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Fatesluc cbasedhrv v2 api25 #2

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merged 2 commits into from
Dec 19, 2022
Merged

Fatesluc cbasedhrv v2 api25 #2

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f165e40
Update interface code to allow FATES API 25
rgknox Dec 12, 2022
60ee280
Update FATES submodule pointer to sci.1.61.0_api.25.0.0
rgknox Dec 12, 2022
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2 changes: 1 addition & 1 deletion components/elm/bld/namelist_files/namelist_defaults.xml
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Expand Up @@ -124,7 +124,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<!-- ================================================================== -->
<!-- FATES default parameter file -->
<!-- ================================================================== -->
<fates_paramfile >lnd/clm2/paramdata/fates_params_12pft_api17.c211116.nc</fates_paramfile>
<fates_paramfile >lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221212.nc</fates_paramfile>

<!-- soil order related parameters (relative to {csmdata}) -->
<fsoilordercon >lnd/clm2/paramdata/CNP_parameters_c131108.nc</fsoilordercon>
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2 changes: 1 addition & 1 deletion components/elm/cime_config/testdefs/testmods_dirs/elm/fates/user_nl_elm
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Expand Up @@ -16,7 +16,7 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_FUEL_AMOUNT', 'FATES_LITTER_IN', 'FATES_LITTER_OUT',
'FATES_SEED_BANK', 'FATES_SEEDS_IN', 'FATES_STOREC', 'FATES_VEGC',
'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
'FATES_CEFFLUX', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
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17 changes: 13 additions & 4 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_eca/user_nl_elm
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Expand Up @@ -18,7 +18,7 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_FUEL_AMOUNT', 'FATES_LITTER_IN', 'FATES_LITTER_OUT',
'FATES_SEED_BANK', 'FATES_SEEDS_IN', 'FATES_STOREC', 'FATES_VEGC',
'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
'FATES_CEFFLUX', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
Expand All @@ -33,7 +33,16 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC','FATES_LITTER_IN_EL','FATES_LITTER_OUT_EL',
'FATES_LEAFN','FATES_LEAFP','FATES_FROOTN','FATES_FROOTP','FATES_NH4UPTAKE',
'FATES_NO3UPTAKE','FATES_NEFFLUX','FATES_PUPTAKE','FATES_PEFFLUX',
'NET_NMIN','NET_PMIN','LITR1P_vr','LITR1C_vr','LITR1N_vr','SOLUTIONP',
'SMIN_NO3','SMIN_NH4','TOTSOMN','TOTSOMP'
'SMIN_NO3','SMIN_NH4','TOTSOMN','TOTSOMP',
'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF',
'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF' ,
'FATES_NDEMAND_SZPF','FATES_NFIX_SYM_SZPF','FATES_NH4UPTAKE','FATES_NO3UPTAKE',
'FATES_NEFFLUX','FATES_NDEMAND','FATES_NFIX_SYM','FATES_STOREN','FATES_STOREN_TF',
'FATES_VEGN','FATES_SAPWOODN','FATES_LEAFN','FATES_FROOTN','FATES_REPRON','FATES_VEGN_SZPF',
'FATES_LEAFN_SZPF','FATES_FROOTN_SZPF','FATES_SAPWOODN_SZPF','FATES_STOREN_SZPF','FATES_STOREN_TF_CANOPY_SZPF',
'FATES_STOREN_TF_USTORY_SZPF','FATES_REPRON_SZPF','FATES_STOREP','FATES_STOREP_TF','FATES_VEGP','FATES_SAPWOODP',
'FATES_LEAFP','FATES_FROOTP','FATES_REPROP','FATES_PUPTAKE','FATES_PEFFLUX','FATES_PDEMAND',
'FATES_VEGP_SZPF','FATES_LEAFP_SZPF','FATES_FROOTP_SZPF','FATES_SAPWOODP_SZPF','FATES_STOREP_SZPF',
'FATES_STOREP_TF_CANOPY_SZPF','FATES_STOREP_TF_USTORY_SZPF','FATES_REPROP_SZPF','FATES_PUPTAKE_SZPF',
'FATES_PEFFLUX_SZPF','FATES_PDEMAND_SZPF'
17 changes: 13 additions & 4 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_rd/user_nl_elm
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_FUEL_AMOUNT', 'FATES_LITTER_IN', 'FATES_LITTER_OUT',
'FATES_SEED_BANK', 'FATES_SEEDS_IN', 'FATES_STOREC', 'FATES_VEGC',
'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
'FATES_CEFFLUX', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
Expand All @@ -33,7 +33,16 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC','FATES_LITTER_IN_EL','FATES_LITTER_OUT_EL',
'FATES_LEAFN','FATES_LEAFP','FATES_FROOTN','FATES_FROOTP','FATES_NH4UPTAKE',
'FATES_NO3UPTAKE','FATES_NEFFLUX','FATES_PUPTAKE','FATES_PEFFLUX',
