Code

Crown damage module#788

Code

Merged

glemieux merged 104 commits intoNGEET:masterNGEET/fates:masterfrom JessicaNeedham:JessicaNeedham-crowndamage_moduleJessicaNeedham/fates:JessicaNeedham-crowndamage_moduleCopy head branch name to clipboardOct 31, 2022

+3,173-1,042

Commits

Commits on Sep 29, 2021

• [ cancel endrun for buggy error check ]

  Show description for 49b41a0
  JessicaNeedham

  committed
  49b41a0

Commits on Sep 30, 2021

• Squashed commit of all crown damage work

  JessicaNeedham

  committed
  e68c22c

• [ Uncomment a check that was breaking runs ]

  Show description for d090bfd
  JessicaNeedham

  committed
  d090bfd

Commits on Oct 1, 2021

• [ Fix bug with understory number densities ]

  Show description for fc3ed80
  

  Jessica Needham

  committed
  fc3ed80

• Merge remote-tracking branch 'jfneedham_repo/JessicaNeedham-crowndamage_module' into JessicaNeedham-crowndamage_module

  

  Jessica Needham

  committed
  ad11283

Commits on Dec 9, 2021

• [moving damage module to biogeochem ]

  Show description for 177876b
  JessicaNeedham

  committed
  177876b

• [bracket the increase in maxCohortsPerPatch in logic so it only increases

  Show description for d700c60
  JessicaNeedham

  committed
  d700c60

• [ Revert number of canopy layers back to 2 ]

  Show description for 63e513d
  JessicaNeedham

  committed
  63e513d

Commits on Dec 15, 2021

• [Change min_n_safemath and min_npm2 to default values. ]

  Show description for 7c585f9
  JessicaNeedham

  committed
  7c585f9

• [ Remove unnecessary history variables]

  Show description for 21b802b
  JessicaNeedham

  committed
  21b802b

Commits on Dec 16, 2021

• Merge remote-tracking branch 'jfneedham_repo/JessicaNeedham-crowndamage_module' into JessicaNeedham-crowndamage_module

  JessicaNeedham

  committed
  86d423e

• [ Add comments to FatesAllometry related to crown damage ]

  Show description for efeb680
  JessicaNeedham

  committed
  efeb680

• [ Correct typo in parameter file ]

  Show description for 7484d25
  JessicaNeedham

  committed
  7484d25

• [Update comments in parameter file with more details on

  Show description for c00b89d
  JessicaNeedham

  committed
  c00b89d

Commits on Dec 17, 2021

• [ Add comments on crowndamage declaration ]

  Show description for 1e1242b
  JessicaNeedham

  committed
  1e1242b

• Merge remote-tracking branch 'ngeet_repo/master'

  JessicaNeedham

  committed
  586cf0c

Commits on Jan 7, 2022

• Merge branch 'master' into damage_temp

  JessicaNeedham

  committed
  b7cb23d

Commits on Jan 10, 2022

• [ Remove old damage history dimensions and fix bugs with

  Show description for b2937ab
  JessicaNeedham

  committed
  b2937ab

• [ update units on damage history variables ]

  Show description for ca903c4
  JessicaNeedham

  committed
  ca903c4

Commits on Jan 28, 2022

• [ Remove branch frac as a cohort variable ]

  Show description for cc5a60b
  JessicaNeedham

  committed
  cc5a60b

Commits on Feb 7, 2022

• Merge remote-tracking branch 'ngeet_repo/master'

  JessicaNeedham

  committed
  092f9df

Commits on Feb 12, 2022

• Merge branch 'master' into branch_frac_fix

  Show description for ada5ce7
  JessicaNeedham

  committed
  ada5ce7

Commits on Feb 14, 2022

• [ Fix merge conflicts in EDCanopySturctureMod ]

  Show description for a5f752b
  JessicaNeedham

  committed
  a5f752b

Commits on Feb 15, 2022

• [ Add damage x damage dimension back ]

  Show description for 14399fc
  JessicaNeedham

  committed
  14399fc

Commits on Feb 16, 2022

• [ Fix bug with if statements in fateshistoryinterface ]

  Show description for 1324109
  JessicaNeedham

  committed
  1324109

• Merge branch 'branch_frac_fix' into JessicaNeedham-crowndamage_module

  Show description for 14ef508
  JessicaNeedham

  committed
  14ef508

Commits on Feb 17, 2022

• [ Remove cdcd dimension ]

  Show description for 6b6ed7f
  JessicaNeedham

  committed
  6b6ed7f

Commits on Feb 28, 2022

• [ update comments on branch_frac ]

  Show description for d15081f
  JessicaNeedham

  committed
  d15081f

Commits on Mar 1, 2022

• [ delete old variables from EDInitMod]

