Leaf Age Response function for all Biogenic VOCs consistent with MEGAN

[quaz115]

See Issue #79 .
@drnimbusrain @MaggieMarvin These are the changes I have added so far for the Leaf Age response function to work for all BVOCs.

Think we need more discussion on how to make it work with the time feature (as I have currently tried to make tdays, i.e. time period between Past and Current LAI (whichever time period we decide to use) to be dynamic and user-defined. This si the only component (LAI and timestep inputs) that would need more work.

@drnimbusrain feel free to point out any further changes I need to make before we can finalize this. I have made this a draft PR currently, but it is almost complete I think

Let me know if you have questions about specific changes

[drnimbusrain]

@quaz115 There are build errors in your codes, as well as formatting issues too. Please make sure you are following the "develop" practices in the README, using things like the pre-commit hooks to check indentation etc.

[quaz115]

@zmoon Even though i made a new conda env which has pre-commit installed, seems like findent isn't working ?

pre-commit install --install-hooks
pre-commit installed at .git/hooks/pre-commit
(CanopyApp) |19:02:01|Quazi.Rasool@hfe03:[canopy-app-LeafAge]> pre-commit run --all-files
trim trailing whitespace.................................................Passed
fix end of files.........................................................Passed
check yaml...............................................................Passed
Format Fortran code using findent........................................Failed
- hook id: wfindent-pypi
- exit code: 1

/home/Quazi.Rasool/.cache/pre-commit/repowh0abga7/py_env-python3.9/bin/wfindent: findent not found, exiting

pyupgrade................................................................Passed
isort....................................................................Passed
black-jupyter............................................................Passed
flake8...................................................................Passed
nbstripout...............................................................Passed

[drnimbusrain]

@quaz115 I tested your repo/branch and using the pre-commit run --all-files on GMU Hopper system and it works OK, and finds wfindent:

fix end of files.........................................................Passed
check yaml...............................................................Passed
Format Fortran code using findent........................................Failed
- hook id: wfindent-pypi
- files were modified by this hook

/home/pcampbe8/.cache/pre-commit/repoevazfzjg/py_env-python3.10/bin/wfindent using: findent version 4.2.3
wfindent: indented files: 28

Of course here I am using a later version of python3.10 in my install of pre-commit, compared to your version of python 3.9 installed in your environment.

Maybe try installing pre-commit again, but with later version of python?

conda install -c conda-forge pre-commit python=3.10.5

[drnimbusrain]

Eventually, when merged this will close #79

[quaz115]

@quaz115 I tested your repo/branch and using the pre-commit run --all-files on GMU Hopper system and it works OK, and finds wfindent:

fix end of files.........................................................Passed
check yaml...............................................................Passed
Format Fortran code using findent........................................Failed
- hook id: wfindent-pypi
- files were modified by this hook

/home/pcampbe8/.cache/pre-commit/repoevazfzjg/py_env-python3.10/bin/wfindent using: findent version 4.2.3
wfindent: indented files: 28

Of course here I am using a later version of python3.10 in my install of pre-commit, compared to your version of python 3.9 installed in your environment.

Maybe try installing pre-commit again, but with later version of python?

conda install -c conda-forge pre-commit python=3.10.5

Had to use 3.11 to make findent work, also resolving other build errros now

[quaz115]

@drnimbusrain It passes all checks and compiles now, but will prefer to merge only after run(s) with this new functionality. Also, let me know when you have reviewed the code changes once and have free time to discuss them sometime early this week.

[drnimbusrain]

Yes, please let us review the code carefully, and it would be best to show tests and results here before merging. I'd like it if Maggie cof help with that too

…

On Sat, Sep 16, 2023, 5:00 PM Quazi Ziaur Rasool ***@***.***> wrote: @drnimbusrain <https://github.com/drnimbusrain> It passes all checks and compiles now, but will prefer to merge only after run(s) with this new functionality. Also, let me know when you have reviewed the code changes once and have free time to discuss them sometime early this week. — Reply to this email directly, view it on GitHub <#92 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGLFYNVHA7MUCTB2FLGAQL3X2YHPFANCNFSM6AAAAAA4Y6U4SY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[drnimbusrain]

@MaggieMarvin Would be great if you could help provide a close code review here, as well as run some tests with for Quazi's PR/branch to gauge if it is working as expected and the impacts.

Thanks!

[drnimbusrain]

@quaz115 Finished my initial review, and looks pretty good. My major comment is that you set the above canopy air temperature to the canopy resolved leaf temperature. I think this should be changed to use the more appropriate 1D/2D 2-meter temperature from model/obs inputs. This seems more relevant, and then the TABOVECANOPY variable does not need to be an array indexed on canopy model levels (modlays, ZK, etc.).

Once updated for this, @MaggieMarvin could review and test the impacts of leaf age factors.

