From cd11062309a9f8239ec75c1cdb39372791727f8b Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Fri, 13 Dec 2024 18:55:29 +0100
Subject: [PATCH 01/11] bugfix BII

---
 .../bii_target_apr24/declarations.gms         |  1 -
 .../bii_target_apr24/equations.gms            |  4 +--
 .../bii_target_apr24/preloop.gms              |  5 ++--
 .../bii_target_apr24/presolve.gms             | 28 +++++++++----------
 .../bii_target_apr24/realization.gms          |  1 +
 .../bii_target_apr24/scaling.gms              |  8 ++++++
 6 files changed, 27 insertions(+), 20 deletions(-)
 create mode 100644 modules/44_biodiversity/bii_target_apr24/scaling.gms

diff --git a/modules/44_biodiversity/bii_target_apr24/declarations.gms b/modules/44_biodiversity/bii_target_apr24/declarations.gms
index 12eb55056c..74275701ab 100644
--- a/modules/44_biodiversity/bii_target_apr24/declarations.gms
+++ b/modules/44_biodiversity/bii_target_apr24/declarations.gms
@@ -16,7 +16,6 @@ positive variables
 parameters
  p44_bii_lower_bound(t,i,biome44) Interpolated lower bound for BII over time (1)
  p44_start_value(i,biome44)       Start value for BII lower bound (1)
- p44_target_value(i,biome44)      Target value for BII lower bound (1)
  i44_biome_share(j,biome44)       Share of biome type in each spatial unit (1)
  i44_biome_area_reg(i,biome44)    Area of range-rarity weighted biome type in each region (mio. ha)
 ;
diff --git a/modules/44_biodiversity/bii_target_apr24/equations.gms b/modules/44_biodiversity/bii_target_apr24/equations.gms
index 19c78350ce..cee2680c23 100644
--- a/modules/44_biodiversity/bii_target_apr24/equations.gms
+++ b/modules/44_biodiversity/bii_target_apr24/equations.gms
@@ -14,13 +14,13 @@
  q44_bii(i2,biome44)$(i44_biome_area_reg(i2,biome44) > 0) .. 
          v44_bii(i2,biome44)
           =e=
-          sum((cell(i2,j2),potnatveg,landcover44), vm_bv(j2,landcover44,potnatveg) * f44_rr_layer(j2) * i44_biome_share(j2,biome44))
+          sum((cell(i2,j2),landcover44,potnatveg), vm_bv(j2,landcover44,potnatveg) * f44_rr_layer(j2) * i44_biome_share(j2,biome44))
           / i44_biome_area_reg(i2,biome44);
 
 *' For each of the 71 biomes, the BII has to meet a minium level based on `s44_bii_lower_bound`.
 *' `v44_bii_missing` is a technical variable to maintain feasibility in case `v44_bii` cannot be increased.
           
- q44_bii_target(i2,biome44)$(i44_biome_area_reg(i2,biome44) > 0) ..          
+ q44_bii_target(i2,biome44) ..          
           v44_bii(i2,biome44) + v44_bii_missing(i2,biome44) =g= sum(ct, p44_bii_lower_bound(ct,i2,biome44));
 
 *' Costs accrue only for `v44_bii_missing`. In the best case costs should be zero or close to zero.
diff --git a/modules/44_biodiversity/bii_target_apr24/preloop.gms b/modules/44_biodiversity/bii_target_apr24/preloop.gms
index f296466db2..b751628362 100644
--- a/modules/44_biodiversity/bii_target_apr24/preloop.gms
+++ b/modules/44_biodiversity/bii_target_apr24/preloop.gms
@@ -6,8 +6,9 @@
 *** |  Contact: magpie@pik-potsdam.de
 
 * Calculate biome share
-i44_biome_share(j,biome44) = 
-   (f44_biome_area(j,biome44) + 1e-10) / sum(biome44_2, f44_biome_area(j,biome44_2) + 1e-10);
+i44_biome_share(j,biome44) = 0;
+i44_biome_share(j,biome44)$(sum(biome44_2, f44_biome_area(j,biome44_2)) > 0) = 
+   f44_biome_area(j,biome44) / sum(biome44_2, f44_biome_area(j,biome44_2));
 
 * Set i44_biome_area_reg
 i44_biome_area_reg(i,biome44) = 
diff --git a/modules/44_biodiversity/bii_target_apr24/presolve.gms b/modules/44_biodiversity/bii_target_apr24/presolve.gms
index f9cd49db45..e3f7741c3b 100644
--- a/modules/44_biodiversity/bii_target_apr24/presolve.gms
+++ b/modules/44_biodiversity/bii_target_apr24/presolve.gms
@@ -13,33 +13,31 @@ loop(i,
       v44_bii_missing.fx(i,biome44) = 0;
     else
       v44_bii.l(i,biome44) = 
-        sum((cell(i,j),potnatveg,landcover44), vm_bv.l(j,landcover44,potnatveg) * f44_rr_layer(j) * i44_biome_share(j,biome44))
+        sum((cell(i,j),landcover44,potnatveg), vm_bv.l(j,landcover44,potnatveg) * f44_rr_layer(j) * i44_biome_share(j,biome44))
         / i44_biome_area_reg(i,biome44);
     );
   );
 );
 
