New outputs: N to food and seed #2074

samsrabin · 2023-07-26T21:53:55Z

Description of changes

In response to a user request for GRAINN_TO_FOOD outputs, this adds *_N_TO_FOOD and *_N_TO_SEED outputs for reproductive N pools. These are off by default, unlike their C counterparts.

Specific notes

CTSM Issues Fixed (include github issue #): None

Are answers expected to change (and if so in what way)? No

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

Testing performed, if any: A simple 5-day test gave the following for the gridcell average of the last day:

Spatial patterns match, but it's weird that the C:N ratio is so high—on the order of 100:1. This could just be a result of looking in what might be the middle of the growing season, before N retranslocation is complete.

samsrabin · 2023-08-03T16:08:36Z

Should probably do aux_clm testing to see whether any diffs are introduced. There shouldn't be any, but one never knows.
Update master_list_nofates.rst (wait on Rework master_list_(no)?fates.rst? #2083)

samsrabin · 2023-08-03T19:44:17Z

Will be unblocked by #2087.

b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

samsrabin · 2023-10-07T17:51:29Z

aux_clm OK; baselines saved as grainN_to_food.a26a5d1b2.

samsrabin · 2023-10-10T19:25:38Z

Tasks from co-review with @slevis-lmwg:

~~Determine why I added get_repr_hist_fname to CNVegNitrogenFluxType%InitHistory(); remove if unneeded.~~ Needed to get _N_TO_FOOD variable names depending on which reproductive pools exist.
~~Add GRAINN_TO_FOOD to first history file in crop testmod.~~ Done with eeab40d.
Do a longer test, examining at-harvest C:N ratios of both TO_FOOD and TO_SEED.

slevis-lmwg · 2023-10-10T19:26:41Z

src/biogeochem/CNPhenologyMod.F90

@@ -3106,8 +3111,15 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, &
                         repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) &
                             + repr_grainc_to_food_perharv(p,h,k)
                     end if
+                     repr_grainn_to_food_thispool = npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k)
                     repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) &
                          + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k)


I asked @samsrabin to remind me the diff between "grain to seed" and "grain to food" and I see here that the two terms summed are the reproductive pool. I'm not sure "seed" is the right term for what's left when you subtract food from the reproductive pool, but that's out of scope for this PR.

src/biogeochem/CNVegNitrogenFluxType.F90

slevis-lmwg · 2023-10-10T19:30:11Z

src/biogeochem/CNVegNitrogenFluxType.F90

+               fname=get_repr_hist_fname(k)//'N_TO_FOOD_PERHARV', &
+               units='gN/m^2', &
+               type2d='mxharvests', &
+               avgflag='I', &


I mentioned PR #2019 which, as written, eliminates 'I' hardwiring in the code; however, we are waiting for a different coding solution from CAM, so no need to worry about that right now.

samsrabin · 2023-10-11T22:12:09Z

Hmm. I'm concerned that the way CLM does C and N allocation to seed vs. grain makes it not fit for purpose with regard to harvested (food) N content. I don't exactly understand all the machinations, but the result is plain enough: At harvest, to-food N is sometimes zero while C is positive. This is not the case for to-seed N and C content (or, of course, seed + food).

Moreover, even if we combine both seed and food to get all grain biomass, C:N looks off. Soybeans typically have C:N ratio of < 10, but from a 5-year run, I'm not seeing mean at-harvest grain C:N below 45:

I still think it's worth adding these outputs, as without them I don't think there's a way to calculate aboveground crop N biomass. But perhaps some metadata of GRAINN_TO_FOOD should disclaim that it's not necessarily realistic.

Tagging @billsacks in case you have any thoughts, as I see you worked on the seed allocation and deficit code, albeit back in 2017.

…ames.

FATES cross-grid seed dispersal This PR enables FATES to disperse seeds across neighboring grid cells using MPI. The API update includes calls to new fates dispersal procedures. There are four parameters that are utilized to control the dispersal kernel, although these were introduced in ctsm5.1.dev130 so no new default FATES parameter file is necessary with this update. A new namelist parameter has been added to enable the use of the seed dispersal mode.

samsrabin · 2023-10-26T19:42:35Z

aux_clm OK as of af4a688.

billsacks · 2023-10-31T16:06:49Z

Tagging @billsacks in case you have any thoughts, as I see you worked on the seed allocation and deficit code, albeit back in 2017.

Sorry for the slow reply. I think I worked on this code as part of getting C & N conservation to work with dynamic crop areas (i.e., dynamic landunits). I think this required me to move the product pools to grid cell level, so I did some rework to accomplish that.

In my notes from that project:

Why is grainn_to_food not treated the same as c, in subtract_cropseed?

