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Re: [lammps-users] Using compute cluster/atom to create group
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Re: [lammps-users] Using compute cluster/atom to create group

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 17 Aug 2017 10:36:46 -0400

On Thu, Aug 17, 2017 at 10:27 AM, Imanuel Kristanto <imanuelkristanto@...24...> wrote:
Dear LAMMPS users,

I have related questions to my previous thread.
In brief, my system is consisted of silver nanoparticles in aggregates. I have used the following command to obtain the histogram of the cluster size:
compute cluster 1 cluster/atom 2.9
compute cc1 1 chunk/atom c_cluster compress yes
compute size 1 property/chunk cc1 count
fix 2 1 ave/histo 10000 1 10000 0 30 30 c_size mode vector ave one beyond ignore file tmp.histo
My question are:
1. Is it possible to use this command to create group (of atoms which belong to the cluster) for each cluster? 

​it should be possible though using an atom style variable. you can define one variable for each cluster id with an _expression_ like c_cluster==1, where​ then the variable evaluates to zero for all atoms that are not part of the cluster. this variable can then be used to define a group. you have to repeat this for each group.
please note, that there is a limit in the number of groups and defining a group per cluster is not always a good idea. many times, there are more effective approaches.

2. Or is it possible to obtain the list of atom-IDs for all atoms assigned to the clusters?



Thank you.
Best Regards,

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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.