Merge pull request #288 from ckoven/flexible_history_bins

runtime-specified history bins for size- and age- resolved output

Author: rgknox

biogeochem/EDCanopyStructureMod.F90

@@ -861,7 +861,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )
     use FatesInterfaceMod    , only : bc_in_type
     use EDPatchDynamicsMod   , only : set_patchno
     use EDPatchDynamicsMod   , only : set_root_fraction
-    use EDTypesMod           , only : sizetype_class_index
+    use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
     use EDGrowthFunctionsMod , only : tree_lai, c_area
     use EDtypesMod           , only : area
     use EDPftvarcon            , only : EDPftvarcon_inst

biogeochem/EDCohortDynamicsMod.F90

@@ -18,7 +18,7 @@ module EDCohortDynamicsMod
   use EDTypesMod            , only : nclmax
   use EDTypesMod            , only : ncwd
   use EDTypesMod            , only : maxCohortsPerPatch
-  use EDTypesMod            , only : sclass_ed,nlevsclass_ed,AREA
+  use EDTypesMod            , only : AREA
   use EDTypesMod            , only : min_npm2, min_nppatch
   use EDTypesMod            , only : min_n_safemath
   use FatesInterfaceMod      , only : hlm_use_planthydro
@@ -28,7 +28,7 @@ module EDCohortDynamicsMod
   use FatesPlantHydraulicsMod, only : initTreeHydStates
   use FatesPlantHydraulicsMod, only : InitHydrCohort
   use FatesPlantHydraulicsMod, only : DeallocateHydrCohort
-  use EDTypesMod             , only : sizetype_class_index
+  use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
 
 
   ! CIME globals

biogeochem/EDPatchDynamicsMod.F90

@@ -1437,7 +1437,7 @@ subroutine fuse_2_patches(dp, rp)
     ! associated with the secnd patch
     !
     ! !USES:
-    use EDTypesMod, only: get_age_class_index
+    use FatesSizeAgeTypeIndicesMod, only: get_age_class_index
     !
     ! !ARGUMENTS:
     type (ed_patch_type) , intent(inout), pointer :: dp ! Donor Patch

main/EDInitMod.F90

@@ -25,6 +25,7 @@ module EDInitMod
   use FatesInterfaceMod         , only : hlm_use_inventory_init
   use FatesInterfaceMod         , only : numpft
   use ChecksBalancesMod         , only : SiteCarbonStock
+  use FatesInterfaceMod         , only : nlevsclass
 
   ! CIME GLOBALS
   use shr_log_mod               , only : errMsg => shr_log_errMsg
@@ -38,6 +39,7 @@ module EDInitMod
         __FILE__
 
   public  :: zero_site
+  public  :: init_site_vars
   public  :: init_patches
   public  :: set_site_properties
   private :: init_cohorts
@@ -48,6 +50,24 @@ module EDInitMod
 
   ! ============================================================================
 
+  subroutine init_site_vars( site_in )
+    !
+    ! !DESCRIPTION:
+    !
+    !
+    ! !ARGUMENTS    
+    type(ed_site_type), intent(inout) ::  site_in
+    !
+    ! !LOCAL VARIABLES:
+    !----------------------------------------------------------------------
+    !
+    allocate(site_in%terminated_nindivs(1:nlevsclass,1:numpft,2))
+    allocate(site_in%demotion_rate(1:nlevsclass))
+    allocate(site_in%promotion_rate(1:nlevsclass))
+    !
+    end subroutine init_site_vars
+
+  ! ============================================================================
   subroutine zero_site( site_in )
     !
     ! !DESCRIPTION:

main/EDMainMod.F90

@@ -34,7 +34,7 @@ module EDMainMod
   use EDPhysiologyMod          , only : recruitment
   use EDPhysiologyMod          , only : trim_canopy
   use SFMainMod                , only : fire_model 
-  use EDTypesMod               , only : get_age_class_index
+  use FatesSizeAgeTypeIndicesMod, only : get_age_class_index
   use EDtypesMod               , only : ncwd
   use EDtypesMod               , only : ed_site_type
   use EDtypesMod               , only : ed_patch_type
@@ -225,7 +225,6 @@ subroutine ed_integrate_state_variables(currentSite, bc_in )
     ! FIX(SPM,032414) refactor so everything goes through interface
     !
     ! !USES:
-    use EDTypesMod, only : ageclass_ed
     !
     ! !ARGUMENTS:
     type(ed_site_type)     , intent(inout) :: currentSite
@@ -381,7 +380,6 @@ subroutine ed_integrate_state_variables(currentSite, bc_in )
        endif
     enddo
 
-
   end subroutine ed_integrate_state_variables
 
   !-------------------------------------------------------------------------------!

