Update to API42 plus fixes for nbp - #43

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mvdebolskiy wants to merge 252 commits into

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mvdebolskiy:tst-mrgnbp

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Commits on Mar 3, 2025

add burn window subroutine
XiulinGao
committed
b5e7aeb
added decision tree to decide which fire happens
XiulinGao
committed
f8685e5
add rxfire burnt area and post-fire mortality
XiulinGao
committed
516e084

Commits on Mar 4, 2025

adding tools-fates-xarray as submodule
glemieux
committed
954d6cd

Commits on Mar 5, 2025

cohort rxfire mortality
XiulinGao
committed
08302ca
patch level dynamic due to rxfire
XiulinGao
committed
fae8b9c
add rxfire relevant variable to cohort
XiulinGao
committed
335874f
add patch level prescribed fire var
XiulinGao
committed
f6f648a
add prescribed fire parameters to SFparams
XiulinGao
committed
35e0c09
add rxfire relevant params in param file
XiulinGao
committed
0ce009f
add prescribed fire mortality and other var for site level tracking
XiulinGao
committed
521b224
add rxfire switch
XiulinGao
committed
9b78204
add relevant var for tracking site dynamics due to rxfire
XiulinGao
committed
eb1b634

Commits on Mar 6, 2025

add prescribed fire relevant history var
XiulinGao
committed
2fc1acd
add prescribed fire relevant to restart hist
XiulinGao
committed
eccc0ed
bug fix
XiulinGao
committed
ddc5bbb
fix typo
XiulinGao
committed
28a1f5a
typo
XiulinGao
committed
de9bff6
add rxfire burnt fraction to patch fusion process
XiulinGao
committed
1c17f3d

Commits on Mar 7, 2025

PR for dynamic L2FR
sharma-bharat
committed
6718800

Commits on Mar 13, 2025

Commits on Mar 14, 2025

update burn window every time
XiulinGao
committed
f1d1d48

Commits on Mar 15, 2025

make min frac burnable to be user parameter
XiulinGao
committed
383c1c1

Commits on Mar 20, 2025

track Rx and Non-Rx fire separately with sum of the two included too
XiulinGao
committed
e100d1e
rename variables for rx and wildfire
XiulinGao
committed
c82e45c
output wildfire and rxfire variables separately with variables for sum of rx and non-rx included
XiulinGao
committed
e16f159
correct prescribed fire typo in param file
XiulinGao
committed
86f17d3
add in-code documentation for explaining how burn window is checked
XiulinGao
committed
d79e39c
fix introduced bug during renaming
XiulinGao
committed
9a87c8b
fix typo
XiulinGao
committed
c8828ac
rename wildfire and rxfire vairables
XiulinGao
committed
dadc679
rename patch level fire occurence and burn frac variables
XiulinGao
committed
157c5f6
correct variable name
XiulinGao
committed
278ea3e
add variables to represent the sum of rx and wildfire
XiulinGao
committed
2ec7a1b

Commits on Mar 24, 2025

update logic to reduce code duplication
glemieux
committed
7ea4ad8
use fates copy of HLM current year for logic check
glemieux
committed
12bbcdd
add flag for carbon only period of ELM AD
glemieux
committed
ff06fd9

Commits on Mar 25, 2025

some suggestions
adrifoster
committed
50c869d

Commits on Mar 26, 2025

Merge pull request #2 from adrifoster/REVIEW_1360
XiulinGao
authored
0ec3152

Commits on Mar 27, 2025

Commits on Mar 31, 2025

update fire mortality var name for wildfire and prescribed fire
XiulinGao
committed
917ff12
cleab up some white space
XiulinGao
committed
96de0b6
merge change
XiulinGao
committed
23b86c0
more white space cleaning
XiulinGao
committed
03bbe72

Commits on Apr 7, 2025

Commits on Apr 10, 2025

Merge branch 'main' into nclmax-3
rgknox
committed
4c75867

Commits on Apr 24, 2025

Commits on May 6, 2025

initializing radiation error diagnostics as ignore instead of zero.
rgknox
committed
4bbe49e