Nice work!

[quaz115]

@quaz115 Finished my initial review, and looks pretty good. My major comment is that you set the above canopy air temperature to the canopy resolved leaf temperature. I think this should be changed to use the more appropriate 1D/2D 2-meter temperature from model/obs inputs. This seems more relevant, and then the TABOVECANOPY variable does not need to be an array indexed on canopy model levels (modlays, ZK, etc.).

Once updated for this, @MaggieMarvin could review and test the impacts of leaf age factors.

Nice work!

@drnimbusrain @MaggieMarvin I have edited the code (compiles as well) based on Patrick's recommendation to pass TEMP2 (above 2-m air temp) for GAMMA_LEAFAGE.

[drnimbusrain]

Looks good, but some other small comments and changes.

[drnimbusrain]

Looks good Quazi, before approving, I'd like it if @MaggieMarvin do a test with the impacts of turning the leaf age factor on and off for isoprene.

Thanks!

[drnimbusrain]

he updated script handles the new daily LAI and creates i

@angehung5 Can you make another PR to @quaz115 's fork of develop, with your updated SE text/nc files(with same daily LAI and pavd updates as before) and updated python script for daily LAI merge from global AWS canopy/GFS files? This will facilitate @quaz115 testing of daily LAI in his develop branch for the leaf age PR.

[quaz115]

@drnimbusrain Attaching the SE US output with @angehung5 's new daily LAI inputs showing difference b/w LEAFAGE OFF vs ON:

[quaz115]

@drnimbusrain @zmoon @MaggieMarvin @angehung5 Feel free to review this, tested with the SE US setup and see if its ready to be merged currently

[drnimbusrain]

@quaz115 Thank you...Some small clarifications and changes.

[drnimbusrain]

@drnimbusrain Attaching the SE US output with @angehung5 's new daily LAI inputs showing difference b/w LEAFAGE OFF vs ON:

@quaz115 Can you comment on these results a bit as to what is being shown, impacts, and if expected results?

[drnimbusrain]

Be sure to run the CI first, seems some small formatting issue with your change: https://github.com/noaa-oar-arl/canopy-app/actions/runs/6776276783/job/18417393784

[drnimbusrain]

@zmoon Can you tell why the CI is failing here?

[quaz115]

@drnimbusrain Attaching the SE US output with @angehung5 's new daily LAI inputs showing difference b/w LEAFAGE OFF vs ON:

@quaz115 Can you comment on these results a bit as to what is being shown, impacts, and if expected results?

@drnimbusrain Normally leaf age response would have a reduction on BVOCs emission rate except for Higher Monoterpene emissions in some cases possibly due to new leaf response as a defense mechanism giving high MT emissions: [Guenther et al. 1991 Also, Guenther et al. 2012: "Table4 shows that new leaves are predicted to have just 5% of the isoprene emission rate, but a factor of 3.5 higher methanol emission rate, in comparison to mature leaves. Monoterpene emissions are predicted to decline with age while sesquiterpene emissions are predicted to increase." So most likely we are seeing this as Fnew and Fgro being higher for these results as a possible reason

[drnimbusrain]

@quaz115 small namelist changes, other than that looks good.

[drnimbusrain]

Suggested change

	file_out = 'output/2022-07-01-11-0000_global_leafageON' !southeast_us'
	file_out = 'output/2022-07-01-11-0000_southeast_us'

[drnimbusrain]

Suggested change

	nlat = 43 !for Global nlat= 1536
	nlat = 43

[drnimbusrain]

Suggested change

	nlon = 86 !for Global nlon= 3072
	nlon = 86

[drnimbusrain]

Suggested change

	leafage_opt = 1
	leafage_opt = 1

[drnimbusrain]

@quaz115 Please also revert these input files back to what they are in default [develop] branch. Thanks!

[quaz115]

this should be uncommented right: file_vars = 'input/gfs.t12z.20220630.sfcf023.canopy.nc' 'input/gfs.t12z.20220701.sfcf000.canopy.nc' 'input/gfs.t12z.20220701.sfcf001.canopy.nc'

[drnimbusrain]

Should look like this:

&FILENAMES
!2D Text and NCF Examples
! Recommend set file_out prefix to initial 'YYYY-MM-DD-HH-MMSS_region_identifier'
  file_vars    = 'input/gfs.t12z.20220630.sfcf023.canopy.nc' 'input/gfs.t12z.20220701.sfcf000.canopy.nc' 'input/gfs.t12z.20220701.sfcf001.canopy.nc'
!  file_vars    = 'input/gfs.t12z.20220630.sfcf023.canopy.txt' 'input/gfs.t12z.20220701.sfcf000.canopy.txt' 'input/gfs.t12z.20220701.sfcf001.canopy.txt'
  file_out     = 'output/2022-07-01-11-0000_southeast_us'