Removed flag update_annualLAImax as implementation was mutating param…

…eters (bad practice) and not actually doing much anyways (simply capping underLAImax and LAImax after year 1).

Breaking change: The capping is now performed at year 0 unconditionally.

R/data.R

@@ -198,8 +198,6 @@
 #'       \item{steps_per_day}{Time resolution of the forcing (day-1).}
 #'       \item{do_U_shaped_mortality}{Flag indicating whether U-shaped
 #'         mortality is used.}
-#'       \item{update_annualLAImax}{Flag indicating whether updating
-#'         LAImax according to mineral N in soil.}
 #'       \item{do_closedN_run}{Flag indicating whether doing N closed
 #'         runs to recover N balance enforcing 0.2 kg N m-2 in the inorganic N pool.}
 #'       \item{code_method_photosynth}{String specifying the method of photosynthesis
@@ -285,7 +283,7 @@
 #'       \item{betaOFF}{Critical soil moisture for phenology offset.}
 #'       \item{seedlingsize}{Initial size of seedlings, in kg C per individual.}
 #'       \item{LNbase}{Basal leaf N per unit area, in kg N m\eqn{^{-2}}.}
-#'       \item{lAImax}{Maximum crown LAI (leaf area index).}
+#'       \item{lAImax}{Maximum crown LAI (leaf area index) (not used, see LAI_light).}
 #'       \item{Nfixrate0}{Reference N fixation rate (kg N kg C\eqn{^{-1}} root).}
 #'       \item{NfixCost0}{Carbon cost of N fixation (kg C kg N\eqn{^{-1}}).}
 #'       \item{phiCSA}{Ratio of sapwood area to leaf area.}

R/run_biomee_f_bysite.R

@@ -417,7 +417,6 @@ prepare_params_siml <- function(params_siml){
     "nyeartrend",
     "steps_per_day",
     "do_U_shaped_mortality",
-    "update_annualLAImax",
     "do_closedN_run",
     "code_method_photosynth",
     "code_method_mortality"

data-raw/generate_biomee_drivers.R

@@ -40,7 +40,6 @@ params_siml_gs_leuning <- tibble(
   nyeartrend = 1,
   steps_per_day = 24,
   do_U_shaped_mortality = TRUE,
-  update_annualLAImax = TRUE,
   do_closedN_run = TRUE,
   method_photosynth = "gs_leuning",
   method_mortality = "dbh"

src/biomee.mod.f90

@@ -119,17 +119,16 @@ subroutine biomee_f(            &
 
     ! Simulation parameters
     myinterface%params_siml%do_U_shaped_mortality = int(params_siml(7)) /= 0
-    myinterface%params_siml%update_annualLAImax   = int(params_siml(8)) /= 0
-    myinterface%params_siml%do_closedN_run        = int(params_siml(9)) /= 0
+    myinterface%params_siml%do_closedN_run        = int(params_siml(8)) /= 0
 
     ! this needs to be consistent with translation to code in run_biomee_f_bysite.R
-    if (int(params_siml(10)) == 1) then
+    if (int(params_siml(9)) == 1) then
       myinterface%params_siml%method_photosynth = "gs_leuning"
     else
       myinterface%params_siml%method_photosynth = "pmodel"
     end if
 
-    select case( int(params_siml(11)) )
+    select case( int(params_siml(10)) )
       case (1)
       myinterface%params_siml%method_mortality = "cstarvation"
       case (2)
@@ -210,7 +209,7 @@ subroutine biomee_f(            &
     myinterface%params_species(:)%CNleafsupport      = real( params_species(:,38))
     myinterface%params_species(:)%rho_wood           = real( params_species(:,39)) ! prescribed
     myinterface%params_species(:)%taperfactor        = real( params_species(:,40))
-    myinterface%params_species(:)%lAImax             = real( params_species(:,41))
+    ! myinterface%params_species(:)%lAImax             = real( params_species(:,41)) ! overriden
     myinterface%params_species(:)%tauNSC             = real( params_species(:,42))
     myinterface%params_species(:)%fNSNmax            = real( params_species(:,43))
     myinterface%params_species(:)%phiCSA             = real( params_species(:,44))

src/biosphere_biomee.mod.f90

@@ -143,8 +143,6 @@ subroutine biosphere_annual( &
     ! Annual calls
     !----------------------------------------------------------------
 
-    if ( myinterface%params_siml%update_annualLAImax ) call vegn_annualLAImax_update( vegn )
-
     !---------------------------------------------
     ! Get annual diagnostics and outputs in once. 
     ! Needs to be called here 

src/datatypes_biomee.mod.f90

@@ -32,7 +32,7 @@ module datatypes_biomee
   !=============== Number of parameters (out) ==============================================
   integer, public, parameter :: nvars_forcing        = 7
   integer, public, parameter :: nvars_site_info      = 3
-  integer, public, parameter :: nvars_params_siml    = 11
+  integer, public, parameter :: nvars_params_siml    = 10
   integer, public, parameter :: nvars_params_tile    = 19
   integer, public, parameter :: nvars_init_soil      = 4
   integer, public, parameter :: nvars_init_cohorts   = 9
@@ -863,7 +863,8 @@ subroutine initialize_PFT_data()
       spdata%prob_g        = 1.0
       spdata%prob_e        = 1.0
 
