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Don't zero out patch%fuel%frac_burnt() before we use it #1302

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merged 6 commits into from
Jan 3, 2025

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adrifoster
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@adrifoster adrifoster commented Dec 11, 2024

Fixes #1301 by checking inside the TransLitterNewPatch for the type of disturbance instead of zero-ing outside of the subroutine.

Description:

Removed the lines in spawn_patches that zero-d the frac_burnt array too soon.
Added checks in TransLitterNewPatch to check for fire disturbance and a fire on the patch:
If no fire, new local variable frac_burnt set to 0.0, otherwise use patch%fuel%frac_burnt

Collaborators:

@glemieux

Expectation of Answer Changes:

Yes - should change answers because before we weren't burning any fuel

Checklist

Contributor

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

Integrator

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

Test Results:

CTSM (or) E3SM (specify which) test hash-tag: ctsm5.3.012

CTSM (or) E3SM (specify which) baseline hash-tag: ctsm5.3.012

FATES baseline hash-tag: sci.1.80.4_api.37.0.0

Test Output:

Running tests now

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I like moving the check into TransLitterNewPatch. That said, do we need to make sure that currentPatch%fuel%frac_burnt is set to zero at the end of spawn_patches or is that already handled elsewhere?

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I like moving the check into TransLitterNewPatch. That said, do we need to make sure that currentPatch%fuel%frac_burnt is set to zero at the end of spawn_patches or is that already handled elsewhere?

I added it to the top of the fire_model subroutine, where we zero other fire-related things. I don't know if this is the right place for it or not...

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glemieux commented Jan 3, 2025

Regression testing on derecho underway.

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glemieux commented Jan 3, 2025

Regression testing agsinst fates-sci.1.80.5_api.37.0.0-tmp-241219.n01.ctsm5.3.016 is showing DIFFs in the following tests:

FAIL ERS_Ld397.f10_f10_mg37.I2000Clm50Fates.derecho_gnu.clm-FatesCold BASELINE fates-sci.1.80.5_api.37.0.0-tmp-241219.n01.ctsm5.3.016: DIFF
FAIL ERS_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdNoComp BASELINE fates-sci.1.80.5_api.37.0.0-tmp-241219.n01.ctsm5.3.016: DIFF
FAIL ERS_Ld397.f45_f45_mg37.I2000Clm50Fates.derecho_intel.clm-FatesColdNoComp BASELINE fates-sci.1.80.5_api.37.0.0-tmp-241219.n01.ctsm5.3.016: DIFF
FAIL SMS_Lm6.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-Fates BASELINE fates-sci.1.80.5_api.37.0.0-tmp-241219.n01.ctsm5.3.016: DIFF

Spot checking the DIFFs, I think these make sense; I'm seeing changes to fire related history. @adrifoster would you take a look when you have a chance to confirm please?

Results: /glade/u/home/glemieux/scratch/ctsm-tests/tests_pr1302

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@glemieux thanks!

yep these look right to me, just to plot some differences:
here are the differences in fire_closs (the new version is higher because now we are actually burning dead fuel):

ERS_Ld397 f10_f10_mg37 I2000Clm50Fates derecho_gnu clm-FatesCold_FATES_FIRE_CLOSS_mean

which does affect ROS and fire intensity:

ERS_Ld397 f10_f10_mg37 I2000Clm50Fates derecho_gnu clm-FatesCold_FATES_ROS_mean

ERS_Ld397 f10_f10_mg37 I2000Clm50Fates derecho_gnu clm-FatesCold_FATES_FIRE_INTENSITY_mean

the new version is lower because fuel is actually lower:

ERS_Ld397 f10_f10_mg37 I2000Clm50Fates derecho_gnu clm-FatesCold_FATES_FUEL_AMOUNT_mean

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glemieux commented Jan 3, 2025

Thanks @adrifoster!

@glemieux glemieux merged commit 1689466 into NGEET:main Jan 3, 2025
1 check was pending
mvdebolskiy added a commit to mvdebolskiy/fates that referenced this pull request Mar 25, 2025
commit 8924c40bbcb1c764434911f74eb578022018bb70
Merge: ecc6815c 23b6f3e1
Author: mvdebolskiy <[email protected]>
Date:   Thu Mar 20 12:18:19 2025 +0100

    Merge pull request #15 from mvdebolskiy/rpointers-update-fates

    Rpointers update fates. also updates to sci.1.81.1_api.38.0.0 on NGEET

commit 23b6f3e17965625e2dd0d03916cf99736d72ea1c
Merge: ecc6815c 6903518a
Author: mvdebolskiy <[email protected]>
Date:   Sat Mar 8 14:20:33 2025 +0100

    Merge commit '6903518a5ebaf711b924583eb109d79805f69e05' into rpointers-update-fates

commit ecc6815c75ede97e23ae660a1980bfa94fc290da
Merge: f2ea09ea 883537bd
Author: mvdebolskiy <[email protected]>
Date:   Thu Feb 27 18:19:26 2025 +0100

    Merge pull request #14 from mvdebolskiy/fix-gnu

    fix logical for ci of gnu compiler

commit 6903518a5ebaf711b924583eb109d79805f69e05
Merge: a91cc42d 57a19619
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 27 08:56:42 2025 -0800

    Merge pull request #1344 from JessicaNeedham/new-namelist

    Add namelist switches and parameter file changes ahead of upcoming PR on Johnson & Berry  electron transport  model

commit 57a196194a79793cbde9d0f4b1ead8680894ab96
Author: Gregory Lemieux <[email protected]>
Date:   Wed Feb 26 14:35:20 2025 -0800

    update patch file and add new archived default

    Add the file to start from the previous API38 default update from sci.1.81.1_api.38.0.0

commit a1929aba0b461bd0eb947f29822812d58b101e10
Author: jessica needham <[email protected]>
Date:   Wed Feb 26 13:40:03 2025 -0800

    make fnps parameter pft specific

commit 0e3ceae19a98f66f6ad1b07a986dbc86c29f2f85
Author: jessica needham <[email protected]>
Date:   Wed Feb 26 12:43:52 2025 -0800

    update param  file with param for later PR

commit 1961dfd74d844b699e2a4ac52a0506ac9f084519
Author: jessica needham <[email protected]>
Date:   Wed Feb 26 11:37:29 2025 -0800

    add new namelist switch  - prep for later PR

commit 883537bd0d18c24e267ac2ca1cf3bb8bfd09faea
Author: mvdebolskiy <[email protected]>
Date:   Tue Feb 25 10:56:14 2025 +0100

    fix logical for ci

commit a91cc42dcd20f878d2412c81f9038636a6030c54
Merge: 655d7846 3b4d20c5
Author: Gregory Lemieux <[email protected]>
Date:   Sun Feb 23 22:08:08 2025 -0800

    Merge pull request #1300 from glemieux/parameter-switch-migration

    Migrate parameter file switches that are moving to HLM namelist

commit 3b4d20c5aeb094c1bde3f0fee3b9ed916e819197
Author: Gregory Lemieux <[email protected]>
Date:   Sat Feb 22 21:42:19 2025 -0700

    correct bad tag merge

commit d88cf4af3af709511779f916875dce2130c7d4eb
Author: Gregory Lemieux <[email protected]>
Date:   Sat Feb 22 21:06:45 2025 -0800

    correct archived parameter file to be api37.1

commit 8fe2fe7b99088726ae02b310652c03376345794a
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 20 10:11:40 2025 -0800

    update archived parameter file to use api37.1 as the base file

commit 601d18b2247922ce1165374a1015df21ea00edc1
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 20 10:09:11 2025 -0800

    update comments in the api38 patch parameter file

commit d87123d55a418e516899eab42fab149da9f7f406
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 20 10:06:16 2025 -0800

    rename patch parameter file and archive default parameter file

commit 928dcd589476cbf316776bfa19291f3bade2c869
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 20 10:03:34 2025 -0800

    update patch parameter file

    The variable additions were incorporated via #1334

commit 2a6b33eeefa719a1b94e800b611e140f70a5053d
Merge: 9cb16111 655d7846
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 20 10:00:18 2025 -0800

    Merge tag 'sci.1.81.1_api.37.1.0' into parameter-switch-migration

    An alternative method of conserving patch area for two-stream radiation.

commit 655d784607f5b590f344696970c3ae1f24092717
Merge: ccc1de04 55544214
Author: Ryan Knox <[email protected]>
Date:   Wed Feb 19 14:40:14 2025 -0500

    Merge pull request #1310 from rgknox/twostream-nveg-fix

    alternative way to adjust area issues in FATES twostream

commit 55544214cc91013fe75931fdb3735f818a735f01
Author: Ryan Knox <[email protected]>
Date:   Wed Feb 19 10:05:55 2025 -0700

    set debug flag to false

commit f3987f2315f0daa60617d73723995dae3fe7ec84
Author: Ryan Knox <[email protected]>
Date:   Wed Feb 19 10:04:40 2025 -0700

    fixed typo in two-stream prep error messages

commit d755072a482501b0fa129d85938d84a04b8808aa
Merge: 11778109 ccc1de04
Author: Ryan Knox <[email protected]>
Date:   Wed Feb 19 09:04:24 2025 -0700

    Merge branch 'main' into twostream-nveg-fix

commit ccc1de04abcc14dcc8a24bb06f271bc04e2bc48c
Merge: 20649ac9 21418e33
Author: Gregory Lemieux <[email protected]>
Date:   Tue Feb 18 14:48:02 2025 -0800

