Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

merge in cstarvation params and main, update xml patch file #9

Merged
Merged
Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
345 commits
Select commit Hold shift + click to select a range
562ed50
Merge tag 'sci.1.65.7_api.25.4.0' into luh2-refactor_merge
glemieux Aug 9, 2023
a3cc2d4
Merge tag 'sci.1.66.0_api.25.5.0' into luh2-refactor_merge
glemieux Aug 9, 2023
4c59f81
Merge tag 'sci.1.67.0_api.25.5.0' into luh2-refactor_merge
glemieux Aug 9, 2023
672bae3
updating parameter file and archives
glemieux Aug 10, 2023
68c7fc6
Merge tag 'sci.1.67.1_api.26.0.0' into luh2-refactor_merge
glemieux Aug 10, 2023
7ba2e79
correct refactor merge issues
glemieux Aug 10, 2023
1502710
correcting additonal bad refactor merge
glemieux Aug 11, 2023
698b91c
Add landuse to initialization procedures
glemieux Aug 15, 2023
0b5d890
Merge branch 'luh2' into luh2-insert_patch
glemieux Aug 15, 2023
c55d7ae
convert insert patch else if to case select
glemieux Aug 15, 2023
33754e1
Merge branch 'luh2' into luh2-fuse-youngest
glemieux Aug 17, 2023
ae880a8
update case names for InsertPatch and clarify comments
glemieux Aug 17, 2023
b640df0
Update the terminate patch process for fusion of different landuse la…
glemieux Aug 18, 2023
de2f8a5
Merge branch 'luh2-fuse-youngest' into luh2-insert-fuse
glemieux Aug 18, 2023
0da2f92
correct case statements and variable name mismatch
glemieux Aug 18, 2023
a9ad185
Merge branch 'luh2-insert_patch' into luh2-insert-fuse
glemieux Aug 18, 2023
cc967cf
fix single line if statements
glemieux Aug 18, 2023
ee47d14
Merge branch 'luh2-fuse-youngest' into luh2-insert-fuse
glemieux Aug 18, 2023
f6687de
adjust patch termination comments
glemieux Aug 18, 2023
0dce77f
correct logic for checking youngest landuse type patch
glemieux Aug 19, 2023
f0e8aa1
add debug check to write statements in fusion
glemieux Aug 21, 2023
ae56d63
Merge up two-stream part 1
rgknox Aug 24, 2023
3e959a8
merge resolution between two-stream and patch/cohort refactor
rgknox Aug 24, 2023
6782b4a
removing layer height profile, for now
rgknox Aug 24, 2023
b1f36bc
add landuse x pft dimension
glemieux Sep 5, 2023
fe3c57f
Merge branch 'main' into two-stream-clean-api26-v2
rgknox Sep 11, 2023
7dc7c47
conflict resolutions for two-stream
rgknox Sep 12, 2023
800136d
pasted code from grazing branch for adding land use dimension to para…
ckoven Aug 10, 2023
e2378fb
changing parameter read infrastructure for maxpatches by landuse cons…
ckoven Sep 12, 2023
4392c39
more changes for maxpatches by landuse consolidation
ckoven Sep 12, 2023
62a6553
fixed/updated clearing matrix logic
ckoven Sep 12, 2023
93fd29d
merged main and resolved conflicts
ckoven Sep 12, 2023
ffdbb86
update patch xml with combined maxpatch variable
glemieux Sep 13, 2023
beeb0fa
align maxpatches by landuse variable names
glemieux Sep 13, 2023
059a03e
fix total area variable name
glemieux Sep 15, 2023
df91bb2
fixed dimension order
ckoven Sep 19, 2023
6d59ea5
add readme to init bld directory
rgknox Sep 19, 2023
3a6b2dc
Updates to two-stream functional unit tests
rgknox Sep 19, 2023
fd0d926
Connected the radiation model switch in the parameter file to the in-…
rgknox Sep 20, 2023
e2aac37
Merge branch 'two-stream-clean-api26-v2' into two-stream-clean-api26
rgknox Sep 20, 2023
d7396b1
Updated radiation model checks to allow for norman and two-stream. Up…
rgknox Sep 21, 2023
bc03f65
Started a new radiation unit test that is used to target specific can…
rgknox Sep 27, 2023
174f292
Updates to two-stream error reporting, checking the linear solution, …
rgknox Sep 29, 2023
b282476
