Add soil NO fluxes into the N cycle. #2290
Conversation
This 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) It is not connected to soil pH from the surface file, that is, it considers the fixed soil pH value of 6.5 given in SoilBiogeochemCompetitionMod.F90 It also includes the dependency of the N mineralization-based term on potential nitrification rates that was implemented in Parton et al. (2001), which was missing from previous versions of CLM5 as pointed out by Nevison et al., (2022). This scheme -with more complexity as it is linked to spatially distributed soil pH and considers weathering effect on denitrification and NH3 volatilization- is described and evaluated 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.
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Thanks for making this PR, @mvalmartin ! We'll start reviewing the code from a scientific and software perspective to see how to move forward. This may be a bit slow with AGU and the holidays. Can you remind me if you've tried spinning these case up from bare ground and creating new initial conditions? I'm curious how much we should expect these nitrogen-focused changes to influence carbon stocks / fluxes? |
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Hi, for the testing I used the spin-up file from Val Martin et al (2023). The changes in the N cycling are not exactly the same but I thought the spin-up file could be used as a good approximation to assess at the spatial distribution, magnitude and seasonality of soil NOx and compared them to other estimates. Perhaps a new spin-up would be necessary to check on the carbon stocks/pools? |
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Hi @mvalmartin, I wanted to let you know that @samsrabin is going to review this PR from the software side. I'll look at it from the science side. Realistically I don't think this with be addressed until after the Feb WG meetings, but it sounds like the the CAMChem group wants this for CESM3 (e.g. before June 2024). Hopefully this timeline is OK with @tilmes? |
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Should we include a namelist variable to define the method by which N gasses are being calculated (e.g. Koven2013 vs. Valmartin2023). This would facilitate backwards capabilities with CLM5 (vs. CLM6). It also makes the code a little harder to read / understand, but is likely a good way to test modifications to the code don't change answers?
| smin_no3_leached => soilbiogeochem_nitrogenflux_inst%smin_no3_leached_col , & ! Input: [real(r8) (:) ] (gN/m2/s) soil mineral NO3 pool loss to leaching | ||
| smin_no3_runoff => soilbiogeochem_nitrogenflux_inst%smin_no3_runoff_col , & ! Input: [real(r8) (:) ] (gN/m2/s) soil mineral NO3 pool loss to runoff | ||
| f_n2o_nit => soilbiogeochem_nitrogenflux_inst%f_n2o_nit_col , & ! Input: [real(r8) (:) ] (gN/m2/s) flux of N2o from nitrification | ||
| !mvm soil NOx 06/19/2023 |
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@mvalmartin here and throughout the PR can you remove the comments with your initials and the date
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Yes, and please also delete commented-out lines of code that your new code is replacing.
| call hist_addfld1d ( fname='RS_DRYDEP_O3', units='s/m', & | ||
| avgflag='A', long_name='Stomatal Resistance Associated with Ozone Dry Deposition Velocity', & | ||
| ptr_patch=this%rs_drydep_patch, default='inactive' ) | ||
| !mvm for soil NOx |
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Should this variable have a more descriptive name (e.g., CRF_DRYDEP_NO), similar to O3, above?
| rc = 1._r8/((1._r8/rsmx(ispec))+(1._r8/rlux(ispec)) + & | ||
| (1._r8/(rdc+rclx(ispec)))+(1._r8/(rac(index_season,wesveg)+rgsx(ispec)))) | ||
| rc = max( 10._r8, rc) | ||
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it seems like setting the parameter ratio_sai_lai for each PFT may be better accomplished on the CLM parameter file, instead of this complicated logic?
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Yes, 2-d variable with dimensions for PFT and season would make it easier for changes and sensitivity tests in the future.
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I can try to do that, I'm not really familiar with the CTSM coding convention though so not sure how to create this 2-D variable with season and PFT.