    Merge pull request #1334 from glemieux/api37.1-parameter-merge

    API 37.1 parameter file merge

commit 21418e336f2c1c739d0e4e87fe6a7f85260e0f7e
Author: Gregory Lemieux <[email protected]>
Date:   Tue Feb 18 11:23:00 2025 -0800

    update the btran model switches in the default parameter file

    This was processed using the pr1262 patch file update

commit 7318f6be347221deb833ad1cb422d46d23baa8e1
Author: Gregory Lemieux <[email protected]>
Date:   Tue Feb 18 11:20:41 2025 -0800

    update 1262 new model switches to match the previous model behavior

commit 9f5bffc7191adbc1052205154bb3906d93b5c1eb
Author: Gregory Lemieux <[email protected]>
Date:   Tue Feb 18 11:05:02 2025 -0800

    update comments for the patch parameter files

    This instructs the user on how best to apply the patches

commit ed07677b15ff46badb8218a5691a0396694cf40d
Author: Gregory Lemieux <[email protected]>
Date:   Tue Feb 18 10:26:38 2025 -0800

    correct error in patch file for PR 1262

    This updates the CDL with the associated new variables as well

commit c510e7d844ece6dfbd80d9922a865246c165287c
Author: Gregory Lemieux <[email protected]>
Date:   Tue Feb 18 10:13:26 2025 -0800

    fates default parameter file minor formatting update

commit b50e3506fc1407658944ff62c12452b2890470e6
Author: Gregory Lemieux <[email protected]>
Date:   Mon Feb 17 22:44:17 2025 -0800

    update base file for #1140 patch parameter file

commit d388be446d6fcf7d4b297fd4a6cddc53c2f12037
Author: Gregory Lemieux <[email protected]>
Date:   Mon Feb 17 17:40:32 2025 -0800

    update patch file names to include only pull request numbers

    Removing the date strings from the patch files as I think it doesn't
    really add anything to help the user.  I also update the base file in
    multiple xml files to use the fates_params_default.cdl so as to build on
    the previous xml files included in this pull request.

commit eb74c653d0a5618464b69ffd4d0d7f5184a2eb12
Author: Gregory Lemieux <[email protected]>
Date:   Mon Feb 17 17:25:43 2025 -0800

    add parameters for pull request 1262

    PR #1262 will be incorporated at a later date, but we are adding
    the parameters to the default here to coincide with a minor API update.

commit 582d8ee98dc9d9bfb9901df8370b980142f64969
Merge: 31c55f90 da70f559
Author: Gregory Lemieux <[email protected]>
Date:   Mon Feb 17 15:25:43 2025 -0800

    Merge remote-tracking branch 'cdkoven/grazing_merge' into api37.1-parameter-merge

commit 31c55f90bee77215d8c7282afa3260bb0b87585f
Merge: 50d9b19e 3c8a9909
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 15:33:02 2025 -0800

    Merge remote-tracking branch 'glemieux/z0mr-param-inconsistant-fix' into api37.1-parameter-merge

commit 50d9b19ea1f2331f2a4f3954a489e1ea39393451
Merge: 02211c28 23330fb3
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 15:32:55 2025 -0800

    Merge remote-tracking branch 'jennyk/jkowalcz-vg-param' into api37.1-parameter-merge

commit 23330fb390e45254216d32a1f209bc13d605a267
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 15:32:10 2025 -0800

    fix fates default param internal name

commit 3c8a9909301e25cda8f59163f85d1e2c7ee3da0e
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 15:30:35 2025 -0800

    correct default param file name

commit 39770b6b0d2cbed6738f22da01d154abba4acb65
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 15:25:39 2025 -0800

    rename patch parameter files

    include the pr number for better traceability

commit 02211c28de266453273483d5501910952a7299d6
Merge: 5a896267 384ef07d
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 15:18:26 2025 -0800

    Merge remote-tracking branch 'glemieux/z0mr-param-inconsistant-fix' into api37.1-parameter-merge

commit 384ef07debe4e5bf7662652e1667df221bd7aee8
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 15:15:27 2025 -0800

    restore cdl ordering

    ordering restore using ncvarsort from sci.1.80.4_api.37.0.0

commit 5a8962679c67cb6004f230d74967e34757db83de
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 14:56:34 2025 -0800

    format update to parameter cdl

    This minor formatting update is after running the patch parameter file
    through UpdateParamAPI.py

commit 46ce070c87b02ba5e84e847344f2a41c9bc89198
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 13:35:16 2025 -0800

    correct new file name in patch file

commit 66c57d20f729e5355343bb0a626d6200dd89b6f7
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 13:34:39 2025 -0800

    add xml patch file for pull request 1263

commit 7e8e112085c4568a3b6a4b593353faef4dfb86b9
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 13:08:19 2025 -0800

    add API36.1 default parameter to the archive

commit 9aaac2041c18ca5dcecb9bdfbba684d80e0af34a
Merge: 9a52e6c5 20649ac9
Author: Gregory Lemieux <[email protected]>
Date:   Fri Feb 14 11:53:48 2025 -0700

    Merge tag 'sci.1.80.14_api.37.0.0' into jkowalcz-vg-param

    Refactors and cleans up the patch numbering and nocomp checks

commit 20649ac98752a619d201bfc7e32c961526b4b721
Merge: eb649284 368906c9
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 13 22:39:00 2025 -0800

    Merge pull request #1226 from rgknox/luh2_nocomp_merge-bcindex

    cleaning up nocomp patch indexing

commit 368906c9d2e4888c82591d7d399fa3b6e90a2faa
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 13 12:27:36 2025 -0700

    add missing nocomp_bareground use statements

commit 315892a66e8da42ef6eb86a48a9ce9f959d807dc
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 13 11:08:35 2025 -0700

    add missing fates constant use statement

commit cfaa1c61cda206a6e6fd32cfaf689b79453c2d8e
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 13 09:42:17 2025 -0700

    correct patch number debug write

commit eb64928484a861cae5491e4597c5e6d5ebe4e2ef
Author: Ryan Knox <[email protected]>
Date:   Thu Feb 13 11:26:28 2025 -0500

    Update CODE_OF_CONDUCT.md

commit 3e01c843033e2dbdddca43f157831647d8fe42dd
Merge: dc16b39d ff845220
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 11 11:12:50 2025 -0500

    conflict resolution for nocomp patch counting branch

commit dc16b39d8a20fc0c7bb5e3873e9702b48ad51f32
Merge: 021c0aab 798acbb5
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 11 11:09:24 2025 -0500

    Merge branch 'main' into luh2_nocomp_merge-bcindex-merged

commit 021c0aab709eefe7f2ffe983d01364797db02005
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 11 10:52:57 2025 -0500

    fixed loop label

commit e828f0549da5df3a37fc982e54aadcaef8a6feb6
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 11 10:51:09 2025 -0500

    fixed loop label

commit d4143dd8899f91d12ed90b8d0c0633496381c80b
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 11 10:46:47 2025 -0500

    Reinstated a patch index order check, enclosed in a debug statement

commit 49a493a41fa0b7c59535eb5cb5b015204854055d
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 11 10:42:03 2025 -0500

    Added description to the new set_patchno

commit b1ccc18d70c5747344299334f34707b4d5603c80
Author: Ryan Knox <[email protected]>
Date:   Sun Feb 2 16:35:45 2025 -0700

    added nocomp filter on history logic

commit ff84522071f01ebbede642f0726b79abc79c0dfa
Merge: fea5f0ab f24f5b51
Author: Adrianna Foster <[email protected]>
Date:   Mon Feb 10 20:48:58 2025 -0700

    Merge pull request #1317 from adrifoster/patch_testing

    Update to cohort insertion and sorting routines

commit f24f5b51baf81388b2699638ee4ef5a499e4e1ce
Merge: 53f03107 fea5f0ab
Author: Adrianna Foster <[email protected]>
Date:   Mon Feb 10 20:47:39 2025 -0700

    merge in main

commit fea5f0ab2ae702d2638eade1d5023524f5c6e632
Merge: 798acbb5 6029b109
Author: Adrianna Foster <[email protected]>
Date:   Mon Feb 10 20:44:29 2025 -0700

    Merge pull request #1327 from adrifoster/preserve_cohort_order

    preserve cohort order when cohorts have identical heights

commit 53f03107fa57c214271b0c04e063802d9f776521
Merge: bb1f9eda 798acbb5
Author: Adrianna Foster <[email protected]>
Date:   Mon Feb 10 17:08:43 2025 -0700

    Merge branch 'main' into patch_testing

commit 6029b109d702e49ebabf5c423de6c1ef01b4f86f
Merge: baa9102f 798acbb5
Author: Adrianna Foster <[email protected]>
Date:   Mon Feb 10 09:34:06 2025 -0700

    Merge branch 'main' into preserve_cohort_order

commit 798acbb55e02d1053720a634281a55f2eeb5821e
Merge: 48b3085f d2b022d4
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 6 11:41:05 2025 -0800

    Merge pull request #1328 from glemieux/github-issue-templates

    Add github issue templates

commit d2b022d481ad484e8838028b4e06ddaee67fb4e7
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 6 11:36:08 2025 -0800

    github-issues: add task template

commit cfc22ce1785c276e5533884184176e5a55131e50
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 6 11:22:22 2025 -0800

    github-issues: add feature request issue template

commit 2183b5955e3c9cbfcde6367afef2fa6b126a3338
Author: Gregory Lemieux <[email protected]>
Date:   Thu Feb 6 10:11:30 2025 -0800

    github-issues: initial commit of issue templates

commit baa9102f82bec8903c198bc3ef5e1d542e0c61ae
Merge: a366ec53 48b3085f
Author: Adrianna Foster <[email protected]>
Date:   Thu Feb 6 11:18:23 2025 -0700

    Merge branch 'main' into preserve_cohort_order

commit bb1f9eda77ed5d2caf2222d08bed37e8fbfd269e
Author: adrifoster <[email protected]>
Date:   Wed Feb 5 10:22:45 2025 -0700

    remove unused variables

commit 11778109f27416d235ce6cc23cea011426a3513e
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 4 14:10:26 2025 -0700

    Adding in another area check for two-stream element nudging

commit 1f3cd3d384eefbed536ef828aa09130cac1b6b37
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 4 13:56:57 2025 -0700

