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Re: [lammps-users] Fragments and Melecules analysis/quantification
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Re: [lammps-users] Fragments and Melecules analysis/quantification


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sun, 20 Aug 2017 09:53:38 -0400



On Fri, Aug 18, 2017 at 1:03 PM, renefbg <renefbg@...6901...> wrote:

Dear all,

Is there a way for LAMMPS (or perhaps VMD) to compute the molecules or fragments existing in each step of the dump file, for example, for the whole simulation?

With a specific determined cutoff distance, could the trajectory file interpret all the fragments/molecules present in each frame and export to a text file or plot it?

As I am currently working on small systems, I can make this evaluation manually, but as the system increases, would be better if the software could supply this info for each timestep.

​can you provide some more context?​ what kind of force field and type of system are you talking about here.

for systems with only atomic interactions there is already compute cluster/atom that steve pointed out and you can output the cluster id together with the atom id.
however, for systems with explicit bonds, it has some limitations, since this is based on a neighbor list where 1-2, 1-3, and 1-4 pairs may be excluded.

it is straightforward to implement a similar compute fragment/atom that is based on the information about explicit bonds rather than distance. please see the attached files, that should be included in a future version of LAMMPS

for systems based on ReaxFF, where bonds are implicit, there is fix reax/c/species.

axel.


 

Thanks.

Rene


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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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