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Oh, I didn't realize this was a time varying variable. Since this is something we're already calculating elsewhere in the model, should we just use the ratio of SAI and LAI for consistency? I realize this may change answers scientifically that you'd want to evaluate? The easier option would be to keep this as is for CLM6/CESM3?
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I left it as it is for now
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The model has another sai = stem area index. Better to call this one stai to prevent confusion?
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| ! Account for nitrification fluxes | ||
| ns%smin_nh4_vr_col(c,j) = ns%smin_nh4_vr_col(c,j) - nf%f_nit_vr_col(c,j) * dt | ||
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remove the unused code below. Alternatively, keep it if we're going to implement a namelist variable to determine how N gasses are being calculated?
| f_nox_denit_atmos => soilbiogeochem_nitrogenflux_inst%f_nox_denit_atmos_col , & ! Input:[real(r8) (:) ] (gN/m2/s) flux of NOx from denitrification; added by mvm for NOx emission | ||
| f_nox_denit => soilbiogeochem_nitrogenflux_inst%f_nox_denit_col , & ! Input:[real(r8) (:) ] (gN/m2/s) flux of NOx from denitrification; added by mvm for NOx emission | ||
| f_nox_nit_atmos => soilbiogeochem_nitrogenflux_inst%f_nox_nit_atmos_col, & ! Input: [real(r8) (:) ] (gN/m2/s) flux of NOx from nitrification; added by mvm for NOx emission | ||
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should there be an f_nox_nit flux (similar to the f_nox_denit to parallel the flux that's lost to the atmosphere?
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in theory it should be a f_nox_nit as well. I'll check the code!
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actually, only the _atmos fluxes are lost to the atmosphere. The f_nox_denit was there for debugging, in case there is an issue with the N balance and can be output during debugging. I'll add f_nox_nit for consistency.
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| ! final ratio expression | ||
| n2_n2o_ratio_denit_vr(c,j) = max(0.16_r8*ratio_k1(c,j), ratio_k1(c,j)*exp(-0.8_r8 * ratio_no3_co2(c,j))) * fr_WFPS(c,j) | ||
| ! n2_n2o_ratio_denit_vr(c,j) = max(0.16_r8*ratio_k1(c,j), ratio_k1(c,j)*exp(-0.8_r8 * ratio_no3_co2(c,j))) * fr_WFPS(c,j) |
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remove unused code or define what's being used with namelist variables
| 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)) | ||
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| !mvm 06/15/2023 NOx FLUXES |
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These are great comments, but they may seem better suited to the tech note?
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I agree for the most part, but I think the comment at line 424 can stay. The other comments are redundant with comments at the variable definition lines; the one at 424 explains what the calculation is doing.
| c = filter_soilc(fc) | ||
| this%denit_col(c) = this%f_denit_col(c) | ||
| !mvm 06/19/2023 for coupling. Total soil N fluxes pass to the atmosphere | ||
| this%soil_nox_total_col(c)=this%f_nox_nit_atmos_col(c)+this%f_nox_denit_atmos_col(c) |
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should this flux be include _atmos somewhere in the name since it's actually the total soil NOx flux to the atmosphere?
| crf_drydep_col(c)= min(1._r8, max(0._r8, crf_drydep_col(c))) | ||
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| f_nox_nit_atmos_vr(c,j) =f_nox_nit_vr(c,j)* crf_drydep_col(c) | ||
| f_nox_denit_atmos_vr(c,j)=f_nox_denit_vr(c,j)*crf_drydep_col(c) |
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I'm confused where the NOx that's trapped in the canopy come back to the soil. Does this just occur because only the f_nox_nit_atmos_vr_col is actually removed from the smin_no3_vr_col pool in N_StateUpdate (below)?
