From 078d94ca80765662cb2686b01cdfee4671e0c408 Mon Sep 17 00:00:00 2001
From: Beni Stocker <benjamin.stocker@gmail.com>
Date: Mon, 29 Apr 2024 23:32:37 +0200
Subject: [PATCH] resolved some bugs after PR from DBEN changes

---
 src/biosphere_biomee.mod.f90  |  46 +++++-------
 src/sofun_r.f90               |  24 +++---
 src/vegetation_biomee.mod.f90 |   8 +-
 src/wrappersc.c               | 134 +++++++++++++++++-----------------
 vignettes/biomee_use.Rmd      |  10 +--
 5 files changed, 102 insertions(+), 120 deletions(-)

diff --git a/src/biosphere_biomee.mod.f90 b/src/biosphere_biomee.mod.f90
index 24af5739..4ee64b84 100644
--- a/src/biosphere_biomee.mod.f90
+++ b/src/biosphere_biomee.mod.f90
@@ -196,39 +196,33 @@ subroutine biosphere_annual(out_biosphere)
     ! update the years of model run
     iyears = iyears + 1
 
-    !---------------------------------------------
-    ! Reset vegetation to initial conditions
-    !---------------------------------------------
+    ! !---------------------------------------------
+    ! ! Reset vegetation to initial conditions
+    ! !---------------------------------------------
 
-    !if (iyears > myinterface%params_siml%spinupyears+31 .and. rand(0)<0.40) &
-    !     call reset_vegn_initial(vegn) ! 0.01, 0.02, 0.04, 0.08, 0.20, 0.40
+    ! !if (iyears > myinterface%params_siml%spinupyears+31 .and. rand(0)<0.40) &
+    ! !     call reset_vegn_initial(vegn) ! 0.01, 0.02, 0.04, 0.08, 0.20, 0.40
 
-    !if (iyears == 700 .or. iyears == 800) &
-    !     call reset_vegn_initial(vegn) 
-    
-    if (myinterface%steering%finalize) then
-      !----------------------------------------------------------------
-      ! Finazlize run: deallocating memory
-      !----------------------------------------------------------------
-      deallocate( vegn )
+    ! !if (iyears == 700 .or. iyears == 800) &
+    ! !     call reset_vegn_initial(vegn) 
 
-    if(myinterface%params_siml%do_reset_veg) then
+    ! if(myinterface%params_siml%do_reset_veg) then
 
-    if (iyears==myinterface%params_siml%spinupyears + 31)  then
-      call reset_vegn_initial(vegn)
-    endif
+    ! if (iyears==myinterface%params_siml%spinupyears + 31)  then
+    !   call reset_vegn_initial(vegn)
+    ! endif
 
-    ! nfrequency = 50 ! 100,75,50,25,15,10 
+    ! ! nfrequency = 50 ! 100,75,50,25,15,10 
 
-    if(myinterface%params_siml%dist_frequency > 0) then
-        do i = myinterface%params_siml%spinupyears + 31 + myinterface%params_siml%dist_frequency, &
-        myinterface%params_siml%spinupyears + myinterface%params_siml%nyeartrend, &
-        myinterface%params_siml%dist_frequency
-      if (iyears == i) call reset_vegn_initial(vegn)
-    enddo
-    endif
+    ! if(myinterface%params_siml%dist_frequency > 0) then
+    !     do i = myinterface%params_siml%spinupyears + 31 + myinterface%params_siml%dist_frequency, &
+    !     myinterface%params_siml%spinupyears + myinterface%params_siml%nyeartrend, &
+    !     myinterface%params_siml%dist_frequency
+    !   if (iyears == i) call reset_vegn_initial(vegn)
+    ! enddo
+    ! endif
 
-    endif
+    ! endif
 
     !----------------------------------------------------------------
     ! Finalize run: deallocating memory
diff --git a/src/sofun_r.f90 b/src/sofun_r.f90
index 8d5f7c5d..a59dc381 100644
--- a/src/sofun_r.f90
+++ b/src/sofun_r.f90
@@ -768,17 +768,11 @@ subroutine biomee_f(            &
       !----------------------------------------------------------------
       ! Output output_annual_cohorts (without subroutine)
       !----------------------------------------------------------------
-      
-      ! To get outputs only after spinupyears make if below and 
-      ! also in run_biomee_f_bysite.R make n_annual_cohorts = as.integer(params_siml$nyeartrend)
+      if (.not. myinterface%steering%spinup) then  ! To get outputs only after spinupyears
 
