New updates on MEGANv2.1 #2588
New updates on MEGANv2.1 #2588
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Thanks for opening this PR @HuiWangWanderInGitHub. We'll start reviewing this PR, but a quick look seems like this should be straightforward to implement. Directions for this are posted on the wiki @olyson, can you help with this? |
wwieder
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Purely samantic question, can we call this PR MEGANv2.2, or is this confusing with broader MEGAN documentation? Also @lkemmons, can you help clarify the prioritization of this PR in relation to the science code freeze (July 31 deadline) for cam-chem? |
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There is a more condensed version of how to update the documentation here: https://docs.google.com/document/d/1aLlu6C6DJiiO2T21qnj54WFCYuSdGw9F/edit Once you've issued a PR for the new documentation and verified the documentation builds successfully, we can take it from there. |
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For naming - Alex recommends calling the updated version 'MEGAN-CLM6' (or
whatever the appropriate label is for the version of CLM/CTSM that it ends
up in). Because the stand-alone MEGAN has features that will never be
implemented in CLM, it is not really appropriate to try to use the v2.x and
v3.x labels here.
I will be happy to help verify results in CAM-chem with these updates, to
work towards getting this in CESM3, and hope that will be possible.
…On Mon, Jun 10, 2024 at 10:03 AM will wieder ***@***.***> wrote:
Purely samantic question, can we call this PR MEGANv2.2, or is this
confusing with broader MEGAN documentation?
Also @lkemmons <https://github.com/lkemmons>, can you help clarify the
prioritization of this PR in relation to the science code freeze (July 31
deadline) for cam-chem?
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samsrabin
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Bring tmp-branch to master Bring in changes that came in on the tmp-240620 branch to master now that cesm3_0_beta01 has been made. The changes are documented in tags and the ChangeLog but include the following tags: tmp-240620.n03.ctsm5.2.007 samrabin -- upland hillslope column fsat values to zero tmp-240620.n02.ctsm5.2.007 erik ------ Another update of git-fleximod tmp-240620.n01.ctsm5.2.007 slevis ---- Merge b4b-dev
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@HuiWangWanderInGitHub
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Large number of tests differ from the baseline (see /glade/derecho/scratch/slevis/tests_0706-132231de).
The former has diffs in FATES variables (clm file) and in lndImp variables (cpl file). UPDATE 1: Same result on izumi with UPDATE 2: I tried the 3 failing tests in vanilla ctsm5.2.008: UPDATE 3: I backed out my last commit and repeated the 3 tests: |
This reverts commit d940ee0 because answers were changing from the baseline in tests ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream
Relax tolerance for truncating small snocan values in CanopyFluxes See the PR ESCOMP#2457 for details.
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The failing test has changed in ctsm5.2.012 to |
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This PR changes the calculation of gamma_sm and of gamma_t. In my troubleshooting I introduced the gamma_sm and the gamma_t changes separately. I also introduced the two new parts of gamma_t (Eopt and gamma_t_LDF) separately. Regardless, the above PEM test gives new results in these three files. The one I'm concerned about is cism because it seems unexpected, but maybe it's fine: |
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@slevis-lmwg there's another issue where we know CISM changes answers on processor count. So do the test without CISM which just means dropping the G at the end of the compset. That will probably mean you have to also run the baseline as well. |
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Thank you for contributing these changes to the model. I included some comments based on clm's coding practices.
But more important concerns:
- As written, the code results in changed answers in a PEM test that I would not have expected (see my corresponding posts about troubleshooting). Am I mistaken? Should we expect changed answers in the cism file?
- When I tried introducing _r8 to all the hardwired reals, I started seeing changed answers in an ERS test in FATES variables, that I would not have expected. Should we expect differences in FATES variables just by adding _r8 to hardwired values?
From master: Now, the diffs from baseline are limited to MEG_ and _voc variables, as expected. |
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I now realize my mistake in thinking that the PEM failure was unexpected: This means that, as written, the code passes the aux_clm tests. |
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@HuiWangWanderInGitHub I'm happy to make the revisions in response to my review; however,
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I used this test to confirm same answers: ./create_test ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream -c /glade/campaign/cgd/tss/ctsm_baselines/ctsm5.2.012 This test had indicated differences with an earlier commit that I subsequently reverted.
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Hi @slevis-lmwg , Thank you so much for your help and sorry for accidentally closing the issue. Here are the names of the unnamed variables: Thank you. |
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@HuiWangWanderInGitHub I will post a new code review with the constants/coefficients that I would prefer ideally to be named. |
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@HuiWangWanderInGitHub thank you for your help trying to resolve these issues.
