Merging soil NO into the new vertical movement scheme for soil nitrate #3341

mvalmartin · 2025-07-16T23:12:02Z

Description of changes

This PR merges the soil NO from #2290 into the NO3 vertical movement scheme in #2992.

The soil NO scheme is based on Parton et al (2001), and includes canopy reduction (Yan et al, 2005) and rain pulses (Yan et al 2005; Hudman et al 2012).

The scheme uses a fixed soil pH value of 6.5, as defined in SoilBiogeochemCompetitionMod.F90

In addition, the scheme does not includes the dependency of the N mineralization-based term on potential nitrification rates proposed in Parton et al. (2001), which is missing in CLM5 as pointed out by Nevison et al., (2022). Although that was implemented in #2290, it is now removed because it substantially affected N plant uptake and the broader carbon cycle.

A more complex version of this scheme, which includes spatially distributed soil pH, weathering effects on denitrification and soil NH3 volatilization, is described and validated in Val Martin et al (2023).

References

Hudman, R. C., Moore, N. E., Mebust, A. K., Martin, R. V., Russell, A. R., Valin, L. C., and Cohen, R. C.: Steps towards a mechanistic model of global soil nitric oxide emissions: implementation and space based-constraints, Atmos. Chem. Phys., 12, 7779–7795, https://doi.org/10.5194/acp-12-7779-2012, 2012.

Nevison, C., Goodale, C., Hess, P., Wieder, W. R., Vira, J., and Groffman, P. M.: Nitrification and Denitrification in the Community Land Model Compared with Observations at Hubbard Brook Forest, Ecol. Appl., 32, e2530, https://doi.org/10.1002/eap.2530, 2022

Parton, W. J., Holland, E. A., Del Grosso, S. J., Hartman, M. D., Martin, R. E., Mosier, A. R., Ojima, D. S., and Schimel, D. S.: Generalized model for NOx and N2O emissions from soils, J. Geophys. Res.-Atmos., 106, 17403–17419, https://doi.org/10.1029/2001JD900101, 2001.

Val Martin, M., Blanc-Betes, E., Fung, K. M., Kantzas, E. P., Kantola, I. B., Chiaravalloti, I., Taylor, L. L., Emmons, L. K., Wieder, W. R., Planavsky, N. J., Masters, M. D., DeLucia, E. H., Tai, A. P. K., and Beerling, D. J.: Improving nitrogen cycling in a land surface model (CLM5) to quantify soil N2O, NO, and NH3 emissions from enhanced rock weathering with croplands, Geosci. Model Dev., 16, 5783–5801, https://doi.org/10.5194/gmd-16-5783-2023, 2023.

Yan, X., Ohara, T., and Akimoto, H.: Statistical modelling of global soil NOx emissions, Global Biogeochem. Cy., 19, GB3019, https://doi.org/10.1029/2004GB002276, 2005.

Specific notes

Contributors other than yourself, if any: @lkemmons, @slevis-lmwg & @wwieder

CTSM Issues Fixed (include github issue #): Unknown

Are answers expected to change (and if so in what way)? I don't think so

Any User Interface Changes (namelist or namelist defaults changes)?
The soil NO scheme can be turned on and off within the user_nl_clm as use_soil_nox=.true. or .false.
As indicated by Jinmu Luo, the soil NO3 vertical movement scheme can also be turned on and off, but the switch is hardwire within SoilNitrogenMovementMod.F90

Does this create a need to change or add documentation? Did you do so?
To be determined

Testing performed, if any:
We performed 15-year runs using the new configuration, with the first 5 year treated as a pseudo-spin up, using the compset 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV

For evaluation we analyzed global annual timeseries and spatial distributions including changes between runs. Simulations were:

Control (no NO3 vertical movement and no soil NOx)
NO3VertMov (only soil NO3 vertical movement activated)
NO3VertMov+SoilNOx (both soil NO3 vertical movemennt and soil NOx activated).

