Hello,
If you want to prescribe boundary conditions over the vertical, I suggest you to have a look at the TELEMAC-3D examples that have USER_BORD3D subroutine in their FORTRAN file, like tetra, stratification or Viollet.
For example, in tetra example, the salinity is prescribed at 40 for planes with number lower than or equal to 4, 30 of planes with number higher than or equal to 5 on the open boundary where tracer is prescribed.
You have to implement what you want to do in the USER_BORD3D subroutine as it is not a standard boundary condition.
Hope this helps,
Chi-Tuan