Adds icepack BGC #6457

njeffery · 2024-05-31T17:15:13Z

Updates the version of icepack to one that includes sea ice BGC. Also added capability to read from an input file atmospheric dust fluxes and dust-iron solubility maps. Added a namelist option to use a spatial field for dust-iron solubility rather than a constant.

Tested in ocean-sea ice BGC active simulations.

[NML]
[non-BFB] only for tests with biogeochemistry and/or sea ice aerosols active

Needs to be tested and merged with main icepack-integration branch BFB in the physics.

Changed back to original formulation.

-bugfix in carbon conservation - Fluxes scaled by aicen not aicen_init -puts snow aerosols into ice rather than ocean for small snow volumes -Changes vertical z-tracer flags so that aerosols and bgc are turned on separately: 1) config_use_column_biogeochemistry indicates biogeochemical tracers are on 2) config_use_zaerosols indicates dust and black carbon are on BFB in the default configuration. nonBFB with zaerosols or column_biogeochemistry

This column_package subroutine was accidentally added during the merge. BFB

Most of the updates are for use in init_zbgc which now initializes many of the configs, indices and size declarations for bgc Contains updates to column package to make puny and accuracy consistent with carbon conservation check BFB with bgc and aerosols off

Removed zsalinity references BFB

…ated-icepack-bgc This version uses a branch of Icepack, not main (see .gitmodules) Modifications bring changes to enable Icepack bgc into master BFB with physics only.

Added flag to turn off BGC coupling between the ocean and sea ice: config_couple_bgc_fields=false Added black carbon conservation analysis member -track ocean black carbon flux Added carbon conservation check options in interfaces for both icepack and column Bugfixes to column package version: 1. Bugfixes to lateral melt BGC snow flux and ice flux 2. Bugfix to add_new_ice_bgc -replaces adjust_tracer_profile with simpler and more accurate version update_vertical_bio_tracers Define carbon molar mass in mpas constants Commented out problematic omp directives in icepack interface Corrections to some bgc Registry descriptions (still more to do) NOTE: Changed submodule path for Icepack to a branch that works with the BGC interface. nonBFB with BGC

-Cleans up some missing bgc info in Registry (more to do) -Adds some additional info to carbon conservation analysis member -Saves bgc ocean fluxes weighted by ice area (for carbon conservation) -Comments out $omp statements around step therm1 (code was crashing -with seg fault) -Removes and cleans up unnecessary write statements for carbon debugging Tested with E3SM-Project/Icepack.git branch njeffery/merge-fixes-to-bgc commit c090b4b20e4ec0317d2c7d742c5ab291ec7a2240 BFB except correcting a seg fault

Now consistent with E3SM master BFB

Small error introduced in last commit - broke compile BFB

Merge remote-tracking branch 'remotes/origin/njeffery/seaice/updated-icepack-bgc' into origin/master

bfb

-First uses init_parameters to initialize bgc namelist parameters -Second (icepack_init_zbgc_tracer_indices) calls bgc indexing and array definitions. -Third defines parameter arrays for bgc (init_zbgc) bfb (round-off level in bgc)

Adds 2 namelist fields: config_use_atm_dust_file - true, use monthly dust climatology config_use_iron_solubility_file -- true, use dust-iron solubility map from file (in icepack: use_atm_dust_sol = .not.config_use_iron_solubility_file) New fields track atmospheric wet and dry dust separately from the coupler to compute the iron contribution. Fraction of iron in dust is also generalized and read from a file. Dust/iron file is identical to the one used by mpas-o. Corrects some units in Registry. BFB with new namelist parameters = false and for all runs without zaerosols or without iron.

This field oceanDustIronFlux will be used by the ocean for dust-iron consistency across the coupled system Also corrects a bug in the calculation of iron from dust introduced in the last commit Works with E3SM-Project/Icepack.git origin/fixes-to-zaerosols-take3 BFB with zaerosols off

-adds subroutine in the icepack interface, init_zbgc_tracer_indices, to replace icepack_init_zbgc_tracer_indices. -moves icepack_init_bgc_trcr from icepack to init_bgc_tracer_indices in mpas_seaice_icepack Tested in GCASE with ice-ocean bgc and aerosols active works with njeffery/Icepack.git branch: fixes-to-bgc-indices

For BGC

github-actions · 2024-05-31T18:05:41Z

PR Preview Action v1.4.7
🚀 Deployed preview to https://E3SM-Project.github.io/E3SM/pr-preview/pr-6457/
on branch `gh-pages` at 2024-07-10 20:32 UTC

eclare108213 · 2024-07-10T18:40:25Z

I am still getting a bgc skl array bounds error in this version of the model with build debug flags on ... Any thoughts about how this should be fixed?