-      !if (.not. myinterface%steering%spinup) then  ! To get outputs only after spinupyears
-      !idx =  yr - myinterface%params_siml%spinupyears
-        
-      ! To get outputs for all runyears idx=yr and also in run_biomee_f_bysite.R make n_annual_cohorts = as.integer(runyears)
-       idx =  yr
+        idx =  yr - myinterface%params_siml%spinupyears
 
-        output_annual_cohorts_year(idx, :)        = dble(out_biosphere%annual_cohorts(:)%year) !xxx commented out for calibration!
+        output_annual_cohorts_year(idx, :)        = dble(out_biosphere%annual_cohorts(:)%year)
         output_annual_cohorts_cID(idx, :)         = dble(out_biosphere%annual_cohorts(:)%cID)
         output_annual_cohorts_PFT(idx, :)         = dble(out_biosphere%annual_cohorts(:)%PFT)
         output_annual_cohorts_layer(idx, :)       = dble(out_biosphere%annual_cohorts(:)%layer)
@@ -794,11 +788,11 @@ subroutine biomee_f(            &
         output_annual_cohorts_Aleaf(idx, :)       = dble(out_biosphere%annual_cohorts(:)%Aleaf)
         output_annual_cohorts_nsc(idx, :)         = dble(out_biosphere%annual_cohorts(:)%nsc)
         output_annual_cohorts_nsn(idx, :)         = dble(out_biosphere%annual_cohorts(:)%nsn)
-        output_annual_cohorts_nsn(idx, :)         = dble(out_biosphere%annual_cohorts(:)%seedC)
-        output_annual_cohorts_nsn(idx, :)         = dble(out_biosphere%annual_cohorts(:)%leafC)
-        output_annual_cohorts_nsn(idx, :)         = dble(out_biosphere%annual_cohorts(:)%rootC)
-        output_annual_cohorts_nsn(idx, :)         = dble(out_biosphere%annual_cohorts(:)%sapwC)
-        output_annual_cohorts_nsn(idx, :)         = dble(out_biosphere%annual_cohorts(:)%woodC)
+        output_annual_cohorts_seedC(idx, :)       = dble(out_biosphere%annual_cohorts(:)%seedC)
+        output_annual_cohorts_leafC(idx, :)       = dble(out_biosphere%annual_cohorts(:)%leafC)
+        output_annual_cohorts_rootC(idx, :)       = dble(out_biosphere%annual_cohorts(:)%rootC)
+        output_annual_cohorts_sapwC(idx, :)       = dble(out_biosphere%annual_cohorts(:)%sapwC)
+        output_annual_cohorts_woodC(idx, :)       = dble(out_biosphere%annual_cohorts(:)%woodC)
         output_annual_cohorts_treeG(idx, :)       = dble(out_biosphere%annual_cohorts(:)%treeG)
         output_annual_cohorts_fseed(idx, :)       = dble(out_biosphere%annual_cohorts(:)%fseed)
         output_annual_cohorts_fleaf(idx, :)       = dble(out_biosphere%annual_cohorts(:)%fleaf)
@@ -811,7 +805,7 @@ subroutine biomee_f(            &
         output_annual_cohorts_Nfix(idx, :)        = dble(out_biosphere%annual_cohorts(:)%Nfix)
         output_annual_cohorts_deathrate(idx, :)   = dble(out_biosphere%annual_cohorts(:)%deathrate)
 
-       !end if
+       end if
 
     end do yearloop
 
diff --git a/src/vegetation_biomee.mod.f90 b/src/vegetation_biomee.mod.f90
index cda3dc90..9968b4ac 100755
--- a/src/vegetation_biomee.mod.f90
+++ b/src/vegetation_biomee.mod.f90
@@ -1892,10 +1892,10 @@ subroutine kill_old_grass(vegn)
       if (.not. OldGrass) k=k+1
     end associate
   enddo
-  if (k==0)then
-     write(*,*)'in kill_old_grass: All cohorts are old grass, No action!'
-     !stop
-  endif
+  ! if (k==0)then
+  !    write(*,*)'in kill_old_grass: All cohorts are old grass, No action!'
+  !    !stop
+  ! endif
 
   ! exclude cohorts that are old grass
   if (k>0 .and. k<vegn%n_cohorts)then
diff --git a/src/wrappersc.c b/src/wrappersc.c
index 6f22edaa..4d9b5fbb 100644
--- a/src/wrappersc.c
+++ b/src/wrappersc.c
@@ -466,76 +466,74 @@ extern SEXP biomee_f_C(
         );
 
     // // Output as list
-    SEXP out_list = PROTECT( allocVector(VECSXP, 64) );  // maybe try  STRSXP instead of VECSXP
+    SEXP out_list = PROTECT( allocVector(VECSXP, 63) );  // maybe try  STRSXP instead of VECSXP
     
