Add namelist switches and parameter file changes ahead of upcoming PR on Johnson & Berry electron transport model by JessicaNeedham · Pull Request #1344 · NGEET/fates (original) (raw)

mvdebolskiy added a commit to mvdebolskiy/fates that referenced this pull request

@mvdebolskiy

commit 8924c40bbcb1c764434911f74eb578022018bb70 Merge: ecc6815c 23b6f3e1 Author: mvdebolskiy 80036033+mvdebolskiy@users.noreply.github.com Date: Thu Mar 20 12🔞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 nomatdebol@gmail.com Date: Sat Mar 8 14:20:33 2025 +0100

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

commit ecc6815c75ede97e23ae660a1980bfa94fc290da Merge: f2ea09ea 883537bd Author: mvdebolskiy 80036033+mvdebolskiy@users.noreply.github.com 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 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 jessiefneedham@gmail.com Date: Wed Feb 26 13:40:03 2025 -0800

make fnps parameter pft specific

commit 0e3ceae19a98f66f6ad1b07a986dbc86c29f2f85 Author: jessica needham jessiefneedham@gmail.com Date: Wed Feb 26 12:43:52 2025 -0800

update param  file with param for later PR

commit 1961dfd74d844b699e2a4ac52a0506ac9f084519 Author: jessica needham jessiefneedham@gmail.com Date: Wed Feb 26 11:37:29 2025 -0800

add new namelist switch  - prep for later PR

commit 883537bd0d18c24e267ac2ca1cf3bb8bfd09faea Author: mvdebolskiy nomatdebol@gmail.com Date: Tue Feb 25 10:56:14 2025 +0100

fix logical for ci

commit a91cc42dcd20f878d2412c81f9038636a6030c54 Merge: 655d7846 3b4d20c5 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Sat Feb 22 21:42:19 2025 -0700

correct bad tag merge

commit d88cf4af3af709511779f916875dce2130c7d4eb Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Sat Feb 22 21:06:45 2025 -0800

correct archived parameter file to be api37.1

commit 8fe2fe7b99088726ae02b310652c03376345794a Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Thu Feb 20 10:09:11 2025 -0800

update comments in the api38 patch parameter file

commit d87123d55a418e516899eab42fab149da9f7f406 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Thu Feb 20 10:06:16 2025 -0800

rename patch parameter file and archive default parameter file

commit 928dcd589476cbf316776bfa19291f3bade2c869 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 rgknox@lbl.gov 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 rgknox@lbl.gov Date: Wed Feb 19 10:05:55 2025 -0700

set debug flag to false

commit f3987f2315f0daa60617d73723995dae3fe7ec84 Author: Ryan Knox rgknox@lbl.gov 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 rgknox@lbl.gov Date: Wed Feb 19 09:04:24 2025 -0700

Merge branch 'main' into twostream-nveg-fix

commit ccc1de04abcc14dcc8a24bb06f271bc04e2bc48c Merge: 20649ac9 21418e33 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Tue Feb 18 10:13:26 2025 -0800

fates default parameter file minor formatting update

commit b50e3506fc1407658944ff62c12452b2890470e6 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Mon Feb 17 22:44:17 2025 -0800

update base file for #1140 patch parameter file

commit d388be446d6fcf7d4b297fd4a6cddc53c2f12037 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Fri Feb 14 15:32:10 2025 -0800

fix fates default param internal name

commit 3c8a9909301e25cda8f59163f85d1e2c7ee3da0e Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Fri Feb 14 15:30:35 2025 -0800

correct default param file name

commit 39770b6b0d2cbed6738f22da01d154abba4acb65 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Fri Feb 14 15🔞26 2025 -0800

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

commit 384ef07debe4e5bf7662652e1667df221bd7aee8 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Fri Feb 14 13:35:16 2025 -0800

correct new file name in patch file

commit 66c57d20f729e5355343bb0a626d6200dd89b6f7 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Fri Feb 14 13:34:39 2025 -0800

add xml patch file for pull request 1263

commit 7e8e112085c4568a3b6a4b593353faef4dfb86b9 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Thu Feb 13 12:27:36 2025 -0700

add missing nocomp_bareground use statements

commit 315892a66e8da42ef6eb86a48a9ce9f959d807dc Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Thu Feb 13 11:08:35 2025 -0700

add missing fates constant use statement

commit cfaa1c61cda206a6e6fd32cfaf689b79453c2d8e Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Thu Feb 13 09:42:17 2025 -0700

correct patch number debug write

commit eb64928484a861cae5491e4597c5e6d5ebe4e2ef Author: Ryan Knox rgknox@lbl.gov Date: Thu Feb 13 11:26:28 2025 -0500

Update CODE_OF_CONDUCT.md

commit 3e01c843033e2dbdddca43f157831647d8fe42dd Merge: dc16b39d ff845220 Author: Ryan Knox rgknox@lbl.gov Date: Tue Feb 11 11:12:50 2025 -0500

conflict resolution for nocomp patch counting branch

commit dc16b39d8a20fc0c7bb5e3873e9702b48ad51f32 Merge: 021c0aab 798acbb5 Author: Ryan Knox rgknox@lbl.gov Date: Tue Feb 11 11:09:24 2025 -0500

Merge branch 'main' into luh2_nocomp_merge-bcindex-merged

commit 021c0aab709eefe7f2ffe983d01364797db02005 Author: Ryan Knox rgknox@lbl.gov Date: Tue Feb 11 10:52:57 2025 -0500

fixed loop label

commit e828f0549da5df3a37fc982e54aadcaef8a6feb6 Author: Ryan Knox rgknox@lbl.gov Date: Tue Feb 11 10:51:09 2025 -0500

fixed loop label

commit d4143dd8899f91d12ed90b8d0c0633496381c80b Author: Ryan Knox rgknox@lbl.gov 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 rgknox@lbl.gov Date: Tue Feb 11 10:42:03 2025 -0500

