Jiang,
The cnoidal wave is a periodic solution of equations (Boussinesq or KdV) falling in the weakly dispersive regime, which Funwave is a member of, so its use for this case is totally appropriate. It would be the Stokes wave regime that would be a stretch, as this range extends to deep water, while the range of validity of Funwave does not.
Jim Kirby
p.s. I don't see anything in particular wrong with your plotted results. Note that the internal wavemaker is linear - you aren't going to get a steady wave at large amplitude since there is going to be an immense amount of energy exchange between Fourier modes, hence the spacial beating effect in your figure.
If you want to try to get a cleaner large amplitude wave, you are going to have to use the option of specifying eta and u at the domain boundary.
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-- Jim Kirby Center for Applied Coastal Research, 259 Academy Street University of Delaware Newark, DE 19716 1-302-562-8113 (cell)