Crown damage module #788

JessicaNeedham · 2021-10-01T20:36:03Z

Description:

This set of changes introduces a crown damage module into FATES. This reduces the crown area and biomass of tissues in the crown -leaves, sapwood, structure, storage and reproductive tissues. Damage can affect canopy or understory cohorts (or both) using the switches hlm_use_canopy_damage and hlm_use_understory_damage. Cohorts are split into damage classes, the number of which is set via the parameter ncrowndamage. The parameter damage_frac sets the fraction of each cohort that gets damaged in each damage event (currently hard coded to be once per year - but working on making this more flexible). The fates_damage_recovery_scalar parameter sets the degree of recovery i.e. allocation to regrow the crown versus staying on damaged allometric trajectory. Two optional parameters can be used to introduce damage-dependent mortality, which captures mortality from damage via mechanisms not represented in FATES. With default parameterisation this would be off.

Collaborators:

@ckoven @glemieux @rgknox @rosiealice

Expectation of Answer Changes:

With the hlm_use_canopy_damage and hlm_use_understory_damage off runs should be bit for bit with master. Currently that is not the case and I'm looking into why.
With these switches on then answers will not be bit for bit with master. There will be more cohorts as damage and recovery involve splitting cohorts into damage classes. Damaged cohorts will have smaller canopies which affects AGB and canopy dynamics. Depending on parameterisation carbon starvation mortality may increase.

Checklist:

My change requires a change to the documentation.
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
If answers were expected to change, evaluation was performed and provided

Test Results:

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

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

FATES baseline hash-tag:

Test Output:

[one of the checks in EDPftvarcon is breaking runs with 1 pft. Cancel out the endrun message as a quick fix. ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ This check is not related to damage work and is being addressed in other issues/PRs ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary: no testing

…ge_module' into JessicaNeedham-crowndamage_module

ckoven

@JessicaNeedham this is really great, thanks! I have some comments/questions, mostly just to improve clarity.

main/DamageMainMod.F90

main/EDTypesMod.F90

ckoven · 2021-10-01T21:43:51Z

main/EDTypesMod.F90

@@ -166,15 +166,15 @@ module EDTypesMod

  ! COHORT TERMINATION

-  real(r8), parameter, public :: min_npm2       = 1.0E-7_r8               ! minimum cohort number density per m2 before termination
+  real(r8), parameter, public :: min_npm2       = 1.0E-12_r8               ! minimum cohort number density per m2 before termination


why does this need to change here? is it a thing to bracket in if statement on the damage, or should we include even when no damage is running? seems like it will change answers if so.

ckoven · 2021-10-01T21:43:57Z

main/EDTypesMod.F90

  real(r8), parameter, public :: min_patch_area = 0.01_r8                 ! smallest allowable patch area before termination
  real(r8), parameter, public :: min_patch_area_forced = 0.0001_r8        ! patch termination will not fuse the youngest patch
                                                                          ! if the area is less than min_patch_area.
                                                                          ! however, it is allowed to fuse the youngest patch
                                                                          ! if the fusion area is less than min_patch_area_forced

  real(r8), parameter, public :: min_nppatch    = min_npm2*min_patch_area ! minimum number of cohorts per patch (min_npm2*min_patch_area)
-  real(r8), parameter, public :: min_n_safemath = 1.0E-12_r8              ! in some cases, we want to immediately remove super small
+  real(r8), parameter, public :: min_n_safemath = 1.0E-15_r8              ! in some cases, we want to immediately remove super small


why does this change? assuming related to the prior one?

main/FatesHistoryInterfaceMod.F90

parameter_files/fates_params_default.cdl

main/EDTypesMod.F90

ckoven · 2021-10-04T21:42:28Z

main/EDTypesMod.F90

@@ -340,6 +342,9 @@ module EDTypesMod
                                                         ! (below ground)
     real(r8) ::  froot_mr                               ! Live fine root   maintenance respiration: kgC/indiv/s

+     !DAMAGE
+     real(r8) :: branch_frac                             ! Fraction of aboveground biomass in branches


I'm not sure I understand why branch_frac needs to be tracked as a cohort-level state variable, rather than a thing that is calculated as a function of PFT parameters and crown damage class? Does it? Also, isn't this the fraction of aboveground woody biomass that is in branches, not the fraction of total aboveground biomass in branches?