Added description to the new set_patchno

commit b1ccc18d70c5747344299334f34707b4d5603c80 Author: Ryan Knox rgknox@lbl.gov Date: Sun Feb 2 16:35:45 2025 -0700

added nocomp filter on history logic

commit ff84522071f01ebbede642f0726b79abc79c0dfa Merge: fea5f0ab f24f5b51 Author: Adrianna Foster afoster@ucar.edu 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 afoster@ucar.edu Date: Mon Feb 10 20:47:39 2025 -0700

merge in main

commit fea5f0ab2ae702d2638eade1d5023524f5c6e632 Merge: 798acbb5 6029b109 Author: Adrianna Foster afoster@ucar.edu 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 afoster@ucar.edu Date: Mon Feb 10 17:08:43 2025 -0700

Merge branch 'main' into patch_testing

commit 6029b109d702e49ebabf5c423de6c1ef01b4f86f Merge: baa9102f 798acbb5 Author: Adrianna Foster afoster@ucar.edu Date: Mon Feb 10 09:34:06 2025 -0700

Merge branch 'main' into preserve_cohort_order

commit 798acbb55e02d1053720a634281a55f2eeb5821e Merge: 48b3085f d2b022d4 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Thu Feb 6 11:36:08 2025 -0800

github-issues: add task template

commit cfc22ce1785c276e5533884184176e5a55131e50 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Thu Feb 6 11:22:22 2025 -0800

github-issues: add feature request issue template

commit 2183b5955e3c9cbfcde6367afef2fa6b126a3338 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Thu Feb 6 10:11:30 2025 -0800

github-issues: initial commit of issue templates

commit baa9102f82bec8903c198bc3ef5e1d542e0c61ae Merge: a366ec53 48b3085f Author: Adrianna Foster afoster@ucar.edu Date: Thu Feb 6 11🔞23 2025 -0700

Merge branch 'main' into preserve_cohort_order

commit bb1f9eda77ed5d2caf2222d08bed37e8fbfd269e Author: adrifoster adrifost@ucar.edu Date: Wed Feb 5 10:22:45 2025 -0700

remove unused variables

commit 11778109f27416d235ce6cc23cea011426a3513e Author: Ryan Knox rgknox@lbl.gov Date: Tue Feb 4 14:10:26 2025 -0700

Adding in another area check for two-stream element nudging

commit 1f3cd3d384eefbed536ef828aa09130cac1b6b37 Author: Ryan Knox rgknox@lbl.gov Date: Tue Feb 4 13:56:57 2025 -0700

Added a very overfull scattering element check

commit a1f84efeea8efe98c9e860a28a21d6827c84c776 Author: Ryan Knox rgknox@lbl.gov Date: Tue Feb 4 15:36:06 2025 -0500

typo correction

commit 48b3085f65bd00f7ee1eb2c134a6af188a639dbc Merge: aa587ccf 694e8064 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Thu Jan 30 16:56:41 2025 -0700

correct location of FATES_NPP_LU calculation

commit 9e8473bcaef65fead3ca486e9972d1ebaf2716a3 Merge: e118d40c aa587ccf Author: Gregory Lemieux glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Wed Jan 29 09:07:30 2025 -0700

add more tests

commit da70f5597bc68fc566c714ded9b667c5025f8240 Author: Charlie Koven ckoven@gmail.com Date: Tue Jan 28 15:29:10 2025 -0800

added herbivory flux to restart data

commit 5d5b0864d9cb1b23462920fbc186729bbdbc7a46 Author: adrifoster adrifost@ucar.edu Date: Tue Jan 28 14:42:22 2025 -0700

add helper method for patch testing

commit 18f36020d74e3017b39e6a5289cce88a4c957543 Author: adrifoster adrifost@ucar.edu Date: Tue Jan 28 13:26:35 2025 -0700

some requested changes

commit 175ffc29494ebf744082d424bfe7e95f9a577b04 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Mon Jan 27 15:44:56 2025 -0800

update fates_turb_z0mr parameter default

commit b619100fb4bd3d0a58bea3cd8f51624e87483733 Author: Charlie Koven ckoven@users.noreply.github.com Date: Mon Jan 27 12:28:48 2025 -0800

Apply suggestions from code review

commit 491c948e4ac5ef0ba13e43230c798a1e660eb65a Author: Adrianna Foster afoster@ucar.edu Date: Mon Jan 27 09🔞35 2025 -0700

more tests

commit a3396709a5726b34d5e88982ee8669dd2f3627f4 Author: Adrianna Foster afoster@ucar.edu Date: Sun Jan 26 14:15:57 2025 -0700

update for tests

commit aa587ccf3a94abbd68dbf3dc7646fa0a61e411ba Merge: a969384b 7ab7a53e Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 ckoven@users.noreply.github.com Date: Thu Jan 23 16:43:18 2025 -0800

Apply suggestions from code review

CamelCase! (camels are grazers too)

Co-authored-by: Gregory Lemieux <7565064+glemieux@users.noreply.github.com>

commit cb1276a2ab9a17f89545c99ea23d2e282c0b2538 Author: Adrianna Foster afoster@ucar.edu Date: Thu Jan 23 15:54:20 2025 -0700

add more units

commit fded3f27fa6c40910ff33f92383085b2d57df057 Author: Adrianna Foster afoster@ucar.edu Date: Thu Jan 23 13:19:56 2025 -0700

remove unused variable

commit c3ddfcec9cc3362e2ad4f4fd6d25ff98e7a1a605 Author: adrifoster adrifost@ucar.edu Date: Thu Jan 23 09:20:29 2025 -0700

clean up

commit 8af82c5f2426b03c8fe10fa88ff9de9be6258d7e Author: adrifoster adrifost@ucar.edu Date: Thu Jan 23 09:06:51 2025 -0700

get rid of tooling

commit b147cd33c7df1e0a7dc68e5ac9f8f4d698d32d66 Author: adrifoster adrifost@ucar.edu Date: Thu Jan 23 09:05:45 2025 -0700

remove old routines

commit cccb7f3e563d88ba4d6567e0eb554f6bf50bcde7 Author: Adrianna Foster afoster@ucar.edu Date: Wed Jan 22 15:17:01 2025 -0700

move to new methods

commit f3ccab240f0bdd51dbf0f61f5f944eaab92b1fb0 Merge: e7ae1323 a969384b Author: Adrianna Foster afoster@ucar.edu Date: Wed Jan 22 10:19:21 2025 -0700