  Show description for a3bb261
  JessicaNeedham

  committed
  a3bb261

Commits on Mar 2, 2022

• [ Remove old history variables ]

  Show description for 36e8faf
  JessicaNeedham

  committed
  36e8faf

Commits on Mar 8, 2022

• Merge remote-tracking branch 'ngeet_repo/master'

  JessicaNeedham

  committed
  6ea0259

• [ and remove the last damage_clux and damage_rate variables ]

  Show description for 7ed9029
  JessicaNeedham

  committed
  7ed9029

• [ Change default damage param values ]

  Show description for 63edb53
  JessicaNeedham

  committed
  63edb53

Commits on Mar 9, 2022

• Merge remote-tracking branch 'ngeet_repo/master'

  JessicaNeedham

  committed
  d59e249

Commits on Mar 10, 2022

• [ remove damage_cflux ]

  Show description for c8d86d1
  JessicaNeedham

  committed
  c8d86d1

Commits on Mar 11, 2022

• Merge branch 'master' into JessicaNeedham-crowndamage_module

  JessicaNeedham

  committed
  4a622fe

Commits on Mar 21, 2022

• Merge branch 'master' into JessicaNeedham-crowndamage_module

  JessicaNeedham

  committed
  64abd25

Commits on Mar 22, 2022

• [ Add damage only dimension back. ]

  Show description for 442639f
  JessicaNeedham

  committed
  442639f

• [ Make crown damage bin edges flexible ]

  Show description for 6f0e682
  JessicaNeedham

  committed
  6f0e682

Commits on Mar 23, 2022

• [ Fixing flexible damage bins ]

  Show description for 78b4f1a
  JessicaNeedham

  committed
  78b4f1a

Commits on Apr 3, 2022

• [Fix bug in defining nlevdamage ]

  Show description for d9ee7ab
  JessicaNeedham

  committed
  d9ee7ab

• [ fixing canopy_too_full error - possibly from bad merge ]

  Show description for f0352aa
  JessicaNeedham

  committed
  f0352aa

Commits on Apr 16, 2022

• [ Fix canopy too full error with damage code ]

  Show description for 8f994c2
  JessicaNeedham

  committed
  8f994c2

Commits on May 13, 2022

• [ make damage timings be controlled by event_code as in

  Show description for f28f532
  JessicaNeedham

  committed
  f28f532

Commits on May 14, 2022

• [ Fixing damage event codes ]

  Show description for 2613582
  JessicaNeedham

  committed
  2613582

Commits on May 26, 2022

• [ create a single hlm_use_crown_damage switch and make a parameter

  Show description for 758d902
  JessicaNeedham

  committed
  758d902

• Merge branch 'master' into crowndamage-deconflict

  Show description for 4d1cd0a
  glemieux

  committed
  4d1cd0a

• converting new procedures to CamelCase

  glemieux

  committed
  ece0c71

• [ change damage bin edges ]

  Show description for f73d65d
  JessicaNeedham

  committed
  f73d65d

• converting logical from CamelCase back to original format

  glemieux

  committed
  59d4357

• adding target_c_area local to UpdateCohortLAI

  glemieux

  committed
  657ba0a

Commits on May 27, 2022

• fixing erroneous damage_time name changes

  glemieux

  committed
  cc2d5f8

• fixing bad merge

  glemieux

  committed
  6b21b53

• [ update UpdateCohortLAI to accommodate extra arguments needed for damage ]

  Show description for a76d62f
  JessicaNeedham

  committed
  a76d62f

• Merge remote-tracking branch 'glemieux_repo/crowndamage-deconflict' into crowndamage-deconflict

  JessicaNeedham

  committed
  f0e8c30

Commits on Jun 21, 2022

• Merge remote-tracking branch 'jfneedham_repo/JessicaNeedham-crowndamage_module' into JessicaNeedham-crowndamage_module

  JessicaNeedham

  committed
  50dc896

Commits on Jun 28, 2022

• First pass at resolving conflicts between the damage module and api 24 changes

  rgknox

  committed
  c1bb091

Commits on Jun 29, 2022

• Updated argument name in UpdateCohortLai

  rgknox

  committed
  e85d1f4

• Added the undamaged class named constant

  rgknox

  committed
  bb345fc

• [ Change tree_sai so that it is affected by damage ]

  Show description for ce6f93b
  JessicaNeedham

  committed
  ce6f93b

Commits on Jun 30, 2022

• Minor variable name change for readability

  rgknox

  committed
  d2dfb73

• Merge branch 'JessicaNeedham-crowndamage_module-merged' of github.com:rgknox/fates into JessicaNeedham-crowndamage_module-merged

  rgknox

  committed
  21ae55e

• Inremental change towards damage recovery refactor

  rgknox

  committed
  71c56b1

• Second pass through splitting allocation and modularizing the recovery code.

