I have three atoms and their coordinates that I would like to delete in LAMMPS. I have tried doing something like:
delete_atoms x y z
But that does not seem to work. I have also tried including the atom type like:
delete_atoms atomtype x y z
but that also does not seem to work.
I had looked in the documentation and it doesn't seem like you can include x/y/z as arguments in the delete_atoms command so I'm not sure what else to do. I had read something about making a group with the atom(s) to be deleted, but I have read the documentation and I'm not sure how to include the atomic coordinates in the group for all three atoms. It also doesn't seem to have x/y/z options for the group command either, though.
You might first create a sphere "region" https://docs.lammps.org/region.html based on your known atomic coordinates. If you need to select multiple, you can create multiple regions and join them with the "union" style. Then delete_atoms may be called on this region. Alternatively, if you know the atom ids you can delete them directly.