    Added a very overfull scattering element check

commit a1f84efeea8efe98c9e860a28a21d6827c84c776
Author: Ryan Knox <[email protected]>
Date:   Tue Feb 4 15:36:06 2025 -0500

    typo correction

commit 48b3085f65bd00f7ee1eb2c134a6af188a639dbc
Merge: aa587ccf 694e8064
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 31 08:33:08 2025 -0800

    Merge pull request #1273 from ckoven/landuse_fixes

    Land Use Fixes

commit 694e8064a4e717a51980d62fd49746c0f858c938
Author: Gregory Lemieux <[email protected]>
Date:   Thu Jan 30 16:56:41 2025 -0700

    correct location of FATES_NPP_LU calculation

commit 9e8473bcaef65fead3ca486e9972d1ebaf2716a3
Merge: e118d40c aa587ccf
Author: Gregory Lemieux <[email protected]>
Date:   Thu Jan 30 11:34:21 2025 -0700

    Merge tag 'sci.1.80.10_api.37.0.0' into landuse_fixes

    Add runtime checks on allometry mode settings

    This adds runtime error and warning messages to avoid erroneous
    `crowndepth` calculations depending on the allometry modes and the
    `h2cd` allometery parameter combination.

commit 53df550191184013c1efee08f5964b4fdf0d91d4
Author: adrifoster <[email protected]>
Date:   Wed Jan 29 09:07:30 2025 -0700

    add more tests

commit da70f5597bc68fc566c714ded9b667c5025f8240
Author: Charlie Koven <[email protected]>
Date:   Tue Jan 28 15:29:10 2025 -0800

    added herbivory flux to restart data

commit 5d5b0864d9cb1b23462920fbc186729bbdbc7a46
Author: adrifoster <[email protected]>
Date:   Tue Jan 28 14:42:22 2025 -0700

    add helper method for patch testing

commit 18f36020d74e3017b39e6a5289cce88a4c957543
Author: adrifoster <[email protected]>
Date:   Tue Jan 28 13:26:35 2025 -0700

    some requested changes

commit 175ffc29494ebf744082d424bfe7e95f9a577b04
Author: Gregory Lemieux <[email protected]>
Date:   Mon Jan 27 15:44:56 2025 -0800

    update fates_turb_z0mr parameter default

commit b619100fb4bd3d0a58bea3cd8f51624e87483733
Author: Charlie Koven <[email protected]>
Date:   Mon Jan 27 12:28:48 2025 -0800

    Apply suggestions from code review

commit 491c948e4ac5ef0ba13e43230c798a1e660eb65a
Author: Adrianna Foster <[email protected]>
Date:   Mon Jan 27 09:18:35 2025 -0700

    more tests

commit a3396709a5726b34d5e88982ee8669dd2f3627f4
Author: Adrianna Foster <[email protected]>
Date:   Sun Jan 26 14:15:57 2025 -0700

    update for tests

commit aa587ccf3a94abbd68dbf3dc7646fa0a61e411ba
Merge: a969384b 7ab7a53e
Author: Gregory Lemieux <[email protected]>
Date:   Sat Jan 25 12:49:03 2025 -0800

    Merge pull request #1314 from mpaiao/mpaiao-pr-dmode-check

    Additional checks for crown depth allometry parameters

commit 76225c9cd4ff67ca80760d751cc4774a5aad16e0
Author: Charlie Koven <[email protected]>
Date:   Thu Jan 23 16:43:18 2025 -0800

    Apply suggestions from code review

    CamelCase! (camels are grazers too)

    Co-authored-by: Gregory Lemieux <[email protected]>

commit cb1276a2ab9a17f89545c99ea23d2e282c0b2538
Author: Adrianna Foster <[email protected]>
Date:   Thu Jan 23 15:54:20 2025 -0700

    add more units

commit fded3f27fa6c40910ff33f92383085b2d57df057
Author: Adrianna Foster <[email protected]>
Date:   Thu Jan 23 13:19:56 2025 -0700

    remove unused variable

commit c3ddfcec9cc3362e2ad4f4fd6d25ff98e7a1a605
Author: adrifoster <[email protected]>
Date:   Thu Jan 23 09:20:29 2025 -0700

    clean up

commit 8af82c5f2426b03c8fe10fa88ff9de9be6258d7e
Author: adrifoster <[email protected]>
Date:   Thu Jan 23 09:06:51 2025 -0700

    get rid of tooling

commit b147cd33c7df1e0a7dc68e5ac9f8f4d698d32d66
Author: adrifoster <[email protected]>
Date:   Thu Jan 23 09:05:45 2025 -0700

    remove old routines

commit cccb7f3e563d88ba4d6567e0eb554f6bf50bcde7
Author: Adrianna Foster <[email protected]>
Date:   Wed Jan 22 15:17:01 2025 -0700

    move to new methods

commit f3ccab240f0bdd51dbf0f61f5f944eaab92b1fb0
Merge: e7ae1323 a969384b
Author: Adrianna Foster <[email protected]>
Date:   Wed Jan 22 10:19:21 2025 -0700

    Merge branch 'main' into patch_testing

commit e7ae13233f500a80783313715d9ceb7cc30f9da2
Author: adrifoster <[email protected]>
Date:   Wed Jan 22 10:18:20 2025 -0700

    add old and new tests

commit 8aa66d15b7ff6ffe6bc95474b1eb7ae46e66232e
Author: adrifoster <[email protected]>
Date:   Wed Jan 22 09:50:40 2025 -0700

    more unit tests

commit b47f60177d53b147af24034550eff25b45195b8a
Author: adrifoster <[email protected]>
Date:   Wed Jan 22 09:50:28 2025 -0700

    add more unit tests

commit a0b1c6071a95f25c4454cf3686b7846932e60c55
Merge: 07b3f99e 6ec0248b
Author: adrifoster <[email protected]>
Date:   Tue Jan 21 19:09:29 2025 -0700

    Merge branch 'patch_testing' of https://github.com/adrifoster/fates into patch_testing

commit 07b3f99edf59c4f07de3903689d606646c806d7c
Author: adrifoster <[email protected]>
Date:   Tue Jan 21 19:09:20 2025 -0700

    update

commit a366ec53da3fdfa197e63c5bc4a79e112a36df16
Author: Adrianna Foster <[email protected]>
Date:   Tue Jan 21 19:07:07 2025 -0700

    preserve cohort order

commit 6ec0248b26e23c4e3078a13357663047ade6e7de
Author: Adrianna Foster <[email protected]>
Date:   Tue Jan 21 19:05:23 2025 -0700

    update tests

commit 4b100b226549ed5c93458edfd541e5ee098b98ad
Author: Charlie Koven <[email protected]>
Date:   Tue Jan 21 16:13:47 2025 -0800

    fix error to EDPhysiologyMod.F90 when nutrients are on

commit 6fa3079dfe123af0e6244a99abf9f59aa478f13b
Author: Gregory Lemieux <[email protected]>
Date:   Tue Jan 21 12:18:15 2025 -0700

    correct woody logic check

commit 63232efa2b01f6436b5669441a23ea91be5e205c
Author: Adrianna Foster <[email protected]>
Date:   Tue Jan 21 08:56:55 2025 -0700

    remove check

commit e118d40cc497fdfcc58021c714eb80ce569b11a2
Author: Charlie Koven <[email protected]>
Date:   Fri Jan 17 12:13:02 2025 -0800

    delete commented-out text in EDPatchDynamicsMod.F90

commit ee0e47fe076927185458efe261d09a0192cdc0a0
Author: Charlie Koven <[email protected]>
Date:   Fri Jan 17 12:10:47 2025 -0800

    fix typos in FatesHistoryInterfaceMod.F90

commit 9cb16111af419bd6e254d97edbea3198790d2674
Merge: a265f96e 01e418cd
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 17 10:03:40 2025 -0800

    Merge pull request #31 from rgknox/parameter-switch-migration

    add leaf biophysics parameters

commit 01e418cdcb1e7af9eda1bbd2814d08e7503a8afb
Author: Ryan Knox <[email protected]>
Date:   Fri Jan 17 11:50:55 2025 -0500

    added grazing parameters

commit e02533bf567aad3fc37efa93a290a9f45a8f2331
Author: Ryan Knox <[email protected]>
Date:   Fri Jan 17 11:27:05 2025 -0500

    added new pft-level switches that control how btran reduces conductance and gross assimilation

commit fcf3f7c5efd43c1b962103d43e6e1eb05cef593e
Author: Adrianna Foster <[email protected]>
Date:   Thu Jan 16 09:04:00 2025 -0700

    update to new routine

commit a969384beafc99834eaa609777fbabd553459011
Merge: f4598102 efb14ac7
Author: Ryan Knox <[email protected]>
Date:   Wed Jan 15 23:01:24 2025 -0500

    Merge pull request #1306 from rgknox/fix-tveg-wgt-satphen

    Fix vegetation temperature weighting during phenology

commit f459810290d837b59e2ea4c24262531163883875
Merge: 505b039d abd56539
Author: Ryan Knox <[email protected]>
Date:   Wed Jan 15 16:03:25 2025 -0500

    Merge pull request #1309 from jennykowalcz/jkowalcz-sapflow

    Add calculation of FATES_SAPFLOW to history interface, add sapwood area as history variable

commit d81ca0f90c32a11e320f7ec7fcb07f6f1b7d4125
Merge: 96df8569 9d03446c
Author: Adrianna Foster <[email protected]>
Date:   Wed Jan 15 13:40:47 2025 -0700

    both changes

commit 96df856995ca51c35cc574713516ee07b34ea50f
Author: Adrianna Foster <[email protected]>
Date:   Wed Jan 15 13:39:44 2025 -0700

    remove nullify

commit 9d03446c3ec39b74093beafae79abcb8a2774e7d
Author: adrifoster <[email protected]>
Date:   Wed Jan 15 13:39:24 2025 -0700

    remove old sort

commit a265f96ed1f24e96ee1a090abcf77b4a855c82fc
Author: Gregory Lemieux <[email protected]>
Date:   Wed Jan 15 09:53:31 2025 -0800

    change photosynthetic acclimation pass name

    This is associated with the hlm-side change from logical to named switch

commit 505b039d8d67deee7c98f1c259d8598070ca6a97
Merge: 1689466c a7208a0d
Author: Ryan Knox <[email protected]>
Date:   Wed Jan 15 11:49:52 2025 -0500

