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remove damage and parameter changes, merge in main #1

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Merged
merged 209 commits into from
Aug 14, 2024
Merged

remove damage and parameter changes, merge in main #1

merged 209 commits into from
Aug 14, 2024

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@rgknox
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@rgknox rgknox commented Aug 14, 2024

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ckoven and others added 30 commits July 14, 2023 13:37
@ckoven
first attempt to reconcile patch initialization logic with land-use +…
0c35e38 
… nocomp
@ckoven
starting to put in logic to handle nocomp PFT transitions during LU c…
2d9dd68 
…hange
@ckoven
fixing some bugs I see while reading through code
9a08430
@ckoven
added new generalized split_patch function
a93efe4
@ckoven
refactored and reused logic to put new patches into linked list
255e709
@ckoven
some compile-time bugfixes
b4159dc
@ckoven
more compile-time bugfixes
148eaf4
@ckoven
adding logic to clean up temporary patches
c594f80
@ckoven
adding logic to handle crop PFTs on crop land use types
e842bdd
@ckoven
adding logic for crops at recruitmetn step
74fefd3
@ckoven
pasted code from grazing branch for adding land use dimension to para…
66a5b2d 
…mter file
@ckoven
passing crop landuse/PFT info through parameter interface
6c43b61
@ckoven
merged main and resolved conflicts
5380c7f
@ckoven
merged luh2 and resolved conflicts (both had new patch insertion subr…
3e9925a 
…outine)
@ckoven
added logic to handle transitioning from a restart with no-land-use t…
6b462cc 
…o land-use
@ckoven
merged luh2 and resolved conflicts
b56044b
@ckoven
added edparamsmod changed to merge
a441e93
@ckoven
fixed merged conflict
b94fefa
@ckoven
Merge branch 'luh1' into luh2_nocomp_merge
7d05c7a
@ckoven
merged luh2 and resolved conflicts
50494e7
@ckoven
added logic to handle case where nocomp and land use are on but not e…
71deea8 
…nough patches for a given land use type to acomodate all PFTs prescribed
@ckoven
error/edge-case handling for if the LU x PFT area dataset has NaNs
01212d1
@ckoven
startign to add logic to handle PFT_level harvest parameters for both…
110ef78 
… logging and land use change
@ckoven
adding parameter values and passing to land use change and logging su…
94ed776 
…broutines
@ckoven
do nocomp PFT shuffle for newly secondary lands as well in case prima…
c823fb6 
…ry and secondary PFT maps differ
@ckoven
Merge branch 'luh2' into luh2_nocomp_merge
4985e94
@ckoven
various compile-time bugfixes
75df884
@ckoven
more compile-time bugfixes
b2e427d
@ckoven
various runtime-failure fixes and attempted fixes
a967b7f
@ckoven
more runtime bugfixes
e1813e8
glemieux and others added 29 commits June 4, 2024 11:12
@glemieux
change nocomp_pft_area_vector check to first diff then sum for better…
9c2444f 
… precision
@glemieux
change check for buffer split to use fraction to keep
737e81d
@glemieux
add check to avoid bareground patches
4b018ea 
This avoids an out-of-bounds indexing error when in landuse mode
@rgknox
Updated some text
e407b81
@rgknox
removed redundant zero flush in history
8d028eb
@glemieux
Merge pull request NGEET#1208 from rgknox/history-zerofixes
b8e4eee 
Updates and fixes to history zeroing and flushing
Merge tag 'sci.1.76.4_api.35.1.0' into luh2_nocomp_merge
3c05ecf 
Updates and fixes to history zeroing and flushing

Includes fixes to how some multi-dimensional history variables are
initialized.  This also introduces a new flush all history subroutine,
to be implimented as an API call in later HLM pull requests.
@glemieux
update split_patches to take optional area input
b43cb3a
@glemieux
fix split patch optional argument name error
29621bc
@glemieux
correct bad merge
9b724ea
@glemieux
refactor checks to determine what is sent to buffer patch
3c02ded
@glemieux
make sure to skip the buffer patch split loop if the buffer patch is …
7add4a1 
…already in the linked list
@glemieux
refactor newp_area calculation to avoid potential precision error
fe795df
@glemieux
move the fraction to keep calculation earlier
28511d1
@glemieux
check absolute value of buffer area to keep
e823830
@glemieux
remove this check as we are now checking the new and remaining areas …
2ec67f9 
…are non-negative
@glemieux
correct whitespace
69e8f6a
@glemieux
Add logic to check for cases in which buffer should be inserted strai…
88ce982 
…ght into the list

This handles cases in which only one pft needs to receive patch area from the buffer,
but due to precision errors, following the splitting routine would result in a very
small patch, technically above the reasonable math precision limit, being held
in the buffer
@glemieux
add sp mode check to litter initialization for bareground patches
c9e7271
@glemieux
initialize current tag for event code logging
bb3d58e
@glemieux
Revert "initialize current tag for event code logging"
4ae398b 
This reverts commit bb3d58e.
@glemieux
Merge pull request NGEET#1116 from ckoven/luh2_nocomp_merge
fd7f343 
V2 Land Use Change
@glemieux
make sure to define state_vector if not in land use mode
a2b71d0
@glemieux
Merge pull request NGEET#1223 from glemieux/landuse-v2-nanfix
1982b00 
Make sure to define `state_vector` if not in land use mode
@glemieux
initialize the transitions matrix to zero
dfe771c
@glemieux
Merge pull request NGEET#1231 from glemieux/init-trans_matrix
e372f0b 
initialize the transitions matrix to zero
@rgknox
Merge branch 'main' into xlg-grass-allometry-rgk
639b3c2
@rgknox
Added parameter checking for sapwood allometry 2 and woody pft, remov…
953eb7c 
…ed crown damage code from grass sapwood allometry
@rgknox
Reverting changes to the parameter file. Those changes will be added …
f73999b 
…to a later PR
@XiulinGao XiulinGao merged commit 8fe0407 into XiulinGao:xlg-grass-allometry Aug 14, 2024
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7 participants

@rgknox @XiulinGao @ckoven @glemieux @mpaiao @adrifoster @samsrabin