This PR updates the AQWA runs for the following cases:

• Ellipsoid comparison to WAMIT looks great. This one is ready for a merge.

• Sphere comparison to WAMIT in surge and pitch differs a bit, any thoughts on this? I've included added mass as an example, but it's also true for radiation damping and excitation.
  AQWA
  
  WAMIT
  

• WEC3 comparison to WAMIT in heave and pitch differs a bit, any thoughts on this? I've included radiation damping as an example, but it's also true for added mass and excitation.
  AQWA
  
  WAMIT
  

Thanks for the input @kmruehl. I was looking mostly at the shapes rather than values so didn't really notice the differences with the sphere (I guess that's why we need the compareBEM function haha) -- thanks for pointing those out. I will try a few things and should be able to figure it out. As for the WEC3, I'm not quite sure what the issue may be, but I'll try adjusting the mesh a bit and see how that changes it.

Thanks! And hopefully the updates to plotBEMIO will make this comparison much easier :)

@jtgrasb I found another run that needs to be updated, the RM3. There is a frequency spike around 2 rad/s that's making the radiation damping IRF unstable, especially in surge and pitch. The excitation magnitude also has a bunch of irregular frequency spikes that are causing the excitation IRF to be unsable.

Radiation Damping These plots compare the WAMIT to the AQWA solution for the RM3.

Excitation These plots compare the WAMIT, NEMOH and Capytaine to the AQWA solution for the RM3.

@jtgrasb #790 has been merged into dev, so please pull this into this PR

@kmruehl Okay, I've pulled the CompareBEMIO updates into this PR, and I will check out the RM3 as well. Thanks!

Great, thank you!

I have fixed the example cases for the sphere and ellipsoid and also improved the example case for the RM3. Unfortunately, the RM3 and WEC3 still have unstable IRF's in surge and pitch that I am working on fixing.

@jtgrasb Have you tried changing the frequency limit for the IRF? If you can't get rid of the IRR problems in Aqwa itself, you can adjust this limit to try and tune the IRF. Not sure what you're using now, but if you set the frequency limit in the IRF to 2rad/s then most IRR spikes are avoided and the IRF may decay better. This worked somewhat in OMT, might be useful here.

@akeeste Thanks for the suggestion! That helped and the IRF looks much better now, so I think it is a good solution for now, but I will keep working to try to figure out the reason for the spikes.

@jtgrasb is this ready for a review?

@kmruehl The sphere and ellipsoid should be fixed, so they are ready for a review. The RM3 case has been improved, but is still seeing some spikes, so it can be reviewed, but it is not perfect yet. I haven't gotten a chance to rerun the WEC3 yet as I've been prioritizing the RM3 case.

Although the WAMIT results seem to avoid the spikes for the RM3, the Capytaine and Nemoh results have similar spikes and just use a frequency limit for the IRF. I will keep looking into potential solutions for the RM3 and WEC3, but I think it is okay to merge for v5.0 for now.