'NET_NMIN','NET_PMIN','LITR1P_vr','LITR1C_vr','LITR1N_vr','SOLUTIONP',
'SMIN_NO3','SMIN_NH4','TOTSOMN','TOTSOMP'
'SMIN_NO3','SMIN_NH4','TOTSOMN','TOTSOMP',
'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF',
'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF' ,
'FATES_NDEMAND_SZPF','FATES_NFIX_SYM_SZPF','FATES_NH4UPTAKE','FATES_NO3UPTAKE',
'FATES_NEFFLUX','FATES_NDEMAND','FATES_NFIX_SYM','FATES_STOREN','FATES_STOREN_TF',
'FATES_VEGN','FATES_SAPWOODN','FATES_LEAFN','FATES_FROOTN','FATES_REPRON','FATES_VEGN_SZPF',
'FATES_LEAFN_SZPF','FATES_FROOTN_SZPF','FATES_SAPWOODN_SZPF','FATES_STOREN_SZPF','FATES_STOREN_TF_CANOPY_SZPF',
'FATES_STOREN_TF_USTORY_SZPF','FATES_REPRON_SZPF','FATES_STOREP','FATES_STOREP_TF','FATES_VEGP','FATES_SAPWOODP',
'FATES_LEAFP','FATES_FROOTP','FATES_REPROP','FATES_PUPTAKE','FATES_PEFFLUX','FATES_PDEMAND',
'FATES_VEGP_SZPF','FATES_LEAFP_SZPF','FATES_FROOTP_SZPF','FATES_SAPWOODP_SZPF','FATES_STOREP_SZPF',
'FATES_STOREP_TF_CANOPY_SZPF','FATES_STOREP_TF_USTORY_SZPF','FATES_REPROP_SZPF','FATES_PUPTAKE_SZPF',
'FATES_PEFFLUX_SZPF','FATES_PDEMAND_SZPF'
2 changes: 1 addition & 1 deletion components/elm/src/external_models/fates
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Submodule fates updated 64 files
+ − .github/images/logo_fates_large.png
+ − .github/images/logo_fates_medium.png
+ − .github/images/logo_fates_small.png
+23 −0 .github/workflows/add-to-gh_projects.yml
+12 −16 README.md
+229 −0 biogeochem/DamageMainMod.F90
+349 −374 biogeochem/EDCanopyStructureMod.F90
+460 −202 biogeochem/EDCohortDynamicsMod.F90
+45 −341 biogeochem/EDLoggingMortalityMod.F90
+130 −84 biogeochem/EDMortalityFunctionsMod.F90
+773 −828 biogeochem/EDPatchDynamicsMod.F90
+543 −215 biogeochem/EDPhysiologyMod.F90
+161 −90 biogeochem/FatesAllometryMod.F90
+316 −615 biogeochem/FatesSoilBGCFluxMod.F90
+3 −1 biogeophys/EDAccumulateFluxesMod.F90
+9 −1 biogeophys/EDBtranMod.F90
+97 −79 biogeophys/EDSurfaceAlbedoMod.F90
+89 −73 biogeophys/FatesPlantHydraulicsMod.F90
+186 −51 biogeophys/FatesPlantRespPhotosynthMod.F90
+22 −20 fire/SFMainMod.F90
+23 −23 fire/SFParamsMod.F90
+8 −6 functional_unit_testing/parteh/f90src/FatesCohortWrapMod.F90
+0 −11 main/ChecksBalancesMod.F90
+123 −65 main/EDInitMod.F90
+257 −174 main/EDMainMod.F90
+211 −114 main/EDParamsMod.F90
+342 −294 main/EDPftvarcon.F90
+155 −100 main/EDTypesMod.F90
+7 −11 main/FatesConstantsMod.F90
+118 −1 main/FatesGlobals.F90
+1,421 −811 main/FatesHistoryInterfaceMod.F90
+29 −6 main/FatesHistoryVariableType.F90
+2 −2 main/FatesHydraulicsMemMod.F90
+31 −1 main/FatesIODimensionsMod.F90
+12 −2 main/FatesIOVariableKindMod.F90
+332 −309 main/FatesInterfaceMod.F90
+67 −48 main/FatesInterfaceTypesMod.F90
+46 −61 main/FatesInventoryInitMod.F90
+108 −6 main/FatesParameterDerivedMod.F90
+22 −21 main/FatesParametersInterface.F90
+486 −258 main/FatesRestartInterfaceMod.F90
+9 −5 main/FatesRestartVariableType.F90
+21 −7 main/FatesRunningMeanMod.F90
+74 −2 main/FatesSizeAgeTypeIndicesMod.F90
+2 −2 main/FatesSynchronizedParamsMod.F90
+1,538 −0 parameter_files/archive/api24.1.0_101722_fates_params_default.cdl
+51 −0 parameter_files/archive/api24.1.0_101722_patch_params.xml
+1,537 −0 parameter_files/archive/api24.2.0_112822_fates_params_default.cdl
+568 −0 parameter_files/archive/apichange_23to24.xml
+72 −0 parameter_files/archive/apichange_24.2to25.xml
+748 −696 parameter_files/fates_params_default.cdl
+31 −21 parameter_files/patch_default_bciopt224.xml
+2 −2 parameter_files/patch_default_e3smtest.xml
+1,077 −939 parteh/PRTAllometricCNPMod.F90
+595 −551 parteh/PRTAllometricCarbonMod.F90
+131 −160 parteh/PRTGenericMod.F90
+94 −40 parteh/PRTLossFluxesMod.F90
+23 −21 parteh/PRTParametersMod.F90
+222 −258 parteh/PRTParamsFATESMod.F90
+113 −24 tools/BatchPatchParams.py
+10 −6 tools/FatesPFTIndexSwapper.py
+448 −0 tools/UpdateParamAPI.py
+3 −1 tools/modify_fates_paramfile.py
+24 −8 tools/ncvarsort.py
12 changes: 9 additions & 3 deletions components/elm/src/main/elmfates_interfaceMod.F90
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Expand Up @@ -915,6 +915,9 @@ subroutine dynamics_driv(this, bounds_clump, top_as_inst, &
! ---------------------------------------------------------------------------------
call fates_hist%flush_hvars(nc,upfreq_in=1)

