Dear Lammps users,

Hope you all are well.

I am simulating a fullerene C60 fall onto a Si crystal surface. And I am trying to analyze amount of vacancies and interstitials using voronoi/atom occupation. The problem is that the Si crystal only takes 50% of the simulation box, so cells of the atoms on the surface extend to empty simulation box space and the voronoi method includes atoms that have left the surface of the crystal after the impact as an interstitials. That’s why I want to limit voronoi calculation for a specific region. But I can’t figure that out myselft.

Hope to find some help.

From the `compute voronoi/atom`

documentation:

Define a computation that calculates the Voronoi tessellation of the atoms in the simulation box. The tessellation is calculated using all atoms in the simulation, but non-zero values are only stored for atoms in the group.

So define a region of interest, then create a group of atoms in that region and then apply the compute to only those atoms. That will result in the compute for all other atoms having a value of 0.

There is nothing you can do about the voronoi cells extending into the empty space. That is how that kind of tesselation works and any restriction would be completely arbitrary and thus you can just as well use the current values.