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New allometric modes #1128

Merged
merged 21 commits into from
Apr 23, 2024
Merged

New allometric modes #1128

merged 21 commits into from
Apr 23, 2024

Commits on Dec 6, 2023

  1. Add new allometric modes for multiple quantities, plus a few minor im…

    …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.
    mpaiao committed Dec 6, 2023
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Commits on Dec 7, 2023

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Commits on Feb 5, 2024

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  3. updating parameters for cstarvation and allometry crown depth modes i…

    …n the xml patch file and cdl
    rgknox committed Feb 5, 2024
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  4. Merge pull request #9 from rgknox/mpaiao-pr-allom-modes-cstarve-merge

    merge in cstarvation params and main, update xml patch file
    mpaiao authored Feb 5, 2024
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  5. Fix crown depth allometry for two stream.

    Fix documentation typos and added suggested values for the new allometry (thanks JessicaNeedham)
    mpaiao committed Feb 5, 2024
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Commits on Feb 6, 2024

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

    … and alpha are incactive
    rgknox committed Feb 6, 2024
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  2. Merge pull request #10 from rgknox/mpaiao-pr-allom-modes-eca

    protections metadata on eca phosphatase
    mpaiao authored Feb 6, 2024
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Commits on Mar 26, 2024

  1. merging in vert resp scaler coeffs

    JessicaNeedham authored and rgknox committed Mar 26, 2024
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  3. updating api update xml files

    rgknox committed Mar 26, 2024
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  4. updated parameter xml names

    rgknox committed Mar 26, 2024
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  6. adding daylight factor

    rgknox committed Mar 26, 2024
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  7. bug fix on parameter printing

    rgknox committed Mar 26, 2024
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Commits on Mar 27, 2024

  1. added carbon starvation mode

    rgknox committed Mar 27, 2024
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  2. Merge pull request #11 from rgknox/mpaiao-pr-allom-modes-moreparams

    added parameters and merged up
    mpaiao authored Mar 27, 2024
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Commits on Apr 11, 2024

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

    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.
    glemieux committed Apr 11, 2024
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Commits on Apr 22, 2024

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

    Fixes exact restart bug for satellite phenology mode
    glemieux committed Apr 22, 2024
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