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NOAA-CEFI-Regional-Ocean-Modeling / ocean_BGC

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Ballast and remin/clean code #79

Closed charliestock closed 2 months ago

charliestock commented 3 months ago

This pull request cleans up the mineral ballasting, remineralization of sinking detritus and iron scavenging sections of COBALTv3. It gets rid of one redundant local variable (z_remin_ramp) and introduces a parameter for the augmentation of scavenging when free iron exceeds fe solubility (fast_fescav_fac).

For fast_fescav_fac have been using a factor of 2 for this in the regional runs, but previous global coarse resolution runs used a factor of 10. I think this parameter is somewhat scale dependent. I used a higher value in prior global runs to try and erode coastal iron signals that were propagating too far into the ocean interior, probably because shelf residence times were under-estimated with coarse resolution. Higher resolution addressed this problem and a factor of 2 seems to work better. I have thus made 2 the default.

Most of this pull request is commenting and clean up. Perhaps most significantly, the comments now include a detailed description of the ligand binding derivation used to calculate the free iron (feprime). This involves solving a system of three equations and results in a quadratic equation for feprime. The comments should now provide enough information for users to be able to understand and verify the derivation.

One thing I did not have time to do yet is to enhance all the variable definitions associated with this pull request. I will handle this in a follow on pull request soon.

This pull request should not change answers!

charliestock commented 2 months ago

This new commit fixes typos in the comments (thanks Jessica), eliminates omegaa and omegac from cobalt_types.F90, and retains the k_no3_denit change in the water column remin (which will change answers very slightly), and introduces k_no3_amx. The last of these changes will have no impact since anammox isn't turned on but, line k_no3_denit, establishes a clear separation between this parameter and the phytoplankton uptake parameters. @jessluo @yichengt900

yichengt900 commented 2 months ago

@charliestock, I like the idea of removing the uses of the phytoplankton parameters beyond their explicit definition. The new commit looks good to me. I will wait a bit for others' comments.