Merge branch 'two-stream-clean' of github.com:rgknox/fates into two-s…
rgknox Oct 4, 2023
e10595c
Applied higher threshold to two-stream closure check, added forced cl…
rgknox Oct 4, 2023
5217289
Set albedo correction to true in fates two-stream
rgknox Oct 4, 2023
f44848b
Merge branch 'two-stream-clean-albedo' into two-stream-clean
rgknox Oct 4, 2023
dd58c11
adding some more comments to spawn_patches
ckoven Oct 5, 2023
853efcf
added restart capability for site-level disturbance rate diagnostic
ckoven Oct 5, 2023
26d6a9f
reset n_dist_types back to 4
ckoven Oct 5, 2023
12132bd
various fixes per review comments
ckoven Oct 5, 2023
3fc589e
minor build fix
glemieux Oct 6, 2023
2ae2f91
manually revert back to previous terminate patches subroutine method
glemieux Oct 6, 2023
bc8fddd
minor comment alignments and fixing bad copies
glemieux Oct 6, 2023
713bbad
small updates to two-stream unit tests
rgknox Oct 6, 2023
40d74ad
remove largestpatch missed in manual reversion
glemieux Oct 6, 2023
f47f009
update last ditch fusion to have donor give reciever the same age_since
glemieux Oct 6, 2023
3c6dee2
Added error tracking in two-stream
rgknox Oct 9, 2023
fbde7c0
Define new fates_param_reader_type type for abstracting param I/O, an…
johnpaulalex Oct 11, 2023
af6a271
Removed canopy_structure() from the restart sequence, it shouldn't be…
rgknox Oct 13, 2023
3d5e878
update diagnostics
glemieux Oct 13, 2023
8cf5d47
remove diagnostic statments
glemieux Oct 16, 2023
438a1e5
Changed ncl_p restart variable to integer, since... its and integer
rgknox Oct 16, 2023
3966cc8
Updates to error tracking of two-stream
rgknox Oct 16, 2023
1f6eb83
Update biogeochem/FatesAllometryMod.F90
rgknox Oct 17, 2023
25923bc
Update radiation/TwoStreamMLPEMod.F90
rgknox Oct 17, 2023
169a8bd
Updates to functional unit test code
rgknox Oct 17, 2023
b74b021
Merge branch 'two-stream-clean-errcheck' into two-stream-clean
rgknox Oct 17, 2023
5d0dddc
adding C-starvation termination mortality to carbon starvation diagno…
ckoven Oct 17, 2023
4d8bebc
Updates to the history file for twostream
rgknox Oct 18, 2023
b3370b9
Cleaning two-stream and radiation drivers to get correct history diag…
rgknox Oct 18, 2023
460645d
more cleaning of radiation history
rgknox Oct 18, 2023
bd33520
updates to the radiation history diagnostics
rgknox Oct 18, 2023
1a3ae69
Changed the avmu radiation parameter to a constant remembered in the …
rgknox Oct 18, 2023
b3eb3f1
remove unnecessary columns from inventory init
JessicaNeedham Oct 18, 2023
10a724c
remove cohort index from inventory init files
JessicaNeedham Oct 19, 2023
97707c0
add script to convert ed to fates inventory init files
JessicaNeedham Oct 19, 2023
156a17a
Added isnan() functions instead of comparing to self
rgknox Oct 19, 2023
c541a74
clean up python script -make simpler
JessicaNeedham Oct 19, 2023
1108024
add height back in
JessicaNeedham Oct 23, 2023
a26146d
Removed old optional two-stream derivations and now using only B1 and…
rgknox Oct 24, 2023
a9260d0
Added checks on scattering coefficient
rgknox Oct 25, 2023
772d57e
Merge branch 'two-stream-clean' into two-stream-clean-v3solution
rgknox Oct 25, 2023
3d0e54d
Remove is_host_file from new fates_param_reader_type API. (because in…
johnpaulalex Oct 25, 2023
df2dee1
fixed typo
rgknox Oct 25, 2023
8ff6444
Merge branch 'two-stream-clean-v3solution' into two-stream-clean
rgknox Oct 25, 2023
391a4f6
merge resolution and reverting of inventory init to not dump output
rgknox Oct 25, 2023
c3da9e6
Updated messaging on the param check failure if the fates_rad_model i…
rgknox Oct 26, 2023
789c36a
Updated fail message on rad parameter bounds
rgknox Oct 26, 2023
7f14138