+if (m_year(t) = s44_start_year AND s44_bii_lower_bound > 0,
 * The start value for the linear interpolation is the BII at biome level in the start year.
-p44_start_value(i,biome44)$(m_year(t) = s44_start_year) = v44_bii.l(i,biome44);
+  p44_start_value(i,biome44) = v44_bii.l(i,biome44);
 * The target value for the linear interpolation is the lower bound defined in `s44_bii_lower_bound`.
-p44_target_value(i,biome44) = s44_bii_lower_bound;
+* Linear increase of BII target values at biome level from start year to target year, and constant values thereafter.
+  p44_bii_lower_bound(t2,i,biome44) = p44_start_value(i,biome44) + ((m_year(t2) - s44_start_year) / (s44_target_year - s44_start_year)) * (s44_bii_lower_bound - p44_start_value(i,biome44));
+  p44_bii_lower_bound(t2,i,biome44)$(m_year(t2) > s44_target_year) = s44_bii_lower_bound;
+* Avoid implausible values
+  p44_bii_lower_bound(t2,i,biome44)$(p44_bii_lower_bound(t2,i,biome44) >= 1) = 1;
+  p44_bii_lower_bound(t2,i,biome44)$(m_year(t2) < s44_start_year) = 0;
+  p44_bii_lower_bound(t2,i,biome44)$(i44_biome_area_reg(i,biome44) <= 0) = 0;
+);
 
 if (m_year(t) <= sm_fix_SSP2,
  v44_bii.lo(i,biome44) = 0;
 else
-* Linear increase of BII target values at biome level from start year to target year, and constant values thereafter.
-  p44_bii_lower_bound(t2,i,biome44) = p44_start_value(i,biome44) + ((m_year(t2) - s44_start_year) / (s44_target_year - s44_start_year)) * (p44_target_value(i,biome44) - p44_start_value(i,biome44));
-  p44_bii_lower_bound(t2,i,biome44)$(m_year(t2) > s44_target_year) = p44_target_value(i,biome44);
+  v44_bii.lo(i,biome44) = p44_bii_lower_bound(t,i,biome44);
   if(c44_bii_decrease = 0,
-    p44_bii_lower_bound(t,i,biome44)$(v44_bii.l(i,biome44) >= p44_target_value(i,biome44)) = v44_bii.l(i,biome44);   
-  elseif c44_bii_decrease = 1,
-    p44_bii_lower_bound(t,i,biome44)$(v44_bii.l(i,biome44) >= p44_target_value(i,biome44)) = p44_target_value(i,biome44);
+    v44_bii.lo(i,biome44)$(v44_bii.l(i,biome44) >= s44_bii_lower_bound) = v44_bii.l(i,biome44);   
   );
-  p44_bii_lower_bound(t,i,biome44)$(p44_bii_lower_bound(t,i,biome44) >= 1) = 1;
-  p44_bii_lower_bound(t,i,biome44)$(m_year(t) < s44_start_year) = 0;
-  p44_bii_lower_bound(t,i,biome44)$(i44_biome_area_reg(i,biome44) <= 0) = 0;
-* The lower bound of `v44_bii` is set to `p44_bii_lower_bound` to avoid a reduction of BII in combination with `v44_bii_missing`.
-  v44_bii.lo(i,biome44) = p44_bii_lower_bound(t,i,biome44);
-  display p44_bii_lower_bound;
 );
 
diff --git a/modules/44_biodiversity/bii_target_apr24/realization.gms b/modules/44_biodiversity/bii_target_apr24/realization.gms
index 1b1298ab5a..f8fbd4252e 100644
--- a/modules/44_biodiversity/bii_target_apr24/realization.gms
+++ b/modules/44_biodiversity/bii_target_apr24/realization.gms
@@ -19,6 +19,7 @@ $Ifi "%phase%" == "sets" $include "./modules/44_biodiversity/bii_target_apr24/se
 $Ifi "%phase%" == "declarations" $include "./modules/44_biodiversity/bii_target_apr24/declarations.gms"
 $Ifi "%phase%" == "input" $include "./modules/44_biodiversity/bii_target_apr24/input.gms"
 $Ifi "%phase%" == "equations" $include "./modules/44_biodiversity/bii_target_apr24/equations.gms"
+$Ifi "%phase%" == "scaling" $include "./modules/44_biodiversity/bii_target_apr24/scaling.gms"
 $Ifi "%phase%" == "preloop" $include "./modules/44_biodiversity/bii_target_apr24/preloop.gms"
 $Ifi "%phase%" == "presolve" $include "./modules/44_biodiversity/bii_target_apr24/presolve.gms"
 $Ifi "%phase%" == "postsolve" $include "./modules/44_biodiversity/bii_target_apr24/postsolve.gms"
diff --git a/modules/44_biodiversity/bii_target_apr24/scaling.gms b/modules/44_biodiversity/bii_target_apr24/scaling.gms
new file mode 100644
index 0000000000..e7cc6622f7
--- /dev/null
+++ b/modules/44_biodiversity/bii_target_apr24/scaling.gms
@@ -0,0 +1,8 @@
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  authors, and contributors see CITATION.cff file. This file is part
+*** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
+*** |  AGPL-3.0, you are granted additional permissions described in the
+*** |  MAgPIE License Exception, version 1.0 (see LICENSE file).
+*** |  Contact: magpie@pik-potsdam.de
+
+q44_bii.scale(i,biome44) = 1e20;