-      spdata%underLAImax = spdata%LAImax
+      spdata%LAImax = MAX(0.5, spdata%LAI_light)
+      spdata%underLAImax = MIN(spdata%LAImax, 1.2)
 
       ! specific root area
       spdata%SRA           = 2.0/(spdata%root_r*spdata%rho_FR)

src/interface_biosphere_biomee.mod.f90

@@ -110,7 +110,7 @@ module md_interface_biomee
     real    :: mortrate_d_u                       ! yearly mortality rate in understory
 
     !===== Population level variables
-    real    :: LAImax, underLAImax                ! max. LAI - Mutated at runtime!!
+    real    :: LAImax, underLAImax                ! max. LAI - Overridden
     real    :: LAI_light                          ! light controlled maximum LAI
     real    :: internal_gap_frac                  ! fraction of internal gaps in the canopy
 

src/params_siml_biomee.mod.f90

@@ -16,7 +16,6 @@ module md_params_siml_biomee
 
     type(steering_parameters) :: steering
     logical :: do_U_shaped_mortality
-    logical :: update_annualLAImax
     logical :: do_closedN_run
     character(len=30) :: method_photosynth
     character(len=30) :: method_mortality

src/vegetation_biomee.mod.f90

@@ -13,7 +13,7 @@ module md_vegetation_biomee
   ! public subroutines
   public :: initialize_cohort_from_biomass, initialize_vegn_tile
   public :: vegn_CNW_budget, vegn_phenology, vegn_growth_EW
-  public :: vegn_reproduction, vegn_annualLAImax_update
+  public :: vegn_reproduction
   public :: vegn_nat_mortality, vegn_species_switch
   public :: relayer_cohorts, vegn_mergecohorts, kill_lowdensity_cohorts
   public :: kill_old_grass
@@ -1976,63 +1976,6 @@ subroutine init_cohort_allometry( cc )
   end subroutine init_cohort_allometry
 
 
-  subroutine vegn_annualLAImax_update( vegn )
-    !////////////////////////////////////////////////////////////////
-    ! used for updating LAImax according to mineral N in soil
-    ! Potential problems:
-    !   1. All species LAImax are updated
-    !   2. For evergreen, LAImax can be less than current LAI.
-    !  Weng, 2017-08-02
-    ! Code from BiomeE-Allocation
-    !---------------------------------------------------------------
-    type(vegn_tile_type), intent(inout) :: vegn
-    ! local variables
-    ! type(cohort_type), pointer :: cc
-    real   :: LAImin, LAIfixedN, LAImineralN
-    real   :: LAI_Nitrogen
-    ! real   :: fixedN, rootN
-    logical:: fixedN_based
-    integer :: i
-    ! Calculating LAI max based on mineral N or mineralN + fixed N
-    fixedN_based =  .False. ! .True. !
-    LAImin       = 0.5
-
-    !fixedN = 0.0
-    !do i = 1,vegn%n_cohorts
-    !      cc => vegn%cohorts(i)
-    !      fixedN = fixedN + cc%annualfixedN * cc%crownarea * cc%nindivs
-    !enddo
-    ! Mineral+fixed N-based LAImax
-    ! LAI_fixedN = sp%Nfixrate0 * sp%LMA * sp%CNleaf0 * sp%leafLS / sp%LMA
-    ! cc%br_max = sp%phiRL*cc%bl_max/(sp%LMA*sp%SRA)
-
-    vegn%previousN = 0.8 * vegn%previousN + 0.2 * vegn%annualN
-    associate (spdata => myinterface%params_species )
-      do i=1,size(spdata)
-        associate (sp => spdata(i))
-
-          LAIfixedN  = 0.5 * sp%Nfixrate0 * sp%CNleaf0 * sp%leafLS
-          LAImineralN = 0.5 * vegn%previousN * sp%CNleaf0 * sp%leafLS / sp%LMA
-
-          !LAImineralN = vegn%previousN/(sp%LMA/(sp%CNleaf0*sp%leafLS)+sp%phiRL*sp%alpha_FR/sp%SRA /sp%CNroot0)
-          LAI_nitrogen = LAIfixedN + LAImineralN
-          ! spdata(i)%LAImax = MAX(LAImin, MIN(LAI_nitrogen, sp%LAI_light))
-
-          ! turn off N limitation
-          sp%LAImax = MAX(LAImin, sp%LAI_light)
-
-          sp%underLAImax = MIN(sp%LAImax, 1.2)
-
-          ! print*,'sp%LAI_light', sp%LAI_light
-
-        end associate
-
-      enddo
-    end associate
-
-  end subroutine vegn_annualLAImax_update
-
-
   function leaf_area_from_biomass(bl,species) result (area)
     !////////////////////////////////////////////////////////////////
     ! Code from BiomeE-Allocation