[VnV][telemac3d] Update Cooper example with better choices for a few keywords

- TREATMENT OF NEGATIVE DEPTHS = 2 (new default value since release 9.0)
to improve mass conservation of water+tracer
- preconditionings = 34 when possible (diffusion of velocities/tracers + PPE
as using conjugate gradients) for great efficiency to converge to the chosen
accuracy (down to 1.E-15 for the diffusion of tracers as easily reached for
this example)