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Add snow-vegetation interactions, NGEE Arctic IM3 #6607

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Add snow-vegetation interactions, NGEE Arctic IM3 #6607

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2faa927
Added downscaling code for coupler bypass
thorntonpe Jul 12, 2024
4188433
Bug fixes for coupler bypass downscaling
thorntonpe Jul 12, 2024
db23793
initial commit of adding shrub bending parameter
rfiorella Mar 6, 2024
f084482
Update snow burial of vegetation parameterization
rfiorella Mar 31, 2024
f9799c6
Update ci-compile-test.yml
rfiorella Mar 29, 2024
7a2dd9c
hard-code pft numbers in pftvarcon for default taper values
rfiorella Apr 2, 2024
702f73c
add bounds checking on bendresist and vegshape parameters
rfiorella Jun 14, 2024
20bb484
Rearrange taper assignment in pftvarcon
rfiorella Aug 22, 2024
e979a2c
Add IM3 ERS developer test to e3sm_land_developer
rfiorella Aug 23, 2024
f0c93cf
Fix new IM3 paramter values in pftvarcon
rfiorella Aug 23, 2024
0f02df7
remove local ci test
rfiorella Aug 28, 2024
01ac9bd
Update comment to correctly reflect references in VegStructUpdateMod
rfiorella Sep 3, 2024
3734c0f
use woody instead of hardcoding to pft number
rfiorella Sep 6, 2024
18fa418
update woody comment description to reflect IM4 changes
rfiorella Sep 6, 2024
f5ee59a
Fix syntax error, missing comment marker
thorntonpe Sep 11, 2024
3cb0e38
Moved tests to e3sm_land_exeshare test suite
peterdschwartz Sep 16, 2024
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5 changes: 3 additions & 2 deletions cime_config/tests.py
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Expand Up @@ -49,6 +49,9 @@
"ERS.f19_g16.I20TRGSWCNPECACNTBC.elm-eca_f19_g16_I20TRGSWCNPECACNTBC",
"ERS.f19_g16.I20TRGSWCNPRDCTCBC.elm-ctc_f19_g16_I20TRGSWCNPRDCTCBC",
"ERS.r05_r05.ICNPRDCTCBC.elm-cbudget",
"ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-snowveg_arctic",
"ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_default_I1850CNPRDCTCBC",
"ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_codetest_I1850CNPRDCTCBC",
)
},

Expand Down Expand Up @@ -94,8 +97,6 @@
"SMS.r05_r05.IELM.elm-topounit",
"ERS.ELM_USRDAT.I1850ELM.elm-usrdat",
"ERS.r05_r05.IELM.elm-lnd_rof_2way",
"ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_default_I1850CNPRDCTCBC",
"ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_codetest_I1850CNPRDCTCBC",
"ERS.r05_r05.IELM.elm-V2_ELM_MOSART_features",
"ERS.ELM_USRDAT.IELM.elm-surface_water_dynamics"
)
Expand Down
10 changes: 10 additions & 0 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/snowveg_arctic/shell_commands
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@@ -0,0 +1,10 @@
./xmlchange LND_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
./xmlchange ATM_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
./xmlchange LND_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
./xmlchange ATM_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
./xmlchange DATM_MODE=CLM1PT
./xmlchange DATM_CLMNCEP_YR_START=2000
./xmlchange DATM_CLMNCEP_YR_END=2000
./xmlchange ELM_USRDAT_NAME=42_FLUXNETSITES
./xmlchange NTASKS=1
./xmlchange NTHRDS=1
8 changes: 8 additions & 0 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/snowveg_arctic/user_nl_elm
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@@ -0,0 +1,8 @@
fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_42_FLUXNETSITES_simyr1850_c170912.nc'
! this test has a parameter file with four new parameters defined for NGEE Arctic IM3
! meant to improve snow-vegetation interactions.
! bendresist -> varies between 0 and 1, represents how much vegetation bends under snow loading
! vegshape -> suggested value 1 (parabolic), but 2 also used previously (Liston and Heimstra, 2011)
! taper -> deadstem height/radius ratio, moved from hardcoded in VegStructUpdateMod to pftvarcon
! stocking -> individual density on landscape (plants/m2), moved from hardcoded in VegStructUpdateMod to pftvarcon
paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_ngeea-im3_c240822.nc'
276 changes: 138 additions & 138 deletions components/elm/src/biogeochem/AllocationMod.F90
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12 changes: 6 additions & 6 deletions components/elm/src/biogeochem/CNAllocationBetrMod.F90
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Expand Up @@ -26,13 +26,13 @@ module CNAllocationBeTRMod
use PhotosynthesisType , only : photosyns_type
use CropType , only : crop_type
use VegetationPropertiesType, only : veg_vp
use LandunitType , only : lun_pp
use LandunitType , only : lun_pp
use ColumnType , only : col_pp
use ColumnDataType , only : col_cf, col_ns, col_nf, col_ps, col_pf
use ColumnDataType , only : col_cf, col_ns, col_nf, col_ps, col_pf
use VegetationType , only : veg_pp
use VegetationDataType , only : veg_cs, veg_ns, veg_nf, veg_ps, veg_pf
use VegetationDataType , only : veg_cf, c13_veg_cf, c14_veg_cf
use VegetationDataType , only : veg_cf, c13_veg_cf, c14_veg_cf

