New allometric modes #1128

mpaiao · 2023-12-08T06:29:04Z

Description:

New allometric function for above-ground biomass (allom_amode = 4), which is similar to Chave et al. (2014), except that the exponent for wood density is independent of the one for "tree size" (i.e., DBHDBHHeight). Although this function could be simplified externally (by incorporating wood density into the scaler), this makes the dependency on wood density more transparent and may make parameter perturbation experiments a bit easier.
New allometric function for leaf biomass and crown area (allom_lmode = 4), which uses tree size as the predictor. In the case of leaf biomass, the function also is a function of top-canopy SLA, using a similar formulation as the one for above-ground biomass.
Crown depth has now allometric modes too (variable allom_dmode). If allom_dmode=1, crown depth is a constant fraction of height (the former default); when allom_dmode=2, crown depth is defined as p1 * Height^p2, following Poorter et al. (2006). Former parameter crown_depth_frac was replaced with parameter allom_h2cd1, and a new parameter allom_h2cd2 was added for the exponent.
All allometric mode variables were converted to integers when they are loaded (parteh/PRTParamsFATESMod.F90). This avoids converting them to integers every time the allometric function is called.
Small edits to CheckParams (parteh/PRTParamsFATESMod.F90).

The current implementation of allom_hmode=2 is a bit unusual because the minus sign of the Weibull function is incorporated in parameter p2 (meaning that p2 must be negative). Added a check to make sure the parameter is negative.
Instead of aborting the run as soon as an inconsistency in parameters is spotted, the subroutine now continues to check other parameters, and report all the errors before stopping the run. This avoids users recompiling/submitting FATES multiple times to fix one inconsistency at a time.

Collaborators:

Expectation of Answer Changes:

Checklist

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The in-code documentation has been updated with descriptive comments
The documentation has been assessed to determine if updates are necessary

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FATES PASS/FAIL regression tests were run
Evaluation of test results for answer changes was performed and results provided

Documentation

Technical Note update:
User's Guide update:

Test Results:

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

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FATES baseline hash-tag:

Test Output:

…provements. 1. New allometric function for above-ground biomass (allom_amode = 4), which is similar to Chave et al. (2014), except that the exponent for wood density is independent of the one for "tree size" (i.e., DBH*DBH*Height). 2. New allometric function for leaf biomass and crown area (allom_lmode = 4), which uses tree size as the predictor. In the case of leaf biomass, the function also is a function of top-canopy SLA, using a similar formulation as the one for above-ground biomass. 3. Crown depth has now allometric modes too (variable allom_dmode). If allom_dmode=1, crown depth is a constant fraction of height; when allom_dmode=2, crown depth is defined as p1 * Height^p2. Former parameter crown_depth_frac was replaced with parameter allom_h2cd1 (p1), a new parameter allom_h2cd2 was added for the exponent. 4. All allometric mode variables were converted to integers when they are loaded. This avoids converting them to integers every time the allometric function is called. 5. Small edit to CheckParams. The current implementation of allom_hmode=2 is a bit unusual because the minus sign of the Weibull function is incorporated in parameter p2 (meaning that p2 must be negative). Also, instead of aborting the run as soon as an inconsistency in parameters is spotted, the subroutine now continues to check other parameters, and report all the errors before stopping the run. This avoids users submitting FATES multiple times to get one inconsistency at a time.

rgknox · 2024-01-15T16:55:23Z

awesome set of updates @mpaiao looking forward to getting this integrated

rgknox · 2024-01-15T17:09:54Z

I was looking through an old issue related to fates Hydro and how it perceives and uses crown depth, see here: #674

I think the things we discuss in that thread are out of scope for this PR, but would be good to re-evaluate and move forward on them though.

rgknox · 2024-01-15T17:13:01Z

Just so people are aware, we don't call the crown depth allometry module in hydro:
https://github.com/NGEET/fates/blob/sci.1.70.0_api.32.0.0/biogeophys/FatesPlantHydraulicsMod.F90#L775-L776

That crown depth routine is really only relevant for fire dynamics, as the radiative transfer doesn't use crown depth in its calculations.

rgknox · 2024-01-15T17:16:06Z

biogeochem/EDCanopyStructureMod.F90

@@ -1616,12 +1625,10 @@ subroutine leaf_area_profile( currentSite )
                ! is obscured by snow.