ns%smin_no3_vr_col(c,j) = ns%smin_no3_vr_col(c,j) - nf%f_nox_nit_atmos_vr_col(c,j) * dt
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Correct, only the NO that is not trapped in the canopy exits the system and is paased into the atmosphere. Both f_nox_nit_atmos and f_nox_denit_atmos leave the system. NO trapped in the canopy ideally should contribute to plant nitrogen uptake, but there are uncertainties in how plants process that nitrogen and how we can parameterize these processes.
| sminn_to_plant_fun_no3_vr(c,j),smin_no3_to_plant_vr(c,j),f_denit_vr(c,j),f_nit_vr(c,j),f_n2o_denit_vr(c,j),f_n2o_nit_vr(c,j),f_nox_denit_vr(c,j),f_nox_nit_vr(c,j),n2_n2o_ratio_denit_vr(c,j),nox_n2o_ratio_vr(c,j),f_n2_denit_vr(c,j),crf_drydep_col(c),pfactor_vr(c,j),pot_f_nox_denit_vr(c,j),pot_f_nox_nit_vr(c,j),pot_f_denit_vr(c,j),pot_f_nit_vr(c,j),(smin_no3_vr(c,j) / dt),actual_immob_no3_vr(c,j) | ||
| call endrun("too much NO3 uptake predicted by FUN") | ||
| end if | ||
| !KO if ((sminn_to_plant_fun_nh4_vr(c,j)-smin_nh4_to_plant_vr(c,j)).gt.0.0000000000001_r8) then |
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maybe remove this redundant line too.
| smin_no3_leached => soilbiogeochem_nitrogenflux_inst%smin_no3_leached_col , & ! Input: [real(r8) (:) ] (gN/m2/s) soil mineral NO3 pool loss to leaching | ||
| smin_no3_runoff => soilbiogeochem_nitrogenflux_inst%smin_no3_runoff_col , & ! Input: [real(r8) (:) ] (gN/m2/s) soil mineral NO3 pool loss to runoff | ||
| f_n2o_nit => soilbiogeochem_nitrogenflux_inst%f_n2o_nit_col , & ! Input: [real(r8) (:) ] (gN/m2/s) flux of N2o from nitrification | ||
| !mvm soil NOx 06/19/2023 |
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Yes, and please also delete commented-out lines of code that your new code is replacing.
| rc = 1._r8/((1._r8/rsmx(ispec))+(1._r8/rlux(ispec)) + & | ||
| (1._r8/(rdc+rclx(ispec)))+(1._r8/(rac(index_season,wesveg)+rgsx(ispec)))) | ||
| rc = max( 10._r8, rc) | ||
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Yes, 2-d variable with dimensions for PFT and season would make it easier for changes and sensitivity tests in the future.
| if (h2osoi_vol(c,j) < 0.30_r8 .and. pfactor_vr(c,j) .eq. 1._r8) then | ||
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| ! If change in soil moisture is > 0.005 (0.5% v/v) and there is precipitation, then start pulsing | ||
| if ( h2osoi_diff(c,j) > 0.005_r8 ) then |
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Please align this and subsequent comments with the lines following.
| pH(bounds%begc:bounds%endc) = 6.5_r8 !!! set all soils with the same pH as placeholder here | ||
| co2diff_con(1) = 0.1325_r8 | ||
| co2diff_con(2) = 0.0009_r8 | ||
| !mvm 06/15/2023 added to correct for missing organic matter turn-over |
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On the parameter file, please!
| 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)) | ||
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| !mvm 06/15/2023 NOx FLUXES |
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I agree for the most part, but I think the comment at line 424 can stay. The other comments are redundant with comments at the variable definition lines; the one at 424 explains what the calculation is doing.