Merge branch 'main' into patch_testing

commit e7ae13233f500a80783313715d9ceb7cc30f9da2 Author: adrifoster adrifost@ucar.edu Date: Wed Jan 22 10🔞20 2025 -0700

add old and new tests

commit 8aa66d15b7ff6ffe6bc95474b1eb7ae46e66232e Author: adrifoster adrifost@ucar.edu Date: Wed Jan 22 09:50:40 2025 -0700

more unit tests

commit b47f60177d53b147af24034550eff25b45195b8a Author: adrifoster adrifost@ucar.edu Date: Wed Jan 22 09:50:28 2025 -0700

add more unit tests

commit a0b1c6071a95f25c4454cf3686b7846932e60c55 Merge: 07b3f99e 6ec0248b Author: adrifoster adrifost@ucar.edu 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 adrifost@ucar.edu Date: Tue Jan 21 19:09:20 2025 -0700

update

commit a366ec53da3fdfa197e63c5bc4a79e112a36df16 Author: Adrianna Foster afoster@ucar.edu Date: Tue Jan 21 19:07:07 2025 -0700

preserve cohort order

commit 6ec0248b26e23c4e3078a13357663047ade6e7de Author: Adrianna Foster afoster@ucar.edu Date: Tue Jan 21 19:05:23 2025 -0700

update tests

commit 4b100b226549ed5c93458edfd541e5ee098b98ad Author: Charlie Koven ckoven@users.noreply.github.com Date: Tue Jan 21 16:13:47 2025 -0800

fix error to EDPhysiologyMod.F90 when nutrients are on

commit 6fa3079dfe123af0e6244a99abf9f59aa478f13b Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Jan 21 12🔞15 2025 -0700

correct woody logic check

commit 63232efa2b01f6436b5669441a23ea91be5e205c Author: Adrianna Foster afoster@ucar.edu Date: Tue Jan 21 08:56:55 2025 -0700

remove check

commit e118d40cc497fdfcc58021c714eb80ce569b11a2 Author: Charlie Koven ckoven@users.noreply.github.com Date: Fri Jan 17 12:13:02 2025 -0800

delete commented-out text in EDPatchDynamicsMod.F90

commit ee0e47fe076927185458efe261d09a0192cdc0a0 Author: Charlie Koven ckoven@users.noreply.github.com Date: Fri Jan 17 12:10:47 2025 -0800

fix typos in FatesHistoryInterfaceMod.F90

commit 9cb16111af419bd6e254d97edbea3198790d2674 Merge: a265f96e 01e418cd Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 rgknox@lbl.gov Date: Fri Jan 17 11:50:55 2025 -0500

added grazing parameters

commit e02533bf567aad3fc37efa93a290a9f45a8f2331 Author: Ryan Knox rgknox@lbl.gov 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 afoster@ucar.edu Date: Thu Jan 16 09:04:00 2025 -0700

update to new routine

commit a969384beafc99834eaa609777fbabd553459011 Merge: f4598102 efb14ac7 Author: Ryan Knox rgknox@lbl.gov 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 rgknox@lbl.gov 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 afoster@ucar.edu Date: Wed Jan 15 13:40:47 2025 -0700

both changes

commit 96df856995ca51c35cc574713516ee07b34ea50f Author: Adrianna Foster afoster@ucar.edu Date: Wed Jan 15 13:39:44 2025 -0700

remove nullify

commit 9d03446c3ec39b74093beafae79abcb8a2774e7d Author: adrifoster adrifost@ucar.edu Date: Wed Jan 15 13:39:24 2025 -0700

remove old sort

commit a265f96ed1f24e96ee1a090abcf77b4a855c82fc Author: Gregory Lemieux glemieux@users.noreply.github.com 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 rgknox@lbl.gov 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 afoster@ucar.edu Date: Wed Jan 15 08:19:26 2025 -0700

merge in changes

commit d2a93bc64583d0b6fb0b34feef392eec2f8cf8e4 Author: Adrianna Foster afoster@ucar.edu Date: Wed Jan 15 08:16:55 2025 -0700

testing

commit b9a46b747d2e542e5448e14d768a4d4999bc8fda Author: adrifoster adrifost@ucar.edu Date: Wed Jan 15 08:00:31 2025 -0700

update

commit 7ab7a53e642d7c07f1f30d3ee7b09607488c7565 Author: Marcos Longo mdplongo@gmail.com 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 mdplongo@gmail.com 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 adrifost@ucar.edu Date: Tue Jan 14 12:13:23 2025 -0700

fix indentation

commit c173889db8b15fb28a92d72e84590ca0cb774696 Author: adrifoster adrifost@ucar.edu Date: Tue Jan 14 12:08:32 2025 -0700

add new insertcohort

commit a7208a0df9a247bf8cfceefe476f9d223d1d8ce2 Author: Ryan Knox rgknox@lbl.gov Date: Tue Jan 14 10:21:05 2025 -0700

small bugfixes adding lai capping

commit b3113b79f8b8138715c83d429304da9075ea2d2c Merge: ac5bf386 1689466c Author: Gregory Lemieux glemieux@users.noreply.github.com 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 rgknox@lbl.gov 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 rgknox@lbl.gov 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 rgknox@lbl.gov 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 ckoven@users.noreply.github.com 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 ckoven@users.noreply.github.com 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 rgknox@lbl.gov Date: Mon Jan 13 11:51:17 2025 -0700

added sp clause to updating sai

commit abd56539e4ccb1755c79b60039e40f7896552e5a Author: [Jennifer Kowalczyk] <[jenniferkowalczyk@lbl.gov]> 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 rgknox@lbl.gov Date: Mon Jan 13 10:27:30 2025 -0500

clean up of tree_lai changes

commit 8b1952747e91b7683613d2454eaaaedcef3c8d11 Merge: 342703ef 1689466c Author: Ryan Knox rgknox@lbl.gov Date: Sun Jan 12 22:07:39 2025 -0500

