Merge pull request #2 from glemieux/fates_sp-deconflict-8abef14

Deconflict PR 632 with FATES master (commit 8abef14)
rgknox · May 27, 2020 · 0f2ea16 · 0f2ea16
2 parents 347270b + 0ffab8b
commit 0f2ea16
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diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,9 @@
+{
+    "title": "The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", 
+    "creators": [
+        {
+            "name": "FATES Development Team"
+        }
+    ],
+    "license":"BSD-3-Clause"
+}
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 # FATES
 ------------------------------
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3825473.svg)](https://doi.org/10.5281/zenodo.3825473)
 
 This repository holds the Functionally Assembled Terrestrial Ecosystem Simulator (FATES).  FATES is a numerical terrestrial ecosystem model. Its development and support is primarily supported by the Department of Energy's Office of Science, through the Next Generation Ecosystem Experiment - Tropics ([NGEE-T](https://ngee-tropics.lbl.gov/)) project.
 

diff --git a/biogeochem/EDCanopyStructureMod.F90 b/biogeochem/EDCanopyStructureMod.F90
@@ -24,10 +24,10 @@ module EDCanopyStructureMod
   use EDTypesMod            , only : nlevleaf
   use EDtypesMod            , only : AREA
   use FatesGlobals          , only : endrun => fates_endrun
-  use FatesInterfaceMod     , only : hlm_days_per_year
-  use FatesInterfaceMod     , only : hlm_use_planthydro
-  use FatesInterfaceMod     , only : hlm_use_cohort_age_tracking
-  use FatesInterfaceMod     , only : numpft
+  use FatesInterfaceTypesMod     , only : hlm_days_per_year
+  use FatesInterfaceTypesMod     , only : hlm_use_planthydro
+  use FatesInterfaceTypesMod     , only : hlm_use_cohort_age_tracking
+  use FatesInterfaceTypesMod     , only : numpft
   use FatesPlantHydraulicsMod, only : UpdateH2OVeg,InitHydrCohort, RecruitWaterStorage
   use EDTypesMod            , only : maxCohortsPerPatch
 
@@ -121,7 +121,7 @@ subroutine canopy_structure( currentSite , bc_in )
 
       use EDParamsMod, only : ED_val_comp_excln
       use EDTypesMod , only : min_patch_area
-      use FatesInterfaceMod, only : bc_in_type
+      use FatesInterfaceTypesMod, only : bc_in_type
       !
       ! !ARGUMENTS    
       type(ed_site_type) , intent(inout), target   :: currentSite
@@ -1256,8 +1256,8 @@ subroutine canopy_summarization( nsites, sites, bc_in )
      ! Much of this routine was once ed_clm_link minus all the IO and history stuff
      ! ---------------------------------------------------------------------------------
 
-    use FatesInterfaceMod    , only : bc_in_type
-    use FatesInterfaceMod    , only : hlm_use_cohort_age_tracking
+    use FatesInterfaceTypesMod    , only : bc_in_type
+    use FatesInterfaceTypesMod    , only : hlm_use_cohort_age_tracking
     use EDPatchDynamicsMod   , only : set_patchno
     use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
     use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
@@ -1874,7 +1874,7 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
 
      use EDTypesMod        , only : ed_patch_type, ed_cohort_type, &
                                     ed_site_type, AREA
-     use FatesInterfaceMod , only : bc_out_type
+     use FatesInterfaceTypesMod , only : bc_out_type
      use EDPftvarcon       , only : EDPftvarcon_inst
 