-    SET_VECTOR_ELT(out_list, 0,  output_hourly_tile);
-    SET_VECTOR_ELT(out_list, 1,  output_daily_tile);
-    SET_VECTOR_ELT(out_list, 2,  output_daily_cohorts_year ); 
-    SET_VECTOR_ELT(out_list, 3,  output_daily_cohorts_doy );  
-    SET_VECTOR_ELT(out_list, 4,  output_daily_cohorts_hour );  
-    SET_VECTOR_ELT(out_list, 5,  output_daily_cohorts_cID );  
-    SET_VECTOR_ELT(out_list, 6,  output_daily_cohorts_PFT );  
-    SET_VECTOR_ELT(out_list, 7,  output_daily_cohorts_layer );  
-    SET_VECTOR_ELT(out_list, 8,  output_daily_cohorts_density );  
-    SET_VECTOR_ELT(out_list, 9,  output_daily_cohorts_f_layer );  
-    SET_VECTOR_ELT(out_list, 10, output_daily_cohorts_LAI );  
-    SET_VECTOR_ELT(out_list, 11, output_daily_cohorts_gpp );  
-    SET_VECTOR_ELT(out_list, 12, output_daily_cohorts_resp );  
-    SET_VECTOR_ELT(out_list, 13, output_daily_cohorts_transp );  
-    SET_VECTOR_ELT(out_list, 14, output_daily_cohorts_NPPleaf );  
-    SET_VECTOR_ELT(out_list, 15, output_daily_cohorts_NPProot );  
-    SET_VECTOR_ELT(out_list, 16, output_daily_cohorts_NPPwood );  
-    SET_VECTOR_ELT(out_list, 17, output_daily_cohorts_NSC );  
-    SET_VECTOR_ELT(out_list, 18, output_daily_cohorts_seedC );  
-    SET_VECTOR_ELT(out_list, 19, output_daily_cohorts_leafC );  
-    SET_VECTOR_ELT(out_list, 20, output_daily_cohorts_rootC );  
-    SET_VECTOR_ELT(out_list, 21, output_daily_cohorts_SW_C );  
-    SET_VECTOR_ELT(out_list, 22, output_daily_cohorts_HW_C );  
-    SET_VECTOR_ELT(out_list, 23, output_daily_cohorts_NSN );  
-    SET_VECTOR_ELT(out_list, 24, output_daily_cohorts_seedN );  
-    SET_VECTOR_ELT(out_list, 25, output_daily_cohorts_leafN );  
-    SET_VECTOR_ELT(out_list, 26, output_daily_cohorts_rootN );  
-    SET_VECTOR_ELT(out_list, 27, output_daily_cohorts_SW_N );  
-    SET_VECTOR_ELT(out_list, 28, output_daily_cohorts_HW_N );  
-
-    SET_VECTOR_ELT(out_list, 29, output_annual_tile);
-
-    SET_VECTOR_ELT(out_list, 30, output_annual_cohorts_year);
-    SET_VECTOR_ELT(out_list, 31, output_annual_cohorts_cID);
-    SET_VECTOR_ELT(out_list, 32, output_annual_cohorts_PFT);
-    SET_VECTOR_ELT(out_list, 33, output_annual_cohorts_layer);
-    SET_VECTOR_ELT(out_list, 34, output_annual_cohorts_density);
-    SET_VECTOR_ELT(out_list, 35, output_annual_cohorts_flayer);
-    SET_VECTOR_ELT(out_list, 36, output_annual_cohorts_DBH);
-    SET_VECTOR_ELT(out_list, 37, output_annual_cohorts_dDBH);
-    SET_VECTOR_ELT(out_list, 38, output_annual_cohorts_height);
-    SET_VECTOR_ELT(out_list, 39, output_annual_cohorts_age);
-    SET_VECTOR_ELT(out_list, 40, output_annual_cohorts_BA);
-    SET_VECTOR_ELT(out_list, 41, output_annual_cohorts_dBA);
-    SET_VECTOR_ELT(out_list, 42, output_annual_cohorts_Acrown);
-    SET_VECTOR_ELT(out_list, 43, output_annual_cohorts_Aleaf);
-    SET_VECTOR_ELT(out_list, 44, output_annual_cohorts_nsc);
-    SET_VECTOR_ELT(out_list, 45, output_annual_cohorts_nsn);
-    SET_VECTOR_ELT(out_list, 46, output_annual_cohorts_seedC);
-    SET_VECTOR_ELT(out_list, 47, output_annual_cohorts_leafC);
-    SET_VECTOR_ELT(out_list, 48, output_annual_cohorts_rootC);
-    SET_VECTOR_ELT(out_list, 49, output_annual_cohorts_sapwC);
-    SET_VECTOR_ELT(out_list, 50, output_annual_cohorts_woodC);
-    SET_VECTOR_ELT(out_list, 51, output_annual_cohorts_treeG);
-    SET_VECTOR_ELT(out_list, 52, output_annual_cohorts_fseed);
-    SET_VECTOR_ELT(out_list, 53, output_annual_cohorts_fleaf);
-    SET_VECTOR_ELT(out_list, 54, output_annual_cohorts_froot);
-    SET_VECTOR_ELT(out_list, 55, output_annual_cohorts_fwood);
-    SET_VECTOR_ELT(out_list, 56, output_annual_cohorts_GPP);
-    SET_VECTOR_ELT(out_list, 57, output_annual_cohorts_NPP);
-    SET_VECTOR_ELT(out_list, 58, output_annual_cohorts_Rauto);
-    SET_VECTOR_ELT(out_list, 59, output_annual_cohorts_Nupt);
-    SET_VECTOR_ELT(out_list, 60, output_annual_cohorts_Nfix);
-    SET_VECTOR_ELT(out_list, 61, output_annual_cohorts_n_deadtrees);
-    SET_VECTOR_ELT(out_list, 62, output_annual_cohorts_c_deadtrees);
-    SET_VECTOR_ELT(out_list, 63, output_annual_cohorts_deathrate);