The main changes in the N cycle (eg soil NO2, denitrification and nitrfication) are driven by the NO3 vertical movement implementation. No significant changes are noticed in the carbon cycle (eg NPP, TOTECOSYSC).

plot_no3vertmov_soilnox_mvalmartin.pdf

ekluzek · 2025-07-22T21:06:16Z

This is based off of: ctsm5.3.040

There is new work to update this to a newer version of CTSM.

slevis-lmwg · 2025-07-22T21:23:27Z

This is based off of: ctsm5.3.040

There is new work to update this to a newer version of CTSM.

True and, more precisely, Maria's branch starts from @jinmuluo's branch #2992 that is based off of ctsm5.3.040.

ekluzek · 2025-07-24T15:31:27Z

Adding next to make sure we know what is happening with all this work.

ekluzek · 2025-07-24T16:19:37Z

@wwieder and @slevis-lmwg will review. @slevis-lmwg meets with the group Monday, and will get more information then.

slevis-lmwg · 2025-07-24T21:55:39Z

@wwieder (in case you want to look)
I made a diff file that compares this PR to #2992, because that's where Maria started from. The diff file is:
/glade/work/slevis/git_people/mvalmartin/ctsm_soilno/dif_from_jinmu

slevis-lmwg

@mvalmartin for starters I want to say that your coding here seems to me well organized, so thank you for this.

In my review I think I only made one comment, but you will find that I repeated it a few times.

Another request is this: Could you document in the PR (if you didn't already) how you tested your code changes? What types of simulations you performed (compsets, lengths, resolutions, ...)? What history fields you looked at to confirm model behavior? What model behavior you expected and what model behavior you saw?

src/biogeochem/CNBalanceCheckMod.F90

slevis-lmwg · 2025-07-24T23:44:52Z

src/biogeochem/DryDepVelocity.F90

+                     if (clmveg == nc3crop .or. clmveg == nc3irrig ) ratio_stai_lai = 0.008_r8 
+                     if (clmveg >= npcropmin .and. clmveg <= npcropmax ) ratio_stai_lai = 0.008_r8 
+
+                     crf_drydep(pi)=(exp(-11.6_r8*elai(pi)*ratio_stai_lai)+exp(-0.32_r8*elai(pi)))/2


This seems to be one big new section of code.

A comment for here and elsewhere:
When possible, we avoid hardwiring values without explanation. As a first step, could you name things like -11.6 and -0.32 to variable names?

I also wonder if values like ratio_stai_lai should be PFT parameters on the parameter file to make this code easier to read? The only odd part is that values change by season for some PFTs?

Thanks for the note and apologies for the slow 'action'. Working on your comments now!

Thanks for the note and apologies for the slow 'action'. Working on your comments now!

@mvalmartin a heads up that I'm about to update your branch to the latest escomp/master tag. I'm mentioning in case you already started making changes to your local copy. If so, you would

"stash" your local changes (git stash)

pull my remote changes (git pull)

bring forward your local changes (git stash pop)

continue making changes as needed (git add, git commit, git push)

I hope all that works without trouble...

If you didn't already start making changes, then you can simply skip the "git stash" and "git stash pop" steps. In other words just

git pull

make changes

git add

git commit

git push

slevis-lmwg · 2025-07-24T23:48:09Z

src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

+                     if ( h2osoi_diff(c,j) > 0.005_r8 ) then
+                     ! Initialize new pulse factor (dry period hours)
+                        if ( ldry_vr(c,j) > 72._r8 ) then
+                           pfactor_vr(c,j) = 13._r8 *LOG(ldry_vr(c,j)) - 53.6_r8


This is another large section of the new code. It would be helpful again here to assign hardwired values to variable names (always with literature references when possible).

Thanks for this comment. In the original code the hardwired values appear as simple scalars in the equations, without variable names or descriptions. I have now added the reference (article and equation number) for each equation to make this clearer.

slevis-lmwg · 2025-07-24T23:50:24Z

src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90

+               afps_vr(c,j) = 1._r8-max(min(h2osoi_vol(c,j)/watsat(c,j), 1._r8), 0._r8)
+               Dr = 0.209_r8*afps_vr(c,j)**(4._r8/3._r8)
+
+               nox_n2o_ratio_vr(c,j) = 15.2_r8 + (35.5_r8 * atan(0.68_r8 * rpi * (10.0_r8 * Dr - 1.86_r8))) / rpi


This is another area with numerous hardwired values that need some kind of documentation, such as assigning variable names and literature refs to them.

