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Drought deciduous phenology updates #958

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Jun 30, 2023
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f9d9220
Changes and updates to drought deciduous phenology to improve process…
mpaiao Dec 1, 2022
046fea5
Merge branch 'main' into mpaiao-drgt-decid
mpaiao Dec 3, 2022
f17e871
Merge branch 'main' into mpaiao-drgt-decid
mpaiao Dec 4, 2022
f785cf0
Fix units for soil matric potential in the output.
mpaiao Dec 6, 2022
8b8b7dc
Minor update to carbon allocation for deciduous PFTs.
mpaiao Dec 6, 2022
1638b65
Bug fixes in the revised carbon allocation.
mpaiao Dec 7, 2022
74a5c61
Drought thresholds are now PFT-specific. Also moved some phenology pa…
mpaiao Dec 21, 2022
b570b36
Bug fix in PRTParamsFATESMod.F90. Missing allocation of phen_moist_th…
mpaiao Dec 21, 2022
95c4a07
Documented and fixed the additional meaning of leaf life span for dro…
mpaiao Mar 6, 2023
010d95a
Multiple updates following PR revision.
mpaiao Apr 4, 2023
b42a6ce
A few bug fixes in the code.
mpaiao Apr 15, 2023
f9af3cc
Merge branch 'main' into mpaiao-pr-drgt-decid
mpaiao Apr 25, 2023
8c76111
Update to the crown damage recovery procedure for drought deciduous. …
mpaiao May 1, 2023
0c2d335
Add parameter patch file
glemieux May 10, 2023
9ec5545
update UpdateParamAPI tool
glemieux May 16, 2023
ea5d83a
update parameter file
glemieux May 16, 2023
21c573b
correct indexing for elongation factor
glemieux May 19, 2023
934ad20
Changed defaults for drought deciduous.
mpaiao May 24, 2023
befe7dd
Adding the fates_rad_model to the parameter file
rgknox Jun 6, 2023
5956465
Merge pull request #2 from rgknox/mpaiao-pr-drgt-decid
mpaiao Jun 6, 2023
afb8194
Added TRS recruitment parameters
rgknox Jun 6, 2023
894206b
Small syntax updates to trs parameter long-names
rgknox Jun 6, 2023
4a14057
Merged in Adam HBs definitions for pft parameters
rgknox Jun 6, 2023
fea2085
Merged in more regeneration parameter definitions and the model switc…
rgknox Jun 6, 2023
fb05618
Merge pull request #3 from rgknox/mpaiao-pr-drgt-decid
mpaiao Jun 6, 2023
074c043
Added AHB parameters to parteh
rgknox Jun 7, 2023
4aae59a
Merge branch 'mpaiao-pr-drgt-decid' of github.com:mpaiao/fates into m…
rgknox Jun 7, 2023
49c30b0
Merge pull request #4 from rgknox/mpaiao-pr-drgt-decid
mpaiao Jun 7, 2023
091627e
Updated memory needed for phenoology restart
rgknox Jun 7, 2023
fad6947
Merge pull request #5 from rgknox/mpaiao-pr-drgt-decid
mpaiao Jun 7, 2023
efde58c
Fix to the restart order issue
rgknox Jun 23, 2023
49f82ab
moved nlevsclass calculation earlier in subroutine
rgknox Jun 23, 2023
180ba13
Moved restart calls for new phen variables to different location
rgknox Jun 26, 2023
fa431f5
removed change of vcmax parameter
rgknox Jun 26, 2023
bd82b5f
updating the default parameter file per fixes in the api update xml t…
rgknox Jun 26, 2023
facbf55
fix to the parameter file
rgknox Jun 27, 2023
0a3c66c
Added future parameters for addressing issue 1014 in an upcoming pull…
mpaiao Jun 27, 2023
6aba10c
Merge resolution
rgknox Jun 27, 2023
59f56ee
reapplied parameter update from xml, something got lost in a merge
rgknox Jun 27, 2023
cbf0d69
add seed dispersal parameters for PR 1005
glemieux Jun 28, 2023
a6008b9
adds two new parameters to address issue 1014
glemieux Jun 28, 2023
e4cf214
provisions for frozen/arid conditions on drought deciduous suction tr…
rgknox Jun 28, 2023
6f44d03
Merge branch 'mpaiao-pr-drgt-decid' of github.com:mpaiao/fates into m…
rgknox Jun 28, 2023
8d2d765
Updating parameter file
rgknox Jun 28, 2023
1864070
simple conflict resolution
rgknox Jun 28, 2023
f87ea87
fixed parameter name
rgknox Jun 28, 2023
5830b35
Update EDPhysiologyMod.F90
mpaiao Jun 28, 2023
a1f3dc5
Merge pull request #6 from rgknox/mpaiao-pr-drgt-decid
mpaiao Jun 28, 2023
6da2d85
correct values assignment error for param patch
glemieux Jun 28, 2023
693061b
Merge branch 'drdt-decid-seed-disp-cp' into mpaiao-pr-drgt-decid
glemieux Jun 28, 2023
516c7e8
fix default param name in file
glemieux Jun 28, 2023
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2 changes: 1 addition & 1 deletion biogeochem/EDCanopyStructureMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -2196,7 +2196,7 @@ subroutine UpdateCohortLAI(currentCohort, canopy_layer_tlai, total_canopy_area)

if (hlm_use_sp .eq. ifalse) then
currentCohort%treesai = tree_sai(currentCohort%pft, currentCohort%dbh, currentCohort%crowndamage, &
currentCohort%canopy_trim, &
currentCohort%canopy_trim, currentCohort%efstem_coh, &
currentCohort%c_area, currentCohort%n, currentCohort%canopy_layer, &
canopy_layer_tlai, currentCohort%treelai , &
currentCohort%vcmax25top,4)
Expand Down
141 changes: 108 additions & 33 deletions biogeochem/EDCohortDynamicsMod.F90

Large diffs are not rendered by default.

