new and fixed parameters for nutrients, phenology, seeds, fire and age-mortality

[rgknox]

Description:

This set of changes focuses only on changes to the default parameter set.

1. New parameters were added for ECA nutrient aquisition. The code will follow, and these parameters are currently unused
2. New parameters for non-woody stem phenology were added, this is coordinated with PR Grass phenology update #554
3. A new parameter that flags if PFTs can experience active crown fires was added, this is coordinated with PR Active crown fire #584
4. Parameter names for seed germination and decay, as well as the units and metadata were fixed, see parameters seed_germination_timescale and seed_decay turnover mixup? #591 and Parameter file definition edits #581

Collaborators:

@qzhu-lbl, @evaleriksen, @pollybuotte, @slevisconsulting , @jkshuman, @glemieux , @xuchongang, @ckoven @rosiealice , @JessicaNeedham

Expectation of Answer Changes:

These changes should not change answers

Checklist:

• I have updated the in-code documentation .AND. (the technical note .OR. the wiki) accordingly.
• I have read the CONTRIBUTING document.
• FATES PASS/FAIL regression tests were run

Test Results:

CTSM (or) E3SM (specify which) test hash-tag:

CTSM (or) E3SM (specify which) baseline hash-tag:

FATES baseline hash-tag:

Test Output:

[jkshuman]

Looks good. Thanks, @rgknox

[glemieux]

Grass phenology related updates look good to go @rgknox

[ckoven]

Hi all,
discussed this with @rgknox and @glemieux. Main remaining question here is what to do about symbiotic N fixation parameters. Right now this PR has two dummy parameters for N fixation, i.e.: https://github.com/NGEET/fates/pull/595/files#diff-a236898dbb7848d5cfdf2610b0ba32c0R321

Is this sufficiently flexible? e.g., @rosiealice does this cover the PFT parameter needs for a FUN-like N fixation scheme? I'm imagining one PFT parameter would be a scalar variable that specifies in some units how much carbon a plant might allocate to N fixation, with zero meaning the plant isn't an N fixer. I could see this having a lower and upper bound to accommodate flexibility in representing obligate vs facultative N fixers, so therefore needing two PFT parameters?

Other PFT parameters might be the N return on the C cost, or the constants controlling the temperature sensitivity of N fixation costs, though I would expect those to be global rather than PFT parameters, and if so, maybe we can add those in once we have a fully developed N fixation model? Does anyone see a need for more than 2 PFT-level N fixation parameters now as we build out the model?

cc @walkeranthonyp @laagee

[pollybuotte]

One question, otherwise looks good. Sorry for the long delay in doing this!

[rgknox]

updates: changed active_crown_fire to a scalar, and fixed the code comment noted by @pollybuotte

[jkshuman]

@rgknox the active_crown_fire parameter will be an "on/off" switch to use the active crown fire portion of the code. It should be switched to a binary logical flag. 1=active crown fire 0=no active crown fire

[rgknox]

@jkshuman , how do those changes look?

[jkshuman]

@rgknox looks good. Thanks.

[rgknox]

working with @JessicaNeedham to incorporate some of her new parameters as well, as some near-term integrations from her that use those parameters are forthcoming

[jkshuman]

@rgknox I am going to pull another parameter out of the fire code. CG_strikes is a scaler on lightning datasets to identify the percentage of cloud to ground strikes. Will be easier to test and modify this if it lives in the param file as a global scaler parameter. Will take care of it this week.
https://github.com/jkshuman/fates/blob/e5e808ca3f7c4f65e4a5fd3d6dbee61a639ac9ab/fire/SFMainMod.F90#L683-L684

[rgknox]

All expected tests pass, b4b. namelist tests do not pass, as expected.

/glade/scratch/rgknox/clmed-tests/fates-sci-1.31.1_api.8.1.0-Ceac01319-F26ab2875.fates.cheyenne.intel

@jkshuman, can you take a look at the new cg_strikes parameter and sign off?

[ckoven]

I think my earlier comments to add size to a couple parameters got lost during the alphabetization step

[rgknox]

see my first question in the discussion of PR 590, here: #590
It may be worth adding the namelist changes to the current PR

[rgknox]

based on feedback so far on #590, I'm not going to add any changes related to hydraulics to this PR.
It looks like we will most likely make changes to the namelist variables, and how we use hlm_use_planthydro. I've mocked up some changes here: rgknox/fates@parameters-eca-phen-fire...rgknox:parameters-nlist-eca-phen-fire

I will go ahead and re-test this PR with @ckoven 's updates, this should be read to merge soon.

[rgknox]

all expected pass, with NLFAILs (expected fail).
/glade/scratch/rgknox/clmed-tests/fates-sci-1.31.1_api.8.1.0-C195c9b2e-F25ff0f6e.fates.cheyenne.intel

[jenniferholm]

Ahh, I just missed this to add in a new parameter. My bad team. There is a fates_leaf level parameter needed for taking into account nutrients effects during photosynthesis. It's "flnr" for fraction of leaf N in Rubisco (gN Rubisco / gN leaf).
But if it's ok, I can just add this as another pull request (when I get closer to finishing the photosynthesis component), right?

[rgknox]

But if it's ok, I can just add this as another pull request (when I get closer to finishing the photosynthesis component), right?

sure, we are bound to have another round of parameter updates in the near future, we just just try to clump them whenever possible