Dust emissions control moved to cmeps Remove the dust emissions namelist items from CTSM and use the namelist in the drv_flds_in for CMEPS. This updates CTSM to use the namelist control in CMEPS (in ESCOMP/CMEPS#429). So the CMEPS external needs to be updated, and the namelist control in CTSM changed to use CMEPS rather than the internal CTSM control settings and the CTSM ones removed. The new XML variable: LND_SETS_DUST_EMIS_DRV_FLDS controls whether dust emission settings are set by CTSM or by CAM. Only one or the other can set them, and it's required so when CAM and CTSM are running together they need to know which one will select. This required some changes for LILAC. The drv_flds_in namelist file is now required for LILAC, and read for dust emissions (and dust emissions only) at the LILAC lnd_comp_esmf.F90 level. Add a unit test for the CMEPS code to make sure it's working correctly. This validates the code both for CAM and CTSM. Fix the cidinahoBR test in the build-namelist unit tester.
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I will submit aux_clm once more to consider this PR ready: @HuiWangWanderInGitHub |
slevis-lmwg
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PR status: ready
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aux_clm results
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@slevis-lmwg this looks to me to be the same as what I saw in my earlier tag here: So yes this is good from a testing perspective. |
samsrabin
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slevis resolved conflicts: doc/ChangeLog doc/ChangeSum
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In preparation for the merge, I have updated to ctsm5.2.019 and submitted aux_clm: OK (same behavior reported earlier in this PR) |
Description of changes
We added new features to MEGANv2.1 for simulating isoprene emissions based on three recent studies conducted at the BAI lab in the University of California, Irvine. The first one is about the drought impact on isoprene (Wang et al., 2022). The second study investigates the effect of temperature history on the emission factors of boreal broadleaf deciduous shrubs (Wang et al., 2024a). The third study explores a different temperature response curve for C3 Arctic grass (Wang et al., 2024b, under press). These changes improved the model's representation of isoprene emissions during drought and in high-latitude ecosystems.
This work is related to issue #1323 and is based on the old MEGANv2.1 framework, but incorporates new scientific insights.
Specific notes
We modified the impact of drought based on the water stress function (β) in the CLM model. We adopted equation (11) from Wang et al., (2022) as:
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, where a1 (=-7.45) and b1(=3.26) are empirical parameters. The function “get_gamma_SM” is modified to simulate the change of substrate supply under the water stress.
Second and third modifications are for the high-latitude isoprene emitters including boreal broadleaf deciduous shrubs (BBDS) and C3 Arctic grass (C3AG). These results come from the Biogenic Emission and Aerosol Response on the North Slope (BEAR-oNS) project. These modifications are implemented in “get_gamma_T” function in the code.
For the BBDS, we included the adaptation of isoprene emission factors to the mean temperature of the previous day with the quation as:
, where T24 (K) denotes the mean air temperature of the preceding day (Wang et al., 2024a).
For the C3AG, we adopted a dynamic temperature response curve adapted to the record of growing temperature as:
. CC3AG is the activation energy for the isoprene temperature response of C3AG and changes with the mean air temperature of the preceding 10 days (T240) as:
The impact of T240 on isoprene emission factor of C3AG is as:
Any User Interface Changes (namelist or namelist defaults changes)?
NO.
Does this create a need to change or add documentation? Did you do so?
I could provide the modification to the scientific document for these changes after they have been added.
Testing performed, if any:
I tested the code on Derecho with the I2000Clm50BgcCrop compsets, and it ran well. The scientific impact of the code for isoprene flux estimations can be found in the corresponding references.
Reference
Wang, H., Lu, X., Seco, R., Stavrakou, T., Karl, T., Jiang, X., et al. (2022). Modeling isoprene emission response to drought and heatwaves within MEGAN using evapotranspiration data and by coupling with the community land model. Journal of Advances in Modeling Earth Systems, 14, e2022MS003174. https://doi.org/10.1029/2022MS003174
Wang, H., Welch, A. M., Nagalingam, S., Leong, C., Kittitananuvong, P., Barsanti, K. C., et al. (2024a). Arctic heatwaves could significantly influence the isoprene emissions from shrubs. Geophysical Research Letters, 51, e2023GL107599. https://doi.org/10.1029/2023GL107599
Wang, H., Welch, A. M., Nagalingam, S., Leong, C., Czimczik, C., Tang, J., et al. (2024b): High temperature sensitivity of Arctic isoprene emissions explained by sedges (accepted by Nature Communications, in press).