    Merge pull request #1269 from ckoven/lai_saturation_bugfix

    handle case where LAI+SAI exceeds array by clipping instead of crashing

commit 464441e5268ed1505e110c65de1f8a45b8cbd1fc
Merge: d2a93bc6 b9a46b74
Author: Adrianna Foster <[email protected]>
Date:   Wed Jan 15 08:19:26 2025 -0700

    merge in changes

commit d2a93bc64583d0b6fb0b34feef392eec2f8cf8e4
Author: Adrianna Foster <[email protected]>
Date:   Wed Jan 15 08:16:55 2025 -0700

    testing

commit b9a46b747d2e542e5448e14d768a4d4999bc8fda
Author: adrifoster <[email protected]>
Date:   Wed Jan 15 08:00:31 2025 -0700

    update

commit 7ab7a53e642d7c07f1f30d3ee7b09607488c7565
Author: Marcos Longo <[email protected]>
Date:   Tue Jan 14 15:38:51 2025 -0800

    Minor edits so the inequality tests are consistent across multiple cases.

commit 0b7df916bde0061c3cb3f5d622140f5016891b97
Author: Marcos Longo <[email protected]>
Date:   Tue Jan 14 14:26:14 2025 -0800

    Include sanity checks for the height:crown depth allometry.  This intends to address
    FATES discussion #1308, by adding multiple checks in subroutine PRTCheckParams.

    1. Fatal error issued if parameters would cause the crown depth to always exceed height or
       to be negative.
    2. Warning issued if parameters could cause crown depth to be capped to height either when
       plants are near recruitment size or when plants are near maximum height.

    if the multiplier is negative,

commit d870f88a678c8000587fa96797bd3a58d4903653
Author: adrifoster <[email protected]>
Date:   Tue Jan 14 12:13:23 2025 -0700

    fix indentation

commit c173889db8b15fb28a92d72e84590ca0cb774696
Author: adrifoster <[email protected]>
Date:   Tue Jan 14 12:08:32 2025 -0700

    add new insertcohort

commit a7208a0df9a247bf8cfceefe476f9d223d1d8ce2
Author: Ryan Knox <[email protected]>
Date:   Tue Jan 14 10:21:05 2025 -0700

    small bugfixes adding lai capping

commit b3113b79f8b8138715c83d429304da9075ea2d2c
Merge: ac5bf386 1689466c
Author: Gregory Lemieux <[email protected]>
Date:   Mon Jan 13 15:27:01 2025 -0800

    Merge tag 'sci.1.80.6_api.37.0.0' into grazing_merge

    Bug fix for issue #1301

    Corrects when the fraction of burnt fuel is zero'd and how the litter
    mass is updated based on that fraction.

commit 6cd15e8f009c4be16ac83e634f98de7695e179d0
Author: Ryan Knox <[email protected]>
Date:   Mon Jan 13 16:02:09 2025 -0700

    added in capping on lai+sai, and also added a check on that cap

commit 2c654d91fc6c87a51392bf826e5d6dfabb47225a
Merge: 58ba459a b6c6b404
Author: Ryan Knox <[email protected]>
Date:   Mon Jan 13 15:37:55 2025 -0700

    Merge branch 'lai_saturation_bugfix' of github.com:ckoven/fates into lai_saturation_bugfix

commit 58ba459a49ae9ac86a52fb06903ef83037c194f7
Author: Ryan Knox <[email protected]>
Date:   Mon Jan 13 12:00:48 2025 -0700

    small comment updates and b4b update for lai capping

commit b6c6b4049366d054f5d2bfc26ff122470c120c98
Merge: 26429c66 e1746673
Author: Charlie Koven <[email protected]>
Date:   Mon Jan 13 11:56:33 2025 -0700

    Merge pull request #27 from rgknox/lai_saturation_bugfix

    force single location for tree_lai and tree_sai

commit 22f7249af0420e6d87f7f7f5cc6c93427be5681e
Merge: 33dcdf69 70c21a3e
Author: Charlie Koven <[email protected]>
Date:   Mon Jan 13 11:53:16 2025 -0700

    Merge pull request #26 from glemieux/landuse_fixes-deconflict

    Landuse fixes history interface deconflict with the latest tag

commit e1746673611788458d979671bff9344bd1a8051d
Author: Ryan Knox <[email protected]>
Date:   Mon Jan 13 11:51:17 2025 -0700

    added sp clause to updating sai

commit abd56539e4ccb1755c79b60039e40f7896552e5a
Author: [Jennifer Kowalczyk] <[[email protected]]>
Date:   Mon Jan 13 09:03:55 2025 -0800

    set basal area and sapwood area history variables back to inactive by default

commit 99359b16f2284d7070a504f5c31c9fd7695d428a
Author: Ryan Knox <[email protected]>
Date:   Mon Jan 13 10:27:30 2025 -0500

    clean up of tree_lai changes

commit 8b1952747e91b7683613d2454eaaaedcef3c8d11
Merge: 342703ef 1689466c
Author: Ryan Knox <[email protected]>
Date:   Sun Jan 12 22:07:39 2025 -0500

    Merge branch 'main' into lai_saturation_bugfix

commit 342703efb1cbd2d80749d8a9b000874905a9378c
Author: Ryan Knox <[email protected]>
Date:   Sun Jan 12 21:55:29 2025 -0500

    forcing tree_lai and tree_sai to be used together

commit ac5bf3864ac8234a7a840b0fc2f436ae9564a329
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 10 17:08:20 2025 -0800

    add api37 parameter file and xml patch file

commit 33dcdf69450abda3e0b619f02dba82dd0e5f8ff7
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 10 11:25:33 2025 -0800

    Update biogeochem/EDLoggingMortalityMod.F90

    Minor typo fix

commit 70c21a3e0fdbc8774f6f782992f41df37ce25805
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 10 10:22:28 2025 -0800

    fix update frequency setting for FATES_NPP_LU

commit 424be2014fdaa4368cd0d64ba424f12c6f05fc27
Author: Adrianna Foster <[email protected]>
Date:   Fri Jan 10 11:03:16 2025 -0700

    update

commit 86ed336c80a2d72cefe0bdaa6b3ba0469e7435b7
Author: Adrianna Foster <[email protected]>
Date:   Fri Jan 10 09:53:03 2025 -0700

    testing

commit a66b53c9cf18b06e79d5612e87266853a92c0185
Author: Adrianna Foster <[email protected]>
Date:   Fri Jan 10 09:52:34 2025 -0700

    update

commit b07e3e7764dc9c44fcd064df307a63a975327c30
Merge: 05f87944 bdbe4438
Author: adrifoster <[email protected]>
Date:   Fri Jan 10 09:09:59 2025 -0700

    merge in changes

commit 05f87944f29b93d185a786d593d5562879c2ccbd
Author: adrifoster <[email protected]>
Date:   Fri Jan 10 09:09:24 2025 -0700

    add unit tests

commit bdbe4438c1bcc805ac3a04dd3a59a9ff6ff62122
Author: Adrianna Foster <[email protected]>
Date:   Fri Jan 10 09:08:44 2025 -0700

    testing

commit 1f51ce7270ad6f7b778f9732da0944dbb492a247
Merge: 0be5cd13 1689466c
Author: Ryan Knox <[email protected]>
Date:   Thu Jan 9 11:45:30 2025 -0500

    merge resolution between nocomp index and firemodel updates

commit d6b41091b4753380a5567863f39559e1a873f88b
Author: Adrianna Foster <[email protected]>
Date:   Wed Jan 8 13:56:08 2025 -0700

    add some tests

commit 0be5cd133070d78d8dee7918ef89c5632d6a6117
Author: Ryan Knox <[email protected]>
Date:   Wed Jan 8 11:00:49 2025 -0700

    more tweaking and cleaning of patch numbering

commit c08819fd3e9931eb7fba62d32409173a76c5c00a
Author: adrifoster <[email protected]>
Date:   Wed Jan 8 09:49:09 2025 -0700

    update names

commit 38531828c6ca496c911fa61ba5c0f318d8161929
Author: adrifoster <[email protected]>
Date:   Wed Jan 8 09:24:51 2025 -0700

    put back tree lai

commit e9aa8479c19664f36ee2bb7cee34a53361e878fb
Author: adrifoster <[email protected]>
Date:   Wed Jan 8 09:24:06 2025 -0700

    put back tree lai

commit 623ce63fb0ed372690116cbd28c99faef82f7fca
Merge: 7613837a 1689466c
Author: adrifoster <[email protected]>
Date:   Tue Jan 7 19:39:12 2025 -0700

    merge in main

commit 7613837ad073dd7fda02a8c4db221506055694b3
Author: adrifoster <[email protected]>
Date:   Tue Jan 7 19:28:14 2025 -0700

    update tests

commit 81e2f7898f6123700174949848914c576e109d0c
Author: adrifoster <[email protected]>
Date:   Tue Jan 7 19:26:28 2025 -0700

    new insert and sort methods

commit e4a163d72f3f21b14bd969d0e462480182470d43
Author: Gregory Lemieux <[email protected]>
Date:   Tue Jan 7 15:55:19 2025 -0800

    move npp by land use out of high frequency section

    This cleans up a bad deconflict merge

commit 69e7433f441dc6fc557d31586e1db4121ea2ddb9
Author: Gregory Lemieux <[email protected]>
Date:   Tue Jan 7 15:35:33 2025 -0800

    remove npp by age from high frequency history

    This is clean up from the deconflict merge

commit d4563be23c1abbb2bb2def84aed36bf5404b26e2
Author: adrifoster <[email protected]>
Date:   Tue Jan 7 15:05:01 2025 -0700

    add more patch types

commit 017e5d53934ef656e0b015929a52182fd5ba9669
Author: adrifoster <[email protected]>
Date:   Tue Jan 7 15:03:53 2025 -0700

    add more patch types

commit 3f4c8ac8f243ae21c40227f7ac00d92a82dbb079
Author: adrifoster <[email protected]>
Date:   Tue Jan 7 14:19:21 2025 -0700

    update testing

commit ef8db940d4bcb3e2a6904b78317a5d06693ae393
Author: adrifoster <[email protected]>
Date:   Tue Jan 7 09:29:04 2025 -0700

    add timing and random modules

commit cd6931f25e988515dd729430021af9607228aade
Author: Gregory Lemieux <[email protected]>
Date:   Mon Jan 6 11:59:21 2025 -0700

    fix bad merge deconflict and remove old secondary history variable

commit 96aeedb42016cb9ff8f36471577aed7f1f66bb43
Author: Gregory Lemieux <[email protected]>
Date:   Mon Jan 6 11:57:47 2025 -0700

    fix npp by age calculation

commit 72bf14ea3e8d76b5b2b63ef96932377736e5bdbb
Author: adrifoster <[email protected]>
Date:   Mon Jan 6 08:58:12 2025 -0700

    update tests

commit 73838b3b0251d1c0890795dd5d383ed8c2a740e4
Merge: 6f4f3f6f 1689466c
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 3 17:00:03 2025 -0800