@njeffery pointed out that the problem code has a loop over nblyr, but skl should only be a single layer. E3SM doesn't run skl and so we'll need to decide what to do about it in the Consortium, independent of E3SM.

jonbob · 2024-07-10T20:00:58Z

@njeffery -- I pushed a couple of commits back to your branch:

Update the bld files to match Registry -- very minor but I did add back the logic for which column physics to use, as we discussed
added support for the file related to the new DustIronMonthlyForcing stream be mesh-dependent and more generalized

I tested the DustIron part in a couple of cases, one where it showed up in the streams.seaice as expected and one where it did not, also expected. But please feel free to rename the variable I added. I also made sure the new file is on the inputdata repo

njeffery

Great. Thanks @jonbob.

njeffery

Perfect.

apcraig · 2024-07-11T16:29:14Z

Is the Icepack version that goes with this commit still https://github.com/E3SM-Project/Icepack/tree/njeffery/fixes-to-bgc? It looks like there are no updates to that branch in the last 3 weeks, is that correct? Also, just FYI, this E3SM PR looks to me like it's not pointing to that version of Icepack. I understand that update may still need to be done and/or there may be other E3SM processes to do so, just wanted to point it out. Thanks.

njeffery · 2024-07-11T16:51:15Z

@apcraig : It's pointing to #31ce422.

apcraig · 2024-07-11T17:28:16Z

@njeffery, I see it now, sorry about my confusion. I needed to "see more commits" on the Icepack diffs link. Thanks. Looks good.

njeffery · 2024-07-11T17:32:18Z

@apcraig : Whew! I had a little panic there for a moment...

proteanplanet · 2024-07-11T17:36:51Z

Can I proceed with the BFB B-case No-BGC test now? I will be merging this branch into a branch from the current E3SM master, and then running a 12-month test of both with BGC switched off.

njeffery · 2024-07-11T18:04:19Z

Yes. Thanks @proteanplanet

rljacob · 2024-07-25T17:39:55Z

status: still getting tested with long comparisons.

njeffery · 2024-07-29T15:23:09Z

@proteanplanet : Let me know if you have any concerns with this PR. It would be great if we could get this through this week. Thanks.

proteanplanet · 2024-07-29T16:35:39Z

B-case tests are in progress on Chrysalis.

proteanplanet

Additions and changes in this branch were cherry picked and tested in a branch from master on July 29, 2024 with BGC switched off. This test was to confirm that when sea ice BGC is switched off and brought into the code as a stealth feature, default B-case simulations using master are unaffected. Two parallel 12-month B-cases were integrated at standard V3 resolution from startup - one forked from master current to 466fa81, the second using the same fork, but with all commits particular to this branch out to cf6f75b. The results are that sea ice is unaffected across 10 metrics, indicating the model climate as a whole is unaffected:

    iceAreaCell 	BFB
    iceVolumeCell 	BFB
    icePressure 	BFB
    uVelocityGeo 	BFB
    vVelocityGeo 	BFB

    totalIceExtent 	BFB
    totalIceVolume 	BFB
    totalSnowVolume 	BFB
    totalKineticEnergy 	BFB
    averageAlbedo 	BFB

Therefore I approve this PR.

njeffery · 2024-07-31T16:01:14Z

@proteanplanet : Great! thank you!

jonbob · 2024-07-31T16:22:18Z

@eclare108213 -- can you sign off on this?

eclare108213

Approved based on extensive testing by @njeffery and @proteanplanet. @apcraig is also testing the icepack changes in CICE, where problems appear to be related to configuration choices rather than to the BGC code itself. If we turn up changes needed in Icepack, we will submit them separately. Kudos to @njeffery -- this has been a HUGE amount of work!

jonbob · 2024-07-31T17:28:15Z

passes e3sm_ice_developer suite on chrysalis with expected NML DIFFs

njeffery · 2024-07-31T19:02:01Z

Yay! Thank you Everyone!

…t (PR #6457) Adds icepack BGC Updates the version of icepack to one that includes sea ice BGC Tested in ocean-sea ice BGC active simulations. [NML] [non-BFB] only for tests with biogeochemistry and/or sea ice aerosols active

jonbob · 2024-07-31T21:14:47Z

merged to next

jonbob · 2024-08-06T16:00:54Z

merged to master and expected DIFFs blessed -- except for one test that is still running on pm-cpu