main/EDParamsMod.F90

@@ -46,6 +46,10 @@ module EDParamsMod
    real(r8),protected :: ED_val_patch_fusion_tol
    real(r8),protected :: ED_val_canopy_closure_thresh ! site-level canopy closure point where trees take on forest (narrow) versus savannah (wide) crown allometry
 
+   ! two special parameters whose size is defined in the parameter file
+   real(r8),protected,allocatable :: ED_val_history_sizeclass_bin_edges(:)
+   real(r8),protected,allocatable :: ED_val_history_ageclass_bin_edges(:)
+
    character(len=param_string_length),parameter :: ED_name_size_diagnostic_scale = "fates_size_diagnostic_scale"
    character(len=param_string_length),parameter :: ED_name_mort_disturb_frac = "fates_mort_disturb_frac"
    character(len=param_string_length),parameter :: ED_name_comp_excln = "fates_comp_excln"
@@ -71,6 +75,10 @@ module EDParamsMod
    character(len=param_string_length),parameter :: ED_name_patch_fusion_tol= "fates_patch_fusion_tol"
    character(len=param_string_length),parameter :: ED_name_canopy_closure_thresh= "fates_canopy_closure_thresh"      
 
+   ! non-scalar parameter names
+   character(len=param_string_length),parameter :: ED_name_history_sizeclass_bin_edges= "fates_history_sizeclass_bin_edges"      
+   character(len=param_string_length),parameter :: ED_name_history_ageclass_bin_edges= "fates_history_ageclass_bin_edges"      
+
    ! Hydraulics Control Parameters (ONLY RELEVANT WHEN USE_FATES_HYDR = TRUE)
    ! ----------------------------------------------------------------------------------------------
    real(r8),protected :: hydr_psi0          !  sapwood water potential at saturation (MPa)
@@ -162,12 +170,15 @@ subroutine FatesRegisterParams(fates_params)
     ! that need to be synced with host values.
 
     use FatesParametersInterface, only : fates_parameters_type, dimension_name_scalar1d, dimension_shape_1d
+    use FatesParametersInterface, only : dimension_name_history_size_bins, dimension_name_history_age_bins
 
     implicit none
 
     class(fates_parameters_type), intent(inout) :: fates_params
 
     character(len=param_string_length), parameter :: dim_names(1) = (/dimension_name_scalar1d/)
+    character(len=param_string_length), parameter :: dim_names_sizeclass(1) = (/dimension_name_history_size_bins/)
+    character(len=param_string_length), parameter :: dim_names_ageclass(1) = (/dimension_name_history_age_bins/)
 
     call FatesParamsInit()
 
@@ -268,6 +279,13 @@ subroutine FatesRegisterParams(fates_params)
          dimension_names=dim_names)
 
 
+    ! non-scalar parameters
+    call fates_params%RegisterParameter(name=ED_name_history_sizeclass_bin_edges, dimension_shape=dimension_shape_1d, &
+         dimension_names=dim_names_sizeclass)
+
+    call fates_params%RegisterParameter(name=ED_name_history_ageclass_bin_edges, dimension_shape=dimension_shape_1d, &
+         dimension_names=dim_names_ageclass)
+
   end subroutine FatesRegisterParams
 
 
@@ -376,6 +394,14 @@ subroutine FatesReceiveParams(fates_params)
     call fates_params%RetreiveParameter(name=logging_name_event_code, &
           data=logging_event_code)
 
+    ! parameters that are arrays of size defined within the params file and thus need allocating as well
+    call fates_params%RetreiveParameterAllocate(name=ED_name_history_sizeclass_bin_edges, &
+          data=ED_val_history_sizeclass_bin_edges)
+
+    call fates_params%RetreiveParameterAllocate(name=ED_name_history_ageclass_bin_edges, &
+          data=ED_val_history_ageclass_bin_edges)
+
+
   end subroutine FatesReceiveParams
 
   ! =====================================================================================

main/EDTypesMod.F90

@@ -100,25 +100,6 @@ module EDTypesMod
   ! special mode to cause PFTs to create seed mass of all currently-existing PFTs
   logical, parameter :: homogenize_seed_pfts  = .false.
 