 

diff --git a/biogeochem/EDCohortDynamicsMod.F90 b/biogeochem/EDCohortDynamicsMod.F90
@@ -6,18 +6,18 @@ module EDCohortDynamicsMod
   ! !USES: 
   use FatesGlobals          , only : endrun => fates_endrun
   use FatesGlobals          , only : fates_log
-  use FatesInterfaceMod     , only : hlm_freq_day
-  use FatesInterfaceMod     , only : bc_in_type
-  use FatesInterfaceMod     , only : hlm_use_planthydro
-  use FatesInterfaceMod     , only : hlm_use_cohort_age_tracking
+  use FatesInterfaceTypesMod     , only : hlm_freq_day
+  use FatesInterfaceTypesMod     , only : bc_in_type
+  use FatesInterfaceTypesMod     , only : hlm_use_planthydro
+  use FatesInterfaceTypesMod     , only : hlm_use_cohort_age_tracking
   use FatesConstantsMod     , only : r8 => fates_r8
   use FatesConstantsMod     , only : fates_unset_int
   use FatesConstantsMod     , only : itrue,ifalse
   use FatesConstantsMod     , only : fates_unset_r8
   use FatesConstantsMod     , only : nearzero
   use FatesConstantsMod     , only : calloc_abs_error
-  use FatesInterfaceMod     , only : hlm_days_per_year
-  use FatesInterfaceMod     , only : nleafage
+  use FatesInterfaceTypesMod     , only : hlm_days_per_year
+  use FatesInterfaceTypesMod     , only : nleafage
   use SFParamsMod           , only : SF_val_CWD_frac
   use EDPftvarcon           , only : EDPftvarcon_inst
   use EDPftvarcon           , only : GetDecompyFrac
@@ -38,17 +38,18 @@ module EDCohortDynamicsMod
   use EDTypesMod            , only : site_fluxdiags_type
   use EDTypesMod            , only : num_elements
   use EDParamsMod           , only : ED_val_cohort_age_fusion_tol
-  use FatesInterfaceMod      , only : hlm_use_planthydro
-  use FatesInterfaceMod      , only : hlm_parteh_mode
+  use FatesInterfaceTypesMod      , only : hlm_use_planthydro
+  use FatesInterfaceTypesMod      , only : hlm_parteh_mode
   use FatesPlantHydraulicsMod, only : FuseCohortHydraulics
   use FatesPlantHydraulicsMod, only : CopyCohortHydraulics
-  use FatesPlantHydraulicsMod, only : updateSizeDepTreeHydProps
-  use FatesPlantHydraulicsMod, only : initTreeHydStates
+  use FatesPlantHydraulicsMod, only : UpdateSizeDepPlantHydProps
+  use FatesPlantHydraulicsMod, only : InitPlantHydStates
   use FatesPlantHydraulicsMod, only : InitHydrCohort
   use FatesPlantHydraulicsMod, only : DeallocateHydrCohort
   use FatesPlantHydraulicsMod, only : AccumulateMortalityWaterStorage
-  use FatesPlantHydraulicsMod, only : UpdateTreeHydrNodes
-  use FatesPlantHydraulicsMod, only : UpdateTreeHydrLenVolCond
+  use FatesPlantHydraulicsMod, only : UpdatePlantHydrNodes
+  use FatesPlantHydraulicsMod, only : UpdatePlantHydrLenVol
+  use FatesPlantHydraulicsMod, only : UpdatePlantKmax
   use FatesPlantHydraulicsMod, only : SavePreviousCompartmentVolumes
   use FatesPlantHydraulicsMod, only : ConstrainRecruitNumber
   use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
@@ -188,7 +189,7 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, coage, dbh,   &
     integer  :: iage                           ! loop counter for leaf age classes 
     real(r8) :: leaf_c                         ! total leaf carbon
     integer  :: tnull,snull                    ! are the tallest and shortest cohorts allocate
-    integer  :: nlevsoi_hyd                    ! number of hydraulically active soil layers 
+    integer  :: nlevrhiz                       ! number of rhizosphere layers
 
     !----------------------------------------------------------------------
 
@@ -300,25 +301,28 @@ subroutine create_cohort(currentSite, patchptr, pft, nn, hite, coage, dbh,   &
 
     if( hlm_use_planthydro.eq.itrue ) then
 
-       nlevsoi_hyd = currentSite%si_hydr%nlevsoi_hyd
+       nlevrhiz = currentSite%si_hydr%nlevrhiz
 
        ! This allocates array spaces
        call InitHydrCohort(currentSite,new_cohort)
 
