More miscellaneous runtime parameter changes for beta05

[gustavo-marques]

• Adds new topographic edits and updated channel list. These lead to slightly improved circulation and hydrograph (Response to bathymetry edits NCAR/omwg_dev#55)
• Enabled COMPUTE_MONIN_OBUKHOV = True to improve the OBL seasonal cycle by limiting the OBL depth to no deeper than the Monin-Obukhov depth. Because of this change, we now need to assure that OBL is always >= than the first thickness (dz) used in the model. This is done by setting MINIMUM_OBL_DEPTH = 2.5.
• Updated background mixing parameters:
  • KV = 1.0E-06
  • KD = 1.0E-07
  • PRANDTL_BKGND = 10
• Enable bug fixes introduced in GFDL to main (2024-11-27) mom-ocean/MOM6#1647

Fixes: #218, #213, #208, #220

[gustavo-marques]

I will add the new files to input_data_list.yaml later today.

[gustavo-marques]

I've added MINIMUM_OBL_DEPTH = 2.5 for cases using tx2_3v2. This solves the issue with the GNU debug test reported in NCAR/MOM6#331

[alperaltuntas]

Thanks, @gustavo-marques. I'll re-run the test suite.

[alperaltuntas]

Dimensional scaling test for the L dimension fails when this PR gets merged. I am investigating.

[alperaltuntas]

@gustavo-marques Is this ready for testing now?

[gustavo-marques]

Yes, thanks!

[gustavo-marques]

With the latest beta05 update, we are getting negative Laplacian viscosities near coastlines. @iangrooms thinks this is a bug; fixing it will take a few days (perhaps more). To avoid additional delays in tag creation, we suggest going back to LEITH_AH.

I am also reverting to using a constant frontal length scale for MLE. As Gokhan pointed out yesterday, the MLE overturning with the variable frontal scale is too strong, reverting the near-surface residual MOC in the Southern Ocean (see plot below).
For now, including this in the tag does not make sense.

[gustavo-marques]

I updated the initial description by removing the following:

• Configured MLE settings (this relies on PR #331):
  • Set MLE_FRONT_LENGTH_FROM_FILE = True
  • Updated MLE_FL_FILE to "mle-lf-clim-tx2_3v2_20250115.nc"
• Enabled Leithy parameterization with:
  • USE_LEITHY = True
  • LEITH_BI_CONST = 90.0
  • LEITHY_CK = 1.0 (full backscatter)
  • LEITH_AH = False