-  !the lower limit of the size classes of ED cohorts
-  !0-10,10-20...
-  integer, parameter :: nlevsclass_ed = 13    ! Number of dbh size classes for size structure analysis
-                                              ! |0-1,1-2,2-3,3-4,4-5,5-10,10-20,20-30,30-40,40-50,50-60,60-70,70-80,80-90,90-100,100+|
-!  real(r8), parameter, dimension(16) ::  sclass_ed  = (/0.0_r8,1.0_r8,2.0_r8,3.0_r8,4.0_r8,5.0_r8,10.0_r8,20.0_r8,30.0_r8,40.0_r8, &
-!                                                       50.0_r8,60.0_r8,70.0_r8,80.0_r8,90.0_r8,100.0_r8/)
-
-  real(r8), parameter, dimension(nlevsclass_ed) ::  sclass_ed  = (/0.0_r8,5.0_r8,10.0_r8,15.0_r8,20.0_r8,30.0_r8,40.0_r8, &
-                                                       50.0_r8,60.0_r8,70.0_r8,80.0_r8,90.0_r8,100.0_r8/)
-
-  integer, parameter :: nlevage_ed = 7  ! Number of patch-age classes for age structured analyses
-  real(r8), parameter, dimension(nlevage_ed) ::  ageclass_ed  = (/0.0_r8,1.0_r8,2._r8,5.0_r8,10.0_r8,20.0_r8,50.0_r8/)
-  
-
- !  integer, parameter :: nlevsclass_ed = 17
- !  real(r8), parameter, dimension(17) ::  sclass_ed  = (/0.1_r8, 5.0_r8,10.0_r8,15.0_r8,20.0_r8,25.0_r8, & 
- !                                                       30.0_r8,35.0_r8,40.0_r8,45.0_r8,50.0_r8,55.0_r8, &
- !                                                       60.0_r8,65.0_r8,70.0_r8,75.0_r8,80.0_r8/)
-
   integer, parameter :: nlevmclass_ed = 5      ! nlev "mortality" classes in ED
                                                ! Number of ways to die
                                                ! (background,hydraulic,carbon,impact,fire)
@@ -552,12 +533,12 @@ module EDTypesMod
 
      ! TERMINATION, RECRUITMENT, DEMOTION, and DISTURBANCE
 
-     real(r8) :: terminated_nindivs(1:nlevsclass_ed,1:maxpft,2) ! number of individuals that were in cohorts which were terminated this timestep, on size x pft x canopy array. 
+     real(r8), allocatable :: terminated_nindivs(:,:,:) ! number of individuals that were in cohorts which were terminated this timestep, on size x pft x canopy array. 
      real(r8) :: termination_carbonflux(2)                     ! carbon flux from live to dead pools associated with termination mortality, per canopy level
      real(r8) :: recruitment_rate(1:maxpft)                     ! number of individuals that were recruited into new cohorts
-     real(r8) :: demotion_rate(1:nlevsclass_ed)                ! rate of individuals demoted from canopy to understory per FATES timestep
+     real(r8), allocatable :: demotion_rate(:)                ! rate of individuals demoted from canopy to understory per FATES timestep
      real(r8) :: demotion_carbonflux                           ! biomass of demoted individuals from canopy to understory [kgC/ha/day]
-     real(r8) :: promotion_rate(1:nlevsclass_ed)               ! rate of individuals promoted from understory to canopy per FATES timestep
+     real(r8), allocatable :: promotion_rate(:)               ! rate of individuals promoted from understory to canopy per FATES timestep
      real(r8) :: promotion_carbonflux                          ! biomass of promoted individuals from understory to canopy [kgC/ha/day]
 
      ! some diagnostic-only (i.e. not resolved by ODE solver) flux of carbon to CWD and litter pools from termination and canopy mortality
@@ -573,67 +554,6 @@ module EDTypesMod
 
 contains
 
-  ! =====================================================================================
-  
-  function get_age_class_index(age) result( patch_age_class ) 
-
-     real(r8), intent(in) :: age
-     
-     integer :: patch_age_class
-
-     patch_age_class = count(age-ageclass_ed.ge.0.0_r8)
-
-  end function get_age_class_index
-
-  ! =====================================================================================
-
-  function get_sizeage_class_index(dbh,age) result(size_by_age_class)
-     
-     ! Arguments
-     real(r8),intent(in) :: dbh
-     real(r8),intent(in) :: age
-
-     integer             :: size_class
-     integer             :: age_class
-     integer             :: size_by_age_class
-     
-     size_class        = get_size_class_index(dbh)
-
-     age_class         = get_age_class_index(age)
-     
-     size_by_age_class = (age_class-1)*nlevsclass_ed + size_class
-
-  end function get_sizeage_class_index
-
-  ! =====================================================================================
-
-  subroutine sizetype_class_index(dbh,pft,size_class,size_by_pft_class)
-    
-    ! Arguments
-    real(r8),intent(in) :: dbh
-    integer,intent(in)  :: pft
-    integer,intent(out) :: size_class
-    integer,intent(out) :: size_by_pft_class
-    
-    size_class        = get_size_class_index(dbh)
-    
-    size_by_pft_class = (pft-1)*nlevsclass_ed+size_class
-
-    return
- end subroutine sizetype_class_index
-
-  ! =====================================================================================
-
-  function get_size_class_index(dbh) result(cohort_size_class)
-
-     real(r8), intent(in) :: dbh
-     
-     integer :: cohort_size_class
-     
-     cohort_size_class = count(dbh-sclass_ed.ge.0.0_r8)
-     
-  end function get_size_class_index
-
   ! =====================================================================================
 
   subroutine val_check_ed_vars(currentPatch,var_aliases,return_code)