Change in crystal structure after combining data files: nanocutting

I made a workpiece via Atomsk and get the sharp tool in Ovito (tool with edge radius: I used comsol with stl file and put atoms using Atomsk. Before combining the tool and workpiece, diamond cubic structures of silicon and diamond tool were maintained along z-direction when view in Ovito. On combing them in Ovito, the atoms at the surface of the tool appear as neighbour diamond cubic(may I say nonperiodic). But when I used slice modifier pipeline in Ovito, the inner atoms in the tool remained cubic diamond structure. My questions is will the neighbour atoms have effect on my simulation results and analysis. Is there any other means to get the models? I tried region commands in Lammps but I couldn’t get the commands right esp. tool with edge radius and angles.

Hi @Tirmidhi,

This questions is only loosely related to LAMMPS as you are mostly concerned with Ovito tools to prepare you configuration.

The effect of the geometry on the simulation results in LAMMPS will depend on your models and periodic boundary conditions so it is impossible to say much without prior knowledge of what simulation you are planning on doing. You question is also very convoluted and it makes it hard to understand what is your problem and what you are trying to get as an input file. You should make it more explicit if you want to get meaningful help.

I suggest you ask the OVITO related questions in the dedicated section of the website (the OVITO section) and come back here with LAMMPS related questions in a new thread if you have any new detailed question with regard to LAMMPS simulation inputs or results.


Dear Germain,
Thanks for your thoughtful insight.