Addressing reviewer comments
rgknox Oct 26, 2023
1aa2ead
removed unused alias in fateshistoryinterface
rgknox Oct 26, 2023
dbb2cfe
fixes to lingering merge conflict resolutions
rgknox Oct 26, 2023
078003d
Added yearly net uptake vector to restart, added a filter on trimming…
rgknox Oct 29, 2023
04577e7
Merge branch 'nocomp-fix-tests' of github.com:rgknox/fates into nocom…
rgknox Oct 29, 2023
701a471
Removed some ed syntax conventions, enabled using height in the inven…
rgknox Oct 31, 2023
9c556ff
added check in inventory init to make sure at least on of dbh or heig…
rgknox Oct 31, 2023
e6bf3ad
Merge pull request #3 from rgknox/jfn-clean-inv-int-rgkedits
JessicaNeedham Nov 1, 2023
6dfe90a
add nearzero to inventory initialization mod
JessicaNeedham Nov 1, 2023
3c78377
Remove the old code path altogether; CESM will be updated at the same…
johnpaulalex Nov 1, 2023
f3c9b54
add timesince to correct "YEAR" calculation for landuse data tool
glemieux Nov 1, 2023
e7e9367
fix LL logic to allow case where all patches and cohorts are identical
JessicaNeedham Nov 2, 2023
8e2e9f7
remove sorting of ll after init data read
JessicaNeedham Nov 2, 2023
35a6abd
Clean writing of inventory files.
JessicaNeedham Nov 2, 2023
00c0ab8
remove another cohort name from write css
JessicaNeedham Nov 2, 2023
44f9a4a
remove debugging checks
JessicaNeedham Nov 3, 2023
90f50ba
turn off hmort when soil is frozen
JessicaNeedham Nov 3, 2023
ef1ee87
remove checks
JessicaNeedham Nov 3, 2023
86eaa05
Remove checks - rename soil temp threshold
JessicaNeedham Nov 4, 2023
3cf49ab
Merge branch 'main' into jfn-hmort-test
JessicaNeedham Nov 4, 2023
63c2c47
revert nlevleaf to 30
JessicaNeedham Nov 4, 2023
03aa382
change >= to > to be consistent with btran calculation
JessicaNeedham Nov 5, 2023
6963650
update soil freezing in btran calculation
JessicaNeedham Nov 5, 2023
83f8156
Adding in protections to avoid Kb==a in two-stream
rgknox Nov 6, 2023
904c0e4
Merge branch 'two-stream-clean' of github.com:rgknox/fates into two-s…
rgknox Nov 6, 2023
7112368
clean up comments and old text in two-stream code
rgknox Nov 6, 2023
6ca1ccb
Conflict resolution two-stream and api30
rgknox Nov 7, 2023
3039873
Merge branch 'main' into nocomp-fix-tests
rgknox Nov 7, 2023
261811b
Fixed keyword name to match
rgknox Nov 8, 2023
80c0fa9
making crown area available in the restart, because its needed
rgknox Nov 8, 2023
2e140be
small tweaks to error tracking in fates two-stream
rgknox Nov 8, 2023
58732e5
correct the way YEAR is updated
glemieux Nov 8, 2023
0913be7
start setting up a refactor of the luh2 shell script
glemieux Nov 8, 2023
17ed1b3
fix how luh2 data tool check luh2 file type
glemieux Nov 8, 2023
77899da
adding attribute copy to luh2 data tool to avoid losing unit data dur…
glemieux Nov 9, 2023
9f6f5c2
cleaning up conservation error diagnostics
rgknox Nov 9, 2023
44ba97a
Merge pull request #1098 from rgknox/nocomp-fix-tests
rgknox Nov 10, 2023
3fa96a3
Tweaking the correction to beam optical depth, needs provisions for n…
rgknox Nov 12, 2023
c0d1856
merge in main
Nov 14, 2023
c37d878
fixing indents
Nov 14, 2023
51c0125
Merge branch 'main' into luh2
glemieux Nov 15, 2023
0344660
update diffs
adrifoster Nov 16, 2023
cb6b677
Initializing two-stream error with the ignore flag
rgknox Nov 17, 2023
bbb0b54
Fixed argument type declaration for the number of cwd pools, identifi…
rgknox Nov 17, 2023
0b105be
Merge pull request #1096 from johnpaulalex/newint
glemieux Nov 17, 2023
24760aa
Tweaks to area squeezing in two-stream
rgknox Nov 21, 2023
d35b9b1
bug fix in area squeezing during two-stream
rgknox Nov 21, 2023
0d7b490
Merge two-stream with api31