! bgc interface & pflotran module switches
use elm_varctl , only : nu_com
use SoilStatetype , only : soilstate_type
Expand Down Expand Up @@ -359,7 +359,7 @@ subroutine Allocation1_PlantNPDemand (bounds, num_soilc, filter_soilc, num_soilp
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type

woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
froot_leaf => veg_vp%froot_leaf , & ! Input: [real(r8) (:) ] allocation parameter: new fine root C per new leaf C (gC/gC)
croot_stem => veg_vp%croot_stem , & ! Input: [real(r8) (:) ] allocation parameter: new coarse root C per new stem C (gC/gC)
stem_leaf => veg_vp%stem_leaf , & ! Input: [real(r8) (:) ] allocation parameter: new stem c per new leaf C (gC/gC)
Expand Down Expand Up @@ -1167,7 +1167,7 @@ subroutine Allocation3_PlantCNPAlloc (bounds , &
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type
!
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
froot_leaf => veg_vp%froot_leaf , & ! Input: [real(r8) (:) ] allocation parameter: new fine root C per new leaf C (gC/gC)
croot_stem => veg_vp%croot_stem , & ! Input: [real(r8) (:) ] allocation parameter: new coarse root C per new stem C (gC/gC)
stem_leaf => veg_vp%stem_leaf , & ! Input: [real(r8) (:) ] allocation parameter: new stem c per new leaf C (gC/gC)
Expand Down
8 changes: 4 additions & 4 deletions components/elm/src/biogeochem/CNGapMortalityBeTRMod.F90
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Expand Up @@ -18,9 +18,9 @@ module CNGapMortalityBeTRMod
use ColumnType , only : col_pp
use ColumnDataType , only : col_cf, col_nf, col_pf
use VegetationPropertiesType , only : veg_vp
use VegetationType , only : veg_pp
use VegetationDataType , only : veg_cs, veg_cf, veg_ns, veg_nf
use VegetationDataType , only : veg_ps, veg_pf
use VegetationType , only : veg_pp
use VegetationDataType , only : veg_cs, veg_cf, veg_ns, veg_nf
use VegetationDataType , only : veg_ps, veg_pf

use PhosphorusFluxType , only : phosphorusflux_type
use PhosphorusStateType , only : phosphorusstate_type
Expand Down Expand Up @@ -121,7 +121,7 @@ subroutine CNGapMortality (&
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type

woody => veg_vp%woody & ! Input: [real(r8) (:) ] binary flag for woody lifeform
woody => veg_vp%woody & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
)

! set the mortality rate based on annual rate
Expand Down
2 changes: 1 addition & 1 deletion components/elm/src/biogeochem/CNNStateUpdate1BeTRMod.F90
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Expand Up @@ -59,7 +59,7 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type

woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)

cascade_donor_pool => decomp_cascade_con%cascade_donor_pool , & ! Input: [integer (:) ] which pool is C taken from for a given decomposition step
cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input: [integer (:) ] which pool is C added to for a given decomposition step
Expand Down
8 changes: 4 additions & 4 deletions components/elm/src/biogeochem/CNPhenologyBeTRMod.F90
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Expand Up @@ -525,7 +525,7 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp , &
prev_dayl => grc_pp%prev_dayl , & ! Input: [real(r8) (:) ] daylength from previous time step (s)

season_decid => veg_vp%season_decid , & ! Input: [real(r8) (:) ] binary flag for seasonal-deciduous leaf habit (0 or 1)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)

t_soisno => col_es%t_soisno , & ! Input: [real(r8) (:,:) ] soil temperature (Kelvin) (-nlevsno+1:nlevgrnd)

Expand Down Expand Up @@ -875,7 +875,7 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
dayl => grc_pp%dayl , & ! Input: [real(r8) (:) ] daylength (s)

leaf_long => veg_vp%leaf_long , & ! Input: [real(r8) (:) ] leaf longevity (yrs)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
stress_decid => veg_vp%stress_decid , & ! Input: [real(r8) (:) ] binary flag for stress-deciduous leaf habit (0 or 1)

soilpsi => soilstate_vars%soilpsi_col , & ! Input: [real(r8) (:,:) ] soil water potential in each soil layer (MPa)
Expand Down Expand Up @@ -2295,7 +2295,7 @@ subroutine CNOnsetGrowth (num_soilp, filter_soilp, &
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type

woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)

onset_flag => cnstate_vars%onset_flag_patch , & ! Input: [real(r8) (:) ] onset flag
onset_counter => cnstate_vars%onset_counter_patch , & ! Input: [real(r8) (:) ] onset days counter
Expand Down Expand Up @@ -2880,7 +2880,7 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type

woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
livewdcn => veg_vp%livewdcn , & ! Input: [real(r8) (:) ] live wood (phloem and ray parenchyma) C:N (gC/gN)
deadwdcn => veg_vp%deadwdcn , & ! Input: [real(r8) (:) ] dead wood (xylem and heartwood) C:N (gC/gN)