Merge branch 'main' into lai_saturation_bugfix

commit 342703efb1cbd2d80749d8a9b000874905a9378c Author: Ryan Knox rgknox@lbl.gov Date: Sun Jan 12 21:55:29 2025 -0500

forcing tree_lai and tree_sai to be used together

commit ac5bf3864ac8234a7a840b0fc2f436ae9564a329 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Fri Jan 10 17:08:20 2025 -0800

add api37 parameter file and xml patch file

commit 33dcdf69450abda3e0b619f02dba82dd0e5f8ff7 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com Date: Fri Jan 10 11:25:33 2025 -0800

Update biogeochem/EDLoggingMortalityMod.F90

Minor typo fix

commit 70c21a3e0fdbc8774f6f782992f41df37ce25805 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Fri Jan 10 10:22:28 2025 -0800

fix update frequency setting for FATES_NPP_LU

commit 424be2014fdaa4368cd0d64ba424f12c6f05fc27 Author: Adrianna Foster afoster@ucar.edu Date: Fri Jan 10 11:03:16 2025 -0700

update

commit 86ed336c80a2d72cefe0bdaa6b3ba0469e7435b7 Author: Adrianna Foster afoster@ucar.edu Date: Fri Jan 10 09:53:03 2025 -0700

testing

commit a66b53c9cf18b06e79d5612e87266853a92c0185 Author: Adrianna Foster afoster@ucar.edu Date: Fri Jan 10 09:52:34 2025 -0700

update

commit b07e3e7764dc9c44fcd064df307a63a975327c30 Merge: 05f87944 bdbe4438 Author: adrifoster adrifost@ucar.edu Date: Fri Jan 10 09:09:59 2025 -0700

merge in changes

commit 05f87944f29b93d185a786d593d5562879c2ccbd Author: adrifoster adrifost@ucar.edu Date: Fri Jan 10 09:09:24 2025 -0700

add unit tests

commit bdbe4438c1bcc805ac3a04dd3a59a9ff6ff62122 Author: Adrianna Foster afoster@ucar.edu Date: Fri Jan 10 09:08:44 2025 -0700

testing

commit 1f51ce7270ad6f7b778f9732da0944dbb492a247 Merge: 0be5cd13 1689466c Author: Ryan Knox rgknox@lbl.gov Date: Thu Jan 9 11:45:30 2025 -0500

merge resolution between nocomp index and firemodel updates

commit d6b41091b4753380a5567863f39559e1a873f88b Author: Adrianna Foster afoster@ucar.edu Date: Wed Jan 8 13:56:08 2025 -0700

add some tests

commit 0be5cd133070d78d8dee7918ef89c5632d6a6117 Author: Ryan Knox rgknox@lbl.gov Date: Wed Jan 8 11:00:49 2025 -0700

more tweaking and cleaning of patch numbering

commit c08819fd3e9931eb7fba62d32409173a76c5c00a Author: adrifoster adrifost@ucar.edu Date: Wed Jan 8 09:49:09 2025 -0700

update names

commit 38531828c6ca496c911fa61ba5c0f318d8161929 Author: adrifoster adrifost@ucar.edu Date: Wed Jan 8 09:24:51 2025 -0700

put back tree lai

commit e9aa8479c19664f36ee2bb7cee34a53361e878fb Author: adrifoster adrifost@ucar.edu Date: Wed Jan 8 09:24:06 2025 -0700

put back tree lai

commit 623ce63fb0ed372690116cbd28c99faef82f7fca Merge: 7613837a 1689466c Author: adrifoster adrifost@ucar.edu Date: Tue Jan 7 19:39:12 2025 -0700

merge in main

commit 7613837ad073dd7fda02a8c4db221506055694b3 Author: adrifoster adrifost@ucar.edu Date: Tue Jan 7 19:28:14 2025 -0700

update tests

commit 81e2f7898f6123700174949848914c576e109d0c Author: adrifoster adrifost@ucar.edu Date: Tue Jan 7 19:26:28 2025 -0700

new insert and sort methods

commit e4a163d72f3f21b14bd969d0e462480182470d43 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Tue Jan 7 15:05:01 2025 -0700

add more patch types

commit 017e5d53934ef656e0b015929a52182fd5ba9669 Author: adrifoster adrifost@ucar.edu Date: Tue Jan 7 15:03:53 2025 -0700

add more patch types

commit 3f4c8ac8f243ae21c40227f7ac00d92a82dbb079 Author: adrifoster adrifost@ucar.edu Date: Tue Jan 7 14:19:21 2025 -0700

update testing

commit ef8db940d4bcb3e2a6904b78317a5d06693ae393 Author: adrifoster adrifost@ucar.edu Date: Tue Jan 7 09:29:04 2025 -0700

add timing and random modules

commit cd6931f25e988515dd729430021af9607228aade Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Mon Jan 6 11:59:21 2025 -0700

fix bad merge deconflict and remove old secondary history variable

commit 96aeedb42016cb9ff8f36471577aed7f1f66bb43 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Mon Jan 6 11:57:47 2025 -0700

fix npp by age calculation

commit 72bf14ea3e8d76b5b2b63ef96932377736e5bdbb Author: adrifoster adrifost@ucar.edu Date: Mon Jan 6 08:58:12 2025 -0700

update tests

commit 73838b3b0251d1c0890795dd5d383ed8c2a740e4 Merge: 6f4f3f6f 1689466c Author: Gregory Lemieux glemieux@users.noreply.github.com 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 7565064+glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Fri Jan 3 13:22:33 2025 -0700

add cohort and patch tests

commit d50c906559947a70cb91048f0d48b2551bd368f4 Merge: 5c6fb7ae 56ecefdb Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Thu Jan 2 15:35:28 2025 -0700

fixing inits

commit 5c6fb7aede1eb478ad02579e5cafe45458fe1787 Merge: 91e4b213 48e9fa47 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Mon Dec 30 15:05:36 2024 -0700

add cohort test

commit b0a316cd5a638b8f20a15d6d62e0245f72e932a2 Author: adrifoster adrifost@ucar.edu Date: Mon Dec 30 13:55:56 2024 -0700