        ! This calculates node heights
-       call UpdateTreeHydrNodes(new_cohort%co_hydr,new_cohort%pft, &
-                                new_cohort%hite,nlevsoi_hyd,bc_in)
+       call UpdatePlantHydrNodes(new_cohort%co_hydr,new_cohort%pft, &
+                                new_cohort%hite,currentSite%si_hydr)
 
-       ! This calculates volumes, lengths and max conductances
-       call UpdateTreeHydrLenVolCond(new_cohort,nlevsoi_hyd,bc_in)
+       ! This calculates volumes and lengths
+       call UpdatePlantHydrLenVol(new_cohort,currentSite%si_hydr)
 
+       ! This updates the Kmax's of the plant's compartments
+       call UpdatePlantKmax(new_cohort%co_hydr,new_cohort,currentSite%si_hydr)
+
        ! Since this is a newly initialized plant, we set the previous compartment-size
        ! equal to the ones we just calculated.
        call SavePreviousCompartmentVolumes(new_cohort%co_hydr)
 
        ! This comes up with starter suctions and then water contents
        ! based on the soil values
-       call initTreeHydStates(currentSite,new_cohort, bc_in)
+       call InitPlantHydStates(currentSite,new_cohort)
 
        if(recruitstatus==1)then
 
@@ -949,7 +953,7 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
      ! !USES:
      use EDParamsMod , only :  ED_val_cohort_size_fusion_tol
      use EDParamsMod , only :  ED_val_cohort_age_fusion_tol
-     use FatesInterfaceMod , only :  hlm_use_cohort_age_tracking
+     use FatesInterfaceTypesMod , only :  hlm_use_cohort_age_tracking
      use FatesConstantsMod , only : itrue
      use FatesConstantsMod, only : days_per_year
      use EDTypesMod  , only : maxCohortsPerPatch
@@ -981,7 +985,6 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
      real(r8) :: leaf_c_target 
      real(r8) :: dynamic_size_fusion_tolerance
      real(r8) :: dynamic_age_fusion_tolerance
-     integer  :: maxCohortsPerPatch_age_tracking
      real(r8) :: dbh
      real(r8) :: leaf_c             ! leaf carbon [kg]
 
@@ -1000,11 +1003,6 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
      ! set the cohort age fusion tolerance (in fraction of years)
      dynamic_age_fusion_tolerance = ED_val_cohort_age_fusion_tol
 
-     if ( hlm_use_cohort_age_tracking .eq. itrue) then
-        maxCohortsPerPatch_age_tracking = 300
-     end if
-
-
 
      !This needs to be a function of the canopy layer, because otherwise, at canopy closure
      !the number of cohorts doubles and very dissimilar cohorts are fused together
@@ -1386,12 +1384,13 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
                                            currentCohort%pft, currentCohort%c_area, currentCohort%n, &
                                            currentCohort%canopy_layer, currentPatch%canopy_layer_tlai, &
                                            currentCohort%vcmax25top  )			    
-                                      call updateSizeDepTreeHydProps(currentSite,currentCohort, bc_in)  				   
+                                      call UpdateSizeDepPlantHydProps(currentSite,currentCohort, bc_in)  				   
                                    endif
-
+                                   
                                    call DeallocateCohort(nextc)
                                    deallocate(nextc)
                                    nullify(nextc)
+
 
                                 endif ! if( currentCohort%isnew.eqv.nextc%isnew ) then
                              endif !canopy layer
@@ -1429,7 +1428,7 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
 
 
            if ( hlm_use_cohort_age_tracking .eq.itrue) then
-              if ( nocohorts > maxCohortsPerPatch_age_tracking ) then
+              if ( nocohorts > maxCohortsPerPatch ) then
                  iterate = 1
                  !---------------------------------------------------------------------!
                  ! Making profile tolerance larger means that more fusion will happen  !