From bec50ed9d0f80c2675da002cbf708350f96ece1b Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 08:52:16 +0100
Subject: [PATCH 02/11] test

---
 modules/10_land/landmatrix_dec18/scaling.gms | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/10_land/landmatrix_dec18/scaling.gms b/modules/10_land/landmatrix_dec18/scaling.gms
index 7cf3630df2..a3971421e3 100644
--- a/modules/10_land/landmatrix_dec18/scaling.gms
+++ b/modules/10_land/landmatrix_dec18/scaling.gms
@@ -6,3 +6,6 @@
 *** |  Contact: magpie@pik-potsdam.de
 
 vm_landdiff.scale = 10e3;
+
+q10_transition_to.scale(j,land_to) = 1e20;
+q10_transition_from.scale(j,land_from) = 1e20;

From a8299bf2ccfe9b1c8ee6026e7afc825c1eeb4fa2 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 10:02:59 +0100
Subject: [PATCH 03/11] update scaling

---
 config/default.cfg                           |  2 +-
 modules/10_land/landmatrix_dec18/scaling.gms |  3 ---
 modules/80_optimization/nlp_apr17/input.gms  |  2 +-
 modules/80_optimization/nlp_apr17/solve.gms  | 12 +++++++-----
 modules/80_optimization/nlp_par/input.gms    |  2 +-
 modules/80_optimization/nlp_par/solve.gms    | 12 +++++++-----
 6 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/config/default.cfg b/config/default.cfg
index 8b5941ac4c..6581d686f4 100644
--- a/config/default.cfg
+++ b/config/default.cfg
@@ -2086,7 +2086,7 @@ cfg$gms$c80_nlp_solver <- "conopt4"              # def = conopt4
 
 # * 1: using optfile for specified solver settings
 # * 0: default settings (optfile will be ignored)
-cfg$gms$s80_optfile <- 0 # def = 0
+cfg$gms$s80_optfile <- 1 # def = 1
 
 # * Optional second solve statement (0=off, 1=on)
 cfg$gms$s80_secondsolve <- 0 # def = 0
diff --git a/modules/10_land/landmatrix_dec18/scaling.gms b/modules/10_land/landmatrix_dec18/scaling.gms
index a3971421e3..7cf3630df2 100644
--- a/modules/10_land/landmatrix_dec18/scaling.gms
+++ b/modules/10_land/landmatrix_dec18/scaling.gms
@@ -6,6 +6,3 @@
 *** |  Contact: magpie@pik-potsdam.de
 
 vm_landdiff.scale = 10e3;
-
-q10_transition_to.scale(j,land_to) = 1e20;
-q10_transition_from.scale(j,land_from) = 1e20;
diff --git a/modules/80_optimization/nlp_apr17/input.gms b/modules/80_optimization/nlp_apr17/input.gms
index 5c645af1c2..07264b2e09 100644
--- a/modules/80_optimization/nlp_apr17/input.gms
+++ b/modules/80_optimization/nlp_apr17/input.gms
@@ -7,6 +7,6 @@
 
 scalars
     s80_maxiter         maximal solve iterations if modelstat is > 2 (1)    / 30 /
-    s80_optfile         switch to use specfied solver settings (1)          / 0 /
+    s80_optfile         switch to use specfied solver settings (1)          / 1 /
     s80_secondsolve     second solve statement (binary)                     / 0 / 
 ;
diff --git a/modules/80_optimization/nlp_apr17/solve.gms b/modules/80_optimization/nlp_apr17/solve.gms
index 7dc3b1198d..3567030625 100644
--- a/modules/80_optimization/nlp_apr17/solve.gms
+++ b/modules/80_optimization/nlp_apr17/solve.gms
@@ -19,14 +19,16 @@ magpie.solprint  = 0 ;
 magpie.holdfixed = 1 ;
 
 $onecho > conopt4.opt
-Lim_Variable = 1.e25
+Tol_Scale_Min = 1e-4;
 $offecho
 
 $onecho > conopt4.op2
-Flg_Prep = FALSE
+Tol_Scale_Min = 1e-4;
+Lim_Variable = 1.e25
 $offecho
 