add cohort factory

commit 50ea2d3193a786a0f2a8784e4b489236a3d7d50d Author: Ryan Knox rgknox@lbl.gov Date: Mon Dec 30 13:55:31 2024 -0700

cleaned out unnecessary patch order checks

commit 56ecefdbde152852a5ad892b71976d310da2c863 Author: adrifoster adrifost@ucar.edu Date: Mon Dec 30 12:01:07 2024 -0700

remove greater than one check

commit 86f8551ec47d33183186e0dc6ac278e463b5d6af Author: adrifoster adrifost@ucar.edu Date: Mon Dec 30 11:59:11 2024 -0700

add factory

commit 6b4c08f3dd07fa8156c654c83baadd1f2eb8ebbe Author: Ryan Knox rgknox@lbl.gov Date: Mon Dec 30 11:49:28 2024 -0700

migrating method of getting patch numbers to be more uniform

commit 7ed9209734bd4fad7a80434ab11b302c7dcf4d97 Author: Ryan Knox rgknox@lbl.gov Date: Sun Dec 29 10🔞32 2024 -0700

bug fixes

commit 599619012345d84af91cfe16eec247b4c513f938 Author: Ryan Knox rgknox@lbl.gov Date: Wed Dec 18 11:17:23 2024 -0700

Fixed null pointer

commit 36a86e66c90324a2d3f195ce715d56ded02ce452 Author: Ryan Knox rgknox@lbl.gov Date: Wed Dec 18 10:28:55 2024 -0700

Update vegetation temperature weighting convention during chill day calculation

commit 4d31bda3caf0a2c330a6c1b5ec0f7500115171fc Author: Ryan Knox rgknox@lbl.gov 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 rgknox@lbl.gov 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 rgknox@lbl.gov Date: Thu Dec 26 13🔞45 2024 -0500

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

Indexing fix in multiple python scripts

commit efb14ac72b7f66e34330fa064a3d42a86443b7e5 Author: Ryan Knox rgknox@lbl.gov Date: Wed Dec 18 11:17:23 2024 -0700

Fixed null pointer

commit 3fbe03b0bccd8bda9df74d9058e237bb81c013c3 Author: Ryan Knox rgknox@lbl.gov Date: Wed Dec 18 10:28:55 2024 -0700

Update vegetation temperature weighting convention during chill day calculation

commit 6a44ef4c27e1060a14d302338240c3bde4ae75c2 Author: Marcos Longo mdplongo@gmail.com Date: Tue Dec 17 13:59:45 2024 -0300

Removing print statement added for debugging.

commit fe1d2e82444da5948123c033779c1da4e56d836f Author: adrifoster adrifost@ucar.edu Date: Mon Dec 16 15:42:56 2024 -0700

pylint

commit da4ed44a85849bcc3ce54627763dbc1799593b8a Author: adrifoster adrifost@ucar.edu Date: Mon Dec 16 15:39:10 2024 -0700

requested changes

commit b1ea3a3f88ee63d477295e8f3b7e5f94c2d2fca2 Author: adrifoster adrifost@ucar.edu Date: Mon Dec 16 15:15:27 2024 -0700

lai test

commit f11b673837aecdec614f7a1a38c55666cda25d16 Author: Adrianna Foster afoster@ucar.edu Date: Mon Dec 16 14:54:38 2024 -0700

remove zero of frac_burnt in split_patch

commit 2b01354acc6be381684d89f42af7720857d54dc6 Merge: 789ecab4 48e9fa47 Author: adrifoster adrifost@ucar.edu Date: Thu Dec 12 16:07:01 2024 -0700

Merge branch 'cmake_bug_fix' into lai_test

commit 48e9fa477ea66d76602ea0e7c723a365134605d5 Author: adrifoster adrifost@ucar.edu Date: Thu Dec 12 16:04:05 2024 -0700

fix

commit 789ecab4c7d84d5fe4942145877c5517b18f16ef Author: adrifoster adrifost@ucar.edu Date: Thu Dec 12 15:07:17 2024 -0700

initial test

commit ef51623f14f9baff293c99e61311ffc2028ce573 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 14:56:26 2024 -0800

move seed regen model switch from EDParamsMod to FatesInterfaceTypesMod

commit c8e0d2bc442b98eb0b551317e3858e3fd1b101fd Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 14:36:48 2024 -0800

move radiation model switch from EDParamsMod to FatesInterfaceTypesMod

commit 1056092410409aa094857e7436edf467ee0215a1 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 14:10:51 2024 -0800

move carbon starvation mortality switch from EDParamsMod to FatesInterfaceTypesMod

commit e6db48f9876522beabad05da5f70e1e489d98c00 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 14:03:18 2024 -0800

move leaf maintenance respiration switch from EDParamsMod to FatesInterfaceTypesMod

commit e63b20d7e968f1b295e709a0ac12d9d48e391a8a Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 13:36:58 2024 -0800

move stomatal model switch from EDParamsMod to FatesInterfaceTypesMod

commit 377b155e8f8611f23c7dfbe3267159bd176e58d6 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 12:27:31 2024 -0800

move stomatal assimiliation switch from EDParamsMod to FatesInterfaceTypesMod

commit 5a6e475740988827e73acccfcf7d4bf6e7a0e6cf Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 12:10:53 2024 -0800

move photosythentic tempsens model switch from EDParamsMod to FatesInterfaceTypesMod

commit 4c565cc1ceba6b1a9d26372d22de8cddd7800689 Author: Adrianna Foster afoster@ucar.edu Date: Wed Dec 11 13:52:40 2024 -0700

suggested changes

commit 2a49f4cb0821fa306dae7bbd1f11be906b4a9680 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Dec 11 11:50:52 2024 -0800

move hydro solver switch from EDParamsMod to FatesInterfaceTypesMod

commit e8ae7468ff323118fcda4807d509fb4009af1e73 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Dec 10 17:06:17 2024 -0800

move daylength factor switch from EDParams to FatesInterfaceMod

commit 8e919983bdc807700374d497d44f6afdef6aec6a Author: Adrianna Foster afoster@ucar.edu Date: Wed Dec 11 11:54:25 2024 -0700