    Merge tag 'sci.1.80.6_api.37.0.0' into landuse_fixes-deconflict

    Bug fix for issue #1301

    Corrects when the fraction of burnt fuel is zero'd and how the litter
    mass is updated based on that fraction.

commit 1689466cfe449bad5c5370420d7a5e4701ae2e05
Merge: d50c9065 f11b6738
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 3 14:51:53 2025 -0800

    Merge pull request #1302 from adrifoster/fuel_frac_fix

    Don't zero out `patch%fuel%frac_burnt()` before we use it

commit ffe501d5eb32560597374da0831caa141c9be2a7
Author: adrifoster <[email protected]>
Date:   Fri Jan 3 13:22:33 2025 -0700

    add cohort and patch tests

commit d50c906559947a70cb91048f0d48b2551bd368f4
Merge: 5c6fb7ae 56ecefdb
Author: Gregory Lemieux <[email protected]>
Date:   Fri Jan 3 09:36:13 2025 -0800

    Merge pull request #1297 from adrifoster/fire_refactor_ros

    Refactor rate of spread subroutine

commit b03b09d77e98ae3f3b928e572c47853f6d014709
Author: adrifoster <[email protected]>
Date:   Thu Jan 2 15:35:28 2025 -0700

    fixing inits

commit 5c6fb7aede1eb478ad02579e5cafe45458fe1787
Merge: 91e4b213 48e9fa47
Author: Gregory Lemieux <[email protected]>
Date:   Thu Jan 2 09:50:23 2025 -0800

    Merge pull request #1303 from adrifoster/cmake_bug_fix

    Fix cmake breaking on functional tests for latest CTSM tag

commit 85837dd416e6f27017377989b4b1aba82878266d
Author: adrifoster <[email protected]>
Date:   Mon Dec 30 15:05:36 2024 -0700

    add cohort test

commit b0a316cd5a638b8f20a15d6d62e0245f72e932a2
Author: adrifoster <[email protected]>
Date:   Mon Dec 30 13:55:56 2024 -0700

    add cohort factory

commit 50ea2d3193a786a0f2a8784e4b489236a3d7d50d
Author: Ryan Knox <[email protected]>
Date:   Mon Dec 30 13:55:31 2024 -0700

    cleaned out unnecessary patch order checks

commit 56ecefdbde152852a5ad892b71976d310da2c863
Author: adrifoster <[email protected]>
Date:   Mon Dec 30 12:01:07 2024 -0700

    remove greater than one check

commit 86f8551ec47d33183186e0dc6ac278e463b5d6af
Author: adrifoster <[email protected]>
Date:   Mon Dec 30 11:59:11 2024 -0700

    add factory

commit 6b4c08f3dd07fa8156c654c83baadd1f2eb8ebbe
Author: Ryan Knox <[email protected]>
Date:   Mon Dec 30 11:49:28 2024 -0700

    migrating method of getting patch numbers to be more uniform

commit 7ed9209734bd4fad7a80434ab11b302c7dcf4d97
Author: Ryan Knox <[email protected]>
Date:   Sun Dec 29 10:18:32 2024 -0700

    bug fixes

commit 599619012345d84af91cfe16eec247b4c513f938
Author: Ryan Knox <[email protected]>
Date:   Wed Dec 18 11:17:23 2024 -0700

    Fixed null pointer

commit 36a86e66c90324a2d3f195ce715d56ded02ce452
Author: Ryan Knox <[email protected]>
Date:   Wed Dec 18 10:28:55 2024 -0700

    Update vegetation temperature weighting convention during chill day calculation

commit 4d31bda3caf0a2c330a6c1b5ec0f7500115171fc
Author: Ryan Knox <[email protected]>
Date:   Sat Dec 28 16:06:43 2024 -0500

    removed instances of iterating patch indices and replaced with usage of cpatch%patchno (which uses a function call to define)

commit 91e4b2130bff87eb843d0151ea37a5f1722e3712
Merge: 3a1f17bb ee9e919c
Author: Ryan Knox <[email protected]>
Date:   Thu Dec 26 13:39:25 2024 -0500

    Merge pull request #1275 from NGEET/ckoven-patch-1

    fix typo in modify_fates_paramfile.py

commit 3a1f17bbbef3c65229b71c00f40fba4c35e22273
Merge: 296e1d6a 6a44ef4c
Author: Ryan Knox <[email protected]>
Date:   Thu Dec 26 13:18:45 2024 -0500

    Merge pull request #1287 from mpaiao/mpaiao-pr-pft-swapper

    Indexing fix in multiple python scripts

commit efb14ac72b7f66e34330fa064a3d42a86443b7e5
Author: Ryan Knox <[email protected]>
Date:   Wed Dec 18 11:17:23 2024 -0700

    Fixed null pointer

commit 3fbe03b0bccd8bda9df74d9058e237bb81c013c3
Author: Ryan Knox <[email protected]>
Date:   Wed Dec 18 10:28:55 2024 -0700

    Update vegetation temperature weighting convention during chill day calculation

commit 6a44ef4c27e1060a14d302338240c3bde4ae75c2
Author: Marcos Longo <[email protected]>
Date:   Tue Dec 17 13:59:45 2024 -0300

    Removing print statement added for debugging.

commit fe1d2e82444da5948123c033779c1da4e56d836f
Author: adrifoster <[email protected]>
Date:   Mon Dec 16 15:42:56 2024 -0700

    pylint

commit da4ed44a85849bcc3ce54627763dbc1799593b8a
Author: adrifoster <[email protected]>
Date:   Mon Dec 16 15:39:10 2024 -0700

    requested changes

commit b1ea3a3f88ee63d477295e8f3b7e5f94c2d2fca2
Author: adrifoster <[email protected]>
Date:   Mon Dec 16 15:15:27 2024 -0700

    lai test

commit f11b673837aecdec614f7a1a38c55666cda25d16
Author: Adrianna Foster <[email protected]>
Date:   Mon Dec 16 14:54:38 2024 -0700

    remove zero of frac_burnt in split_patch

commit 2b01354acc6be381684d89f42af7720857d54dc6
Merge: 789ecab4 48e9fa47
Author: adrifoster <[email protected]>
Date:   Thu Dec 12 16:07:01 2024 -0700

    Merge branch 'cmake_bug_fix' into lai_test

commit 48e9fa477ea66d76602ea0e7c723a365134605d5
Author: adrifoster <[email protected]>
Date:   Thu Dec 12 16:04:05 2024 -0700

    fix

commit 789ecab4c7d84d5fe4942145877c5517b18f16ef
Author: adrifoster <[email protected]>
Date:   Thu Dec 12 15:07:17 2024 -0700

    initial test

commit ef51623f14f9baff293c99e61311ffc2028ce573
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 14:56:26 2024 -0800

    move seed regen model switch from EDParamsMod to FatesInterfaceTypesMod

commit c8e0d2bc442b98eb0b551317e3858e3fd1b101fd
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 14:36:48 2024 -0800

    move radiation model switch from EDParamsMod to FatesInterfaceTypesMod

commit 1056092410409aa094857e7436edf467ee0215a1
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 14:10:51 2024 -0800

    move carbon starvation mortality switch from EDParamsMod to FatesInterfaceTypesMod

commit e6db48f9876522beabad05da5f70e1e489d98c00
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 14:03:18 2024 -0800

    move leaf maintenance respiration switch from EDParamsMod to FatesInterfaceTypesMod

commit e63b20d7e968f1b295e709a0ac12d9d48e391a8a
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 13:36:58 2024 -0800

    move stomatal model switch from EDParamsMod to FatesInterfaceTypesMod

commit 377b155e8f8611f23c7dfbe3267159bd176e58d6
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 12:27:31 2024 -0800

    move stomatal assimiliation switch from EDParamsMod to FatesInterfaceTypesMod

commit 5a6e475740988827e73acccfcf7d4bf6e7a0e6cf
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 12:10:53 2024 -0800

    move photosythentic tempsens model switch from EDParamsMod to FatesInterfaceTypesMod

commit 4c565cc1ceba6b1a9d26372d22de8cddd7800689
Author: Adrianna Foster <[email protected]>
Date:   Wed Dec 11 13:52:40 2024 -0700

    suggested changes

commit 2a49f4cb0821fa306dae7bbd1f11be906b4a9680
Author: Gregory Lemieux <[email protected]>
Date:   Wed Dec 11 11:50:52 2024 -0800