 $onecho > conopt4.op3
+Tol_Scale_Min = 1e-4;
 Flg_NoDefc = TRUE
 $offecho
 
@@ -58,15 +60,15 @@ if (magpie.modelstat > 2,
       option nlp = conopt4;
       magpie.optfile = 0;
     elseif s80_resolve_option = 2,
-      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE";
+      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 1";
       option nlp = conopt4;
       magpie.optfile = 1;
     elseif s80_resolve_option = 3,
-      display "Modelstat > 2 | Retry solve with CONOPT4 w/o preprocessing";
+      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 2";
       option nlp = conopt4;
       magpie.optfile = 2;
     elseif s80_resolve_option = 4,
-      display "Modelstat > 2 | Retry solve with CONOPT4 w/o search for definitional constraints";
+      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 3";
       option nlp = conopt4;
       magpie.optfile = 3;
     elseif s80_resolve_option = 5,
diff --git a/modules/80_optimization/nlp_par/input.gms b/modules/80_optimization/nlp_par/input.gms
index 1004040b7e..f282808333 100644
--- a/modules/80_optimization/nlp_par/input.gms
+++ b/modules/80_optimization/nlp_par/input.gms
@@ -7,6 +7,6 @@
 
 scalars
     s80_maxiter         maximal solve iterations if modelstat is > 2 (1)  / 30 /
-    s80_optfile         switch to use specfied solver settings (1)        / 0 /
+    s80_optfile         switch to use specfied solver settings (1)        / 1 /
     s80_secondsolve     second solve statement (binary)                   / 0 / 
 ;
diff --git a/modules/80_optimization/nlp_par/solve.gms b/modules/80_optimization/nlp_par/solve.gms
index 60d888a72e..5c4afe4c53 100644
--- a/modules/80_optimization/nlp_par/solve.gms
+++ b/modules/80_optimization/nlp_par/solve.gms
@@ -22,14 +22,16 @@ magpie.holdfixed = 1 ;
 magpie.savepoint = 0;
 
 $onecho > conopt4.opt
-Lim_Variable = 1.e25
+Tol_Scale_Min = 1e-4;
 $offecho
 
 $onecho > conopt4.op2
-Flg_Prep = FALSE
+Tol_Scale_Min = 1e-4;
+Lim_Variable = 1.e25
 $offecho
 
 $onecho > conopt4.op3
+Tol_Scale_Min = 1e-4;
 Flg_NoDefc = TRUE
 $offecho
 
@@ -107,15 +109,15 @@ repeat
           option nlp = conopt4;
           magpie.optfile = 0;         
         elseif p80_resolve_option(h) = 2, 
-          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE";
+          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 1";
           option nlp = conopt4;
           magpie.optfile = 1;         
         elseif p80_resolve_option(h) = 3, 
-          display "Modelstat > 2 | Retry solve with CONOPT4 w/o preprocessing";
+          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 2";
           option nlp = conopt4;
           magpie.optfile = 2;         
         elseif p80_resolve_option(h) = 4, 
-          display "Modelstat > 2 | Retry solve with CONOPT4 w/o search for definitional constraints";
+          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 3";
           option nlp = conopt4;
           magpie.optfile = 3;         
         elseif p80_resolve_option(h) = 5, 

From 6846f7a763c74bc8fcb3502a932387a3d97c54ce Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 10:56:44 +0100
Subject: [PATCH 04/11] test

---
 config/default.cfg                                   | 2 +-
 modules/44_biodiversity/bii_target_apr24/scaling.gms | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/default.cfg b/config/default.cfg
index 6581d686f4..8b5941ac4c 100644
--- a/config/default.cfg
+++ b/config/default.cfg
@@ -2086,7 +2086,7 @@ cfg$gms$c80_nlp_solver <- "conopt4"              # def = conopt4
 
 # * 1: using optfile for specified solver settings
 # * 0: default settings (optfile will be ignored)
-cfg$gms$s80_optfile <- 1 # def = 1
+cfg$gms$s80_optfile <- 0 # def = 0
 
 # * Optional second solve statement (0=off, 1=on)
 cfg$gms$s80_secondsolve <- 0 # def = 0
diff --git a/modules/44_biodiversity/bii_target_apr24/scaling.gms b/modules/44_biodiversity/bii_target_apr24/scaling.gms
index e7cc6622f7..b954d39231 100644
--- a/modules/44_biodiversity/bii_target_apr24/scaling.gms
+++ b/modules/44_biodiversity/bii_target_apr24/scaling.gms
@@ -5,4 +5,4 @@
 *** |  MAgPIE License Exception, version 1.0 (see LICENSE file).
 *** |  Contact: magpie@pik-potsdam.de
 
-q44_bii.scale(i,biome44) = 1e20;
+q44_bii.scale(i,biome44) = 1e10;

From 9b3a59c54c43f18c995ac85bae4db5c715be2189 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 12:38:21 +0100
Subject: [PATCH 05/11] revert

---
 modules/80_optimization/nlp_apr17/input.gms |  2 +-
 modules/80_optimization/nlp_apr17/solve.gms | 12 +++++-------
 modules/80_optimization/nlp_par/input.gms   |  2 +-
 modules/80_optimization/nlp_par/solve.gms   | 12 +++++-------
 4 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/modules/80_optimization/nlp_apr17/input.gms b/modules/80_optimization/nlp_apr17/input.gms
index 07264b2e09..5c645af1c2 100644
--- a/modules/80_optimization/nlp_apr17/input.gms
+++ b/modules/80_optimization/nlp_apr17/input.gms
@@ -7,6 +7,6 @@
 
 scalars
     s80_maxiter         maximal solve iterations if modelstat is > 2 (1)    / 30 /
-    s80_optfile         switch to use specfied solver settings (1)          / 1 /
+    s80_optfile         switch to use specfied solver settings (1)          / 0 /
     s80_secondsolve     second solve statement (binary)                     / 0 / 
 ;
diff --git a/modules/80_optimization/nlp_apr17/solve.gms b/modules/80_optimization/nlp_apr17/solve.gms
index 3567030625..7dc3b1198d 100644
--- a/modules/80_optimization/nlp_apr17/solve.gms
+++ b/modules/80_optimization/nlp_apr17/solve.gms
@@ -19,16 +19,14 @@ magpie.solprint  = 0 ;
 magpie.holdfixed = 1 ;
 
