Calculating free energy difference on clustered atoms

Dear LAMMPS users,

I have a system consists of silver atom in clusters and free silver ions.
Throughout NVT run, the silver ions is forming aggregates with free silver ions or on the available silver clusters.

I have used the following commands to group the clusters:

compute cluster 1 cluster/atom 2.9
compute cc2 1 chunk/atom c_cluster compress yes

variable agg1 atom “c_cc2==1”

variable agg2 atom “c_cc2==2”
variable agg3 atom “c_cc2==3”
variable agg4 atom “c_cc2==4” #which then used to define the group

Since there is a limit in number of groups which can be created (32 atoms), there will be clusters which can’t be grouped. My purpose to create the groups is to calculate the free energy difference (before and after the aggregation). Any suggestion to address the group limit are welcome.

Thank you.

Dear LAMMPS users,

I have a system consists of silver atom in clusters and free silver ions.
Throughout NVT run, the silver ions is forming aggregates with free silver
ions or on the available silver clusters.

I have used the following commands to group the clusters:

compute cluster 1 cluster/atom 2.9
compute cc2 1 chunk/atom c_cluster compress yes
variable agg1 atom "c_cc2==1"
variable agg2 atom "c_cc2==2"
variable agg3 atom "c_cc2==3"
variable agg4 atom "c_cc2==4" #which then used to define the group
...

Since there is a limit in number of groups which can be created (32
atoms), there will be clusters which can't be grouped. My purpose to create
the groups is to calculate the free energy difference (before and after the
aggregation). Any suggestion to address the group limit are welcome.

​you cannot lift the group limit without rewriting large chunks of LAMMPS,
breaking compatibility with all off-site add-ons and possibly some
operating systems.
that is why the chunk infrastructure was introduced. you can do pretty much
everything that you would do with groups using chunks.

axel.

Dear Axel,

Thank you very much for your suggestion and clarification.