! Frequency 5 is routine that processes FATES history
! on the dynamics (daily) step, but before disturbance
call fates_hist%flush_hvars(nc,upfreq_in=5)

! ---------------------------------------------------------------------------------
! Part II: Call the FATES model now that input boundary conditions have been
Expand Down Expand Up @@ -948,7 +951,8 @@ subroutine dynamics_driv(this, bounds_clump, top_as_inst, &
! ---------------------------------------------------------------------------------
call fates_hist%update_history_dyn( nc, &
this%fates(nc)%nsites, &
this%fates(nc)%sites)
this%fates(nc)%sites, &
this%fates(nc)%bc_in)

if (masterproc) then
write(iulog, *) 'FATES dynamics complete'
Expand Down Expand Up @@ -1585,7 +1589,8 @@ subroutine restart( this, bounds_proc, ncid, flag, &
end do
call fates_hist%update_history_dyn( nc, &
this%fates(nc)%nsites, &
this%fates(nc)%sites)
this%fates(nc)%sites, &
this%fates(nc)%bc_in)


end if
Expand Down Expand Up @@ -1742,7 +1747,8 @@ subroutine init_coldstart(this, canopystate_inst, soilstate_inst, frictionvel_in
end do
call fates_hist%update_history_dyn( nc, &
this%fates(nc)%nsites, &
this%fates(nc)%sites)
this%fates(nc)%sites, &
this%fates(nc)%bc_in)



Expand Down