I've simplified the code so that branch_frac is no longer a cohort variable. Also updated comments where it is declared.

[ ] Fixes: [NGT-ED Github issue #] User interface changes?: [ No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary: no testing

…ases when damage module is on. ] [don't change maxCohortsPerPatch in EDTypesMod but instead in FatesInterfaceMod ] Fixes: [NGT-ED Github issue #] User interface changes?: [No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[Increased it to 3 to work with Ryan's bci param file but reverting it to 2 for PR ] Fixes: [NGT-ED Github issue #] User interface changes?: [No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[Can't remember why I changed these. Possibly to do with termination mortality? ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ Remove the crowndamage x crowndamage dimension, remove unecessary history variables and put all damage history variables in an if statement ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary: no testing

…ge_module' into JessicaNeedham-crowndamage_module

[ ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ crowndamage to crown damage ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

frequency of damage events. ] [ ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary: no testing

damage history outputs ] [ Remove damage only history dimension. Fix bug with crownarea by damage and mortality. ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ update damage history variable units to be in line with recent history output refactor ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary: no testing

[ Branch frac does not need to be associated with cohorts. This simplifies many of the calls to allometry functions. ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

Conflicts: biogeochem/EDCanopyStructureMod.F90 biogeochem/FatesAllometryMod.F90 main/EDParamsMod.F90 main/EDTypesMod.F90

[Add cohort crowndamage status to calls to tree_sai ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ Needed for damage transition matrix ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

[ because damage history variables are defined in an if statment they need to be references by this%hvars and not hio_ ] Fixes: [NGT-ED Github issue #] User interface changes?: [Yes (describe what changes), No] Code review: [Names] Test suite: [suite name, machine, compilers] Test baseline: Test namelist changes: Test answer changes: [bit for bit, roundoff, climate changing] Test summary:no testing

Conflicts: main/FatesIODimensionsMod.F90 main/FatesInterfaceMod.F90

…albeit not compatible with tree damage

damage class widths

…ge_module' into JessicaNeedham-crowndamage_module

glemieux

Initial review due to regression test failure in debug mode. One other minor suggestion as well.

biogeophys/FatesPlantRespPhotosynthMod.F90

main/FatesParameterDerivedMod.F90

Refactor damage check to enable the use of `sap_c_` variables regardless of run mode

Fixes exact restart issues with the vegetation temperature for run modes with bareground patches

glemieux · 2022-10-25T16:34:32Z

Regression testing on Cheyenne is complete. All expected tests pass b4b. Note that the tree damage test mod which wasn't generating baselines prior to this PR is now running and generating baselines successfully. Also, the addition of MORTALITY_CROWNAREA_CANOPY and MORTALITY_CROWNAREA_UNDERSTORY is resulting in expected FIELDLIST DIFFs for those test mods that includes all active history output.

One minor clarification: for some reason the P144x2 mimics fates test mod didn't have a baseline when I ran the initial comparison, which resulted in an NLCOMP DIFF and BFAIL. I regenerated that baseline and re-ran the comparison which is comping back b4b, but the NLCOMP DIFF is still showing up with the automated check. Looking at the TestStatus.log for that test, you can see these diffs are from that original failed comparison against the missing baseline and thus can be ignored.