zero frac_burnt at top of fire mod

commit f5119a37e88edea4b33d1a1c2257e13bc1f81cb4 Author: Adrianna Foster afoster@ucar.edu Date: Wed Dec 11 10:02:56 2024 -0700

fix typo

commit e04e140cc4527fb8e60cc34558f05c728dbd2339 Author: Adrianna Foster afoster@ucar.edu Date: Wed Dec 11 09:57:40 2024 -0700

add idisttype

commit 79fb219b1f0882d098aeff5e6364398fcdcc6ef6 Author: Adrianna Foster afoster@ucar.edu Date: Wed Dec 11 09:30:12 2024 -0700

initial fix

commit 723c6d8031eb32ce7380a3636109486d8f5fd3e1 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Dec 10 16:49:12 2024 -0800

remove parameter file switches that are moving to HLM namelist

commit e7a7c54492897ecd519fd16eb29c035c65d2e5c3 Author: adrifoster adrifost@ucar.edu Date: Mon Dec 9 15:24:22 2024 -0700

update test

commit 296e1d6a45f05a800073d376286d0537d2290e96 Merge: 02ee145d 77e89489 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Fri Dec 6 14:43:45 2024 -0700

remove blank line

commit a2ce597e7826d32e9d9e64ba8ace9252fcbb1e87 Author: adrifoster adrifost@ucar.edu Date: Fri Dec 6 14:42:26 2024 -0700

add tests

commit 0aef731e31e7d82393d6ca6cc3175859efb5adb1 Author: adrifoster adrifost@ucar.edu Date: Fri Dec 6 13:10:01 2024 -0700

test for propagating flux

commit c2f6a999c9a1bd56f5792391d8fcdcdc2a613a68 Merge: 31a4bb64 a1c587d3 Author: adrifoster adrifost@ucar.edu 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 adrifost@ucar.edu Date: Fri Dec 6 11:25:37 2024 -0700

add ros tests

commit a1c587d3bc64df236db5a733d57f0121bde90d5c Author: Adrianna Foster afoster@ucar.edu Date: Fri Dec 6 11:16:03 2024 -0700

Update FatesHistoryInterfaceMod.F90

commit 211dedae8c66aec70b2d1e17c2e273a6059575ee Merge: acde77c0 02ee145d Author: Adrianna Foster afoster@ucar.edu Date: Fri Dec 6 11:06:33 2024 -0700

Merge branch 'main' into fire_refactor_ros

commit acde77c0504ddda06115ad8149a57b447191d4a6 Author: Adrianna Foster afoster@ucar.edu Date: Fri Dec 6 09:42:20 2024 -0700

fix bugs

commit 426899be6b5409211411eaa6bd3a414868663d2d Author: Adrianna Foster afoster@ucar.edu Date: Fri Dec 6 09:32:07 2024 -0700

full refactor of ros

commit d5c1ac9c5b53b341c947075b232aded043e88e7d Merge: bc037997 8fb9f1fc Author: Adrianna Foster afoster@ucar.edu Date: Fri Dec 6 09:19:56 2024 -0700

merge in changes

commit bc0379972b51dd0e67a18f59c3edda306a6f0cf2 Author: Adrianna Foster afoster@ucar.edu Date: Fri Dec 6 09:19:00 2024 -0700

add ros

commit 8fb9f1fcea7d152feed1983eb4db287ed4076754 Merge: 4b5a6707 51a6a37a Author: adrifoster adrifost@ucar.edu 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 adrifost@ucar.edu Date: Thu Dec 5 11:03:56 2024 -0700

updates

commit 51a6a37a1df69f696cc43e1eb7d2648ca2e00cd7 Author: Adrianna Foster afoster@ucar.edu Date: Thu Dec 5 10:11:07 2024 -0700

bug fix

commit 599cc11df1968473aaf20f1ffc86f673a659209e Merge: ac035e01 8bca0fb1 Author: Adrianna Foster afoster@ucar.edu 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 afoster@ucar.edu Date: Tue Dec 3 13:32:37 2024 -0700

Merge branch 'main' into fire_refactor_ros

commit 77e894898e17395033d43ae0911a4bbc455eb9fb Merge: 914393a4 02ee145d Author: Gregory Lemieux glemieux@users.noreply.github.com 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 7565064+glemieux@users.noreply.github.com 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 92333861+sshu88@users.noreply.github.com Date: Mon Dec 2 13:49:17 2024 -0800

Update FatesConstantsMod.F90

Define named constants for "harvest_tag"

commit 0eb912c11c467b63b9cce294521f36e6da47b0c2 Author: Shijie Shu 92333861+sshu88@users.noreply.github.com 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 7565064+glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Mon Dec 2 12:16:03 2024 -0700

create temp variable

commit 8bca0fb17b8b389cbf1cdd41a9d0a759a779d482 Author: adrifoster adrifost@ucar.edu Date: Mon Dec 2 12:09:52 2024 -0700

updates

commit ab2d78189c0792f15d6e98fd576b624bf487b996 Author: [Jennifer Kowalczyk] <[jenniferkowalczyk@lbl.gov]> Date: Mon Nov 25 11:34:22 2024 -0800

add calculation of sapflow_si

commit ddcbf3e49721efc82755e154999db0be0d38b2a8 Author: [Jennifer Kowalczyk] <[jenniferkowalczyk@lbl.gov]> Date: Fri Nov 22 09:50:56 2024 -0800

bug fix

commit 9f70f21f15c659ab510be02fa51a5bce6a80ac1e Author: [Jennifer Kowalczyk] <[jenniferkowalczyk@lbl.gov]> Date: Fri Nov 22 09:14:32 2024 -0800

add sapwood area by scpf to history

commit df6c5e7c9c6ecf1a998c199a72e031175ae856ac Author: Shijie Shu 92333861+sshu88@users.noreply.github.com 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 jessiefneedham@gmail.com Date: Wed Nov 20 09:44:31 2024 -0800

reverse logic for if statement

commit e7b332f8f97cfd48e38bef0f512a5997831398d9 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Wed Nov 20 09:39:17 2024 -0800

fix if then typo around Kb_sing

commit c07ef109fdd344cef02760a4e4c1031a9dcae6d3 Author: jessica needham jessiefneedham@gmail.com 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 rgknox@lbl.gov 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 7565064+glemieux@users.noreply.github.com 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 mdplongo@gmail.com 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 mdplongo@gmail.com Date: Mon Nov 18 10:09:46 2024 -0800

