Hi Ali,
Could you please post the Wilson loop plots which can be generated by
“gnuplot wanniercenter3D_Chern.gnu”?
There could be Weyl point happening which would generate the singularity of the Berry curvature. You could check with the “FindNodes_calc=T” by setting Nk1=10;Nk2=10;Nk3=10.
By the way, when using Chern_3D_calc=T, you don’t have to set Nk3. Only Nk1 and Nk2 are relevant.