Danica says: N should be treated the same as C... that's something they wanted to add

Then my notes went on to say that I want to rework this so that N is treated the same as C. And it looks like I did some rework to that end; in particular, it looks like I put in a removal of grainn_to_seed from the N crop product pool.

My notes lead me to think that, as of the time of this work (clm4_5_14_r220, in January 2017), it should have been the case that C and N were treated in the same way for crop seeding. But it's very possible that (1) I'm making an incorrect assumption about that from what I can glean from my 7-year-old notes; (2) I intended to make the treatment the same but there was still some mistake / discrepancy; and/or (3) C and N were treated the same at that time, but have diverged in some way since then.

I'd be happy to discuss this further if it would be useful.

samsrabin · 2023-10-31T16:55:11Z

@billsacks Thanks for that context—it's so great that you have notes going back that far!

As far as I can tell, everything that happens to repr_grainn_to_food_patch happens to the C equivalent and vice versa: e.g., "Send the remaining grain to the food product pool", the update of reproductive[cn]_patch in [CN]StateUpdate1(). I think the difference must come in how the seed deficit is calculated. But again, things seem to be the same mechanically—although I haven't taken as close a look.

Does it all derive from leafcn, then? That seems to be the driver of seed deficit via seed[cn]_to_leaf.

billsacks · 2023-10-31T19:04:57Z

Interesting, thanks for your analysis. I don't remember enough about this to weigh in further, but let me know if you want to talk about it.

samsrabin · 2023-11-01T17:21:47Z

@slevis-lmwg This is ready for re-review (commits beginning b95b986).

slevis-lmwg

I looked over the latest changes and have no concerns.

Add sowing window input files Previously, one could run crops with either (a) sowing windows defined by the hemisphere-specific start and end dates on the paramfile or (b) prescribed sowing dates specified by input file stream_fldFileName_sdate. This PR replaces the latter with two new input files, stream_fldFileName_swindow_start and stream_fldFileName_swindow_end.

samsrabin added 3 commits July 26, 2023 15:15

Add N_TO_FOOD outputs.

93e82dc

Add N_TO_SEED outputs.

2cd8339

Make N_TO_FOOD and N_TO_SEED outputs default inactive.

f737631

samsrabin self-assigned this Jul 26, 2023

samsrabin added 3 commits July 26, 2023 16:16

Fix indentation of a block.

8ae1ecb

Merge branch 'master-upstream' into grainN-to-food

bda8cf1

Add N_TO_FOOD perharv and ann.

01731b7

samsrabin removed the PR status: ready PR: this is ready to merge in, with all tests satisfactory and reviews complete label Aug 3, 2023

samsrabin added the blocked: dependency Wait to work on this until dependency is resolved label Aug 3, 2023

samsrabin mentioned this pull request Aug 3, 2023

Rework master_list* files etc. #2087

Merged

samsrabin removed the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Aug 17, 2023

samsrabin removed the blocked: dependency Wait to work on this until dependency is resolved label Sep 25, 2023

samsrabin added 2 commits October 6, 2023 13:11

Merge tag 'ctsm5.1.dev142' into grainN-to-food

a26a5d1

b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

Update history_fields .rst files.

bf9f4d8

samsrabin requested a review from slevis-lmwg October 10, 2023 19:20

Add GRAINN_TO_FOOD to first history file in crop testmod.

eeab40d

slevis-lmwg approved these changes Oct 10, 2023

View reviewed changes

samsrabin added 2 commits October 17, 2023 13:24

Added TO_SEED _ANN and _PERHARV outputs.

d0c44a1

Fix in-progress attempt to add note to N_TO_FOOD longnames.

b95b986

samsrabin added 4 commits October 25, 2023 10:15

Add "not scientifically supported" to reproductive N hist field longn…

205848b

…ames.

Move GRAINC_TO_SEED_ANN to same place as GRAINC_TO_SEED.

ae8f46a

Added *C_TO_SEED_PERHARV hist fields.

af4a688

samsrabin requested a review from slevis-lmwg November 1, 2023 17:21

slevis-lmwg approved these changes Nov 1, 2023

View reviewed changes

samsrabin added the PR status: ready PR: this is ready to merge in, with all tests satisfactory and reviews complete label Nov 1, 2023

samsrabin added 3 commits November 2, 2023 15:02

Updated history_fields*.rst files.

1e2c520

Update ChangeLog and ChangeSum.

333c0d6

samsrabin merged commit 6743205 into ESCOMP:master Nov 3, 2023
2 checks passed

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

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New outputs: N to food and seed #2074

New outputs: N to food and seed #2074

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New outputs: N to food and seed #2074

New outputs: N to food and seed #2074

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Description of changes

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