Fix typo in my last update

commit f36f34a550242b8dc7c6b5c8aec7910aa0757fdf Author: Marcos Longo mdplongo@gmail.com 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 mdplongo@gmail.com Date: Mon Nov 18 10:02:52 2024 -0800

Replacing datatype with typecode in ncvarsort.py

commit 612d4e010edb270895518885bb2e81a1d284f855 Author: Marcos Longo mdplongo@gmail.com 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 mdplongo@gmail.com 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 mdplongo@gmail.com 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 mdplongo@gmail.com 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 mdplongo@gmail.com 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 mdplongo@gmail.com 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 mdplongo@gmail.com Date: Mon Nov 18 09🔞02 2024 -0800

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

commit 291096a6b7960e6e122c4a142e48a37a305d3027 Author: Marcos Longo mdplongo@gmail.com 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 adrifost@ucar.edu Date: Thu Nov 14 18:14:37 2024 -0700

minor updates

commit 205fc9892ccfaa55eab3b7e7c1ae9f17c94c22c2 Author: adrifoster adrifost@ucar.edu Date: Thu Nov 14 16:03:02 2024 -0700

initial cleanup

commit de5f266a54df9a0464608f709486cda96f7526db Merge: e3e7d2cd 9d28eb6c Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Wed Nov 13 15:33:11 2024 -0800

formatting space alignment

commit 2202c461b5fb6fa1aa9398a5b19624771a3169f9 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Wed Nov 13 15:30:18 2024 -0800

update subroutine case to PascalCase

commit e3e7d2cd86a66f8ca0e8f6dc4a823246a2bdb95b Merge: 1be39629 bdb253fd Author: Adrianna Foster afoster@ucar.edu 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 glemieux@users.noreply.github.com Date: Tue Nov 12 16:30:56 2024 -0800

remove the need for a check variable

commit 4b6fd9b7ff5826b630a179d48e8e74ba9b9d7a3d Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Nov 12 16:26:05 2024 -0800

refactor singularity check loop

commit bdb253fd9262cbb721a3f2ef033e16d73c2cd77e Author: Adrianna Foster afoster@ucar.edu Date: Tue Nov 12 10:58:38 2024 -0700

fix capitalization

commit 128e0a92566888f1edb0d35a50f42f6bdf33decd Author: Adrianna Foster afoster@ucar.edu Date: Tue Nov 12 09:40:34 2024 -0700

fix class vs. type

commit fb6ab8c2f744fdebe42e5ab2881c0c34333180b7 Merge: 00d02de3 d422c126 Author: Adrianna Foster afoster@ucar.edu 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 rgknox@lbl.gov 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 afoster@ucar.edu Date: Mon Nov 4 10:07:27 2024 -0700

Merge branch 'main' into fire_refactor_fuel

commit 52842b37843522995796fa7a1144e31ee2054130 Author: Adrianna Foster afoster@ucar.edu Date: Mon Nov 4 10:06:17 2024 -0700

fix variable names

commit 1be3962933351b94fef134d607ac7d821d884f96 Merge: 468ebcaf f208cb87 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com Date: Fri Nov 1 15🔞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 ckoven@users.noreply.github.com 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 samrabin@ucar.edu Date: Fri Nov 1 12:21:17 2024 -0600

Undo an indentation change.

commit f19848b02d55a82a1a32cfb2af06c6a57d6338ab Author: Sam Rabin samrabin@ucar.edu Date: Fri Nov 1 12:17:46 2024 -0600

Simplify "prevent conversion of bare ground land" logic.

commit 52462b5b4c7aab61ddef6bd6675e5161a28dba44 Author: Sam Rabin samrabin@ucar.edu Date: Fri Nov 1 12:15:39 2024 -0600

Fix typo in comment.

commit 9d28eb6c2a770fa8feac4c08adb973c2d6a9ad92 Merge: 9080ba37 50bf6b93 Author: Charlie Koven ckoven@users.noreply.github.com Date: Thu Oct 31 13:05:59 2024 -0700

Merge pull request #24 from rgknox/growth_respiration

Growth respiration

commit cd33abc9676b5178d5839eddbd347285f3a89abb Author: Ryan Knox rgknox@lbl.gov Date: Thu Oct 31 15:32:17 2024 -0400

Added recursive checks for singularity in two-stream

commit de6102884790bb60681b11d20151fb462c1a70b5 Merge: e0c70580 468ebcaf Author: adrifoster adrifost@ucar.edu Date: Thu Oct 31 10:15:22 2024 -0600

Merge branch 'main' into fire_refactor_fuel

commit e0c705804511eb9945517c93333e5f8a5b8a7794 Author: adrifoster adrifost@ucar.edu Date: Thu Oct 31 10:14:49 2024 -0600

fix comment

commit 50bf6b93050fe3675f253418afdd6d275d5457b3 Author: Ryan Knox rgknox@lbl.gov Date: Wed Oct 30 23:15:04 2024 -0400

syntax updates and minor bug fix for respiration update

commit e7b236b8412f46332fb76ebf1d63551ad887b9a2 Author: Charles D Koven cdkoven@lbl.gov Date: Wed Oct 30 19:39:29 2024 -0700

added grazing carbon flux history variable

commit a9758b3f4aa92d76e0ed983ea3d923b83dc344a3 Author: Ryan Knox rgknox@lbl.gov 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 rgknox@lbl.gov Date: Wed Oct 30 22:32:43 2024 -0400

various bug fixes for growth respiration update

commit ee9e919c9bead499d6f688175d902f21d814ff5a Author: Charlie Koven ckoven@users.noreply.github.com Date: Wed Oct 30 14:05:58 2024 -0700

fix typo in modify_fates_paramfile.py

commit 366b73a24b9de701abde7e1a5cdc1b23e29cfcfb Merge: 1d520346 f5bd6250 Author: Ryan Knox rgknox@lbl.gov Date: Wed Oct 30 15:17:51 2024 -0400