 $onecho > conopt4.opt
-Tol_Scale_Min = 1e-4;
+Lim_Variable = 1.e25
 $offecho
 
 $onecho > conopt4.op2
-Tol_Scale_Min = 1e-4;
-Lim_Variable = 1.e25
+Flg_Prep = FALSE
 $offecho
 
 $onecho > conopt4.op3
-Tol_Scale_Min = 1e-4;
 Flg_NoDefc = TRUE
 $offecho
 
@@ -60,15 +58,15 @@ if (magpie.modelstat > 2,
       option nlp = conopt4;
       magpie.optfile = 0;
     elseif s80_resolve_option = 2,
-      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 1";
+      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE";
       option nlp = conopt4;
       magpie.optfile = 1;
     elseif s80_resolve_option = 3,
-      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 2";
+      display "Modelstat > 2 | Retry solve with CONOPT4 w/o preprocessing";
       option nlp = conopt4;
       magpie.optfile = 2;
     elseif s80_resolve_option = 4,
-      display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 3";
+      display "Modelstat > 2 | Retry solve with CONOPT4 w/o search for definitional constraints";
       option nlp = conopt4;
       magpie.optfile = 3;
     elseif s80_resolve_option = 5,
diff --git a/modules/80_optimization/nlp_par/input.gms b/modules/80_optimization/nlp_par/input.gms
index f282808333..1004040b7e 100644
--- a/modules/80_optimization/nlp_par/input.gms
+++ b/modules/80_optimization/nlp_par/input.gms
@@ -7,6 +7,6 @@
 
 scalars
     s80_maxiter         maximal solve iterations if modelstat is > 2 (1)  / 30 /
-    s80_optfile         switch to use specfied solver settings (1)        / 1 /
+    s80_optfile         switch to use specfied solver settings (1)        / 0 /
     s80_secondsolve     second solve statement (binary)                   / 0 / 
 ;
diff --git a/modules/80_optimization/nlp_par/solve.gms b/modules/80_optimization/nlp_par/solve.gms
index 5c4afe4c53..60d888a72e 100644
--- a/modules/80_optimization/nlp_par/solve.gms
+++ b/modules/80_optimization/nlp_par/solve.gms
@@ -22,16 +22,14 @@ magpie.holdfixed = 1 ;
 magpie.savepoint = 0;
 
 $onecho > conopt4.opt
-Tol_Scale_Min = 1e-4;
+Lim_Variable = 1.e25
 $offecho
 
 $onecho > conopt4.op2
-Tol_Scale_Min = 1e-4;
-Lim_Variable = 1.e25
+Flg_Prep = FALSE
 $offecho
 
 $onecho > conopt4.op3
-Tol_Scale_Min = 1e-4;
 Flg_NoDefc = TRUE
 $offecho
 
@@ -109,15 +107,15 @@ repeat
           option nlp = conopt4;
           magpie.optfile = 0;         
         elseif p80_resolve_option(h) = 2, 
-          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 1";
+          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE";
           option nlp = conopt4;
           magpie.optfile = 1;         
         elseif p80_resolve_option(h) = 3, 
-          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 2";
+          display "Modelstat > 2 | Retry solve with CONOPT4 w/o preprocessing";
           option nlp = conopt4;
           magpie.optfile = 2;         
         elseif p80_resolve_option(h) = 4, 
-          display "Modelstat > 2 | Retry solve with CONOPT4 OPTFILE 3";
+          display "Modelstat > 2 | Retry solve with CONOPT4 w/o search for definitional constraints";
           option nlp = conopt4;
           magpie.optfile = 3;         
         elseif p80_resolve_option(h) = 5, 

From 55f248b4fba4ef023b4802352342bcce4fa314a7 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 12:43:41 +0100
Subject: [PATCH 06/11] cleanup

---
 CHANGELOG.md                                  |  2 +-
 .../bii_target/declarations.gms               |  1 -
 .../44_biodiversity/bii_target/equations.gms  |  4 +--
 .../44_biodiversity/bii_target/preloop.gms    |  9 +++---
 .../44_biodiversity/bii_target/presolve.gms   | 31 +++++++++----------
 .../bii_target/realization.gms                |  1 +
 .../44_biodiversity/bii_target/scaling.gms    |  8 +++++
 7 files changed, 32 insertions(+), 24 deletions(-)
 create mode 100644 modules/44_biodiversity/bii_target/scaling.gms

