Arctic changes branch with Kattge in place of Leuning in LUNA #990

ekluzek · 2020-04-23T20:31:34Z

Description of changes

This is @lmbirch89 branch from #947 with the exception that Kattge is used in place of Leuning in LUNA. Also the startup initial values in the luna bug fix branch #961 is used in place of the updated values by @lmbirch89. The LUNA bug fixes have already come in, so these are some changes to improve arctic plants.

I did also merge in #961 just to make sure that the only differences to it were formatting changes.

Specific notes

Contributors other than yourself, if any: @lmbirch

CTSM Issues Fixed (include github issue #):
Fixes #807
Fixes #1307

Are answers expected to change (and if so in what way)? Yes (for CLM5.1 compsets using LUNA)

Any User Interface Changes (namelist or namelist defaults changes)? No

Testing performed, if any: running regular testing on cheyenne

Abz update

update branch

merging 4/13

…ts324

…ange anything of substance

wwieder

@ekluzek This looks good. I think there are some changes to hard coded parameters in PhotosynthesisMod that should not be changed for Kattge. Maybe @lmbirch89 can confirm.

src/biogeophys/PhotosynthesisMod.F90

ekluzek · 2020-04-24T19:28:56Z

Ahh, thanks for correcting that @lmbirch89 and @wwieder. I was wondering about those lines, but wasn't sure. I'll change them and also add some notes about how they go with Kattge vs. Leuning.

That's why we want to make these changes easy to see and for people to correct it.

wwieder · 2020-04-24T19:41:55Z

OK, once your finalize this @ekluzek @olyson can run a new spinup and historical simulation. We just need to make sure this uses the new parameter file provided in the PR from @lmbirch89 .

XueliHuo · 2020-12-10T21:06:12Z

There is a tag named as branch_tags/lmbirch_wkattge.n01_ctsm5.1.dev006.
It is described as

Update lmbirch_wkattge branch to ctsm5.1.dev006
Due to a subtle code bug, CNFireLi2021 was using the btran2 calculating
routine from the base class rather than the new one that is specific to
this formulation

To my understanding, the tag is the result of merging tag 'ctsm5.1.dev006' into lmbirch_wkattge branch. It is a tag of lmbirch_wkattge branch rather than the master branch.

ekluzek · 2020-12-10T21:17:12Z

Yes, these changes aren't in the master branch (i.e. main development) as of yet. We do have them in the PPE branch that is updated to a newer version ctsm5.1.dev012. The part of Leah's original changes that are in place are the bug fixes for LUNA, that we could say were clearly bug fixes rather than tuning of the arctic vegetation patterns.

So @amfox37 would the PPE branch do for what you want to do with this? It has some other changes, but all of them will be eventually coming to CTSM main-development. If so I can point you to that branch.

The other option if you just need this in a more recent version of CTSM, I could do that update on this branch. That shouldn't be very hard, and it's something I have to do eventually anyway. So let me know if that would be helpful as well.

Outside of that this will come to main development eventually, but there are other higher immediate priorities right now. So it won't be until early 2021. But, we could point you to the PPE branch immediately or update this branch to the latest in the next week or so.

XueliHuo · 2020-12-10T22:19:50Z

We do need the version that includes the tuning of arctic vegetation pattern. If you could update the Arctic vegetation pattern change in a more recent version of CTSM in the next week, we would appreciate it so much.

We understand that there are other higher immediate priorities right now. So if you could not make this happen in the next week or so, could you give any comment on the disadvantage of using this tag

branch_tags/lmbirch_wkattge.n01_ctsm5.1.dev006

?

ekluzek · 2020-12-10T22:26:37Z

There's a couple important changes that go in a few tags after that one (branch_tags/lmbirch_wkattge.n01_ctsm5.1.dev006). I would recommend using this tag: branch_tags/PPE.n01_ctsm5.1.dev012, which includes these lmbirch_wkatttge changes in it. From the description of what you want to do it sounds like that should work.

