Add FAN and fertilizer for crops #5981

bbye · 2023-10-11T01:05:57Z

Adds Flow of Agriculture Nitrogen (ammonia emissions) to crop model.
Adds gridded fertilizer for nitrogen and phosphorus.
Adds manure application.

All tests with CN biogeochemistry will have a namelist change.
[NML]
[non-BFB] for crop tests

This adds the first round of the Flow of Agricultural Nitrogen (FAN) code which includes three new files, two with the FAN algorithms and one with the data stream.

Adds gridded nitrogen and phosphorus fertilizer. Adds fixed manure application if FAN is not used. If FAN is on, then uses FAN manure applications.

This commit allows ammonia emissions from FAN to couple with the atmosphere. Note that this feature is off by default and has not been tested with the full atmosphere or chemistry model.

There are several items addressed in this commit to improve the crop model. 1. First it resolves a bug in the crop model preventing bfb restart 2. Adds the missing components needed to collapse crop types that are not calibrated into ones that are known to the model. This allows placeholders of cfts so we don't have to keep changing the surface data files. 3. Resolves an issue with the cropseedc, cropseedn, and cropseedp so they don't keep growing negative every time the initial seed is given at planting.

This is the last of the FAN subroutine. It updates the mksurfdat routine to include the gridded fertilizer. Also updates some parameter and surface data files with the fertilizer. Finally, a test for FAN is included (default mode) only.

Bugfixes to get tests to pass

bbye · 2023-10-11T01:09:58Z

The land developer tests all passed, with diffs for all the smallvilleIA tests due to the new fertilizer datasets. All the tests with CN also fail the namelist check because there is a new fan namelist.

A description of the feature can be found at: https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/2237465109/B14+Flow+of+Agriculture+Nitrogen+Design+Document

evasinha

Great job @bbye for getting the FAN implemented in E3SM and submitting the PR.

I only have minor edits for your consideration.

evasinha · 2023-10-16T19:44:08Z

components/elm/src/biogeochem/CNNitrogenFluxType.F90

Please add units for manure_n_transf_col , nh3_otherfert_col, and nh3_total_col

Parenthesis are missing or not closed for few units.

Thanks, this was due to a copy paste, it's fixed now.

evasinha · 2023-10-16T19:48:27Z

components/elm/src/biogeochem/CNNitrogenStateType.F90

Minor typo - 'ammoniacal'

This is the actual spelling (I looked it up to make sure), it refers to the ammonia component of nitrogen

evasinha · 2023-10-16T20:49:57Z

components/elm/src/biogeochem/FanUpdateMod.F90

For the FanMod.F90 and FanUpdateMod.F90, please consider listing name of all subroutines after contains.

For e.g.,

contains procedure , public :: fanInit

I didn't do this because I think it's generally done when defining a type. All the public subroutines are listed at the beginning of the module and I added some extra description about the flow of the FAN model in each of FanUpdateMod and FanMod.

The listing of public functions is before the "contains" and there is a small block in each of the new files like this one in FanMod.F90.

private public update_org_n public eval_fluxes_storage public update_npool public update_4pool public update_urea

You might want to add an inline comment for each of those explaining what they do.

Ok, I went through FanMod and FanUpdateMod and added inline comments to all the public functions to briefly explain what they do.

evasinha · 2023-10-16T20:54:52Z

components/elm/src/data_types/ColumnDataType.F90

Minor typo - The comment for tan_s3 ! (gN/m2) total ammoniacal N in FAN pool S2 incorrectly calls it FAN pool S2. Same typo was in components/elm/src/biogeochem/CNNitrogenStateType.F90

Initialization of all FAN variables - should it be nan or spval?

Thanks, the typos are fixed and the initialization was changed to spval.

evasinha · 2023-10-16T21:04:28Z

components/elm/src/biogeochem/FanMod.F90

This module has various subroutines and functions. Consider adding short notes on the top that explain the flow through various subroutines.

Thanks, I added more description about the flow of the modules.

evasinha · 2023-10-16T21:20:49Z

components/elm/src/data_types/VegetationDataType.F90

Lines 9397 to 9430 can all be in a single crop_prog loop instead of five separate if loops for crop_prog.

Thanks, this is now one loop.

Fixes some initialization, loop configuration, typos, and adds some more text describing FAN module.

evasinha

All comments have been addressed. I approve the PR for merging to the master.

Add more comments to FanMod and FanUpdateMod

mingxuanwupnnl · 2023-10-28T05:37:48Z

Nice to see that this feature will be in master. Will this be turned on by default for BGC?

bbye · 2023-11-17T15:25:35Z

@mingxuanwupnnl Sorry, I just saw your comment. This feature won't be on by default in v3 sims because it requires the crop model to be turned on and that won't be on by default in v3. However, we are planning to do some simulations with the crop model on and we can have FAN on with those.