Commits on May 15, 2025

change name of new bc out flux subroutine for more detail
glemieux
committed
3072e4b
add missing use statments for uptake
glemieux
committed
c7cda2e

Commits on May 21, 2025

change crop PFT to back to cool C3 grass (PFT 13 now)
ckoven
committed
2284f9b

Commits on May 24, 2025

remote bc_in argument from FuseCohortHydraulics
glemieux
committed
26e2586
remove bc_in argument from UpdateSizeDepPlanyHydProps
glemieux
committed
93f9c31

Commits on May 27, 2025

remove unused bc_in from canopy_summarization
glemieux
committed
2ee65cd

Commits on May 29, 2025

changed external seed rain to only fall on a given PFT's nocomp patch
ckoven
committed
cd24a49
Revert "remove unused bc_in from canopy_summarization"
glemieux
committed
e43e22f
remove unused bc_in arguments for history procedures
glemieux
committed
deb8994
remove unused bc_in arguments from seed related procedures
glemieux
committed
2546661
remove unused bc_in from recruitwuptake procedure
glemieux
committed
bb3e552
remove unused bc_in from damage and litter flux procedure
glemieux
committed
bd63aa4

Commits on Jun 4, 2025

remove unused bc_out in history sub procedures
glemieux
committed
9c90594

Commits on Jun 5, 2025

Commits on Jun 6, 2025

remove homogenize_seed_pfts option
glemieux
committed
7929e6e
Remove deprecated quadratic smoothing parameters
glemieux
committed
169f08c

Commits on Jun 9, 2025

Commits on Jun 10, 2025

fix to event based logging harvest
JessicaNeedham
committed
39bafa3

Commits on Jun 11, 2025

fix breaking changes
adrifoster
committed
bd2c170
fix issues with cmakelists
adrifoster
committed
1eb49d8
final fixes
adrifoster
committed
5374f39

Commits on Jun 12, 2025

Commits on Jun 13, 2025

fix hlm_regen use
adrifoster
committed
6c6e967
refactor canopy promotion/demotion for simplicity, stability and code reusability.
rgknox
committed
38fefa7
small fixes to canopy structure
rgknox
committed
0e3bdd4
added argument to sorting that turns it into a check instead of an execution
rgknox
committed
527fbee
resolved conflict on nclmax
rgknox
committed
fa8a0c3
Functional test fix: DATM file now found when using -r.
samsrabin
committed
6cc3141
Functional tests now work if called from somewhere other than testing/.
samsrabin
committed
a2c2a2d
Functional tests: Simplify an error.
samsrabin
committed
c0af355
run_functional_tests.py: Add optional --config-file argument.
samsrabin
committed
08c1dbc
Functional tests: Error if Fortran executable fails.
samsrabin
committed
a80dd9e
Functional tests: Fortran now errors instead of just stopping.
samsrabin
committed
d34666c
Functional tests: Download datm_file if needed. KLUDGE!
samsrabin
committed
3b47323

Commits on Jun 14, 2025

minor fixes and corrections to promotion/demotion refactor
rgknox
committed
d70ccca

Commits on Jun 16, 2025

removed termination during promotion/demotion
rgknox
committed
cbca268
Rename is_wild_fire() to fire_has_ignitions_and_intensity().
samsrabin
committed
7dbfcca
fire_has_ignitions_and_intensity(): Remove unused rx/not distinction.
samsrabin
committed
6d23025
fire_has_ignitions_and_intensity(): Compile fix.
samsrabin
committed
e8de4c7
Delete fire_has_ignitions_and_intensity().
samsrabin
committed
8a23189
Merge pull request #4 from samsrabin/rxfire_on_spitfire_refactor-ssr
XiulinGao
authored
e14c0be

Commits on Jun 17, 2025

add ignition check for wildfire occurence
XiulinGao
committed
2e6521f

Commits on Jun 18, 2025

Merge branch 'main' into pr/adrifoster/1423
glemieux
committed
a0b3984
fixing duplicates that came up with main merge
glemieux
committed
ea26256
Merge pull request #1423 from adrifoster/fix_testing
glemieux
authored
5ab1ef1