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e8993779c4..65e1c7fa0f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,7 +16,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 -
 
 ### fixed
--
+- **44_biodiversity** bugfix i44_biome_share, code cleanup, added scaling of `q44_bii`
 
 ## [4.9.0] - 2024-12-05
 
diff --git a/modules/44_biodiversity/bii_target/declarations.gms b/modules/44_biodiversity/bii_target/declarations.gms
index 7f4552e059..4134fc41a6 100644
--- a/modules/44_biodiversity/bii_target/declarations.gms
+++ b/modules/44_biodiversity/bii_target/declarations.gms
@@ -16,7 +16,6 @@ positive variables
 parameters
  p44_bii_lower_bound(t,i,biome44) Interpolated lower bound for BII over time (1)
  p44_start_value(i,biome44)       Start value for BII lower bound (1)
- p44_target_value(i,biome44)      Target value for BII lower bound (1)
  i44_biome_share(j,biome44)       Share of biome type in each spatial unit (1)
  i44_biome_area_reg(i,biome44)    Area of range-rarity weighted biome type in each region (mio. ha)
 ;
diff --git a/modules/44_biodiversity/bii_target/equations.gms b/modules/44_biodiversity/bii_target/equations.gms
index d372e2a7c3..f0ce37c2be 100644
--- a/modules/44_biodiversity/bii_target/equations.gms
+++ b/modules/44_biodiversity/bii_target/equations.gms
@@ -13,13 +13,13 @@
  q44_bii(i2,biome44)$(i44_biome_area_reg(i2,biome44) > 0) .. 
           v44_bii(i2,biome44)
           =e=
-          sum((cell(i2,j2),potnatveg,landcover44), vm_bv(j2,landcover44,potnatveg) * i44_biome_share(j2,biome44))
+          sum((cell(i2,j2),landcover44,potnatveg), vm_bv(j2,landcover44,potnatveg) * i44_biome_share(j2,biome44))
           / i44_biome_area_reg(i2,biome44);
 
 *' For each of the 71 biomes, the BII has to meet a minium level based on `s44_bii_lower_bound`.
 *' `v44_bii_missing` is a technical variable to maintain feasibility in case `v44_bii` cannot be increased.
           
- q44_bii_target(i2,biome44)$(i44_biome_area_reg(i2,biome44) > 0) ..          
+ q44_bii_target(i2,biome44) ..          
           v44_bii(i2,biome44) + v44_bii_missing(i2,biome44) =g= sum(ct, p44_bii_lower_bound(ct,i2,biome44));
 
 *' Costs accrue only for `v44_bii_missing`. In the best case costs should be zero or close to zero.
diff --git a/modules/44_biodiversity/bii_target/preloop.gms b/modules/44_biodiversity/bii_target/preloop.gms
index 962ffcaea1..b751628362 100644
--- a/modules/44_biodiversity/bii_target/preloop.gms
+++ b/modules/44_biodiversity/bii_target/preloop.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
@@ -6,11 +6,12 @@
 *** |  Contact: magpie@pik-potsdam.de
 
 * Calculate biome share
-i44_biome_share(j,biome44) = 
-   (f44_biome_area(j,biome44) + 1e-10) / sum(biome44_2, f44_biome_area(j,biome44_2) + 1e-10);
+i44_biome_share(j,biome44) = 0;
+i44_biome_share(j,biome44)$(sum(biome44_2, f44_biome_area(j,biome44_2)) > 0) = 
+   f44_biome_area(j,biome44) / sum(biome44_2, f44_biome_area(j,biome44_2));
 
 * Set i44_biome_area_reg
 i44_biome_area_reg(i,biome44) = 
-  sum((cell(i,j),land), pcm_land(j,land) * i44_biome_share(j,biome44));
+  sum((cell(i,j),land), pcm_land(j,land) * f44_rr_layer(j) * i44_biome_share(j,biome44));
 
 p44_bii_lower_bound(t,i,biome44) = 0;
diff --git a/modules/44_biodiversity/bii_target/presolve.gms b/modules/44_biodiversity/bii_target/presolve.gms
index edca9fc629..e3f7741c3b 100644
--- a/modules/44_biodiversity/bii_target/presolve.gms
+++ b/modules/44_biodiversity/bii_target/presolve.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
@@ -13,32 +13,31 @@ loop(i,
       v44_bii_missing.fx(i,biome44) = 0;
     else
       v44_bii.l(i,biome44) = 
-        sum((cell(i,j),potnatveg,landcover44), vm_bv.l(j,landcover44,potnatveg) * i44_biome_share(j,biome44))
+        sum((cell(i,j),landcover44,potnatveg), vm_bv.l(j,landcover44,potnatveg) * f44_rr_layer(j) * i44_biome_share(j,biome44))
         / i44_biome_area_reg(i,biome44);
     );
   );
 );
 
