Hi Pilou,
You are right, for the friction we assume in Sisyphe turbulent rough boundary layer(which is generally the case, even for a 1mm bed roughness).
For a smooth turbulent flow, you would have to program the White Coolebroke law based on what is done in Telemac 2D(see friction_calc.f).
When dealing with cohesive sediment myself, I generally assume a skin bed roughness of about 1 mm even if the grain is very small, there are always some irregularitiees in nature (presence of shells or con-cohesive). There are two ways to do this:
1. turn off the skin friction correction and assume a Nikuradse friction law (ks=ksp=1mm)
2. Keep the skin friction correction and increase either the diameter or the KSPRATIO.The cohesive grain diameter is only used to determine the skin friction (KSPRATIO= 100 for D=.01 mm)
Good luck, Cath