you have to define depends solely
on the force field, not on your geometry or whether it has periodic
boundaries or not.
and from what i understand, there are only 12 distinct atom types for
the force field you are using.

actually, two would be sufficient, if it wasn't for the fact, that the
force field you want to use does not 100% comply with the regular
stillinger-weber formalism.
the normal SW setup consists of a pair wise additive term that is
element specific and an angle dependent term with a fixed equilibrium
angle and which depends in essence only on the central atom type. i.e.
you can have a parameterization for diamond or graphite, but not one
for both.

the force field that you want to use, however, allows for multiple
equilibrium angle values and works around the limitation of the SW
formalism by defining multiple atom types to differentiate between
those.

>
> 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 think that your problem is in the defining of the geometry and how
you assign atom types.
it is highly unlikely that you need more atom types. i think you are
misinterpreting what is an atom type.

since LAMMPS is open source, you are also free to modify it to serve
your needs better. in any case, you have not so far produced a
*convincing* proof, that there is something wrong with LAMMPS, or that
something needs to be improved on the LAMMPS side. unless you do, i
will assume, that this is something that needs to be addressed on your
side.

axel.

>
> 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
>



-- 
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.