This is a significant update in the BGC including refactoring Icepack interfaces. Deprecate skl BGC but leave code alone for now hoping we get help from the community to validate the latest code. Add BGC parameters to icepack_parameters.F90 Update BGC physics, consistent with E3SM-Project/E3SM#6457. Remove redundant arguments in BGC interfaces. icepack_aerosol.F90 revised subroutine update_snow_bgc icepack_algae.F90 revised subroutine zbio revised subroutine z_biogeochemistry revised subroutine algal_dyn add subroutine bgc_carbon_sum icepack_brine.F90 revise subroutine prepare_hbrine revise subroutine update_hbrine icepack_mechred.F90 add mbio calculation to subroutine ridge_shift add flux_bio calculation to subroutine ridge_ice icepack_therm_itd.F90 update calculation of dvssl and dvint in subroutine lateral_melt icepack_zbgc.F90 lots of stuff icepack_zbgc_shared.F90 lots of stuff Remove redundant arguments in non-BGC interfaces. icepack_atmo.F90 icepack_fsd.F90 icepack_isotope.F90 icepack_itd.F90 icepack_meltpond_topo.F90 icepack_mushy_physics.F90 icepack_snow.F90 icepack_therm_bl99.F90 icepack_therm_mushy.F90 icepack_therm_shared.F90 icepack_therm_vertical.F90 icepack_tracers.F90 icepack_wavefracspec.F90 Generalize merge_fluxes to make all arguments optional Fix bug in subroutine snow_redist computation of hsn_new when nslyr=1 Update the Icepack driver consistent with Icepack interface changes Update zbgc initialization in the Icepack driver, move bgc parameter intiialization to icepack_init_parameters, update icepack_init_zbgc call. Update some calls to icepack_warnings_setabort to add file and line number. Update warning package to improve OpenMP robustness. Fixes potential race conditions that show up when lots of output is produced. Modified congel implementation in subroutine thickness_changes in icepack_therm_vertical.F90 to recover bit-for-bit results. New congel and new bgc implementation were bit-for-bit independently, but when combining the changes, the intel compiler (with -O2) introduces non bit-for-bit changes (roundoff). Update bgc namelist defaults and settings in icepack_in Update bgc tracer sizing in set_env files Update testing, remove skl tests, add zaero tests. --------- Co-authored-by: Elizabeth Hunke <[email protected]> Co-authored-by: David Bailey <[email protected]> Co-authored-by: Nicole Jeffery <[email protected]>

njeffery added 22 commits October 11, 2023 17:00

Adds mpas interface for icepack bgc

246b7f5

Needs to be tested and merged with main icepack-integration branch BFB in the physics.

merged conflicts by hand

df74186

Clean-up from the merge

e09f187

Modified algal growth by mistake in merge.

e5b6cda

Changed back to original formulation.

Removed init_column_package_tracer_indices from mpas_seaice_icepack

fb48cef

This column_package subroutine was accidentally added during the merge. BFB

Added bgc parameter checks

5f73ff0

Removed zsalinity references BFB

Merge remote-tracking branch 'origin/master' into njeffery/seaice/upd…

bae58ce

…ated-icepack-bgc This version uses a branch of Icepack, not main (see .gitmodules) Modifications bring changes to enable Icepack bgc into master BFB with physics only.

Changed Icepack submodule url

2305a7d

Now consistent with E3SM master BFB

Corrects error in black carbon conservation member

6357063

Small error introduced in last commit - broke compile BFB

Bring "update to icepack bgc" up to date with master

16ea615

Merge remote-tracking branch 'remotes/origin/njeffery/seaice/updated-icepack-bgc' into origin/master

Adds ^xpmem and grid TL319_r05_IcoswISC30E3r5

d6411d8

bfb

Split init_zbgc into three calls

2272b67

-First uses init_parameters to initialize bgc namelist parameters -Second (icepack_init_zbgc_tracer_indices) calls bgc indexing and array definitions. -Third defines parameter arrays for bgc (init_zbgc) bfb (round-off level in bgc)

Updates .gitmodules to zbgc-enabled icepack submodule branch

73788b9

Reverts the previous commit

393d0ed

Updating Icepack to hash #2e5d5a27

4873471

For BGC

njeffery requested review from eclare108213 and proteanplanet May 31, 2024 17:15

njeffery assigned njeffery and jonbob May 31, 2024

njeffery added BGC mpas-seaice non-BFB PR makes roundoff changes to answers. labels May 31, 2024

Add mesh-dependent dust_iron_file to streams

4c94ac4

njeffery commented Jul 10, 2024

View reviewed changes

proteanplanet approved these changes Jul 31, 2024

View reviewed changes

jonbob added the NML label Jul 31, 2024

eclare108213 approved these changes Jul 31, 2024

View reviewed changes

jonbob merged commit ebb7301 into master Aug 6, 2024
21 checks passed

jonbob deleted the njeffery/seaice/update-icepack-bgc-v3-indices branch August 6, 2024 15:51

apcraig mentioned this pull request Aug 9, 2024

BGC update CICE-Consortium/Icepack#497

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Adds icepack BGC #6457

Adds icepack BGC #6457

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Adds icepack BGC #6457

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