In this case too. In the original code the hardwired values appear as simple scalars in the equations, without variable names or descriptions. I added the reference (article and equation number) for each equation to make this clearer.

wwieder

I wonder we can rebase this PR can be to Jinmu's branch / PR #2992 so we just see the changes that were made for the NOx scheme? Maybe this will be be easier once Jinmu's PR comes to main?

wwieder · 2025-07-28T15:30:11Z

src/biogeochem/DryDepVelocity.F90

+                     if (clmveg == nc3crop .or. clmveg == nc3irrig ) ratio_stai_lai = 0.008_r8 
+                     if (clmveg >= npcropmin .and. clmveg <= npcropmax ) ratio_stai_lai = 0.008_r8 
+
+                     crf_drydep(pi)=(exp(-11.6_r8*elai(pi)*ratio_stai_lai)+exp(-0.32_r8*elai(pi)))/2


I also wonder if values like ratio_stai_lai should be PFT parameters on the parameter file to make this code easier to read? The only odd part is that values change by season for some PFTs?

slevis-lmwg · 2025-08-04T19:05:05Z

@mvalmartin I will need "collaborator access" to your branch for when I end up working on it. This is how you give me access:

At the top of your PR, click on your branch: mvalmartin:ctsm_soilno
Now at the top-middle click Settings and then Collaborators and follow the prompts to add me (@slevis-lmwg) as a collaborator

mvalmartin · 2025-08-05T14:34:57Z

@slevis-lmwg, I added you as collaborator in the PR, you should have received an invitation. Please let me know if you can't still access it. Thanks!

…_soilno slevis resolved conflicts: src/main/controlMod.F90

slevis-lmwg · 2025-08-05T18:08:57Z

@mvalmartin thank you. I confirmed my access by merging the latest updates from @jinmuluo's branch to your branch here. A few points:

I will make such merges a few more times occasionally, including after merging @jinmuluo's branch to master eventually.
Do "git pull" in your local copy of ctsm_soilno to have the latest code from here.
Then modify ctsm_soilno as necessary (e.g. revisions in response to the code reviews above) and git push back to here, so that I can in turn git pull to my local copy of ctsm_soilno and that way stay up-to-date.

Incorporating a new vertical movement scheme for soil nitrate Work by Jinmu Luo of Cornell University. use_nvmovement defaults to .false. and can be changed in user_nl_clm. use_nvmovement cannot be true while use_nitrif_denitrif is false. We test the flag as .true. in two new tests: ERP_D_Ld5.f10_f10_mg37.I1850Clm60BgcCrop.derecho_intel.clm-nvmovement--clm-matrixcnOn ERP_D.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-decStart--clm-nvmovement PR ESCOMP#2992

slevis-lmwg · 2025-08-26T22:28:29Z

Updated to ctsm5.3.073 and started ./run_sys_tests -s aux_clm -c ctsm5.3.073 --skip-generate
So far I see many RUN failures in the following tests, so debugging likely comes next...

izumi tests_0829-095644iz
derecho, still NLCOMP diffs? tests_0829-095437de
Troubleshooting with SMS.f10_f10_mg37.I2000Clm50BgcCrop.derecho_intel.clm-crop (see latest submit 2025/9/3)

Update .gitmodules to cesm3_0_alpha07c Update ccs_config_cesm1.0.48 to ccs_config_cesm1.0.56. Update cime6.1.112 to cime6.1.113. Answers change in gnu and nvhpc tests on derecho (details in the PR). New bugs found and reported in issues ESCOMP#3453 FAIL MKSURFDATAESMF_...intel NLCOMP ESCOMP#3454 FAIL SUBSETDATA* tests NLCOMP PR ESCOMP#3422

…to add information about the schemes and parameters

slevis-lmwg

@mvalmartin thank you for these updates.

