How to derive potential energy profile in the z-direction

LAMMPS LAMMPS Beginners
1

Hello all.

I tried to derive GB mobility based on paper "Modelling Simul. Mater. Sci. Eng. 21 (2013) 045017
"
This paper said that to derive GB position, they derive potential energy profile in the z-direction and GB position have maximum potential energy.

So I tried to derive potential energy profile in the z- direction by lammps but it was not easy.
The lammps manual only show the method to derive total potential energy or potential energy per atom.

How to derive potential energy profile in the z-direction and find where GB is.

Thank you

2

You can compute this kind of profile with the “chunk” feature in LAMMPS using 1d binning.
For an overview, a few representative examples, and links to individual command documentation, please see: 8.3.2. Use chunks to calculate system properties — LAMMPS documentation

3

Thank you for your advice!

Using chunck command, I write

PE

compute PE all pe/atom
variable temp atom c_PE

compute layers all chunk/atom bin/1d z lower 0.001 units reduced
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.mp

then I could derive potential energy profile.

But in result, there are a few ‘0 potential energy’ bins.
Is there any problem in my code?

Best

4

This explanation for this is so very obvious, that you should figure it out by yourself.

5

Okay, I will try it.

Thank you very much!