+    // SET_VECTOR_ELT(out_list, 0,  output_hourly_tile);
+    SET_VECTOR_ELT(out_list, 0,  output_daily_tile);
+    SET_VECTOR_ELT(out_list, 1,  output_daily_cohorts_year ); 
+    SET_VECTOR_ELT(out_list, 2,  output_daily_cohorts_doy );  
+    SET_VECTOR_ELT(out_list, 3,  output_daily_cohorts_hour );  
+    SET_VECTOR_ELT(out_list, 4,  output_daily_cohorts_cID );  
+    SET_VECTOR_ELT(out_list, 5,  output_daily_cohorts_PFT );  
+    SET_VECTOR_ELT(out_list, 6,  output_daily_cohorts_layer );  
+    SET_VECTOR_ELT(out_list, 7,  output_daily_cohorts_density );  
+    SET_VECTOR_ELT(out_list, 8,  output_daily_cohorts_f_layer );  
+    SET_VECTOR_ELT(out_list, 9, output_daily_cohorts_LAI );  
+    SET_VECTOR_ELT(out_list, 10, output_daily_cohorts_gpp );  
+    SET_VECTOR_ELT(out_list, 11, output_daily_cohorts_resp );  
+    SET_VECTOR_ELT(out_list, 12, output_daily_cohorts_transp );  
+    SET_VECTOR_ELT(out_list, 13, output_daily_cohorts_NPPleaf );  
+    SET_VECTOR_ELT(out_list, 14, output_daily_cohorts_NPProot );  
+    SET_VECTOR_ELT(out_list, 15, output_daily_cohorts_NPPwood );  
+    SET_VECTOR_ELT(out_list, 16, output_daily_cohorts_NSC );  
+    SET_VECTOR_ELT(out_list, 17, output_daily_cohorts_seedC );  
+    SET_VECTOR_ELT(out_list, 18, output_daily_cohorts_leafC );  
+    SET_VECTOR_ELT(out_list, 19, output_daily_cohorts_rootC );  
+    SET_VECTOR_ELT(out_list, 20, output_daily_cohorts_SW_C );  
+    SET_VECTOR_ELT(out_list, 21, output_daily_cohorts_HW_C );  
+    SET_VECTOR_ELT(out_list, 22, output_daily_cohorts_NSN );  
+    SET_VECTOR_ELT(out_list, 23, output_daily_cohorts_seedN );  
+    SET_VECTOR_ELT(out_list, 24, output_daily_cohorts_leafN );  
+    SET_VECTOR_ELT(out_list, 25, output_daily_cohorts_rootN );  
+    SET_VECTOR_ELT(out_list, 26, output_daily_cohorts_SW_N );  
+    SET_VECTOR_ELT(out_list, 27, output_daily_cohorts_HW_N );  
+    SET_VECTOR_ELT(out_list, 28, output_annual_tile);
+    SET_VECTOR_ELT(out_list, 29, output_annual_cohorts_year);
+    SET_VECTOR_ELT(out_list, 30, output_annual_cohorts_cID);
+    SET_VECTOR_ELT(out_list, 31, output_annual_cohorts_PFT);
+    SET_VECTOR_ELT(out_list, 32, output_annual_cohorts_layer);
+    SET_VECTOR_ELT(out_list, 33, output_annual_cohorts_density);
+    SET_VECTOR_ELT(out_list, 34, output_annual_cohorts_flayer);
+    SET_VECTOR_ELT(out_list, 35, output_annual_cohorts_DBH);
+    SET_VECTOR_ELT(out_list, 36, output_annual_cohorts_dDBH);
+    SET_VECTOR_ELT(out_list, 37, output_annual_cohorts_height);
+    SET_VECTOR_ELT(out_list, 38, output_annual_cohorts_age);
+    SET_VECTOR_ELT(out_list, 39, output_annual_cohorts_BA);
+    SET_VECTOR_ELT(out_list, 40, output_annual_cohorts_dBA);
+    SET_VECTOR_ELT(out_list, 41, output_annual_cohorts_Acrown);
+    SET_VECTOR_ELT(out_list, 42, output_annual_cohorts_Aleaf);
+    SET_VECTOR_ELT(out_list, 43, output_annual_cohorts_nsc);
+    SET_VECTOR_ELT(out_list, 44, output_annual_cohorts_nsn);
+    SET_VECTOR_ELT(out_list, 45, output_annual_cohorts_seedC);
+    SET_VECTOR_ELT(out_list, 46, output_annual_cohorts_leafC);
+    SET_VECTOR_ELT(out_list, 47, output_annual_cohorts_rootC);
+    SET_VECTOR_ELT(out_list, 48, output_annual_cohorts_sapwC);
+    SET_VECTOR_ELT(out_list, 49, output_annual_cohorts_woodC);
+    SET_VECTOR_ELT(out_list, 50, output_annual_cohorts_treeG);
+    SET_VECTOR_ELT(out_list, 51, output_annual_cohorts_fseed);
+    SET_VECTOR_ELT(out_list, 52, output_annual_cohorts_fleaf);
+    SET_VECTOR_ELT(out_list, 53, output_annual_cohorts_froot);
+    SET_VECTOR_ELT(out_list, 54, output_annual_cohorts_fwood);
+    SET_VECTOR_ELT(out_list, 55, output_annual_cohorts_GPP);
+    SET_VECTOR_ELT(out_list, 56, output_annual_cohorts_NPP);
+    SET_VECTOR_ELT(out_list, 57, output_annual_cohorts_Rauto);
+    SET_VECTOR_ELT(out_list, 58, output_annual_cohorts_Nupt);
+    SET_VECTOR_ELT(out_list, 59, output_annual_cohorts_Nfix);
+    SET_VECTOR_ELT(out_list, 60, output_annual_cohorts_n_deadtrees);
+    SET_VECTOR_ELT(out_list, 61, output_annual_cohorts_c_deadtrees);
+    SET_VECTOR_ELT(out_list, 62, output_annual_cohorts_deathrate);
     
