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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: Wed, 25 Oct 2017 18:14:06 -0400

On Wed, Oct 25, 2017 at 5:11 PM, Lijie Tu <lt374@...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.


> Thanks,
> Lijie
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Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.