Commits on Jun 20, 2025

Move functional test plotting functions to new module.
samsrabin
committed
4c334ac

Commits on Jun 21, 2025

Add FunctionalTestWithDrivers to handle fuel test.
samsrabin
committed
c65df33
Move config file check to check_arg_validity().
samsrabin
committed
5e124f4

Commits on Jun 22, 2025

Simplify FunctionalTestWithDrivers.__init__().
samsrabin
committed
7404a9d
FunctionalClass: Revert unused changes.
samsrabin
committed
620abe9

Commits on Jun 23, 2025

Commits on Jun 24, 2025

removed commented fire_closs terms
rgknox
committed
cc8bd8b
Merge pull request #1371 from ckoven/nocomp_seeds
glemieux
authored
b5d17b4

Commits on Jun 25, 2025

Merge pull request #28 from rgknox/nbp_totecosysc
ckoven
authored
63e3358

Commits on Jun 26, 2025

Update PULL_REQUEST_TEMPLATE with sp mode b4b check
glemieux
authored
bfb8534

Commits on Jun 27, 2025

Merge pull request #1430 from NGEET/glemieux-patch-1
glemieux
authored
a461955

Commits on Jun 30, 2025

Commits on Jul 1, 2025

Remove Python download of datm_file.
samsrabin
committed
8caf366
Remove datm_file_url.
samsrabin
committed
e0037fa
removed currentSite%resources_management%trunk_product_site variable and related history var
ckoven
committed
dc466d5

Commits on Jul 2, 2025

hotfix: add missing right paranthesis
glemieux
committed
527f9ad
Merge pull request #1436 from glemieux/hotfix-missing-paran
glemieux
authored
230446e

Commits on Jul 8, 2025

Fixes to vegc canlayer diagnostics
rgknox
committed
768e345

Commits on Jul 14, 2025

Commits on Jul 15, 2025

Commits on Jul 16, 2025

Merge pull request #1438 from rgknox/vegc-canlayer
glemieux
authored
27c11f8

Commits on Jul 17, 2025

Commits on Jul 21, 2025

Merge pull request #1426 from samsrabin/fix_testing_ssr
glemieux
authored
49cd7d0

Commits on Jul 22, 2025

Commits on Jul 24, 2025

various fixes associated with l2fr-cnp
rgknox
committed
c5d9081

Commits on Jul 28, 2025

Merge tag 'sci.1.86.3_api.40.0.0' into parameter-deprecated-quadsmooth
glemieux
committed
232ac3b

Commits on Jul 29, 2025

Commits on Jul 30, 2025

Merge remote-tracking branch 'ckoven/croppft' into api40.1-super-pr
glemieux
committed
6ff9b12

Commits on Jul 31, 2025

Merge tag 'sci.1.86.3_api.40.0.0' into rxfire_on_spitfire_refactor
glemieux
committed
5acefc3

Commits on Aug 1, 2025

correct rxfire module and function definition statements
glemieux
committed
5fa7c33
remove defunct is_wildfire
glemieux
committed
100c4be

Commits on Aug 4, 2025

Commits on Aug 5, 2025

convert parameter file switch to hlm namelist option
glemieux
committed
4637bba
build fixes
glemieux
committed
f10139d
correct minor variable name typo
glemieux
committed
c99b998
correct argument name typo
glemieux
committed
1664bbc

Commits on Aug 7, 2025

Commits on Aug 11, 2025

Merge pull request #14 from glemieux/check-order-optional
rgknox
authored
8073789
wrapped sort checker behind a debug flag
rgknox
committed
5b14b2f
Update biogeochem/EDCanopyStructureMod.F90

rgknox
and
glemieux
authored
1a5304b
fixed error message to report error correctly (bias instead of abs)
rgknox
committed
a37d8e7
Merge branch 'nclmax-3-sortfixes' of github.com:rgknox/fates into nclmax-3-sortfixes
rgknox
committed
d3b3f20
Updated trivial scenarios for prom/dem with probability case
rgknox
committed
ead5055