-    UNPROTECT(65);
+    UNPROTECT(64);
 
     return out_list;
 }
diff --git a/vignettes/biomee_use.Rmd b/vignettes/biomee_use.Rmd
index e41155c4..a1ff41c6 100644
--- a/vignettes/biomee_use.Rmd
+++ b/vignettes/biomee_use.Rmd
@@ -23,7 +23,7 @@ The `rsofun` package and framework includes two main models. The `pmodel` and `b
 
 ## Demo data
 
-The package includes two demo datasets to run and validate pmodel output. These files can be directly loaded into your workspace by typing:
+The package includes two demo datasets to run. These files can be directly loaded into your workspace by typing:
 
 ```{r eval = FALSE}
 library(rsofun)
@@ -218,9 +218,7 @@ ggplot() +
             aes(x = year, y = GPP),
             color = "grey50") +
   theme_classic() + 
-  labs(x = "Year", y = "GPP") +
-  geom_hline(yintercept = biomee_validation_2$data[[1]]$targets_obs[1],
-              lty=2)        # plot observation
+  labs(x = "Year", y = "GPP")
 
 ggplot() +
   geom_line(data = biomee_p_model_output,
@@ -229,7 +227,5 @@ ggplot() +
             aes(x = year, y = plantC),
             color = "grey50") +
   theme_classic() + 
-  labs(x = "Year", y = "plantC") +
-  geom_hline(yintercept = biomee_validation_2$data[[1]]$targets_obs[4],
-             lty = 2)        # plot observation
+  labs(x = "Year", y = "plantC")
 ```
\ No newline at end of file