Update Icepack z-biogeochemistry and z-aerosols with the MPAS-Sea ice column package #34
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… standard dEdd config
Update to Consortium Main Aug 17, 2022
clean up trailing blanks
Add calls to icepack_init_radiation to icepack driver
Add some SNICAR SSP table checks, aborts, etc
new namelist variables and options. Add new namelist to icepack_in. Add snicar and snicartest options. Minor updates to namelist output
Update snow table implementation and add SNICAR SSP Tables
Update ssp data for dEdd_snicar
…ata for use_snicar
Add additional SNICAR SSP fields for aerosols, BGC
…o cice-consortium/E3SM-icepack-initial-integration Merge Icepack main #23b6c1272b50d42cad, includes thin ice enthalpy fix and zsalinity deprecation
…o e3sm230830 Update to Icepack Consortium #7952807, Sept 13, 2023
Merge Consortium Icepack #23b6c1272b50d4, Aug 30, 2023
Update to Consortium #795280797a Sept 13, 2023
…gration version Some changes to z-aerosols in snow to be consistent with colpkg. Still needs to be tested.
Adjust icepack interface for E3SM
Update documentation
…o upd230930 Merge Consortium main #390fb5518326217c2501dbf5 to branch, Sept 30, 2023
Update Icepack Consortium main #390fb5518326217c2501dbf5, Sept 30, 2023
Modifications are bfb in the physics. BGC/Zaerosol changes make icepack consistent with mpas-seaice colpkg. Still needs testing once merged with mpas-seaice interface changes.
…k' into njeffery/merge-bgc merges icepack bgc changes with icepack-integration branch
Rayleigh_criteria was a field in zsalinity
Most of the updates are for use in init_zbgc which now initializes many of the configs, indices and size declarations for bgc -Puts dust/BC into sea ice for thin snow layers rather than ocean -make "puny" and "accuracy" consistent with carbon conservation check -corrects algal parameter f_v = 0.7854 to 0.7854_dbl_kind -adds stationary fraction for nitrate when derived from nitrification -corrects carbon conservation error - flux_bio should be defined with the new brine height -corrects algal source and sink reaction terms -Adds DIC loss term -updates algal_vel parameter value -Corrects initial default values for DIC -Corrects merging of bgc flux fields for aicen not aice_init BFB with no BGC or aerosols
Bugfix in BGC, nonBFB. BFB without BGC active
Bugfixes in bgc tracers -corrected bgc ocean flux during lateral melt -updated add_new_ice_bgc for compatibility with floe size distribution -replace and greaty simplify adjust_tracer_profile with update_vertical_bio_tracers -remove bgc tracers for small ice areas (corrects carbon conservation) -pass carbon molar mass to icepack Bugfixes in zaerosol snow tracers -the two BGC snow layers are now fixed fractions of the snow thickness -added missing snow bgc flux during ridging Added diagnostics and updates to write statements Verified carbon conservation in 20-day ocean-ice test. nonBFB with bgc on. BFB with bgc off.
Corrects division by zero in ice_algae and add_new_ice_bgc Remove small bgc values and track flux properly for conservation Remove small area bgc and account for fluxes Clean write statements nonBGC in ice bgc
Comments out bgc aborts that could just be warnings Fixes icepack setaborts subroutine to "add" warning strings Fixes missing "add" to some bgc warning messages Avoids division by small number in update vertical bio tracers Code was seg faulting with debug_compile=true around icepack write statements
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I don't think this is being merged to the correct place, E3SM-Project/Icepack/main should probably remain synced to Consortium/Icepack/main. Should we merge this to Consortium Icepack main first? Or to a branch on E3SM/Icepack? Are there things in particular that needed to be reviewed, tested, refactored? How should we proceed, maybe we should chat sometime. |
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This PR is showing all of the commits from the last 2 years, so the base code definitely needs to be resync'ed first. Rebased? @njeffery has been developing and testing in E3SM, so it makes sense to merge there then pull back to the Consortium, although our preference is to test and merge in the Consortium then PR to E3SM. Either way, we'll need an iteration to resync the two repos, whether it's done as part of this PR or separately. @njeffery is your origin code from E3SM's fork or from the Consortium? |
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I'm not clear on the history of the branch, but maybe it would be good to clarify and clean up if needed. I know we could create a clean branch. The best process depends how we're going to proceed. Icepack in E3SM is a submodule. If we want these mods to be added just to the E3SM version of Icepack, we need to create a "clean" branch in E3SM/Icepack based on the current E3SM version so the E3SM submodule can be updated. We don't want to merge this to E3SM/Icepack/main (as the PR currently does). We would probably test with Consortium/Icepack/main at the same time to make sure these mods work both in E3SM and in Consortium. Alternatively, this could be merged into the Consortium/Icepack/main then E3SM/Icepack/main could be resynced and the E3SM Icepack submodule could be updated. But E3SM would then get all the latest mods from the Consortium (although that's probably not a lot of stuff). I think that's how we "planned" to do things wrt E3SM/Consortium. So, those seem like the two main options (push to E3SM and Consortium separately or push to Consortium then use in E3SM). In either case, I think we should test with both E3SM and within the Consortium (Icepack and CICE) before we finalize the PR. But open to other ideas about how to best proceed. |
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The BGC updates went directly into E3SM via @njeffery's branch, then were merged into the CICE Consortium's repo which is now being resynced with E3SM. Closing this PR. |
PR checklist
Short (1 sentence) summary of your PR:
Updates Icepack z-bgc and z-aerosols to the latest mpas-sea ice column package version
Developer(s):
Nicole Jeffery
Suggest PR reviewers from list in the column to the right.
Elizabeth and Tony
Please copy the PR test results link or provide a summary of testing completed below.
https://acme-climate.atlassian.net/wiki/spaces/ICE/pages/4225073188/icepack.GMPAS.EC30to60E2r2.BGC+and+GMPAS.EC30to60E2r2
How much do the PR code changes differ from the unmodified code?
Does this PR create or have dependencies on CICE or any other models?
Does this PR add any new test cases?
Is the documentation being updated? ("Documentation" includes information on the wiki or in the .rst files from doc/source/, which are used to create the online technical docs at https://readthedocs.org/projects/cice-consortium-cice/.)
Please provide any additional information or relevant details below:
ECH edited to fix checkboxes