rgknox Nov 21, 2023
133d57f
Merge pull request #1121 from rgknox/ncwd-ndk-fix
glemieux Nov 21, 2023
30cc0ca
Merge pull request #1112 from glemieux/tools/luh2-yearfix
glemieux Nov 21, 2023
a4c3f34
Merge pull request #1104 from JessicaNeedham/jfn-clean-inv-int
glemieux Nov 22, 2023
5551a70
Merge pull request #1115 from JessicaNeedham/jfn-hmort-test
glemieux Nov 22, 2023
91bf5b4
Merge remote-tracking branch 'ckoven/cstarv_term_reporting' into jkow…
Nov 22, 2023
ad307d2
debug
Nov 22, 2023
019fa58
added comments
Nov 22, 2023
e5f6160
debug
Nov 22, 2023
31ed39b
cleaned up canopy mask logic
rgknox Nov 22, 2023
38c3f1f
Added in code to preserve leaf to cohort scaling in norman mode, will…
rgknox Nov 28, 2023
33c83cb
trivial merge resolution between two-stream and inventory uppdates
rgknox Nov 28, 2023
3c361de
add graceful failure if the HLM state name is not found in the fates …
glemieux Nov 29, 2023
cde7e7d
correct findloc check for landuse state name check
glemieux Nov 29, 2023
ef1c454
Merge tag 'sci.1.69.0_api.31.0.0' into luh2
glemieux Nov 29, 2023
1cf7bca
fix merge that snuck in old anthro disturbance label
glemieux Nov 30, 2023
ea24aa8
rename the parameter patch file to reflect the actual next tag
glemieux Nov 30, 2023
46ecf39
altnerate reverted form of leaf layer calculation
rgknox Nov 30, 2023
624293b
testing out b4b corrections
rgknox Dec 1, 2023
5f4a8b6
Reverted incorrect nscalar
rgknox Dec 1, 2023
33cb3ae
Merge branch 'two-stream-clean' into two-stream-clean-b4b
rgknox Dec 2, 2023
b88f636
More b4b attempts at two-stream
rgknox Dec 4, 2023
bf99977
Added crown area by size class and PFT to the output.
mpaiao Dec 6, 2023
0ab1f80
Fix units for FATES_CROWNAREA_CANOPY_SZ and FATES_CROWNAREA_USTORY_SZ.
mpaiao Dec 6, 2023
da1b798
Prevent hydraulic failure mortality to occur in deciduous plants when…
mpaiao Dec 6, 2023
8756dc1
Fix typo.
mpaiao Dec 6, 2023
3c0051e
debugging logic ends
rgknox Dec 7, 2023
c71dadb
more b4b attempts at two-stream
rgknox Dec 8, 2023
e0c564f
Merge branch 'two-stream-clean-b4b' into two-stream-clean-b4b2
rgknox Dec 8, 2023
1d64107
making switches in b4b check consistent
rgknox Dec 8, 2023
d4ac49b
reverting history code in two-stream to match main for b4b
rgknox Dec 8, 2023
da54174
attempts to revert history code in 2str to get b4b
rgknox Dec 8, 2023
0683cd1
Added new carbon starvation model.
mpaiao Dec 9, 2023
6849406
Edited carbon starvation mortality so the parameters are a bit more t…
mpaiao Dec 9, 2023
1df494a
small b4b changes to two-stream
rgknox Dec 12, 2023
56aa325
Creating seperate module for norman rad
rgknox Dec 12, 2023
8cc57c9
fixed some typos
rgknox Dec 13, 2023
7abc732
cleaning up photosynthesis code w/two-stream
rgknox Dec 13, 2023
40f1a2a
Merge branch 'two-stream-clean-b4b-hist' into two-stream-clean-b4b2
rgknox Dec 13, 2023
a3754a1
Reverted history code to be as similar to base as possible
rgknox Dec 13, 2023
a972ff3
more two-stream b4b work
rgknox Dec 14, 2023
c34773a
reinstated ed_laisun_z and ed_laisha_z for b4b tests
rgknox Dec 14, 2023
0c1e890
reverting canopy mask for b4b
rgknox Dec 14, 2023
4966a98
refactor to replace findloc intrinsic
glemieux Dec 14, 2023
ece937c
fix array size call
glemieux Dec 15, 2023
89aecd1
reworking towards b4b
rgknox Dec 15, 2023
c6da2fe
b4b stuff
rgknox Dec 15, 2023
56eec56
Reduce the sum of fates_maxpatches_per_landuse to 16 as default
glemieux Dec 15, 2023
7a7a8a3
rename the patch paramfile for api 32
glemieux Dec 15, 2023
f6b879e
b4b stuff for two-stream
rgknox Dec 18, 2023
140e6ff
b4b for two-stream
rgknox Dec 18, 2023
b1a14a7
Edited function storage_fraction_of_target to remove upper threshold.