merge resolution between growth_respiration and main

commit 1d520346dfda16a5a9ef61391829935f6c12cc73 Author: Ryan Knox rgknox@lbl.gov Date: Wed Oct 30 15:02:42 2024 -0400

removing resp_g_acc, it is unnecessary

commit f5a7caad435700def48cf5ff8ac7ba3853e9d8be Author: Ryan Knox rgknox@lbl.gov Date: Wed Oct 30 14:04:24 2024 -0400

removing resp_g_acc

commit a0dea3b51a2370ba13ce811d6c90b662f3c06833 Author: Ryan Knox rgknox@lbl.gov 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 adrifost@ucar.edu Date: Wed Oct 30 10:42:20 2024 -0600

more updates

commit 920c549ba2f67ffe2f26c38de6ffa44b52b1fb07 Author: adrifoster adrifost@ucar.edu Date: Wed Oct 30 10:14:37 2024 -0600

big fixes

commit 0831336228bd243c25ed9c16cf94c6962ff1c87e Merge: b4367834 230fd170 Author: adrifoster adrifost@ucar.edu Date: Wed Oct 30 09:46:07 2024 -0600

updates to testing

commit 56882373d160aa8ea085b0a743793ea015349974 Author: Charles D Koven cdkoven@lbl.gov 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 cdkoven@lbl.gov 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 cdkoven@lbl.gov 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 cdkoven@lbl.gov Date: Fri Oct 25 08:16:34 2024 -0700

removing logic that prevents harvest at too-small rates

commit 59be47049fae2d2c138b9b5be0cfea7d8db3f64c Author: Charles D Koven cdkoven@lbl.gov Date: Fri Oct 25 08:14:26 2024 -0700

handling open canopy initial landuse harvest conversion case

commit 1895896ea6810755b82ad4a082615b99540e498c Author: Charles D Koven cdkoven@lbl.gov Date: Fri Oct 25 08:13:06 2024 -0700

adding variable names from luh2 harvest drivers

commit dacea7ccc6d9e6fcb0b5f855227c0b628d1e378b Author: Charles D Koven cdkoven@lbl.gov 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 cdkoven@lbl.gov Date: Tue Oct 22 15:55:16 2024 -0700

fixed harvest rates when bare ground >0

commit 468ebcafab8f4e45ac61f2ceae54101f0d6d922c Merge: 230fd170 464a7ec3 Author: Gregory Lemieux 7565064+glemieux@users.noreply.github.com 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 adrifost@ucar.edu Date: Tue Oct 29 15:17:43 2024 -0600

updating variable names

commit 6f6ac0b4d7f7ee040e389431468408514adf2de4 Author: adrifoster adrifost@ucar.edu Date: Tue Oct 29 15:01:26 2024 -0600

other updates

commit 195dce4336af0dc38fadee26f0ec8c5135ded387 Author: adrifoster adrifost@ucar.edu Date: Tue Oct 29 14:56:45 2024 -0600

change total_loading to non_trunk_loading

commit b5f39560228a8de2caf203b7098c0a271c729b9c Author: adrifoster adrifost@ucar.edu Date: Tue Oct 29 14:52:37 2024 -0600

update nfsc variable name

commit 464a7ec3da81e164fa4159d9288f9ac37bf471fb Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Oct 29 13:40:23 2024 -0700

add truncated version of suggested header comments to .gitmodules

commit 710ae0d3411819eeef94111c94b681cd846f084b Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Oct 29 13:36:56 2024 -0700

minor format update

commit 58b9e81a369d4eb75b7e077580644ad23e72a6d1 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Oct 29 13:31:19 2024 -0700

update landuse tool version

commit e65a3a9b48dffb7930b916515dc0d4ce49bd12f6 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Tue Oct 29 13:23:07 2024 -0700

add tag

commit 9080ba37506445d2bdaa11d68e0b43316cfbc75b Author: Charlie Koven ckoven@users.noreply.github.com Date: Tue Oct 29 11:34:17 2024 -0700

Apply suggestions from code review

Co-authored-by: Jessica Needham <10586303+JessicaNeedham@users.noreply.github.com>

commit 9cdc98a1b504bda1ae46fedd68f607cc48bd18c1 Merge: 588a9805 078b99d6 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com 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 7565064+glemieux@users.noreply.github.com 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 7565064+glemieux@users.noreply.github.com 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 glemieux@users.noreply.github.com Date: Sun Oct 27 23:13:16 2024 -0600

correct hlm swich check in history interface

commit 756434035f397e45b93eb49fb488e2834831983a Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Fri Oct 25 11:00:47 2024 -0700

correct pseudo age calculation statement

commit 69592f2db229d8aa83f0ff68381a299c6f7f9300 Author: Gregory Lemieux glemieux@users.noreply.github.com Date: Thu Oct 24 15:38:47 2024 -0700

convert new function name to PascalCase

commit ea2224983e410cf2c2a85aa3cc9b60a68e3fda43 Author: Gregory Lemieux glemieux@users.noreply.github.com 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 cdkoven@lbl.gov 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 xiulin.gao.edu@gmail.com Date: Wed Oct 23 15:58:08 2024 -0700

update in-code documentation

commit 862706823d734664c30f4dfc7287931f62906bbb Author: Xiulin Gao xiulin.gao.edu@gmail.com Date: Wed Oct 23 15:54:55 2024 -0700

correct area calculation

commit 67459866e922528d7c18e5bc2d110316f4777b76 Merge: 454b189d 147d411e Author: Charlie Koven ckoven@users.noreply.github.com 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 rgknox@lbl.gov Date: Wed Oct 23 12🔞32 2024 -0600

Fixed restart issues for sp and allvars with integrated flux

commit a001c7150ed7536af8eee2c6c4120c2cb9e9fc30 Author: Xiulin Gao xiulin.gao.edu@gmail.com 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 rgknox@lbl.gov Date: Fri Oct 18 10:58:36 2024 -0600

Merge branch 'main' into new_patch_insertion

commit 454b189d830c08cc3b3d006a989f4fcb7c8fa450 Author: Ryan Knox <rgknox@lbl…