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[lammps-users] Calculating free energy difference on clustered atoms
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[lammps-users] Calculating free energy difference on clustered atoms


From: Imanuel Kristanto <imanuelkristanto@...24...>
Date: Tue, 29 Aug 2017 23:27:04 +0900

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.

--
Best Regards,
Kristanto