diff --git a/biogeochem/EDLoggingMortalityMod.F90 b/biogeochem/EDLoggingMortalityMod.F90
@@ -38,14 +38,14 @@ module EDLoggingMortalityMod
    use EDParamsMod       , only : logging_mechanical_frac 
    use EDParamsMod       , only : logging_coll_under_frac 
    use EDParamsMod       , only : logging_dbhmax_infra
-   use FatesInterfaceMod , only : hlm_current_year
-   use FatesInterfaceMod , only : hlm_current_month
-   use FatesInterfaceMod , only : hlm_current_day
-   use FatesInterfaceMod , only : hlm_model_day
-   use FatesInterfaceMod , only : hlm_day_of_year 
-   use FatesInterfaceMod , only : hlm_days_per_year
-   use FatesInterfaceMod , only : hlm_use_logging 
-   use FatesInterfaceMod , only : hlm_use_planthydro
+   use FatesInterfaceTypesMod , only : hlm_current_year
+   use FatesInterfaceTypesMod , only : hlm_current_month
+   use FatesInterfaceTypesMod , only : hlm_current_day
+   use FatesInterfaceTypesMod , only : hlm_model_day
+   use FatesInterfaceTypesMod , only : hlm_day_of_year 
+   use FatesInterfaceTypesMod , only : hlm_days_per_year
+   use FatesInterfaceTypesMod , only : hlm_use_logging 
+   use FatesInterfaceTypesMod , only : hlm_use_planthydro
    use FatesConstantsMod , only : itrue,ifalse
    use FatesGlobals      , only : endrun => fates_endrun 
    use FatesGlobals      , only : fates_log

diff --git a/biogeochem/EDMortalityFunctionsMod.F90 b/biogeochem/EDMortalityFunctionsMod.F90
@@ -13,13 +13,13 @@ module EDMortalityFunctionsMod
    use FatesConstantsMod     , only : itrue,ifalse
    use FatesAllometryMod     , only : bleaf
    use FatesAllometryMod     , only : storage_fraction_of_target
-   use FatesInterfaceMod     , only : bc_in_type
-   use FatesInterfaceMod     , only : hlm_use_ed_prescribed_phys
-   use FatesInterfaceMod     , only : hlm_freq_day
-   use FatesInterfaceMod     , only : hlm_use_planthydro
+   use FatesInterfaceTypesMod     , only : bc_in_type
+   use FatesInterfaceTypesMod     , only : hlm_use_ed_prescribed_phys
+   use FatesInterfaceTypesMod     , only : hlm_freq_day
+   use FatesInterfaceTypesMod     , only : hlm_use_planthydro
    use EDLoggingMortalityMod , only : LoggingMortality_frac
    use EDParamsMod           , only : fates_mortality_disturbance_fraction
-   use FatesInterfaceMod     , only : bc_in_type
+   use FatesInterfaceTypesMod     , only : bc_in_type
 
    use PRTGenericMod,          only : all_carbon_elements
    use PRTGenericMod,          only : store_organ
@@ -50,7 +50,7 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
     ! ============================================================================
 
     use FatesConstantsMod,  only : tfrz => t_water_freeze_k_1atm
-    use FatesInterfaceMod        , only : hlm_hio_ignore_val   
+    use FatesInterfaceTypesMod        , only : hlm_hio_ignore_val   
     use FatesConstantsMod,  only : fates_check_param_set
 
     type (ed_cohort_type), intent(in) :: cohort_in 
@@ -62,7 +62,7 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
     real(r8),intent(out) :: smort  ! size dependent senescence term
     real(r8),intent(out) :: asmort ! age dependent senescence term 
 