  rgknox

  committed
  010a95f

• Minor updates to damage recovery

  rgknox

  committed
  02b661a

• Applying the phase argument to carbon allocation in parteh

  rgknox

  committed
  db14473

• cleaning up damage boundary condition to parteh, adding in phase hooks to parteh_mode=2, even if its incompatible at the moment

  rgknox

  committed
  daafba1

Commits on Jul 1, 2022

• Various merge resolutions and fixes for new damge recovery scheme

  rgknox

  committed
  f6bfc64

• Moving DamageRecovery to cohortdynamics

  rgknox

  committed
  b660f7b

• resolution on moving damagerecovery

  rgknox

  committed
  bfe205c

• Removed check on use_tree_damage, which is allowed now

  rgknox

  committed
  84e84b9

• Fixes to use_tree_damage

  rgknox

  committed
  650077a

Commits on Jul 3, 2022

• Making tree_sai in canopy_trim use actual area

  rgknox

  committed
  71c41c6

Commits on Jul 5, 2022

• argument re-ordering in crowndamage allometry argument and adding in the call to initalize the derived damage parameter

  rgknox

  committed
  52f5b87

Commits on Jul 6, 2022

• Removed a redundant (double) allocation call

  rgknox

  committed
  b266106

• Removed patch level damage code, in preparation for moving it to a pre-disturbance part of the dynamics code.

  rgknox

  committed
  34a6fe3

• Added declaration of global hlm_use_tree_damage

  rgknox

  committed
  3351666

• First pass at the new damage application routine

  rgknox

  committed
  b9d7b97

Commits on Jul 11, 2022

• Adding variable definitions to the damage generation routine

  rgknox

  committed
  3e2aeab

Commits on Jul 12, 2022

• Added module use statements to damage and litter generation module

  rgknox

  committed
  85f7e55

Commits on Sep 13, 2022

• conflict resolutions on damage branch

  rgknox

  committed
  c263eac

Commits on Sep 16, 2022

• Syntax updates for tree damage mode

  rgknox

  committed
  eadc895

• slight correction to crown damage calc

  rgknox

  committed
  32a5a4d

• Fixes to allocation phases vis-a-vis recovery

  rgknox

  committed
  cf91237

• Subtle fixes to the allocation phasing and damage

  rgknox

  committed
  dc3e5f4

• Fixes, yet again, to allocation and phasing

  rgknox

  committed
  d5e9ad4

• Changes to sapwood respiration to account for aboveground damage.

  

  Jessica F Needham

  committed
  38d9f32

Commits on Sep 17, 2022

• Fix the sapwood respiration bug

  

  Jessica F Needham

  committed
  6fc3bef

Commits on Sep 20, 2022

• Slight update to allow FATES CNP to work with new phased allocation, albeit not compatible with tree damage

  rgknox

  committed
  c955cf1

• Added user name checks for damage mode and parteh 2

  rgknox

  committed
  ae40104

• Updated error statement for fates cnp and tree damage

  rgknox

  committed
  2b064f0

• Conflict resolutions

  rgknox

  committed
  79f3065

Commits on Sep 21, 2022

• reverting nlevleaf

  rgknox

  committed
  f998407

Commits on Sep 22, 2022

• Changing how damage fraction is calculated to account for variable

  Show description for 35dad01
  

  Jessica F Needham

  committed
  35dad01

• Merge remote-tracking branch 'jfneedham_repo/JessicaNeedham-crowndamage_module' into JessicaNeedham-crowndamage_module

  

  Jessica F Needham

  committed
  86dd566

Commits on Sep 24, 2022

• Tidy up some debugging print statements

  

  Jessica F Needham

  committed
  bec8928

Commits on Sep 26, 2022

• Fix damage transition matrix to account for flexible damage bins

  

  Jessica F Needham

  committed
  3efa3d0

• add crowndamage to allometry calls in EDPhysiologyMod

  

  Jessica F Needham

  committed
  0251401

Commits on Sep 27, 2022

• Update sapwood respiration to fix damage related bug

  

  Jessica F Needham

  committed
  de822e4

Commits on Oct 4, 2022

• Tidy comments on damage code

  

  Jessica F Needham

  committed
  e5b0121

Commits on Oct 24, 2022

• Update biogeophys/FatesPlantRespPhotosynthMod.F90

  Show description for 9dddd74
  glemieux

  authored
  9dddd74

• fix whitespace and add comment

  glemieux

  committed
  ab4e75b

• add debug check

  glemieux

  committed
  b1e4a1a

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

  Show description for adfba93
  glemieux

  committed
  adfba93