…tilizer_for_crops' into next (PR #5981) Adds Flow of Agriculture Nitrogen (ammonia emissions) to crop model. Adds gridded fertilizer for nitrogen and phosphorus. Adds manure application. All tests with CN biogeochemistry will have a namelist change. [BFB] except for crop tests. [NML] diff

peterdschwartz · 2023-11-21T21:11:55Z

merged to next

peterdschwartz · 2023-11-22T15:45:11Z

@bbye some tests failed due to missing inputdata file
file not found: stream_fldfilename_fan = /sems-data-store/ACME/inputdata/lnd/clm2/ndepdata/fan_nitrogen_e3sm_f19_c20191010.nc

peterdschwartz · 2023-11-22T16:10:56Z

@bbye I went ahead and added that file to the data server. Just have to check if any others are missing

peterdschwartz · 2023-11-22T16:42:57Z

@bbye Also, it seems that .case.setup will still fail before it can even attempt to download the file, so it needs to be copied to every inputdata manually?? If so, it may need to be reworked, and I may just revert it today.

I always get the error message

ERROR: Command: '/global/u2/p/pschwar3/E3SM/components/elm/bld/build-namelist -infile /pscratch/sd/p/pschwar3/fantest/ERS.f19_g16.I1850GSWCNPECACNTBC.pm-cpu_intel.elm-eca_f19_g16_I1850GSWCNPECACNTBC.C.20231122_111411_ugxi8j/Buildconf/elmconf/namelist  -csmdata /global/cfs/cdirs/e3sm/inputdata -inputdata /pscratch/sd/p/pschwar3/fantest/ERS.f19_g16.I1850GSWCNPECACNTBC.pm-cpu_intel.elm-eca_f19_g16_I1850GSWCNPECACNTBC.C.20231122_111411_ugxi8j/Buildconf/elm.input_data_list -ignore_ic_year -namelist " &elm_inparm  start_ymd=00010101  /" -use_case 1850_control  -res 1.9x2.5  -clm_start_type default -envxml_dir /pscratch/sd/p/pschwar3/fantest/ERS.f19_g16.I1850GSWCNPECACNTBC.pm-cpu_intel.elm-eca_f19_g16_I1850GSWCNPECACNTBC.C.20231122_111411_ugxi8j -l_ncpl 48 -r_ncpl 8 -lnd_frac /global/cfs/cdirs/e3sm/inputdata/share/domains/domain.lnd.fv1.9x2.5_gx1v6.090206.nc -glc_nec 0 -co2_ppmv 284.7 -co2_type constant  -ncpl_base_period day  -config /pscratch/sd/p/pschwar3/fantest/ERS.f19_g16.I1850GSWCNPECACNTBC.pm-cpu_intel.elm-eca_f19_g16_I1850GSWCNPECACNTBC.C.20231122_111411_ugxi8j/Buildconf/elmconf/config_cache.xml -bgc bgc -nutrient cnp -nutrient_comp_pathway eca -soil_decomp century -methane  -mask gx1v6' failed with error 'File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /global/u2/p/pschwar3/E3SM/components/elm/bld/ELMBuildNamelist.pm line 3674.
ERROR : CLM build-namelist::ELMBuildNamelist::add_default() : file not found: stream_fldfilename_fan = /global/cfs/cdirs/e3sm/inputdata/lnd/clm2/ndepdata/fan_nitrogen_e3sm_f19_c20191010.nc' from dir '/pscratch/sd/p/pschwar3/fantest/ERS.f19_g16.I1850GSWCNPECACNTBC.pm-cpu_intel.elm-eca_f19_g16_I1850GSWCNPECACNTBC.C.20231122_111411_ugxi8j/Buildconf/elmconf'

Attempting to use ./check_input_data --download doesn't help -- maybe due to setup failing before it can generate elm.input_data_list

…_and_Fertilizer_for_crops' into next (PR #5981)" This reverts commit f1eaf60, reversing changes made to 892e777.

peterdschwartz · 2023-11-22T19:02:54Z

Reverted this PR for now. Need to investigate how the changes to the namelists are done.

peterdschwartz · 2023-11-28T17:57:35Z

In E3SM/components/elm/bld/ELMBuildNamelist.pm the add_default function checks if a file exists. Commenting out this check will allow the case to setup and download the missing lnd/clm2/ndepdata/fan_nitrogen_e3sm_f19_c20191010.nc as expected.

Maybe there's a better solution, but having a missing file result in a fatal error seems to contradict the idea behind being able to download files from the data server to begin with.

rljacob · 2023-11-28T18:06:39Z

That sounds like the right solution.

peterdschwartz · 2023-11-30T17:06:23Z

Update: There's another error message for a couple of pm-cpu_gnu tests where the fan atm is enabled but use_fan is disabled. I believe I tracked it down to shr_fan_readnl not initializing fan_nh3_to_atm so that if the drv_flds_in file does not exist fan_nh3_to_atm defaults to .true. for this compiler.