mpaiao Dec 18, 2023
ae8f117
bug fix
Dec 18, 2023
81be091
Merge pull request #1040 from ckoven/luh2
glemieux Dec 19, 2023
b83584d
Updated parameter file with complete description for stress/drought-d…
mpaiao Dec 19, 2023
36105c3
more b4b stuff
rgknox Dec 19, 2023
312593f
revert history to match main
rgknox Dec 20, 2023
36be028
merge two-stream with lu1
rgknox Dec 20, 2023
62a37f9
removed solver error (redundant with conservation error)
rgknox Dec 20, 2023
85e7c18
corrected comments
Dec 21, 2023
052d52c
fixed error in variable declaration, added c-starve related terminati…
Dec 21, 2023
d9113d1
bug fix
Dec 21, 2023
d9edfc5
bug fix; added error check for termination_type
Dec 21, 2023
f479db4
bug fix
Dec 21, 2023
893d8cf
merge updates on two-stream with luh2, as well as consolidation of ra…
rgknox Dec 21, 2023
b743547
two-stream cleaning up
rgknox Dec 22, 2023
0366819
adding text around preserve_b4b
rgknox Dec 27, 2023
5e4c6df
removed redundant declaration
rgknox Dec 27, 2023
ea34893
Revised quadratic equation solver for handling exceptions.
mpaiao Jan 2, 2024
cf8ca94
Updated reference to numerical recipes in the comment.
mpaiao Jan 2, 2024
0979a67
Added info on section where the solution can be found.
mpaiao Jan 2, 2024
f416029
Updating scipy module importing to work for both new and old conventions
rgknox Jan 3, 2024
9fa0153
added try clause to scipy module loading
rgknox Jan 3, 2024
64eb770
deleted unnecessary comment
rgknox Jan 3, 2024
6935a40
removed unncecessary comment
rgknox Jan 3, 2024
5daf737
set intent in on veg_tempk
rgknox Jan 3, 2024
1642919
removed unused global declarations in history
rgknox Jan 3, 2024
200f024
removing hlm_numSWb use in code, it is redundant
rgknox Jan 3, 2024
f6832c3
two-stream responding to reviewer comments
rgknox Jan 4, 2024
d127f51
resolving more reviewer comments
rgknox Jan 4, 2024
d514afb
Merge tag 'sci.1.70.0_api.32.0.0' into jkowalcz-ckoven-cstarv_term_re…
glemieux Jan 4, 2024
3e4ff34
update FatesPFTIndexSwapper.py to work with landuse
JessicaNeedham Jan 4, 2024
698a8df
Merge pull request #1145 from JessicaNeedham/jfn-fatespftindexswapper…
glemieux Jan 8, 2024
0079a85
Fixing zero protections on two-stream zenith calcualtions
rgknox Jan 10, 2024
9c6f822
Merge branch 'main' into two-stream-clean-b4b-nohist
rgknox Jan 10, 2024
af2c3b9
Fixes to nan checks in fates two-stream
rgknox Jan 12, 2024
7b2cdbe
fixed try statement on module importing in python scipy
rgknox Jan 12, 2024
18f0a64
Updating comments following @JessicaNeedham suggestions.