    move hydro solver switch from EDParamsMod to FatesInterfaceTypesMod

commit e8ae7468ff323118fcda4807d509fb4009af1e73
Author: Gregory Lemieux <[email protected]>
Date:   Tue Dec 10 17:06:17 2024 -0800

    move daylength factor switch from EDParams to FatesInterfaceMod

commit 8e919983bdc807700374d497d44f6afdef6aec6a
Author: Adrianna Foster <[email protected]>
Date:   Wed Dec 11 11:54:25 2024 -0700

    zero frac_burnt at top of fire mod

commit f5119a37e88edea4b33d1a1c2257e13bc1f81cb4
Author: Adrianna Foster <[email protected]>
Date:   Wed Dec 11 10:02:56 2024 -0700

    fix typo

commit e04e140cc4527fb8e60cc34558f05c728dbd2339
Author: Adrianna Foster <[email protected]>
Date:   Wed Dec 11 09:57:40 2024 -0700

    add idisttype

commit 79fb219b1f0882d098aeff5e6364398fcdcc6ef6
Author: Adrianna Foster <[email protected]>
Date:   Wed Dec 11 09:30:12 2024 -0700

    initial fix

commit 723c6d8031eb32ce7380a3636109486d8f5fd3e1
Author: Gregory Lemieux <[email protected]>
Date:   Tue Dec 10 16:49:12 2024 -0800

    remove parameter file switches that are moving to HLM namelist

commit e7a7c54492897ecd519fd16eb29c035c65d2e5c3
Author: adrifoster <[email protected]>
Date:   Mon Dec 9 15:24:22 2024 -0700

    update test

commit 296e1d6a45f05a800073d376286d0537d2290e96
Merge: 02ee145d 77e89489
Author: Gregory Lemieux <[email protected]>
Date:   Mon Dec 9 11:27:03 2024 -0800

    Merge pull request #1291 from sshu88/fatesluc_cbasedhrv_v2

    Bug fix for issue #1289

commit 2b62d7adb56ce6d0946ed5b8c98279a91aa85dd1
Author: adrifoster <[email protected]>
Date:   Fri Dec 6 14:43:45 2024 -0700

    remove blank line

commit a2ce597e7826d32e9d9e64ba8ace9252fcbb1e87
Author: adrifoster <[email protected]>
Date:   Fri Dec 6 14:42:26 2024 -0700

    add tests

commit 0aef731e31e7d82393d6ca6cc3175859efb5adb1
Author: adrifoster <[email protected]>
Date:   Fri Dec 6 13:10:01 2024 -0700

    test for propagating flux

commit c2f6a999c9a1bd56f5792391d8fcdcdc2a613a68
Merge: 31a4bb64 a1c587d3
Author: adrifoster <[email protected]>
Date:   Fri Dec 6 11:25:46 2024 -0700

    Merge branch 'fire_refactor_ros' of https://github.com/adrifoster/fates into fire_refactor_ros

commit 31a4bb649bb3c8830afebb51de4cd51836ecaa82
Author: adrifoster <[email protected]>
Date:   Fri Dec 6 11:25:37 2024 -0700

    add ros tests

commit a1c587d3bc64df236db5a733d57f0121bde90d5c
Author: Adrianna Foster <[email protected]>
Date:   Fri Dec 6 11:16:03 2024 -0700

    Update FatesHistoryInterfaceMod.F90

commit 211dedae8c66aec70b2d1e17c2e273a6059575ee
Merge: acde77c0 02ee145d
Author: Adrianna Foster <[email protected]>
Date:   Fri Dec 6 11:06:33 2024 -0700

    Merge branch 'main' into fire_refactor_ros

commit acde77c0504ddda06115ad8149a57b447191d4a6
Author: Adrianna Foster <[email protected]>
Date:   Fri Dec 6 09:42:20 2024 -0700

    fix bugs

commit 426899be6b5409211411eaa6bd3a414868663d2d
Author: Adrianna Foster <[email protected]>
Date:   Fri Dec 6 09:32:07 2024 -0700

    full refactor of ros

commit d5c1ac9c5b53b341c947075b232aded043e88e7d
Merge: bc037997 8fb9f1fc
Author: Adrianna Foster <[email protected]>
Date:   Fri Dec 6 09:19:56 2024 -0700

    merge in changes

commit bc0379972b51dd0e67a18f59c3edda306a6f0cf2
Author: Adrianna Foster <[email protected]>
Date:   Fri Dec 6 09:19:00 2024 -0700

    add ros

commit 8fb9f1fcea7d152feed1983eb4db287ed4076754
Merge: 4b5a6707 51a6a37a
Author: adrifoster <[email protected]>
Date:   Thu Dec 5 11:04:05 2024 -0700

    Merge branch 'fire_refactor_ros' of https://github.com/adrifoster/fates into fire_refactor_ros

commit 4b5a67074ec927e50045e6f9bb554e180c6bb832
Merge: 8bca0fb1 f7ed823c
Author: adrifoster <[email protected]>
Date:   Thu Dec 5 11:03:56 2024 -0700

    updates

commit 51a6a37a1df69f696cc43e1eb7d2648ca2e00cd7
Author: Adrianna Foster <[email protected]>
Date:   Thu Dec 5 10:11:07 2024 -0700

    bug fix

commit 599cc11df1968473aaf20f1ffc86f673a659209e
Merge: ac035e01 8bca0fb1
Author: Adrianna Foster <[email protected]>
Date:   Tue Dec 3 13:32:50 2024 -0700

    Merge branch 'fire_refactor_ros' of https://github.com/adrifoster/fates into fire_refactor_ros

commit ac035e0166bd8216be1a812e23ab565e3d4402d0
Merge: a3cf233b 08f2410f
Author: Adrianna Foster <[email protected]>
Date:   Tue Dec 3 13:32:37 2024 -0700

    Merge branch 'main' into fire_refactor_ros

commit 77e894898e17395033d43ae0911a4bbc455eb9fb
Merge: 914393a4 02ee145d
Author: Gregory Lemieux <[email protected]>
Date:   Mon Dec 2 16:11:34 2024 -0800

    Merge tag 'sci.1.80.3_api.37.0.0' into fatesluc_cbasedhrv_v2

    Two-stream singularity correction update

    This implements a more comprehensive avoidance of singularities with
    two-stream radiation across bands.

commit 02ee145db8d10928e357952533cbdb55bc716d1b
Merge: 0802e4b3 e7b332f8
Author: Gregory Lemieux <[email protected]>
Date:   Mon Dec 2 14:43:06 2024 -0800

    Merge pull request #1277 from rgknox/two-stream-singularity-fix

    comprehensive correction for singularity in two-stream

commit 914393a4c69bf1f00e01750cecce69012d3b915d
Author: Shijie Shu <[email protected]>
Date:   Mon Dec 2 13:49:17 2024 -0800

    Update FatesConstantsMod.F90

    Define named constants for "harvest_tag"

commit 0eb912c11c467b63b9cce294521f36e6da47b0c2
Author: Shijie Shu <[email protected]>
Date:   Mon Dec 2 13:46:00 2024 -0800

    Update EDLoggingMortalityMod.F90

    Use named integer constants for "harvest_tag"

commit 0802e4b35cf6a686c91555ec02579bab460c269f
Merge: 08f2410f c1d04c44
Author: Gregory Lemieux <[email protected]>
Date:   Mon Dec 2 11:30:51 2024 -0800

    Merge pull request #1290 from JessicaNeedham/jfn-cnp-alloc-fix

    Fix CNP allocation weights when reproductive fraction is 1

commit f7ed823ce551c3aa6c19f5cbb253d0f63f962071
Author: adrifoster <[email protected]>
Date:   Mon Dec 2 12:16:03 2024 -0700

    create temp variable

commit 8bca0fb17b8b389cbf1cdd41a9d0a759a779d482
Author: adrifoster <[email protected]>
Date:   Mon Dec 2 12:09:52 2024 -0700

    updates

commit ab2d78189c0792f15d6e98fd576b624bf487b996
Author: [Jennifer Kowalczyk] <[[email protected]]>
Date:   Mon Nov 25 11:34:22 2024 -0800

    add calculation of sapflow_si

commit ddcbf3e49721efc82755e154999db0be0d38b2a8
Author: [Jennifer Kowalczyk] <[[email protected]]>
Date:   Fri Nov 22 09:50:56 2024 -0800

    bug fix

commit 9f70f21f15c659ab510be02fa51a5bce6a80ac1e
Author: [Jennifer Kowalczyk] <[[email protected]]>
Date:   Fri Nov 22 09:14:32 2024 -0800

    add sapwood area by scpf to history

commit df6c5e7c9c6ecf1a998c199a72e031175ae856ac
Author: Shijie Shu <[email protected]>
Date:   Wed Nov 20 11:03:59 2024 -0800

    Bug fix for issue #1289

    Fix the issue of no wood product when forced by area-based harvest.
    https://github.com/NGEET/fates/issues/1289

commit c1d04c44a5feb75e7154d9e404d80adced0a99a1
Author: jessica needham <[email protected]>
Date:   Wed Nov 20 09:44:31 2024 -0800

    reverse logic for if statement

commit e7b332f8f97cfd48e38bef0f512a5997831398d9
Author: Gregory Lemieux <[email protected]>
Date:   Wed Nov 20 09:39:42 2024 -0800

    fix Kb_sing calculation

    Using a do loop in place of broadcasting is necessary here
    per the fortran standard since the pointers and arrays are
    not contiguous in memory.

commit 589f263667c9b29dd4ae69a0eba3b1689568ea25
Author: Gregory Lemieux <[email protected]>
Date:   Wed Nov 20 09:39:17 2024 -0800

    fix if then typo around Kb_sing

commit c07ef109fdd344cef02760a4e4c1031a9dcae6d3
Author: jessica needham <[email protected]>
Date:   Tue Nov 19 11:40:21 2024 -0800

    fix CNP allocation when reproductive frac is 1

commit a1e17977d7a57ffbd2ac3de3d7dff8d456f3d460
Merge: cd33abc9 c81282b0
Author: Ryan Knox <[email protected]>
Date:   Mon Nov 18 13:36:52 2024 -0500

    Merge pull request #13 from glemieux/two-stream-sing-fix-refactor

    Two stream singularity fix refactor

commit 08f2410fd2a9e04920eedb4cc2d51a09f68127ec
Merge: de5f266a 1365dee1
Author: Gregory Lemieux <[email protected]>
Date:   Mon Nov 18 10:33:06 2024 -0800

    Merge pull request #1268 from XiulinGao/xlg-grass-sapwood-area-fix

    calculate sapwood cross-sectional area for grass PFT

commit 9b2384c921ee80b66a1d452ba38abaaf5ef93470
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 10:27:52 2024 -0800

    Multiple fixes to ncvarsort.py to be compatible with scipy.io.netcdf

commit 14a5cb44c5d82c0eac2920058a5c1a121e39b95a
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 10:09:46 2024 -0800

    Fix typo in my last update

commit f36f34a550242b8dc7c6b5c8aec7910aa0757fdf
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 10:08:24 2024 -0800

    More fixes in ncvarsort.py to be compatible to scipy.io.netcdf

commit 7bf2f7cd75414edb3662f83f01b07d1b3da1f431
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 10:02:52 2024 -0800

    Replacing datatype with typecode in ncvarsort.py

commit 612d4e010edb270895518885bb2e81a1d284f855
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 09:57:58 2024 -0800

    Bug fix when retrieving variables in ncvarsort.py.