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@mvalmartin and @samsrabin, what's our best plan moving forward? Some of the requests are easy (remove your name and date from line changes). Others may be more challenging (adding parameters to parameters to the parameter file and using namelist flags)? We're pretty swamped with SE needs for CESM3, so any work your group can contribute would be appreciated, Maria. That said, some of this may be simpler for someone who's more familiar with CTSM coding conventions? Happy to hear your thoughts on this. |
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I have to admit that some of my coding practices are rustic :) I can modify some of the code in the next days -before I start lecturing again. I'm not fully familiar with the CTSM coding conventions so may need some help, specially about adding the namelist or parameters in the file. I'll do my best though. |
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Definitely feel free to ping me if you need help with the parameter file! Or anything else for that matter. You can mention me here or send me an email. |
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@samlevis will you look at how this may integrate with #640? I'm assuming Matrix will come in before this PR is ready. |
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Hi @mvalmartin , One more question that came up in a conversation with @ekluzek and @tilmes was that we don't have the rest of the CESM PR here, but can you also open a PR on CMEPS for passing these fluxes through the coupler? |
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Thanks! I added it into my to do list! |
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@mvalmartin thank you for this contribution! From my perspective, once
- revisions have been made to address the code reviews,
- the PR has been updated to the latest clm tag
- test-suites have passed and
- this PR can be merged to clm's main trunk (aka master),
- I will need to figure out how to make this PR compatible with the cn-matrix_v3 branch (PR #640), which will be coming into main soon.
| write(iulog,*)'net flux = ',(col_ninputs(c)-col_noutputs(c))*dt | ||
| write(iulog,*)'inputs,ffix,nfix,ndep = ',ffix_to_sminn(c)*dt,nfix_to_sminn(c)*dt,ndep_to_sminn(c)*dt | ||
| write(iulog,*)'outputs,lch,roff,dnit = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt | ||
| write(iulog,*)'outputs,lch,roff,dnit = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,denit(c)*dt |
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Make sure that denit is calculated somewhere. I did not see it anywhere but may have missed it.
| rc = 1._r8/((1._r8/rsmx(ispec))+(1._r8/rlux(ispec)) + & | ||
| (1._r8/(rdc+rclx(ispec)))+(1._r8/(rac(index_season,wesveg)+rgsx(ispec)))) | ||
| rc = max( 10._r8, rc) | ||
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The model has another sai = stem area index. Better to call this one stai to prevent confusion?
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Hi @slevis-lmwg, @wwieder and @samsrabin, Apologies I'm slow working on this and on top of that my ctsm with soil NOx version was implemented in cheyenne and had a hard time to make it run in derecho. I also need to admit that github is not my forte and need some guidance here.... So, I started transfering the soil NOx code while addressing the previous comments from @wwieder and @samsrabin (eg remove my 'mvm' notes, etc) in a new version that works in derecho /glade/derecho/scratch/mariavm/derecho_ctsm/ Is that a good approach? I see @slevis-lmwg requested some additional modifications, so are those on top of @wwieder and @samsrabin comments or those previous ones have already been addressed? I still need to open the a PR on CMEPS for passing these fluxes through the coupler but wanted to get everything sorted in ctsm_soilnox sorted first but should I go ahead and request it? Thanks a lot! Maria |
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@mvalmartin please view my two suggestions as additional to prior comments, though I entered this discussion late and do not necessarily know what's going on. And my review's 5-point task list indicates requirements for getting code into "main" without indicating or making assumptions about who will complete each step. Seems fine to me that you made a new version that works on derecho, though keep in mind that /scratch has a scrubber, so you may lose work on that disk. That version will need to come to github to this or a follow-up PR, right? |
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Hi @wwieder, @samsrabin, @slevis-lmwg, @ekluzek and @tilmes, I have implemented the soil NOx scheme in a new version of ctsm as I couldn't make my old version run in derecho for testing. It is in here: /glade/work/mariavm/derecho_ctsm_soilnox I have also incorporated most of your modifications except 'creating a namelist variable to define the method by which N gases are calculated (e.g., Koven2013 vs. Valmartin2023)' as that was beyond my current expertise and time available to learn! The only thing left is to couple soil_nox_atmos from CTSM to CAM. Do you need to push this version to github? Thanks a lot and apologies for the delay! Maria |
