" Simulation cell is degenerate in the deformed configuration"
Actually, I have changed the Dimensionality from default 3D to 2D but the problem sill exists. So, any helpful comment is highly appreciated.
at the moment both version (OVITO 2.9 and the current developer version) do not support 2D configurations in the Wigner-Seitz defect analysis. But it might well be added in a future release. If you like, you can upload an example of your data here so we can look into the problem.
Thank you very much for your email. So, I can use my 3d model instead!