Using compute cluster/atom to create group

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

Thank you.

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?

​axel​

Dear Axel,

Well noted and thank you very much for your suggestion.

Best Regards,
Kristanto