Transforming a monoclinic supercell to orthogonal


I am trying to create an Al slab with two layers of oxide on top and bottom similar to the one created in the paper using LAMMPS Version: LAMMPS-64bit-8Feb2019.exe:

Verners, O., Psofogiannakis, G., & van Duin, A. C. (2015). Comparative molecular dynamics study of fcc-Al hydrogen embrittlement. Corrosion Science, 98, 40-49.

My problem is the oxide slab has a non-orthogonal crystal structure (monoclinic), so it doesn’t line up with a rectangular surface. Is there a way to convert a monoclinic supercell into an equivalent orthogonal one?

I have tried ‘trimming’ the ends of the cell by deleting atoms, but this doesn’t run correctly in LAMMPS (large outputs for temp, energy and pressure).

This is my input code, and attached is the forcefield and data files:

ffield.reax.txt (24.3 KB)

al2o3 (175 KB)

in.nvt-nve-npt (547 Bytes)

al2o3_trimmed (38.4 KB)


the problem is that your cell does not correctly continue with periodic boundaries in the y direction. since you have a 120 degree (instead of 90 degree) cell angle, this is easily done with a replication in y direction. please try the following script to process your data file and check out if the new data file is making problems.

atom_style full
read_data al2o3
comm_modify cutoff 10.0
replicate 1 2 1
change_box all xy final 0.0
change_box all ortho
set group all image 0 0 0

1 Like

Hi Axel,

This works. Thanks very much for your help.