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


From: Imanuel Kristanto <imanuelkristanto@...24...>
Date: Wed, 30 Aug 2017 13:36:16 +0900

Dear Axel,

Thank you very much for your suggestion and clarification.



On Tue, Aug 29, 2017 at 11:44 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Tue, Aug 29, 2017 at 10:27 AM, Imanuel Kristanto <imanuelkristanto@...24...> wrote:
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.

 

Thank you.

--
Best Regards,
Kristanto

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



--
Best Regards,
Kristanto