Commits on Aug 12, 2025

add check to avoid new cohorts during restart
glemieux
committed
21a709f

Commits on Aug 13, 2025

Commits on Aug 21, 2025

merge resolution
rgknox
committed
1670ba6
fixed zstar history
rgknox
committed
ba3fd1d

Commits on Aug 26, 2025

Merge pull request #1424 from rgknox/nclmax-3-sortfixes
glemieux
authored
315e0d6

Commits on Sep 4, 2025

Commits on Sep 5, 2025

Commits on Sep 10, 2025

changing gpp and ar output boundary flux to use the massbalance data already available
rgknox
committed
0d7c607

Commits on Sep 11, 2025

bug fixes for changes to nbp bc_out variables
rgknox
committed
58e0d67
Merge pull request #34 from rgknox/nbp-gpp-restart-fix
glemieux
authored
a3ed667

Commits on Sep 12, 2025

Commits on Sep 14, 2025

Merge branch 'main' into nbp-gpp-restart-fix
rgknox
committed
659b51b
zeroing cmass%gpp for mass checking on restart
rgknox
committed
638ae67
Merge branch 'nbp-gpp-restart-fix' of github.com:rgknox/fates into nbp-gpp-restart-fix
rgknox
committed
f847ef7

Commits on Sep 16, 2025

Commits on Sep 22, 2025

Merge pull request #1448 from glemieux/nbp-gpp-restart-fix
glemieux
authored
f6355b1

Commits on Sep 23, 2025

Commits on Sep 30, 2025

Commits on Oct 10, 2025

Commits on Oct 12, 2025

small fix to ignore val global
rgknox
committed
8fa0c36
small fixes for rad_error and parprofile refactors
rgknox
committed
7ba3727

Commits on Oct 13, 2025

Commits on Oct 14, 2025

Commits on Oct 21, 2025

Merge branch 'main' into cnp-l2fr-conly
rgknox
committed
22a5839

Commits on Oct 27, 2025

update secondary young frac calculation
Jessica Needham
committed
edaf2a4
changed l2fr fusion to only happen during CNP runs (for b4b)
rgknox
committed
8c5a24c

Commits on Oct 29, 2025

Merge pull request #1443 from rgknox/cnp-l2fr-conly
rgknox
authored
5bb36cb

Commits on Oct 30, 2025

Merge pull request #1495 from JessicaNeedham/jfn-ngeet-harvestbugfix
glemieux
authored
75a465c

Commits on Nov 3, 2025

Update main/ChecksBalancesMod.F90
glemieux
authored
283bc8e

Commits on Nov 17, 2025

Merge tag 'sci.1.88.1_api.42.0.0' into Fix-inventory-init-grid-matching
glemieux
committed
5638bd5

Commits on Nov 19, 2025

Commits on Nov 20, 2025

Merge pull request #1476 from XiulinGao/correct-wind-speed-unit
glemieux
authored
56add1b

Commits on Nov 24, 2025

Merge remote-tracking branch 'upstream/main' into update-ctsm-5.3.084
mvdebolskiy
committed
5ac9b1d
update paramfilename
mvdebolskiy
committed
d41f9ec

Commits on Nov 25, 2025

fix compile errors.
mvdebolskiy
committed
24c40f6
Merge remote-tracking branch 'rgknox/nbp-gpp-restart-fix-extended-v2' into tst-mrgnbp
mvdebolskiy
committed
c41ccc0

Commits on Nov 26, 2025

move bc_out gpp and ar calculation earlier in the ed_update_site call
glemieux
committed
95c4bcb
Added is restarting arguments
rgknox
committed
759ed00
Merge remote-tracking branch 'rgknox/nbp-gpp-restart-fix-extended-v2' into tst-mrgnbp
mvdebolskiy
committed
d3cfa86
fix args
mvdebolskiy
committed
2740db2
Revert "fix args"
mvdebolskiy
committed
fc07a7d
fix arg processing
mvdebolskiy
committed
5d3546d

Commits on Dec 3, 2025

Merge branch 'noresm' into tst-mrgnbp
mvdebolskiy
authored
184a676