-
+    integer  :: ifp
     real(r8) :: frac  ! relativised stored carbohydrate
     real(r8) :: leaf_c_target      ! target leaf biomass kgC
     real(r8) :: store_c
@@ -128,9 +128,9 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
     hf_flc_threshold = EDPftvarcon_inst%hf_flc_threshold(cohort_in%pft)
     if(hlm_use_planthydro.eq.itrue)then
      !note the flc is set as the fraction of max conductivity in hydro
-     min_fmc_ag = minval(cohort_in%co_hydr%flc_ag(:))
-     min_fmc_tr = minval(cohort_in%co_hydr%flc_troot(:))
-     min_fmc_ar = minval(cohort_in%co_hydr%flc_aroot(:))
+     min_fmc_ag = minval(cohort_in%co_hydr%ftc_ag(:))
+     min_fmc_tr = cohort_in%co_hydr%ftc_troot
+     min_fmc_ar = minval(cohort_in%co_hydr%ftc_aroot(:))
      min_fmc = min(min_fmc_ag, min_fmc_tr)
      min_fmc = min(min_fmc, min_fmc_ar)
      flc = 1.0_r8-min_fmc
@@ -173,7 +173,8 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
     !           Eastern US carbon sink.  Glob. Change Biol., 12, 2370-2390,              
     !           doi: 10.1111/j.1365-2486.2006.01254.x                                    
 
-    temp_in_C = bc_in%t_veg24_si - tfrz
+    ifp = cohort_in%patchptr%patchno
+    temp_in_C = bc_in%t_veg24_pa(ifp) - tfrz
     temp_dep_fraction  = max(0.0_r8, min(1.0_r8, 1.0_r8 - (temp_in_C - &
                          EDPftvarcon_inst%freezetol(cohort_in%pft))/frost_mort_buffer) )
     frmort    = EDPftvarcon_inst%mort_scalar_coldstress(cohort_in%pft) * temp_dep_fraction
@@ -217,7 +218,7 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
     !
     ! !USES:
 
-    use FatesInterfaceMod, only : hlm_freq_day
+    use FatesInterfaceTypesMod, only : hlm_freq_day
     !
     ! !ARGUMENTS    
     type(ed_site_type), intent(inout), target  :: currentSite

diff --git a/biogeochem/EDPatchDynamicsMod.F90 b/biogeochem/EDPatchDynamicsMod.F90
@@ -4,7 +4,7 @@ module EDPatchDynamicsMod
   ! Controls formation, creation, fusing and termination of patch level processes. 
   ! ============================================================================
   use FatesGlobals         , only : fates_log 
-  use FatesInterfaceMod    , only : hlm_freq_day
+  use FatesInterfaceTypesMod    , only : hlm_freq_day
   use EDPftvarcon          , only : EDPftvarcon_inst
   use EDPftvarcon          , only : GetDecompyFrac
   use EDCohortDynamicsMod  , only : fuse_cohorts, sort_cohorts, insert_cohort
@@ -37,11 +37,11 @@ module EDPatchDynamicsMod
   use EDTypesMod           , only : dl_sf
   use EDTypesMod           , only : dump_patch
   use FatesConstantsMod    , only : rsnbl_math_prec
-  use FatesInterfaceMod    , only : hlm_use_planthydro
-  use FatesInterfaceMod    , only : hlm_numSWb
-  use FatesInterfaceMod    , only : bc_in_type
-  use FatesInterfaceMod    , only : hlm_days_per_year
-  use FatesInterfaceMod    , only : numpft
+  use FatesInterfaceTypesMod    , only : hlm_use_planthydro
+  use FatesInterfaceTypesMod    , only : hlm_numSWb
+  use FatesInterfaceTypesMod    , only : bc_in_type
+  use FatesInterfaceTypesMod    , only : hlm_days_per_year
+  use FatesInterfaceTypesMod    , only : numpft
   use FatesGlobals         , only : endrun => fates_endrun
   use FatesConstantsMod    , only : r8 => fates_r8
   use FatesConstantsMod    , only : itrue, ifalse
@@ -75,7 +75,7 @@ module EDPatchDynamicsMod
   use PRTGenericMod,          only : repro_organ
   use PRTGenericMod,          only : struct_organ
   use PRTLossFluxesMod,       only : PRTBurnLosses
-  use FatesInterfaceMod,      only : hlm_parteh_mode
+  use FatesInterfaceTypesMod,      only : hlm_parteh_mode
   use PRTGenericMod,          only : prt_carbon_allom_hyp   
   use PRTGenericMod,          only : prt_cnp_flex_allom_hyp