    Fixing a bug I introduced when I replaced variable retrieval with variables.get.
    I had forgotten to replace square brackets with parentheses.

commit b417a78e8ce657826517dae1558efe0b3bff5060
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 09:54:56 2024 -0800

    Dropping attribute size from "the_dim" in ncvartsort.py

    Apparently this is different between scipy/io/netcdf and netCDF4

commit f2b44986fa34a34342dd1b6c826eecbd3b8e76b6
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 09:51:41 2024 -0800

    Force integer in createDimension in ncvarsort.py

    I copied this from FatesPFTIndexSwapper.py, because the code was giving an
    attribute error.

commit 5cb89ad14775b291450869401a3ef0d2db5aa2dc
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 09:47:42 2024 -0800

    Additional edits to ncvarsort.py to align with the scipy/io/netcdf library.

commit 7d30a3fb6c43f0bef6cb6a37b64e427d514dc677
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 09:37:44 2024 -0800

    Append extension nc to the temporary files. In some combinations of python/netcdf libraries,
    the lack of nc extension has caused the function to crash.

commit 7539b402ae06ef790560d0a81b303cc886a25101
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 09:32:12 2024 -0800

    Updating ncvarsort.py so it uses the same netcdf libraries as other python scripts.

commit fd7922f234822c7fe1c21fdc65660e82b4f17767
Author: Marcos Longo <[email protected]>
Date:   Mon Nov 18 09:18:02 2024 -0800

    Editing modify_fates_paramfile.py similarly to FatesPFTIndexSwapper.py for scalars.

commit 291096a6b7960e6e122c4a142e48a37a305d3027
Author: Marcos Longo <[email protected]>
Date:   Sun Nov 17 17:54:45 2024 -0800

    Minor fix in FatesPFTIndexSwapper.py. At least with my scipy configuration, the code
    would crash with scalars. The updates should be equivalent to the old code but do not
    cause errors.

commit a3cf233b1b84e115d8acc46c80ce13f4a0fe50bc
Author: adrifoster <[email protected]>
Date:   Thu Nov 14 18:14:37 2024 -0700

    minor updates

commit 205fc9892ccfaa55eab3b7e7c1ae9f17c94c22c2
Author: adrifoster <[email protected]>
Date:   Thu Nov 14 16:03:02 2024 -0700

    initial cleanup

commit de5f266a54df9a0464608f709486cda96f7526db
Merge: e3e7d2cd 9d28eb6c
Author: Gregory Lemieux <[email protected]>
Date:   Thu Nov 14 08:57:38 2024 -0800

    Merge pull request #1197 from ckoven/growth_respiration

    Move growth respiration to daily timestep

commit 1365dee1ccdc99710d563dcef95a2f1065065764
Author: Gregory Lemieux <[email protected]>
Date:   Wed Nov 13 15:33:11 2024 -0800

    formatting space alignment

commit 2202c461b5fb6fa1aa9398a5b19624771a3169f9
Author: Gregory Lemieux <[email protected]>
Date:   Wed Nov 13 15:30:18 2024 -0800

    update subroutine case to PascalCase

commit e3e7d2cd86a66f8ca0e8f6dc4a823246a2bdb95b
Merge: 1be39629 bdb253fd
Author: Adrianna Foster <[email protected]>
Date:   Wed Nov 13 09:44:43 2024 -0700

    Merge pull request #1247 from adrifoster/fire_refactor_fuel

    Refactor spitfire fuel calculations

commit c81282b04bfee06c8513d61990f1e5606548b3bd
Author: Gregory Lemieux <[email protected]>
Date:   Tue Nov 12 16:30:56 2024 -0800

    remove the need for a check variable

commit 4b6fd9b7ff5826b630a179d48e8e74ba9b9d7a3d
Author: Gregory Lemieux <[email protected]>
Date:   Tue Nov 12 16:26:05 2024 -0800

    refactor singularity check loop

commit bdb253fd9262cbb721a3f2ef033e16d73c2cd77e
Author: Adrianna Foster <[email protected]>
Date:   Tue Nov 12 10:58:38 2024 -0700

    fix capitalization

commit 128e0a92566888f1edb0d35a50f42f6bdf33decd
Author: Adrianna Foster <[email protected]>
Date:   Tue Nov 12 09:40:34 2024 -0700

    fix class vs. type

commit fb6ab8c2f744fdebe42e5ab2881c0c34333180b7
Merge: 00d02de3 d422c126
Author: Adrianna Foster <[email protected]>
Date:   Fri Nov 8 09:34:34 2024 -0700

    Merge branch 'fire_refactor_fuel' of https://github.com/adrifoster/fates into fire_refactor_fuel

commit a05f1429cc250e5e1c7bf83ae4a9af3c4d7aae1f
Author: Ryan Knox <[email protected]>
Date:   Mon Nov 4 17:38:51 2024 -0500

    alternative way to adjust area issues in FATES twostream

commit d422c126e3ebba0a6bd01398d3e2b0b763d9ecc1
Merge: 52842b37 1be39629
Author: Adrianna Foster <[email protected]>
Date:   Mon Nov 4 10:07:27 2024 -0700

    Merge branch 'main' into fire_refactor_fuel

commit 52842b37843522995796fa7a1144e31ee2054130
Author: Adrianna Foster <[email protected]>
Date:   Mon Nov 4 10:06:17 2024 -0700

    fix variable names

commit 1be3962933351b94fef134d607ac7d821d884f96
Merge: 468ebcaf f208cb87
Author: Gregory Lemieux <[email protected]>
Date:   Fri Nov 1 15:18:08 2024 -0700

    Merge pull request #1244 from JessicaNeedham/jfn-invinit-write-fix

    Fix write of inventory init files

commit 6f4f3f6f67cd167f767a782b85c899e7f04701f6
Merge: 56882373 111278a4
Author: Charlie Koven <[email protected]>
Date:   Fri Nov 1 11:25:42 2024 -0700

    Merge pull request #25 from samsrabin/landuse_fixes-ssr

    Minor changes to landuse_fixes branch

commit 111278a4238051be3b3974001ccd25b3aaf825f2
Author: Sam Rabin <[email protected]>
Date:   Fri Nov 1 12:21:17 2024 -0600

    Undo an indentation change.

commit f19848b02d55a82a1a32cfb2af06c6a57d6338ab
Author: Sam Rabin <[email protected]>
Date:   Fri Nov 1 12:17:46 2024 -0600

    Simplify "prevent conversion of bare ground land" logic.

commit 52462b5b4c7aab61ddef6bd6675e5161a28dba44
Author: Sam Rabin <[email protected]>
Date:   Fri Nov 1 12:15:39 2024 -0600

    Fix typo in comment.

commit 9d28eb6c2a770fa8feac4c08adb973c2d6a9ad92
Merge: 9080ba37 50bf6b93
Author: Charlie Koven <[email protected]>
Date:   Thu Oct 31 13:05:59 2024 -0700

    Merge pull request #24 from rgknox/growth_respiration

    Growth respiration

commit cd33abc9676b5178d5839eddbd347285f3a89abb
Author: Ryan Knox <[email protected]>
Date:   Thu Oct 31 15:32:17 2024 -0400

    Added recursive checks for singularity in two-stream

commit de6102884790bb60681b11d20151fb462c1a70b5
Merge: e0c70580 468ebcaf
Author: adrifoster <[email protected]>
Date:   Thu Oct 31 10:15:22 2024 -0600

    Merge branch 'main' into fire_refactor_fuel

commit e0c705804511eb9945517c93333e5f8a5b8a7794
Author: adrifoster <[email protected]>
Date:   Thu Oct 31 10:14:49 2024 -0600

    fix comment

commit 50bf6b93050fe3675f253418afdd6d275d5457b3
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 30 23:15:04 2024 -0400

    syntax updates and minor bug fix for respiration update

commit e7b236b8412f46332fb76ebf1d63551ad887b9a2
Author: Charles D Koven <[email protected]>
Date:   Wed Oct 30 19:39:29 2024 -0700

    added grazing carbon flux history variable

commit a9758b3f4aa92d76e0ed983ea3d923b83dc344a3
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 30 22:33:43 2024 -0400

