[lammps-users] knowing surroundig atoms ID of a given atom (NEB method)

Hi,

I am trying to automatize the NEB method for study the energy barrier of vacancies in a FCC metal.

The idea is to pick a random atom, get its coordinates and remove it. Then identify all the nearest neighbors and run the NEB method for each of them migrating in the vacancy spot in order to get the vacancy migration energy barrier. My questions are basically 2:

  1. Is there a better algorithm to perform a NEB method on a vacancy multiple times?
  2. Is there a way to get the ID of all the nearest neighbors of a given atom far from the boundaries?

Thank you.

Regards,

Stefano

Hi,

I am trying to automatize the NEB method for study the energy barrier of vacancies in a FCC metal.

The idea is to pick a random atom, get its coordinates and remove it. Then identify all the nearest neighbors and run the NEB method for each of them migrating in the vacancy spot in order to get the vacancy migration energy barrier. My questions are basically 2:

  1. Is there a better algorithm to perform a NEB method on a vacancy multiple times?

that is a question about the “science of the problem” and thus independent from using LAMMPS and therefore (mostly) off-topic for this mailing list. since I have next to no personal experience with the NEB method, I cannot make any “best practices” suggestions.

  1. Is there a way to get the ID of all the nearest neighbors of a given atom far from the boundaries?

please note that while LAMMPS has some scripting capability, this is quite beyond what can be done with it. this seems to require “real” programming.
you could try using the LAMMPS python scripting where it is possible get access to the neighbor lists, but that is quite complex and seems overkill.
I would instead just write a standalone script to generate the original fcc structure and then the vacancies and the necessary input files. that is much easier done this way.

axel.