Hello,
This is an interesting topic. The stratification can be set up by giving initial values plane by plane, in the subroutine condim.f.
Up to now we did tests on stratifications, e.g. their tilting under the action of wind, but nothing on internal waves. The extra difficulty will be to follow the stratification with the mesh, this is an opportunity to test the option programmed at HR-Wallingford : MESH TRANSFORMATION = 5, which is a mesh adaptation after the values of a tracer.
Extracting cross-sections can be done with Tecplot and probably many other programs, but you can do it with Postel-3D, which provides cross sections as selafin format files, which can be seen by Fudaa, BlueKenue, etc. You can look at example "stratification" in Telemac-3D, where an example of Postel-3D steering file is "p3d_stratification.cas".
With best regards,
Jean-Michel Hervouet