New allometric modes #1128
New allometric modes #1128
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…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.
glemieux
added
parameter file
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awesome set of updates @mpaiao looking forward to getting this integrated |
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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. |
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Just so people are aware, we don't call the crown depth allometry module in hydro: That crown depth routine is really only relevant for fire dynamics, as the radiative transfer doesn't use crown depth in its calculations. |
biogeochem/EDCanopyStructureMod.F90
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| @@ -1616,12 +1625,10 @@ subroutine leaf_area_profile( currentSite ) | |||
| ! is obscured by snow. | |||
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| 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 ) | |||
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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
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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.
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@rgknox Should I go ahead and edit subroutine VegAreaLayer now that two-stream has been merged?
| @@ -305,7 +306,7 @@ subroutine h2d_allom(h,ipft,d,dddh) | |||
| p3 => prt_params%allom_d2h3(ipft), & | |||
| allom_hmode => prt_params%allom_hmode(ipft)) | |||
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| select case(int(allom_hmode)) | |||
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agreed, smarter to convert the switch on the read in, no need to convert over and over again in the dynamics loop
| @@ -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) | |||
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Noting that height capping is compatible with this scheme and implementation makes sense.
| !--- Local variables | ||
| real(r8) :: duse | ||
| !---~--- | ||
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header and descriptions are nice and verbose, units, refs, great
| return | ||
| end subroutine size2dbh | ||
| ! ============================================================================ | ||
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You were very determined to find the inverse solution for dbh and h @mpaiao , not easy, kudos
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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.
| write(fates_log(),*) '---~---' | ||
| write(fates_log(),*) '' | ||
| write(fates_log(),*) '' | ||
| nerror = nerror + 1 |
| if (nerror > 0) then | ||
| write(fates_log(),*) 'One or more parameter errors found. Aborting.' | ||
| call endrun(msg=errMsg(sourcefile, __LINE__)) | ||
| end if |
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double checked to make sure that all checks removed endrun and added nerror, looks good
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@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 |
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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.
| ! degradation on water, energy, and carbon cycling of the Amazon | ||
| ! tropical forests. J. Geophys. Res.-Biogeosci. 125: | ||
| ! e2020JG005677. doi:10.1029/2020JG005677. | ||
| ! |
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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.
| 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
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
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I re-ran the fates regression tests on Location: |
Description:
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.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.allom_dmode=1, crown depth is a constant fraction of height (the former default); whenallom_dmode=2, crown depth is defined as p1 * Height^p2, following Poorter et al. (2006). Former parametercrown_depth_fracwas replaced with parameterallom_h2cd1, and a new parameterallom_h2cd2was added for the exponent.Collaborators:
Expectation of Answer Changes:
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