8 changes: 7 additions & 1 deletion biogeochem/EDMortalityFunctionsMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,13 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
! Carbon Starvation induced mortality.
if ( cohort_in%dbh > 0._r8 ) then

call bleaf(cohort_in%dbh,cohort_in%pft,cohort_in%crowndamage,cohort_in%canopy_trim,target_leaf_c)
! We compare storage with leaf biomass if plant were fully flushed, otherwise
! mortality would be underestimated for plants that lost all leaves and have no
! storage to flush new ones.
! MLO. Why isn't this comparing with storage allometry (i.e., accounting for
! cushion)?
call bleaf(cohort_in%dbh,cohort_in%pft,cohort_in%crowndamage,cohort_in%canopy_trim, &
1.0_r8, target_leaf_c)
store_c = cohort_in%prt%GetState(store_organ,carbon12_element)

call storage_fraction_of_target(target_leaf_c, store_c, frac)
Expand Down
1,176 changes: 719 additions & 457 deletions biogeochem/EDPhysiologyMod.F90

Large diffs are not rendered by default.

151 changes: 100 additions & 51 deletions biogeochem/FatesAllometryMod.F90

Large diffs are not rendered by default.

6 changes: 3 additions & 3 deletions biogeophys/FatesPlantHydraulicsMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -982,7 +982,7 @@ subroutine UpdatePlantHydrLenVol(ccohort,csite_hydr)
! Lets also avoid super-low targets that have very low trimming functions

call bleaf(ccohort%dbh,ccohort%pft,ccohort%crowndamage, &
max(ccohort%canopy_trim,min_trim),leaf_c_target)
max(ccohort%canopy_trim,min_trim),ccohort%efleaf_coh, leaf_c_target)

if( (ccohort%status_coh == leaves_on) .or. ccohort_hydr%is_newly_recruited ) then
ccohort_hydr%v_ag(1:n_hypool_leaf) = max(leaf_c,min_leaf_frac*leaf_c_target) * &
Expand All @@ -998,7 +998,7 @@ subroutine UpdatePlantHydrLenVol(ccohort,csite_hydr)

! calculate the sapwood cross-sectional area
call bsap_allom(ccohort%dbh,ccohort%pft,ccohort%crowndamage, &
ccohort%canopy_trim,a_sapwood_target,sapw_c_target)
ccohort%canopy_trim, ccohort%efstem_coh, a_sapwood_target,sapw_c_target)

! uncomment this if you want to use
! the actual sapwood, which may be lower than target due to branchfall.
Expand Down Expand Up @@ -2980,7 +2980,7 @@ subroutine UpdatePlantKmax(ccohort_hydr,ccohort,csite_hydr)

! Get the cross-section of the plant's sapwood area [m2]
call bsap_allom(ccohort%dbh,pft,ccohort%crowndamage, &
ccohort%canopy_trim,a_sapwood,c_sap_dummy)
ccohort%canopy_trim, ccohort%efstem_coh, a_sapwood,c_sap_dummy)

! Leaf Maximum Hydraulic Conductance
! The starting hypothesis is that there is no resistance inside the
Expand Down
5 changes: 4 additions & 1 deletion biogeophys/FatesPlantRespPhotosynthMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -413,8 +413,11 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
ft = currentCohort%pft
cl = currentCohort%canopy_layer

! MLO. Assuming target to be related to leaf biomass when leaves are fully
! flushed. But unsure whether this call is correct or not, shouldn't we get
! the target value directly from the bstore_allom?
call bleaf(currentCohort%dbh,currentCohort%pft,&
currentCohort%crowndamage,currentCohort%canopy_trim,store_c_target)
currentCohort%crowndamage,currentCohort%canopy_trim,1.0_r8,store_c_target)
! call bstore_allom(currentCohort%dbh,currentCohort%pft, &
! currentCohort%canopy_trim,store_c_target)

Expand Down
193 changes: 127 additions & 66 deletions main/EDInitMod.F90

Large diffs are not rendered by default.

3 changes: 2 additions & 1 deletion main/EDMainMod.F90
Original file line number Diff line number Diff line change
Expand Up @@ -531,11 +531,12 @@ subroutine ed_integrate_state_variables(currentSite, bc_in, bc_out )

! Conduct Maintenance Turnover (parteh)
if(debug) call currentCohort%prt%CheckMassConservation(ft,3)
if(any(currentSite%dstatus == [phen_dstat_moiston,phen_dstat_timeon])) then
if(any(currentSite%dstatus(ft) == [phen_dstat_moiston,phen_dstat_timeon])) then
is_drought = .false.
else
is_drought = .true.
end if

call PRTMaintTurnover(currentCohort%prt,ft,is_drought)

! -----------------------------------------------------------------------------------
Expand Down
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