mpaiao Jan 15, 2024
05d98ad
Edited comments for clarity (thanks for the suggestion, @JessicaNeedham)
mpaiao Jan 16, 2024
7d518ac
Merge pull request #1141 from rgknox/two-stream-clean-b4b-nohist
rgknox Jan 16, 2024
27691d2
Merge tag 'sci.1.71.0_api.33.0.0' into jkowalcz-ckoven-cstarv_term_re…
glemieux Jan 18, 2024
7805da8
Merge pull request #1131 from mpaiao/mpaiao-pr-outcrown
rgknox Jan 19, 2024
d446945
Merge pull request #1138 from mpaiao/mpaiao-pr-ddparam
rgknox Jan 19, 2024
a882f41
resolved strange conflict between quadratic pr and main by reverting …
rgknox Jan 19, 2024
a470a43
shorten history variable name
Jan 19, 2024
4d052e7
clean up loops to avoid duplication
Jan 19, 2024
24d3ea8
Merge pull request #7 from rgknox/mpaiao-pr-quadratic
mpaiao Jan 19, 2024
d3e850e
update long name for termination mortality history variables
Jan 19, 2024
b01c842
update comments
Jan 19, 2024
a9bbfd8
Merge pull request #1144 from mpaiao/mpaiao-pr-quadratic
rgknox Jan 20, 2024
53b88e2
Edited hydraulic failure mortality so deciduousness prevents mortalit…
mpaiao Jan 24, 2024
6120cad
Merge tag 'sci.1.71.2_api.33.0.0' into mpaiao-pr-hfm+phenology
glemieux Jan 29, 2024
bee1769
implement @mpaiao suggested fix for deconflict
glemieux Jan 29, 2024
1777702
remove hmort setting missed in previous deconflict
glemieux Jan 29, 2024
464af4c
Merge pull request #1142 from jennykowalcz/jkowalcz-ckoven-cstarv_ter…
glemieux Jan 30, 2024
0bdb724
Merge pull request #1130 from mpaiao/mpaiao-pr-hfm+phenology
glemieux Jan 30, 2024
94fa571
temporary override of cstarvation mode
rgknox Jan 31, 2024
447d83b
Reverted parameter file temporarily for cstarvation mode
rgknox Jan 31, 2024
50f33e7
merge resolution
rgknox Jan 31, 2024
c51af01
Merge pull request #8 from rgknox/mpaiao-pr-cstarve-hardc
mpaiao Jan 31, 2024
42d804b
Merge pull request #1132 from mpaiao/mpaiao-pr-cstarve
rgknox Jan 31, 2024
8531dda
merge resolution between allometry modes and two-stream
rgknox Feb 5, 2024
118b411
enabling cstarvation mode switch in-code
rgknox Feb 5, 2024
f450fb7
updating parameters for cstarvation and allometry crown depth modes i…
rgknox Feb 5, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Merge tag 'sci.1.67.0_api.25.5.0' into luh2-refactor_merge
This tag adds environmentaly sensitive tree recruitment, work by Adam Hanbury-Brown. These features are not enabled by default, but can be set with the regeneration_model integer switch in the parameter file.
  • Loading branch information
glemieux committed Aug 9, 2023
commit 4c59f81c3332e749e763db71211669ee9cbadb39
14 changes: 14 additions & 0 deletions biogeochem/EDPatchDynamicsMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,8 @@ module EDPatchDynamicsMod
use EDParamsMod, only : maxpatch_primaryland, maxpatch_secondaryland
use EDParamsMod, only : maxpatch_pastureland, maxpatch_rangeland, maxpatch_cropland
use EDParamsMod, only : maxpatch_total
use FatesRunningMeanMod, only : ema_sdlng_mdd
use FatesRunningMeanMod, only : ema_sdlng_emerg_h2o, ema_sdlng_mort_par, ema_sdlng2sap_par
use FatesRunningMeanMod, only : ema_24hr, fixed_24hr, ema_lpa, ema_longterm

! CIME globals
Expand Down Expand Up @@ -679,6 +681,18 @@ subroutine spawn_patches( currentSite, bc_in)
call new_patch%tveg_longterm%CopyFromDonor(currentPatch%tveg_longterm)


if ( regeneration_model == TRS_regeneration ) then
call new_patch%seedling_layer_par24%CopyFromDonor(currentPatch%seedling_layer_par24)
call new_patch%sdlng_mort_par%CopyFromDonor(currentPatch%sdlng_mort_par)
call new_patch%sdlng2sap_par%CopyFromDonor(currentPatch%sdlng2sap_par)
do pft = 1,numpft
call new_patch%sdlng_emerg_smp(pft)%p%CopyFromDonor(currentPatch%sdlng_emerg_smp(pft)%p)
call new_patch%sdlng_mdd(pft)%p%CopyFromDonor(currentPatch%sdlng_mdd(pft)%p)
enddo
end if

call new_patch%tveg_longterm%CopyFromDonor(currentPatch%tveg_longterm)

! --------------------------------------------------------------------------
! The newly formed patch from disturbance (new_patch), has now been given
! some litter from dead plants and pre-existing litter from the donor patches.