Just haven't been able to properly test the fix the past couple of days due to perlmutter being down for maintenance

rljacob · 2023-12-04T19:53:34Z

@peterdschwartz any further progress?

peterdschwartz · 2023-12-04T20:18:57Z

@rljacob Yes, I did fix the other error message. I'll push the new commit to @bbye branch after I do a test merge and run all the tests on pm gnu

ELMBuilNamelist.pm : removed fatal_error call if missing files so that they can be downloaded from data server. shr_fan_mod.F90 : initialized fan_nh3_to_atm to .false. in case drv_flds_in doesn't exist for certain configs.

peterdschwartz · 2023-12-05T19:29:33Z

With the last round of testing, there were a few parameter and surfdata_map files that had to be added to the data server, and so far that seems to have fixed all the fails (though still waiting on a few).

Hopefully it's straightforward to push these changes to your fork @bbye

bbye · 2023-12-05T19:31:06Z

Thanks @peterdschwartz! I appreciate your help getting the PR fixed.

…rate_FAN_and_Fertilizer_for_crops' into next (PR #5981)"" This reverts commit 8bba792.

…tilizer_for_crops' into next (PR #5981) Adds Flow of Agriculture Nitrogen (ammonia emissions) to crop model. Adds gridded fertilizer for nitrogen and phosphorus. Adds manure application. All tests with CN biogeochemistry will have a namelist change. [non-BFB] for crop tests. [NML]

peterdschwartz · 2023-12-07T19:24:42Z

Merged to next. Sucessfully re-ran the new FAN test to make sure the revert and re-merge worked as intended, so hopefully everything checks out tomorrow

peterdschwartz · 2023-12-08T18:40:14Z

Merged to master. Submitted bless requests except for pm-cpu_intel which hasn't finished yet

bbye · 2023-12-08T19:41:01Z

Thank you Peter for your help getting this PR in!

bbye added 6 commits September 27, 2023 17:09

Initial FAN implimentation

fe887f9

This adds the first round of the Flow of Agricultural Nitrogen (FAN) code which includes three new files, two with the FAN algorithms and one with the data stream.

Add Nitrogen and Phosphorus Fertilizer

f17c9b0

Adds gridded nitrogen and phosphorus fertilizer. Adds fixed manure application if FAN is not used. If FAN is on, then uses FAN manure applications.

Connect FAN to the atmosphere

718ec6c

This commit allows ammonia emissions from FAN to couple with the atmosphere. Note that this feature is off by default and has not been tested with the full atmosphere or chemistry model.

Adds finishing touches to FAN implementation

0203540

This is the last of the FAN subroutine. It updates the mksurfdat routine to include the gridded fertilizer. Also updates some parameter and surface data files with the fertilizer. Finally, a test for FAN is included (default mode) only.

Bugfixes to get tests to pass

1ea4a6d

Bugfixes to get tests to pass

bbye added the Land label Oct 11, 2023

bbye requested a review from evasinha October 11, 2023 01:06

bbye assigned peterdschwartz Oct 11, 2023

bbye changed the title ~~bbye/lnd/integrate fan and fertilizer for crops~~ Add FAN and fertilizer for crops Oct 12, 2023

rljacob added the enhancement label Oct 12, 2023

evasinha added 2 commits October 16, 2023 14:02

Update ColumnDataType.F90

2595884

Update ColumnDataType.F90

3d833c1

evasinha reviewed Oct 16, 2023

View reviewed changes

Minor edits to Fan module

c5f9489

Fixes some initialization, loop configuration, typos, and adds some more text describing FAN module.

evasinha approved these changes Oct 26, 2023

View reviewed changes

Add more comments

2d55ed6

Add more comments to FanMod and FanUpdateMod

rljacob approved these changes Nov 16, 2023

View reviewed changes

peterdschwartz added a commit that referenced this pull request Nov 22, 2023

Revert "Merge remote-tracking branch 'bbyefork/bbye/lnd/integrate_FAN…

8bba792

…_and_Fertilizer_for_crops' into next (PR #5981)" This reverts commit f1eaf60, reversing changes made to 892e777.

Fix two errors

123e652

ELMBuilNamelist.pm : removed fatal_error call if missing files so that they can be downloaded from data server. shr_fan_mod.F90 : initialized fan_nh3_to_atm to .false. in case drv_flds_in doesn't exist for certain configs.

peterdschwartz added a commit that referenced this pull request Dec 7, 2023

Revert "Revert "Merge remote-tracking branch 'bbyefork/bbye/lnd/integ…

3539050

…rate_FAN_and_Fertilizer_for_crops' into next (PR #5981)"" This reverts commit 8bba792.

peterdschwartz merged commit fa40af6 into E3SM-Project:master Dec 8, 2023
2 checks passed

mahf708 mentioned this pull request Dec 13, 2023

Enable rough topograph and add remaining atm and lnd settings for v3b02 #6113

Merged

bishtgautam mentioned this pull request Jan 3, 2024

mksurfdata.pl is broken #6137

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Add FAN and fertilizer for crops #5981

Add FAN and fertilizer for crops #5981

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Add FAN and fertilizer for crops #5981

Add FAN and fertilizer for crops #5981

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