                layer_top_height = currentCohort%height - &
-                     ( real(iv-1,r8)/currentCohort%NV * currentCohort%height *  &
-                     prt_params%crown_depth_frac(currentCohort%pft) )
+                     ( real(iv-1,r8)/currentCohort%NV * crown_depth )


nice update here @mpaiao

This will have a conflict with the new two-stream PR. I created a new subroutine that calculates the leaf area of crown layers, and it will need to leverage your fixes, see: https://github.com/NGEET/fates/pull/1141/files#diff-4fd8508e4a25680b45ecbfec6b6d80980a5b1e358af731203ee9d29266be46dbR2655

Thanks for spotting this, @rgknox. Once the two-stream PR is integrated, I can update this part. I will leave this conversation open so we don't forget.

@rgknox Should I go ahead and edit subroutine VegAreaLayer now that two-stream has been merged?

rgknox · 2024-01-15T17:17:15Z

biogeochem/FatesAllometryMod.F90

@@ -305,7 +306,7 @@ subroutine h2d_allom(h,ipft,d,dddh)
                p3          => prt_params%allom_d2h3(ipft), &
                allom_hmode => prt_params%allom_hmode(ipft))

-      select case(int(allom_hmode))


agreed, smarter to convert the switch on the read in, no need to convert over and over again in the dynamics loop

rgknox · 2024-01-15T17:28:12Z

biogeochem/FatesAllometryMod.F90

@@ -522,6 +534,12 @@ subroutine carea_allom(dbh,nplant,site_spread,ipft,crowndamage,c_area,inverse)
          call carea_2pwr(dbh_eff,site_spread,d2bl_p2,d2bl_ediff,d2ca_min,d2ca_max, &
               crowndamage, c_area, do_inverse)
          capped_allom = .true.
+       case (4)
+          dbh_eff = min(dbh,dbh_maxh)


Noting that height capping is compatible with this scheme and implementation makes sense.

rgknox · 2024-01-15T17:29:44Z

biogeochem/FatesAllometryMod.F90

+     !--- Local variables
+     real(r8) :: duse
+     !---~---
+


header and descriptions are nice and verbose, units, refs, great

biogeochem/FatesAllometryMod.F90

rgknox · 2024-01-15T17:47:09Z

biogeochem/FatesAllometryMod.F90

+      return
+   end subroutine size2dbh
+   ! ============================================================================
+


You were very determined to find the inverse solution for dbh and h @mpaiao , not easy, kudos

This one is totally borrowed from ED2 solvers, I just adapted it here. This allometric function is well behaved and should quickly converge with the Newton method, but I thought I should keep the full root finding approach in case we want to adapt for less well-behaved functions anywhere in FATES in the future.

rgknox · 2024-01-15T17:50:33Z

parteh/PRTParamsFATESMod.F90

+              write(fates_log(),*) '---~---'
+              write(fates_log(),*) ''
+              write(fates_log(),*) ''
+              nerror = nerror + 1


rgknox · 2024-01-15T17:53:52Z

parteh/PRTParamsFATESMod.F90

+     if (nerror > 0) then
+        write(fates_log(),*) 'One or more parameter errors found. Aborting.'
+        call endrun(msg=errMsg(sourcefile, __LINE__))
+     end if


double checked to make sure that all checks removed endrun and added nerror, looks good

rgknox · 2024-01-15T17:56:03Z

@mpaiao these changes look pretty clean to me. The root finding method is complicated, and I did not go through it in detail. But I did see that it was borrowed from ed2? If so, that is great, since its already been vetted. After discussion, I realized that the 2 is a derivative of an x^2. There is no precedent of explaining that in the other methods, so I have no further comments. Approvinng

JessicaNeedham

Thanks @mpaiao - these are great changes/additions. I was wondering whether we want to put suggested parameter values for various allometry options, since default parameters will be wacky with some of the options. We already do this for the Chave d2h and dh2bagw but we could add it in for some others as well. Maybe out of scope for this PR, but might be helpful in future.

biogeochem/FatesAllometryMod.F90

JessicaNeedham · 2024-01-24T01:10:29Z

biogeochem/FatesAllometryMod.F90

+     !    degradation on water, energy, and carbon cycling of the Amazon 
+     !    tropical forests. J. Geophys. Res.-Biogeosci. 125:
+     !    e2020JG005677. doi:10.1029/2020JG005677.
+     !


