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Hello,
That is an interesting case! A few questions:
  - Please can you confirm the draft of the vessel?
  - Are all of the openings submerged?
  - If I understand your description and the images well, there is a partition running port-starboard across the middle of the vessel. Is this modelled with diffracting elements?
Applying the Generate Internal Lid option is a good choice. I suspect the spiky radiation damping may be due to the interior surfaces, assuming that they are modelled with diffracting panels.
We would recommend that you give the vessel plates a thickness, and then detach the inside surfaces so that you can specify them as non-diffracting in the hydrodynamic analysis. I've set up a simplified model to check this:
Zoomed in on the central partition and openings, you can see that there is a thickness to the plates:
The faces are grouped so that the exterior faces form one surface body, while the edges of the openings and all of the interior faces form another surface body. In the Aqwa Workbench editor I changed the Surface Type of the interior surface body from 'Program Controlled' to 'Non-Diffracting'. In this way the interior faces are not included in the radiation-diffraction analysis, but the hydrostatic stiffness is calculated for the flooded vessel, so the RAOs should be reasonably accurate.
However, we cannot account for any sloshing of the fluid inside the vessel using this approach. I think the only way to do this would be to create an internal tank (or two) to represent the flooded volumes, but there would be no flow (or continuity) between the outside seawater region and the inside fluid.
Mike