Folder location: /glade/u/home/glemieux/scratch/ctsm-tests/tests_pr788-crowndamage-2

JessicaNeedham and others added 5 commits September 29, 2021 16:27

Squashed commit of all crown damage work

e68c22c

Merge remote-tracking branch 'jfneedham_repo/JessicaNeedham-crowndama…

ad11283

…ge_module' into JessicaNeedham-crowndamage_module

JessicaNeedham marked this pull request as ready for review October 1, 2021 20:46

glemieux added the PR status: Not Ready The author is signaling that this PR is a work in progress and not ready for integration. label Oct 1, 2021

ckoven reviewed Oct 4, 2021

View reviewed changes

JessicaNeedham and others added 21 commits December 9, 2021 09:44

Merge remote-tracking branch 'jfneedham_repo/JessicaNeedham-crowndama…

86d423e

…ge_module' into JessicaNeedham-crowndamage_module

Merge remote-tracking branch 'ngeet_repo/master'

586cf0c

Merge branch 'master' into damage_temp

b7cb23d

Merge remote-tracking branch 'ngeet_repo/master'

092f9df

Merge branch 'master' into branch_frac_fix

ada5ce7

Conflicts: biogeochem/EDCanopyStructureMod.F90 biogeochem/FatesAllometryMod.F90 main/EDParamsMod.F90 main/EDTypesMod.F90

Merge branch 'branch_frac_fix' into JessicaNeedham-crowndamage_module

14ef508

Conflicts: main/FatesIODimensionsMod.F90 main/FatesInterfaceMod.F90

rgknox and others added 18 commits September 15, 2022 22:16

slight correction to crown damage calc

32a5a4d

Fixes to allocation phases vis-a-vis recovery

cf91237

Subtle fixes to the allocation phasing and damage

dc3e5f4

Fixes, yet again, to allocation and phasing

d5e9ad4

Changes to sapwood respiration to account for aboveground damage.

38d9f32

Fix the sapwood respiration bug

6fc3bef

Slight update to allow FATES CNP to work with new phased allocation, …

c955cf1

…albeit not compatible with tree damage

Added user name checks for damage mode and parteh 2

ae40104

Updated error statement for fates cnp and tree damage

2b064f0

Conflict resolutions

79f3065

reverting nlevleaf

f998407

Changing how damage fraction is calculated to account for variable

35dad01

damage class widths

Merge remote-tracking branch 'jfneedham_repo/JessicaNeedham-crowndama…

86dd566

…ge_module' into JessicaNeedham-crowndamage_module

Tidy up some debugging print statements

bec8928

Fix damage transition matrix to account for flexible damage bins

3efa3d0

add crowndamage to allometry calls in EDPhysiologyMod

0251401

Update sapwood respiration to fix damage related bug

de822e4

Tidy comments on damage code

e5b0121

glemieux requested changes Oct 24, 2022

View reviewed changes

biogeophys/FatesPlantRespPhotosynthMod.F90 Outdated Show resolved Hide resolved

main/FatesParameterDerivedMod.F90 Outdated Show resolved Hide resolved

glemieux and others added 4 commits October 24, 2022 14:53

Update biogeophys/FatesPlantRespPhotosynthMod.F90

9dddd74

Refactor damage check to enable the use of `sap_c_` variables regardless of run mode

fix whitespace and add comment

ab4e75b

add debug check

b1e4a1a

Merge tag 'sci.1.59.7_api.24.1.0' into JessicaNeedham-crowndamage_module

adfba93

Fixes exact restart issues with the vegetation temperature for run modes with bareground patches

glemieux approved these changes Oct 25, 2022

View reviewed changes

glemieux merged commit 3374ba3 into NGEET:master Oct 31, 2022

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Crown damage module #788

Crown damage module #788

JessicaNeedham commented Oct 1, 2021 •

edited by glemieux

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Crown damage module #788

Crown damage module #788

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JessicaNeedham commented Oct 1, 2021 • edited by glemieux Loading

Description:

Collaborators:

Expectation of Answer Changes:

Checklist:

Test Results:

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