I am trying to calculate the vacancy formation energy in the alloy (Let’s say AB alloy). I’d like to remove one A atom only in the system (Then, I’d like to run multiple times to increase statistic with different seed number).
Is it possible to delete A atom (or B atom) only in AB alloy whenever I run the simulation? I can add a specific atom type by using create_atoms command, but I don’t know how to delete a specific atom type.
You can delete atoms that are in a specific group, and a group can be defined based on atom type or in even more complex ways using an atom style variable. Please see the discussion of issue #1425 on the LAMMPS GitHub project for an example of such a use of an atom style variable.
Dear Dr. Axel Kohlmeyer,
Thanks for your answer. That works very well if I want to delete fraction of atoms. However, if I want to remove only 1 atom in the alloy (for instance, If I run the simulation 1000 times with different configuration of alloy, I always want a A atom to be removed in AB alloy), I think this is not a efficient way to do it. I would appreciate for your comments.
you are not paying sufficient attention to what i was telling you.
the example quoted was only for illustration of how complex a selection of atoms you can have.
however, what is important to you is the fact, that you can create a group (even if it only contains one atom) and then delete the atoms in that group. that is the basic principle of how you can delete arbitrary atoms. now it is all a matter of being smart about how to define this group, for which you can use different methods including some atom style variable command.
if you expected that you will get a viable solution from cut-n-paste, then i have to disappoint you. you will have to do your part of the thinking as well.