Expand Down
2 changes: 1 addition & 1 deletion components/elm/src/biogeochem/CarbonStateUpdate1Mod.F90
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Expand Up @@ -200,7 +200,7 @@ subroutine CarbonStateUpdate1(bounds, &

associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
cascade_donor_pool => decomp_cascade_con%cascade_donor_pool , & ! Input: [integer (:) ] which pool is C taken from for a given decomposition step
cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input: [integer (:) ] which pool is C added to for a given decomposition step
harvdate => crop_vars%harvdate_patch & ! Input: [integer (:) ] harvest date
Expand Down
4 changes: 2 additions & 2 deletions components/elm/src/biogeochem/GrowthRespMod.F90
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Expand Up @@ -51,7 +51,7 @@ subroutine GrowthResp(num_soilp, filter_soilp)
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:)] pft vegetation type

woody => veg_vp%woody , & ! Input: [real(r8) (:)] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:)] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)

cpool_to_leafc => veg_cf%cpool_to_leafc , & ! Input: [real(r8) (:)]
cpool_to_leafc_storage => veg_cf%cpool_to_leafc_storage , & ! Input: [real(r8) (:)]
Expand Down Expand Up @@ -98,7 +98,7 @@ subroutine GrowthResp(num_soilp, filter_soilp)
)

! Loop through patches
! start pft loop
! start pft loop
do fp = 1,num_soilp

p = filter_soilp(fp)
Expand Down
6 changes: 3 additions & 3 deletions components/elm/src/biogeochem/MaintenanceRespMod.F90
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Expand Up @@ -70,7 +70,7 @@ subroutine readMaintenanceRespParams ( ncid )
call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(__FILE__, __LINE__))
br_mr_Inst = tempr

end subroutine readMaintenanceRespParams

!-----------------------------------------------------------------------
Expand Down Expand Up @@ -107,7 +107,7 @@ subroutine MaintenanceResp(bounds, &

associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] patch vegetation type
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)
br_xr => veg_vp%br_xr , & ! Input: [real(r8) (:) ] base rate for excess respiration
frac_veg_nosno => canopystate_vars%frac_veg_nosno_patch , & ! Input: [integer (:) ] fraction of vegetation not covered by snow (0 OR 1) [-]
laisun => canopystate_vars%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index
Expand Down Expand Up @@ -160,7 +160,7 @@ subroutine MaintenanceResp(bounds, &
! calculate temperature corrections for each soil layer, for use in
! estimating fine root maintenance respiration with depth
tcsoi(c,j) = Q10**((t_soisno(c,j)-SHR_CONST_TKFRZ - 20.0_r8)/10.0_r8)

end do
end do

Expand Down
10 changes: 5 additions & 5 deletions components/elm/src/biogeochem/NitrogenStateUpdate1Mod.F90
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Expand Up @@ -130,7 +130,7 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp
associate( &
ivt => veg_pp%itype , & ! Input: [integer (:) ] pft vegetation type

woody => veg_vp%woody , & ! Input: [real(r8) (:) ] binary flag for woody lifeform (1=woody, 0=not woody)
woody => veg_vp%woody , & ! Input: [real(r8) (:) ] woody lifeform flag (0 = non-woody, 1 = tree, 2 = shrub)

cascade_donor_pool => decomp_cascade_con%cascade_donor_pool , & ! Input: [integer (:) ] which pool is C taken from for a given decomposition step
cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input: [integer (:) ] which pool is C added to for a given decomposition step
Expand All @@ -147,7 +147,7 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp
do j = 1, nlevdecomp
do fc = 1,num_soilc
c = filter_soilc(fc)

! N deposition and fixation (put all into NH4 pool)
col_ns%smin_nh4_vr(c,j) = col_ns%smin_nh4_vr(c,j) + col_nf%ndep_to_sminn(c)*dt * ndep_prof(c,j)
col_ns%smin_nh4_vr(c,j) = col_ns%smin_nh4_vr(c,j) + col_nf%nfix_to_sminn(c)*dt * nfixation_prof(c,j)
Expand Down Expand Up @@ -219,7 +219,7 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp
end do
end if
end do

do j = 1, nlevdecomp
! column loop
do fc = 1,num_soilc
Expand Down Expand Up @@ -254,8 +254,8 @@ subroutine NitrogenStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp

end do ! end of column loop
end do
endif !end if is_active_betr_bgc

endif !end if is_active_betr_bgc

! forest fertilization
call get_curr_date(kyr, kmo, kda, mcsec)
Expand Down
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