XueliHuo · 2020-12-10T22:39:08Z

Thanks. Just want to confirm that what you mean by

We do have them in the PPE branch that is updated to a newer version ctsm5.1.dev012. The part of Leah's original changes that are in place are the bug fixes for LUNA

is the PPE branch includes Leah's arctic vegetation changes while the part of Leah's original changes that are in place in main development (master branch) are only the bug fixes for LUNA.

Right ?

ekluzek · 2020-12-10T22:42:55Z

@XueliHuo yes exactly. That's why I recommend you use the PPE tag.

XueliHuo · 2020-12-10T22:44:49Z

Okay. Thank you so much. This is very useful.

wwieder · 2020-12-11T13:54:22Z

@ekluzek thanks for pointing @XueliHuo to the right tag.

@XueliHuo I just want to clarify that this a development branch of the model and that 'tuning of arctic vegetation pattern' has not really been done. This branch uses new parameter files that do a better job of keeping arctic C3 grasses alive following the other changes to Arctic phenology that Leah made. These changes (to leaf C:N and SLA) seem justified by quickly collected observations, but I would not consider this a well tuned model. That said, I think it's likely the best we can offer right now for what you're trying to do.

Will

XueliHuo · 2020-12-11T17:47:40Z

Thanks @wwieder for the clarification. Another question is will there be an announcement somewhere (github CTSM wiki page, the tag page or ?) when the 'tuning of arctic vegetation pattern' is really been done ?

wwieder · 2020-12-11T23:54:08Z

This will be 'finished' after the PPE experiment and released to the community with great fan-fare. It may be when we finalize and release the CTSM5.1 tag (or a later development tag) depending on how long it takes to finish the parameter estimate work.

…

On Fri, Dec 11, 2020 at 10:47 AM XueliHuo ***@***.***> wrote: Thanks @wwieder <https://github.com/wwieder> for the clarification. Another question is will there be an announcement somewhere (github CTSM wiki page, the tag page or ?) when the 'tuning of arctic vegetation pattern' is really been done ? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#990 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5IWJHYG5BJBKPYJZE4FB3SUJLMXANCNFSM4MPNNOYA> .

dlawrenncar · 2020-12-14T17:36:10Z

And this presumes that the PPE tuning actually works, which it may or may not and also may or may not generate better behavior in the Arctic. So, I think the best way to look at this is to consider this tag as our best current effort to tune the Arctic vegetation. On Fri, Dec 11, 2020 at 4:54 PM will wieder <notifications@github.com> wrote:

…

This will be 'finished' after the PPE experiment and released to the community with great fan-fare. It may be when we finalize and release the CTSM5.1 tag (or a later development tag) depending on how long it takes to finish the parameter estimate work. On Fri, Dec 11, 2020 at 10:47 AM XueliHuo ***@***.***> wrote: > Thanks @wwieder <https://github.com/wwieder> for the clarification. > Another question is will there be an announcement somewhere (github CTSM > wiki page, the tag page or ?) when the 'tuning of arctic vegetation > pattern' is really been done ? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#990 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AB5IWJHYG5BJBKPYJZE4FB3SUJLMXANCNFSM4MPNNOYA > > . > — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#990 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFABYVCU243FFZWADRPOAM3SUKWLHANCNFSM4MPNNOYA> .

Refactor ozone code, and misc. small fixes (1) Restructure ozone code (ESCOMP#1276) in preparation for new ozone parameterization. (2) Fix non-standard hexadecimal constant (ESCOMP#1271), needed for gfortran 10 (3) Remove support for CISM1 (ESCOMP#1226) (4) Move final WaterGridcellBalance call out to clm_driver (resolves ESCOMP#1286) (5) Only add WA and QCHARGE history fields if use_aquifer_layer is true (resolves ESCOMP#1281) (6) Consolidate conditional structures for VIC initialization (resolves ESCOMP#1287) Conflicts: bld/namelist_files/namelist_defaults_ctsm.xml bld/unit_testers/build-namelist_test.pl

