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:
- Is it possible to use this command to create group (of atoms which belong to the cluster) for each cluster?
- 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