Expand Down
19 changes: 13 additions & 6 deletions main/EDInitMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@ module EDInitMod
use FatesConstantsMod , only : primaryland
use FatesConstantsMod , only : nearzero
use FatesConstantsMod , only : n_landuse_cats
use FatesConstantsMod , only : fates_unset_r8
use FatesConstantsMod , only : nearzero
use FatesGlobals , only : endrun => fates_endrun
use EDTypesMod , only : nclmax
use FatesGlobals , only : fates_log
Expand Down Expand Up @@ -709,13 +711,18 @@ subroutine init_patches( nsites, sites, bc_in)
! Initialize the litter pools to zero, these
! pools will be populated by looping over the existing patches
! and transfering in mass
if(hlm_use_sp.eq.itrue)then
litt_init = fates_unset_r8
else
litt_init = 0._r8
end if
do el=1,num_elements
call newp%litter(el)%InitConditions(init_leaf_fines=0._r8, &
init_root_fines=0._r8, &
init_ag_cwd=0._r8, &
init_bg_cwd=0._r8, &
init_seed=0._r8, &
init_seed_germ=0._r8)
call newp%litter(el)%InitConditions(init_leaf_fines=litt_init, &
init_root_fines=litt_init, &
init_ag_cwd=litt_init, &
init_bg_cwd=litt_init, &
init_seed=litt_init, &
init_seed_germ=litt_init)
end do

sitep => sites(s)
Expand Down
22 changes: 12 additions & 10 deletions main/FatesRestartInterfaceMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -10,20 +10,22 @@ module FatesRestartInterfaceMod
use FatesConstantsMod, only : fates_unset_r8, fates_unset_int
use FatesConstantsMod, only : primaryland
use FatesConstantsMod, only : nearzero
use FatesConstantsMod, only : default_regeneration
use FatesConstantsMod, only : TRS_regeneration
use FatesGlobals, only : fates_log
use FatesGlobals, only : endrun => fates_endrun
use FatesIODimensionsMod, only : fates_io_dimension_type
use FatesIOVariableKindMod, only : fates_io_variable_kind_type
use FatesRestartVariableMod, only : fates_restart_variable_type
use FatesInterfaceTypesMod, only : nlevcoage
use FatesInterfaceTypesMod, only : bc_in_type
use FatesInterfaceTypesMod, only : bc_out_type
use FatesInterfaceTypesMod, only : hlm_use_planthydro
use FatesInterfaceTypesMod, only : hlm_parteh_mode
use FatesInterfaceTypesMod, only : hlm_use_sp
use FatesInterfaceTypesMod, only : hlm_use_nocomp, hlm_use_fixed_biogeog
use FatesInterfaceTypesMod, only : fates_maxElementsPerSite
use FatesInterfaceTypesMod, only : hlm_use_tree_damage
use FatesInterfaceTypesMod, only : nlevcoage
use FatesInterfaceTypesMod, only : bc_in_type
use FatesInterfaceTypesMod, only : bc_out_type
use FatesInterfaceTypesMod, only : hlm_use_planthydro
use FatesInterfaceTypesMod, only : hlm_parteh_mode
use FatesInterfaceTypesMod, only : hlm_use_sp
use FatesInterfaceTypesMod, only : hlm_use_nocomp, hlm_use_fixed_biogeog
use FatesInterfaceTypesMod, only : fates_maxElementsPerSite
use FatesInterfaceTypesMod, only : hlm_use_tree_damage
use EDCohortDynamicsMod, only : UpdateCohortBioPhysRates
use FatesHydraulicsMemMod, only : nshell
use FatesHydraulicsMemMod, only : n_hypool_ag
Expand All @@ -37,7 +39,7 @@ module FatesRestartInterfaceMod
use EDCohortDynamicsMod, only : InitPRTObject
use EDCohortDynamicsMod, only : InitPRTBoundaryConditions
use FatesPlantHydraulicsMod, only : InitHydrCohort
use FatesInterfaceTypesMod, only : nlevsclass
use FatesInterfaceTypesMod, only : nlevsclass
use FatesInterfaceTypesMod, only : nlevdamage
use FatesLitterMod, only : litter_type
use FatesLitterMod, only : ncwd
Expand Down
You are viewing a condensed version of this merge commit. You can view the full changes here.