Configurations Analysis

LAMMPS LAMMPS General Discussion
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1

Dear All,
I’m new at this code and I’m having some issue to understand how to prepare the right input in order to study a particular system: I have a layered oxide and I would like to delete one or more atoms and calculate which configuration is the most stable. For a better explanation here an example:
In my system there are 30 atoms in 30 specific positions that can be deleted, by removing one of these atoms I’ll obtain a system with a void and 29/30 atoms. I would like to calculate which configuration is the most stable.
Is it a feasible calculation with LAMMPS? Does it require a particular script or there is a keyword specific for this case?

Thanks a lot for your help!

2

This kind of study is usually done with some kind of loop. You would first prepare and relax the full system and then save it as a restart file. Then you can do a loop over the list of atom IDs that you want to try deleting. Inside the loop you start with a “clear” command and then read the restart file and then delete the indicated atom and perform your relaxation/minimization/equilibration/whatever. After the loop has completed you can post-process the log file to extract the optimized energies for the different defect systems.

More information about loops is in the manual and some of the examples in the examples folder use loops.