Problem in non periodicity of boundary while visualizing in OVITO

OVITO
1

Dear all, I have created a script to create an FCC (Ni) system using LAMMPS such that 111 direction is along x direction to calculate surface Energy. On visualizing the structures in OVITO, I’m not convinced that it is FCC.

The atoms in boundaries are not FCC and some atoms are missing. I am guessing that it is due to PBC and missing atoms at bottom appears on top. But my guide told me that’s not how it works.

I want to confirm if the way I wrote the script is wrong. and how else can I write the script, to get pure FCC.

I have attached dump file (dump_bulk.dat) and script (input.txt).

Thanks in advance.

PS: Please add Common neighbor analysis modifier to check the type of structures.

dump_bulk.dat (993.6 KB)
input.txt (3.5 KB)

2

Hi @nitheesh_rkm,

Your mentor is correct. 2 things to consider here:

  • You might have atoms sitting exactly at the edge of the rotated cell. This is known to cause issues in LAMMPS when computing periodicity due to finite number rounding. A common solution is to use the keyword origin in the lattice command with some small displacement of the origin of the cell.
  • More importantly, you have a 3 cell periodicity in your rotated cell along the z axis, so you need your number of replicated cells to be a multiple of 3 along that axis. 5 will not do.
1 Like
3

Got it. Thanks, Germain