+if (m_year(t) = s44_start_year AND s44_bii_lower_bound > 0,
 * The start value for the linear interpolation is the BII at biome level in the start year.
-p44_start_value(i,biome44)$(m_year(t) = s44_start_year) = v44_bii.l(i,biome44);
+  p44_start_value(i,biome44) = v44_bii.l(i,biome44);
 * The target value for the linear interpolation is the lower bound defined in `s44_bii_lower_bound`.
-p44_target_value(i,biome44) = s44_bii_lower_bound;
+* Linear increase of BII target values at biome level from start year to target year, and constant values thereafter.
+  p44_bii_lower_bound(t2,i,biome44) = p44_start_value(i,biome44) + ((m_year(t2) - s44_start_year) / (s44_target_year - s44_start_year)) * (s44_bii_lower_bound - p44_start_value(i,biome44));
+  p44_bii_lower_bound(t2,i,biome44)$(m_year(t2) > s44_target_year) = s44_bii_lower_bound;
+* Avoid implausible values
+  p44_bii_lower_bound(t2,i,biome44)$(p44_bii_lower_bound(t2,i,biome44) >= 1) = 1;
+  p44_bii_lower_bound(t2,i,biome44)$(m_year(t2) < s44_start_year) = 0;
+  p44_bii_lower_bound(t2,i,biome44)$(i44_biome_area_reg(i,biome44) <= 0) = 0;
+);
 
 if (m_year(t) <= sm_fix_SSP2,
  v44_bii.lo(i,biome44) = 0;
 else
-* Linear increase of BII target values at biome level from start year to target year, and constant values thereafter.
-  p44_bii_lower_bound(t2,i,biome44) = p44_start_value(i,biome44) + ((m_year(t2) - s44_start_year) / (s44_target_year - s44_start_year)) * (p44_target_value(i,biome44) - p44_start_value(i,biome44));
-  p44_bii_lower_bound(t2,i,biome44)$(m_year(t2) > s44_target_year) = p44_target_value(i,biome44);
+  v44_bii.lo(i,biome44) = p44_bii_lower_bound(t,i,biome44);
   if(c44_bii_decrease = 0,
-    p44_bii_lower_bound(t,i,biome44)$(v44_bii.l(i,biome44) >= p44_target_value(i,biome44)) = v44_bii.l(i,biome44);   
-  elseif c44_bii_decrease = 1,
-    p44_bii_lower_bound(t,i,biome44)$(v44_bii.l(i,biome44) >= p44_target_value(i,biome44)) = p44_target_value(i,biome44);
+    v44_bii.lo(i,biome44)$(v44_bii.l(i,biome44) >= s44_bii_lower_bound) = v44_bii.l(i,biome44);   
   );
-  p44_bii_lower_bound(t,i,biome44)$(p44_bii_lower_bound(t,i,biome44) >= 1) = 1;
-  p44_bii_lower_bound(t,i,biome44)$(m_year(t) < s44_start_year) = 0;
-  p44_bii_lower_bound(t,i,biome44)$(i44_biome_area_reg(i,biome44) <= 0) = 0;
-* The lower bound of `v44_bii` is set to `p44_bii_lower_bound` to avoid a reduction of BII in combination with `v44_bii_missing`.
-  v44_bii.lo(i,biome44) = p44_bii_lower_bound(t,i,biome44);
-  display p44_bii_lower_bound;
 );
+
diff --git a/modules/44_biodiversity/bii_target/realization.gms b/modules/44_biodiversity/bii_target/realization.gms
index ff48d813de..7e1ef74dd4 100644
--- a/modules/44_biodiversity/bii_target/realization.gms
+++ b/modules/44_biodiversity/bii_target/realization.gms
@@ -19,6 +19,7 @@ $Ifi "%phase%" == "sets" $include "./modules/44_biodiversity/bii_target/sets.gms
 $Ifi "%phase%" == "declarations" $include "./modules/44_biodiversity/bii_target/declarations.gms"
 $Ifi "%phase%" == "input" $include "./modules/44_biodiversity/bii_target/input.gms"
 $Ifi "%phase%" == "equations" $include "./modules/44_biodiversity/bii_target/equations.gms"
+$Ifi "%phase%" == "scaling" $include "./modules/44_biodiversity/bii_target/scaling.gms"
 $Ifi "%phase%" == "preloop" $include "./modules/44_biodiversity/bii_target/preloop.gms"
 $Ifi "%phase%" == "presolve" $include "./modules/44_biodiversity/bii_target/presolve.gms"
 $Ifi "%phase%" == "postsolve" $include "./modules/44_biodiversity/bii_target/postsolve.gms"
diff --git a/modules/44_biodiversity/bii_target/scaling.gms b/modules/44_biodiversity/bii_target/scaling.gms
new file mode 100644
index 0000000000..b954d39231
--- /dev/null
+++ b/modules/44_biodiversity/bii_target/scaling.gms
@@ -0,0 +1,8 @@
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  authors, and contributors see CITATION.cff file. This file is part
+*** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
+*** |  AGPL-3.0, you are granted additional permissions described in the
+*** |  MAgPIE License Exception, version 1.0 (see LICENSE file).
+*** |  Contact: magpie@pik-potsdam.de
+
+q44_bii.scale(i,biome44) = 1e10;

From b3a7ba7c669b5f3eb61e2a15bc1e8360579b175f Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 12:46:08 +0100
Subject: [PATCH 07/11] bugfix