The new leaf biomass allometry looks great to me. One minor suggestion is to put suggested parameter values. It looks like the default d2bl1, d2bl2 and d2bl3 will give very high biomass with this equation so some suggested values for users wishing to use this option could be helpful.

biogeochem/FatesAllometryMod.F90

JessicaNeedham · 2024-01-24T01:20:04Z

parteh/PRTParamsFATESMod.F90

+              write(fates_log(),*) '---~---'
+              write(fates_log(),*) ''
+              write(fates_log(),*) ''
+              nerror = nerror + 1


…n the xml patch file and cdl

merge in cstarvation params and main, update xml patch file

Fix documentation typos and added suggested values for the new allometry (thanks JessicaNeedham)

… and alpha are incactive

protections metadata on eca phosphatase

added parameters and merged up

biogeochem/FatesAllometryMod.F90

biogeochem/EDCanopyStructureMod.F90

Bug fix. Adrianna Foster identified that trunks should be removed from the patch-level variable sum_fuel before being used to calculate rate of spread and fuel consumption.

Fixes exact restart bug for satellite phenology mode

glemieux · 2024-04-23T00:21:11Z

I re-ran the fates regression tests on derecho since it had been a while since the last tests Ryan ran. As expected, all expected tests passed b4b.

Location: /glade/u/home/glemieux/scratch/ctsm-tests/tests_pr1128-fates-2

mpaiao added 2 commits December 6, 2023 07:44

Fix swapped arguments for leaf biomass allometry.

d29e182

glemieux added parameter file Pertaining to changes to the FATES parameter file enhancement labels Dec 8, 2023

rgknox self-assigned this Jan 15, 2024

rgknox reviewed Jan 15, 2024

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rgknox and others added 7 commits February 5, 2024 11:54

merge resolution between allometry modes and two-stream

8531dda

enabling cstarvation mode switch in-code

118b411

updating parameters for cstarvation and allometry crown depth modes i…

f450fb7

…n the xml patch file and cdl

Merge pull request #9 from rgknox/mpaiao-pr-allom-modes-cstarve-merge

92d0dff

merge in cstarvation params and main, update xml patch file

Fix crown depth allometry for two stream.

c644186

Fix documentation typos and added suggested values for the new allometry (thanks JessicaNeedham)

Add in parameter file checks and metadata that ECA phosphatase lambda…

e35f44c

… and alpha are incactive

Merge pull request #10 from rgknox/mpaiao-pr-allom-modes-eca

37db010

protections metadata on eca phosphatase

This was referenced Mar 18, 2024

Update default allometry parameters for tree PFTs #1093

Merged

Adding day length factor switch #1161

Merged

FATES API35 parameter file update ESCOMP/CTSM#2436

Merged

JessicaNeedham and others added 10 commits March 26, 2024 10:53

merging in vert resp scaler coeffs

e1e9b07

added leaf vertical scaling parameter coefficients in read-in and xml

dc1d029

updating api update xml files

7ab9bcc

updated parameter xml names

e218fb3

Applied batch patch script to api34 update

4942a17

adding daylight factor

48f0a81

bug fix on parameter printing

7444f26

merge resolution between allom mode updates and api34

1aef70f

added carbon starvation mode

97dc27a

Merge pull request #11 from rgknox/mpaiao-pr-allom-modes-moreparams

6573572

added parameters and merged up

rgknox closed this Apr 1, 2024

rgknox reopened this Apr 1, 2024

mpaiao commented Apr 1, 2024

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glemieux self-assigned this Apr 9, 2024

Merge tag 'sci.1.72.6_api.34.0.0' into mpaiao-pr-allom-modes

90350db

Bug fix. Adrianna Foster identified that trunks should be removed from the patch-level variable sum_fuel before being used to calculate rate of spread and fuel consumption.

Merge tag 'sci.1.72.7_api.34.0.0' into mpaiao-pr-allom-modes

0827f05

Fixes exact restart bug for satellite phenology mode

glemieux merged commit adfa664 into NGEET:main Apr 23, 2024
1 check was pending

mpaiao deleted the mpaiao-pr-allom-modes branch November 18, 2024 15:58

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New allometric modes #1128

New allometric modes #1128

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New allometric modes #1128

New allometric modes #1128

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mpaiao commented Dec 8, 2023

Description:

Collaborators:

Expectation of Answer Changes:

Checklist

Documentation

Test Results:

rgknox commented Jan 15, 2024

rgknox commented Jan 15, 2024

rgknox commented Jan 15, 2024

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