Another request that @samsrabin reminded me of when he reviewed @jinmuluo's PR is to pick more descriptive variable names for the code, rather than using the symbols used in the literature.

(No immediate rush, as I am working on other things at the moment, plus there are tests that this PR fails that I need to look into.)

slevis-lmwg · 2025-09-02T19:02:23Z

src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90

               fno3_co2 = max(0.16_r8*ratio_k1(c,j), ratio_k1(c,j)*exp(-0.8_r8 * ratio_no3_co2(c,j)))
               n2_n2o_ratio_denit_vr(c,j) = max(0.1_r8,fno3_co2*fr_WFPS(c,j))
-
+               ! Dr from Zhao et al. (2017) Equation A2 https://doi.org/10.5194/acp-17-9781-2017


@mvalmartin
@samsrabin reminded me of this when he reviewed @jinmuluo's PR:
Please pick more descriptive variable names for the code, rather than using the symbols used in the literature (such as Dr here).

slevis-lmwg · 2025-09-16T20:58:20Z

@mvalmartin
other activities have lowered this PR's priority for me right now. If you could investigate why tests like SMS.f10_f10_mg37.I2000Clm50BgcCrop.derecho_intel.clm-crop fail, that would help move this work forward. To run this test, go to the /cime/scripts directory and run
create_test SMS.f10_f10_mg37.I2000Clm50BgcCrop.derecho_intel.clm-crop
The failure has been in the RUN phase.

slevis-lmwg assigned slevis-lmwg and mvalmartin Jul 17, 2025

slevis-lmwg added the science Enhancement to or bug impacting science label Jul 17, 2025

slevis-lmwg added this to LMWG: Sprint Planning Board Jul 17, 2025

github-project-automation bot moved this to Todo in LMWG: Sprint Planning Board Jul 17, 2025

slevis-lmwg added the enhancement new capability or improved behavior of existing capability label Jul 17, 2025

Add soil NOx scheme and integrate with soil NO3 vertical movement

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slevis-lmwg mentioned this pull request Jul 21, 2025

Add soil NO fluxes into the N cycle. #2290

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slevis-lmwg moved this from Todo to In Progress in LMWG: Sprint Planning Board Jul 22, 2025

ekluzek added the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Jul 24, 2025

ekluzek removed the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Jul 24, 2025

ekluzek requested review from slevis-lmwg and wwieder July 24, 2025 16:17

ekluzek added this to the ctsm6.1.0 milestone Jul 24, 2025

slevis-lmwg requested changes Jul 24, 2025

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wwieder reviewed Jul 28, 2025

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wwieder mentioned this pull request Jul 28, 2025

1-deg I-case spin-up and historical to test new CLM6 paramfile (ctsm53026_BNF_[AD, SASU, pSASU, hist]) NCAR/LMWG_dev#91

Open

slevis-lmwg mentioned this pull request Jul 28, 2025

ctsm5.3.072: Incorporating a new vertical movement scheme for soil nitrate #2992

Merged

slevis-lmwg moved this from In Progress to Stalled in LMWG: Sprint Planning Board Jul 28, 2025

Merge remote-tracking branch 'jinmuluo/n-vertical-movement' into ctsm…

d6a4af3

…_soilno slevis resolved conflicts: src/main/controlMod.F90

slevis-lmwg moved this from Stalled to In Progress in LMWG: Sprint Planning Board Aug 26, 2025

slevis-lmwg and others added 3 commits August 26, 2025 17:09

Correction of conflict that slipped past the git merge

4d3b1ca

Updated Nitrogen Competition, NitrifDenit and Dry Deposition modules …

8fac120

…to add information about the schemes and parameters

slevis-lmwg requested changes Sep 2, 2025

View reviewed changes

slevis-lmwg moved this from In Progress to Stalled in LMWG: Sprint Planning Board Sep 16, 2025

Merging soil NO into the new vertical movement scheme for soil nitrate #3341

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Merging soil NO into the new vertical movement scheme for soil nitrate #3341

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Description of changes

Specific notes

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