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@mvalmartin It sounds like you have a new branch, right? And the one in this PR is not being used anymore? In that case, I think it would be best to close this pull request, then submit a new one with your new branch (including a link to this PR). |
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I'd agree, letting us see your update would be helpful. That's likely easiest if you just open a new PR. |
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It seems worth including some of our email discussion with @lkemmons & @tilmes. Louisa wrote: @wwieder responded: If you can provide SE support, especially for the technical bits that Maria's struggling with, that would be excellent and certainly help us out. Could Francis (of someone else) help move this PR through the pipeline? I think the prioritization of somewhat comes down to the CAM-Chem group and Dave (@dlawrenncar). Can we delay the science freeze to accommodate this request? How high a priority is it for the science you'd like to do with CESM3.0 (as opposed to CESM3.1)? |
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After further discussing this PR at our SE meeting today I think it's clear that the LMWG will not be able to get this PR onto main by the June 30 code freeze. I'm happy to outline what needs to happen to bring in this work and make it available to the community, but it's a larger discussion about deadlines and priorities for the default configuration of CESM3. |
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Thanks for the update. We will work on implementing and fully evaluating this after the freeze. |
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I had previously promised to add the page on how to add namelist items to CLM. I just found where that is, so I'm posting here in case it's helpful. As one thing we had talked about was putting namelist control around this new feature. https://wiki.ucar.edu/display/ccsm/Adding+New+Namelist+Items+to+CLM |
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@lkemmons thanks for offering to pick up this work. I don't know if it's easiest to merge the latest work you referenced in your comment here into this PR, or close this PR and open a new one? Either way, it would be nice to see where comments from the previous code review were addressed. Separately, I want to emphasize that besides the logistics of merging the PR we also need to:
Accomplishing these additional tasks seems unlikely on a July 31 timeline, but we can't even begin to evaluate this until we see an updated PR on the core of the soil BGC work. |
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@lkemmons you were going to work on this one have you made any progress on it? This seems like something that will need to come in later after the current "chill" activity happens. |
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@ekluzek Sorry, I have not found time to work on this. |
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@wwieder I'm taking the lack of urgency in this for CESM3.0 and without there being dedicated work being done on this -- that should be slated for a ctsm7.0.0 milestone. Does that seem correct to you? |
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@mvalmartin plans to visit NCAR/ACOM this summer and complete this implementation then. |
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@mvalmartin is back in Boulder and working on this! |
Yes, I'm happy to help. |
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I also want to make clear that although I hope to have this available for the CLM6 release, it will be off by default in CESM3, as the code freeze for science changes has already passed. |
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This PR is replaced by #3341 and, I think, could be closed. |
6 participants
This 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)
It is not connected to soil pH from the surface file, that is, it considers the fixed soil pH value of 6.5 given in
SoilBiogeochemCompetitionMod.F90
It also includes the dependency of the N mineralization-based term on potential nitrification rates that was implemented in Parton et al. (2001), which was missing
from previous versions of CLM5 as pointed out by Nevison et al., (2022).
This scheme -with more complexity as it is linked to spatially distributed soil pH and considers weathering effect on denitrification and NH3 volatilization- is described and evaluated 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.
Description of changes
Specific notes
Contributors other than yourself, if any:
CTSM Issues Fixed (include github issue #):
Are answers expected to change (and if so in what way)?
Any User Interface Changes (namelist or namelist defaults changes)?
Testing performed, if any:
(List what testing you did to show your changes worked as expected)
(This can be manual testing or running of the different test suites)
(Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide)
(aux_clm on cheyenne for intel/gnu and izumi for intel/gnu/nag/pgi is the standard for tags on master)
NOTE: Be sure to check your coding style against the standard
(https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines) and review
the list of common problems to watch out for
(https://github.com/ESCOMP/CTSM/wiki/List-of-common-problems).