Implemented new nuopc/cmeps single column functionality. In config/cesm/config_files.xml - single point domains are only used for mct/cpl7. For cmeps single point meshes are now generated on the fly and component domains files are no longer needed. env_run.xml variables PTS_LAT, PTS_LON and PTS_DOMAINFILE are used to determine if there is a single point or single column run. If PTS_LAT and PTS_LON are not -999 and PTS_DOMAINFILE is UNSET, then you have a single point run and the exact values of PTS_LAT and PTS_LON are used. If PTS_LAT and PTS_LON are not -999 and PTS_DOMAINFILE is not UNSET, then then the cmeps driver will recognize the nearest neighbor values of PTS_LAT and PTS_LON in PTS_DOMAINFILE as the single column lat and lon to use.

Remove unnecessary settings of nextsw_cday Remove setting of nextsw_cday in initialization: this hasn't been needed ever since we stopped calculating albedos in initialization. Also remove nextsw_cday from clm_time_manager: this was being set but was never referenced from here: instead, nextsw_cday was being passed as an argument to clm_drv. Also, updates cime to a branch tag where I have fixed the --retry option to create_test.

ekluzek · 2021-04-15T21:03:14Z

OK, there are a couple things I noted that I should fix before bringing this to main-dev. But, they should all be simple things to do. I can also add #1307 to this one.

ekluzek · 2021-04-16T23:00:56Z

@ekluzek This looks good. I think there are some changes to hard coded parameters in PhotosynthesisMod that should not be changed for Kattge. Maybe @lmbirch89 can confirm.

It appears to me this is done now. The only change in Photosynthesis are commented out lines that tell what the values for Leuning would be.

@wwieder can you confirm this is correct, and mark this PR as approved by you?

src/biogeophys/TemperatureType.F90

…t will work for different soil depths

…he upper_soil_layer was exactly 3 as ERS_Ly5_P144x1.f10_f10_mg37.IHistClm51BgcCrop.cheyenne_intel.clm-cropMonthOutput passes and with identical answers to previously

wwieder

looks good @ekluzek

lmbirch89 and others added 22 commits March 21, 2020 11:24

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Set vxmax/jmax to same as lunadaylbugs branch

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Use Kattge instead of Leuning in Luna

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ekluzek added enhancement new capability or improved behavior of existing capability type: -discussion PR status: ready PR: this is ready to merge in, with all tests satisfactory and reviews complete labels Apr 23, 2020

ekluzek self-assigned this Apr 23, 2020

wwieder requested changes Apr 24, 2020

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ekluzek added 3 commits March 6, 2021 14:42

ekluzek added 2 commits April 16, 2021 00:48

Turn reseed_dead_plants on for AD spinup mode fixes ESCOMP#1307

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Remove KO comments and commented out code

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ekluzek commented Apr 17, 2021

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ekluzek added 2 commits April 19, 2021 00:34

Set upper_soil_layer with a function call at initialization so that i…

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…t will work for different soil depths

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…he upper_soil_layer was exactly 3 as ERS_Ly5_P144x1.f10_f10_mg37.IHistClm51BgcCrop.cheyenne_intel.clm-cropMonthOutput passes and with identical answers to previously

ekluzek mentioned this pull request Apr 19, 2021

Use of floating point flag onset_thresh is confusing in CNPhenologyMod #1346

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ekluzek requested a review from wwieder April 19, 2021 21:11

wwieder approved these changes Apr 19, 2021

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ekluzek merged commit c877c22 into ESCOMP:master Apr 19, 2021

ekluzek deleted the lmbirch_wkattge branch April 19, 2021 22:04

ekluzek mentioned this pull request Jun 11, 2021

Some cleanup for arctic luna changes #1399

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samsrabin added the science Enhancement to or bug impacting science label Aug 8, 2024

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Arctic changes branch with Kattge in place of Leuning in LUNA #990

Arctic changes branch with Kattge in place of Leuning in LUNA #990

ekluzek commented Apr 23, 2020 •

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Arctic changes branch with Kattge in place of Leuning in LUNA #990

Arctic changes branch with Kattge in place of Leuning in LUNA #990

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ekluzek commented Apr 23, 2020 • edited Loading

Description of changes

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