    Added hard-coded override to revert to original format for inventory files

commit 3f688d70d1563e3688434a3c923393c088f408e3
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 30 22:32:43 2024 -0400

    various bug fixes for growth respiration update

commit ee9e919c9bead499d6f688175d902f21d814ff5a
Author: Charlie Koven <[email protected]>
Date:   Wed Oct 30 14:05:58 2024 -0700

    fix typo in modify_fates_paramfile.py

commit 366b73a24b9de701abde7e1a5cdc1b23e29cfcfb
Merge: 1d520346 f5bd6250
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 30 15:17:51 2024 -0400

    merge resolution between growth_respiration and main

commit 1d520346dfda16a5a9ef61391829935f6c12cc73
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 30 15:02:42 2024 -0400

    removing resp_g_acc, it is unnecessary

commit f5a7caad435700def48cf5ff8ac7ba3853e9d8be
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 30 14:04:24 2024 -0400

    removing resp_g_acc

commit a0dea3b51a2370ba13ce811d6c90b662f3c06833
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 30 13:27:02 2024 -0400

    Added respiration excess to sub-daily npp tracking by holding it like gpp does. Fixed some output units.  Fixed carbon flux tracking when we bypass (ie st3 and satphen).

commit 7fc224251a876748cdd6bda6e4ea504f234121eb
Author: adrifoster <[email protected]>
Date:   Wed Oct 30 10:42:20 2024 -0600

    more updates

commit 920c549ba2f67ffe2f26c38de6ffa44b52b1fb07
Author: adrifoster <[email protected]>
Date:   Wed Oct 30 10:14:37 2024 -0600

    big fixes

commit 0831336228bd243c25ed9c16cf94c6962ff1c87e
Merge: b4367834 230fd170
Author: adrifoster <[email protected]>
Date:   Wed Oct 30 09:46:07 2024 -0600

    updates to testing

commit 56882373d160aa8ea085b0a743793ea015349974
Author: Charles D Koven <[email protected]>
Date:   Fri Oct 25 09:17:06 2024 -0700

    added two more hist vars: GPP and NPP, by land use type

commit a580785d5ca49b04079dd3f4a77a21d8e024119e
Author: Charles D Koven <[email protected]>
Date:   Fri Oct 25 09:03:37 2024 -0700

    added two new hist vars: biomass and burned area, by land use type

commit cff10057db186bb40c2d1cbdd5151ac1977a6420
Author: Charles D Koven <[email protected]>
Date:   Fri Oct 25 08:42:22 2024 -0700

    deleting most of the secondary-specific hist vars, in prep for adding some as lu-dim vars

commit e1711ab7db7b3600afc7ee330e0572ca55eb5d1e
Author: Charles D Koven <[email protected]>
Date:   Fri Oct 25 08:16:34 2024 -0700

    removing logic that prevents harvest at too-small rates

commit 59be47049fae2d2c138b9b5be0cfea7d8db3f64c
Author: Charles D Koven <[email protected]>
Date:   Fri Oct 25 08:14:26 2024 -0700

    handling open canopy initial landuse harvest conversion case

commit 1895896ea6810755b82ad4a082615b99540e498c
Author: Charles D Koven <[email protected]>
Date:   Fri Oct 25 08:13:06 2024 -0700

    adding variable names from luh2 harvest drivers

commit dacea7ccc6d9e6fcb0b5f855227c0b628d1e378b
Author: Charles D Koven <[email protected]>
Date:   Tue Oct 22 16:25:22 2024 -0700

    added primary lands age dist history diagnostic, and updated some var names on secondary diags

commit 6dc557e31011efa4bf888e372651bed17647d89f
Author: Charles D Koven <[email protected]>
Date:   Tue Oct 22 15:55:16 2024 -0700

    fixed harvest rates when bare ground >0

commit 468ebcafab8f4e45ac61f2ceae54101f0d6d922c
Merge: 230fd170 464a7ec3
Author: Gregory Lemieux <[email protected]>
Date:   Tue Oct 29 15:25:44 2024 -0700

    Merge pull request #1239 from glemieux/tool-landuse-submodule

    Add external land use data tool as a submodule to fates

commit b4367834abf505eb4e5f53af9bc7e4b83af4685c
Author: adrifoster <[email protected]>
Date:   Tue Oct 29 15:17:43 2024 -0600

    updating variable names

commit 6f6ac0b4d7f7ee040e389431468408514adf2de4
Author: adrifoster <[email protected]>
Date:   Tue Oct 29 15:01:26 2024 -0600

    other updates

commit 195dce4336af0dc38fadee26f0ec8c5135ded387
Author: adrifoster <[email protected]>
Date:   Tue Oct 29 14:56:45 2024 -0600

    change total_loading to non_trunk_loading

commit b5f39560228a8de2caf203b7098c0a271c729b9c
Author: adrifoster <[email protected]>
Date:   Tue Oct 29 14:52:37 2024 -0600

    update nfsc variable name

commit 464a7ec3da81e164fa4159d9288f9ac37bf471fb
Author: Gregory Lemieux <[email protected]>
Date:   Tue Oct 29 13:40:23 2024 -0700

    add truncated version of suggested header comments to .gitmodules

commit 710ae0d3411819eeef94111c94b681cd846f084b
Author: Gregory Lemieux <[email protected]>
Date:   Tue Oct 29 13:36:56 2024 -0700

    minor format update

commit 58b9e81a369d4eb75b7e077580644ad23e72a6d1
Author: Gregory Lemieux <[email protected]>
Date:   Tue Oct 29 13:31:19 2024 -0700

    update landuse tool version

commit e65a3a9b48dffb7930b916515dc0d4ce49bd12f6
Author: Gregory Lemieux <[email protected]>
Date:   Tue Oct 29 13:23:07 2024 -0700

    add tag

commit 9080ba37506445d2bdaa11d68e0b43316cfbc75b
Author: Charlie Koven <[email protected]>
Date:   Tue Oct 29 11:34:17 2024 -0700

    Apply suggestions from code review

    Co-authored-by: Jessica Needham <[email protected]>

commit 9cdc98a1b504bda1ae46fedd68f607cc48bd18c1
Merge: 588a9805 078b99d6
Author: Gregory Lemieux <[email protected]>
Date:   Mon Oct 28 15:57:45 2024 -0700

    Merge branch 'tool-landuse-submodule' into submodule-fxtest

commit 078b99d6611ecbeb42061e1a20af5f1cd5c399ee
Merge: 6fe16854 230fd170
Author: Gregory Lemieux <[email protected]>
Date:   Mon Oct 28 15:48:19 2024 -0700

    Merge tag 'sci.1.79.1_api.36.1.0_tools.2.1.0' into tool-landuse-submodule

    Refactor fates testing scripts

commit 230fd1706189a0457e20d4741a36fd907fd5a5f7
Merge: 4ffab323 d10f218f
Author: Gregory Lemieux <[email protected]>
Date:   Mon Oct 28 13:28:00 2024 -0700

    Merge pull request #1245 from adrifoster/testing_refator

    Refactor to testing scripts.

commit 4ffab3230518253bbed9aaaab055037f5dc7bb33
Merge: f5bd6250 ec61b062
Author: Gregory Lemieux <[email protected]>
Date:   Mon Oct 28 09:59:46 2024 -0700

    Merge pull request #1155 from ckoven/new_patch_insertion

    New patch insertion method

commit ec61b062917ac6db42dc7641e687ed40ffa6c5c8
Author: Gregory Lemieux <[email protected]>
Date:   Sun Oct 27 23:13:16 2024 -0600

    correct hlm swich check in history interface

commit 756434035f397e45b93eb49fb488e2834831983a
Author: Gregory Lemieux <[email protected]>
Date:   Fri Oct 25 11:00:47 2024 -0700

    correct pseudo age calculation statement

commit 69592f2db229d8aa83f0ff68381a299c6f7f9300
Author: Gregory Lemieux <[email protected]>
Date:   Thu Oct 24 15:38:47 2024 -0700

    convert new function name to PascalCase

commit ea2224983e410cf2c2a85aa3cc9b60a68e3fda43
Author: Gregory Lemieux <[email protected]>
Date:   Thu Oct 24 15:33:37 2024 -0700

    change pseudoage calculation to align to current linked list scheme

    The current scheme assumes that "older" patches are lower in patch
    number index and "younger" patches are larger in patch number index.

commit 26429c66cf223dbf68db41cc244c4c58014fec3a
Author: Charles D Koven <[email protected]>
Date:   Tue Oct 22 10:31:13 2024 -0700

    handle case where LAI+SAI exceeds array by clipping LAI+SAI instead of crashing

commit 0628cb76b1df8dc6a99a31799439de1a9a9609bf
Author: Xiulin Gao <[email protected]>
Date:   Wed Oct 23 15:58:08 2024 -0700

    update in-code documentation

commit 862706823d734664c30f4dfc7287931f62906bbb
Author: Xiulin Gao <[email protected]>
Date:   Wed Oct 23 15:54:55 2024 -0700

    correct area calculation

commit 67459866e922528d7c18e5bc2d110316f4777b76
Merge: 454b189d 147d411e
Author: Charlie Koven <[email protected]>
Date:   Wed Oct 23 11:33:21 2024 -0700

    Merge pull request #23 from rgknox/new_patch_insertion

    integrated flux error fix, merge

commit 147d411ee56a4cb0777a9ba248e8a41a196495e7
Author: Ryan Knox <[email protected]>
Date:   Wed Oct 23 12:18:32 2024 -0600

    Fixed restart issues for sp and allvars with integrated flux

commit a001c7150ed7536af8eee2c6c4120c2cb9e9fc30
Author: Xiulin Gao <[email protected]>
Date:   Wed Oct 23 10:28:52 2024 -0700

    add subroutine to calculate sapwood cross-sectional area for grass PFT

commit 3fbc57fbec584e641574ea44409013f151ac9d8c
Merge: 454b189d f5bd6250
Author: Ryan Knox <[email protected]>
Date:   Fri Oct 18 10:58:36 2024 -0600

    Merge branch 'main' into new_patch_insertion

commit 454b189d830c08cc3b3d006a989f4fcb7c8fa450
Author: Ryan Knox <rgknox@lbl…
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Dead fuels never actually consumed in fires
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