---
 modules/44_biodiversity/bii_target/preloop.gms            | 2 +-
 modules/44_biodiversity/bii_target/presolve.gms           | 2 +-
 modules/44_biodiversity/bii_target_apr24/declarations.gms | 2 +-
 modules/44_biodiversity/bii_target_apr24/equations.gms    | 2 +-
 modules/44_biodiversity/bii_target_apr24/input.gms        | 2 +-
 modules/44_biodiversity/bii_target_apr24/postsolve.gms    | 2 +-
 modules/44_biodiversity/bii_target_apr24/preloop.gms      | 2 +-
 modules/44_biodiversity/bii_target_apr24/presolve.gms     | 2 +-
 modules/44_biodiversity/bii_target_apr24/realization.gms  | 2 +-
 modules/44_biodiversity/bii_target_apr24/sets.gms         | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/44_biodiversity/bii_target/preloop.gms b/modules/44_biodiversity/bii_target/preloop.gms
index b751628362..7cab290a5d 100644
--- a/modules/44_biodiversity/bii_target/preloop.gms
+++ b/modules/44_biodiversity/bii_target/preloop.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target/presolve.gms b/modules/44_biodiversity/bii_target/presolve.gms
index e3f7741c3b..c5d6f8dd08 100644
--- a/modules/44_biodiversity/bii_target/presolve.gms
+++ b/modules/44_biodiversity/bii_target/presolve.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/declarations.gms b/modules/44_biodiversity/bii_target_apr24/declarations.gms
index 74275701ab..01351790de 100644
--- a/modules/44_biodiversity/bii_target_apr24/declarations.gms
+++ b/modules/44_biodiversity/bii_target_apr24/declarations.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/equations.gms b/modules/44_biodiversity/bii_target_apr24/equations.gms
index cee2680c23..4c34556907 100644
--- a/modules/44_biodiversity/bii_target_apr24/equations.gms
+++ b/modules/44_biodiversity/bii_target_apr24/equations.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/input.gms b/modules/44_biodiversity/bii_target_apr24/input.gms
index 042c3e03fb..099ce53b9d 100644
--- a/modules/44_biodiversity/bii_target_apr24/input.gms
+++ b/modules/44_biodiversity/bii_target_apr24/input.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/postsolve.gms b/modules/44_biodiversity/bii_target_apr24/postsolve.gms
index 1974fa3da6..3d8723d8f2 100644
--- a/modules/44_biodiversity/bii_target_apr24/postsolve.gms
+++ b/modules/44_biodiversity/bii_target_apr24/postsolve.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/preloop.gms b/modules/44_biodiversity/bii_target_apr24/preloop.gms
index b751628362..7cab290a5d 100644
--- a/modules/44_biodiversity/bii_target_apr24/preloop.gms
+++ b/modules/44_biodiversity/bii_target_apr24/preloop.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/presolve.gms b/modules/44_biodiversity/bii_target_apr24/presolve.gms
index e3f7741c3b..c5d6f8dd08 100644
--- a/modules/44_biodiversity/bii_target_apr24/presolve.gms
+++ b/modules/44_biodiversity/bii_target_apr24/presolve.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/realization.gms b/modules/44_biodiversity/bii_target_apr24/realization.gms
index f8fbd4252e..6963031558 100644
--- a/modules/44_biodiversity/bii_target_apr24/realization.gms
+++ b/modules/44_biodiversity/bii_target_apr24/realization.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the
diff --git a/modules/44_biodiversity/bii_target_apr24/sets.gms b/modules/44_biodiversity/bii_target_apr24/sets.gms
index 4e19d2313d..69751ecef9 100644
--- a/modules/44_biodiversity/bii_target_apr24/sets.gms
+++ b/modules/44_biodiversity/bii_target_apr24/sets.gms
@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
 *** |  authors, and contributors see CITATION.cff file. This file is part
 *** |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
 *** |  AGPL-3.0, you are granted additional permissions described in the

From 043e72abd1b5926f525dccb567857d8f13816e10 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 12:47:45 +0100
Subject: [PATCH 08/11] bugfix

---
 modules/44_biodiversity/bii_target/preloop.gms  | 2 +-
 modules/44_biodiversity/bii_target/presolve.gms | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/44_biodiversity/bii_target/preloop.gms b/modules/44_biodiversity/bii_target/preloop.gms
index 7cab290a5d..8d54341f40 100644
--- a/modules/44_biodiversity/bii_target/preloop.gms
+++ b/modules/44_biodiversity/bii_target/preloop.gms
@@ -12,6 +12,6 @@ i44_biome_share(j,biome44)$(sum(biome44_2, f44_biome_area(j,biome44_2)) > 0) =
 
 * Set i44_biome_area_reg
 i44_biome_area_reg(i,biome44) = 
-  sum((cell(i,j),land), pcm_land(j,land) * f44_rr_layer(j) * i44_biome_share(j,biome44));
+  sum((cell(i,j),land), pcm_land(j,land) * i44_biome_share(j,biome44));
 
 p44_bii_lower_bound(t,i,biome44) = 0;
diff --git a/modules/44_biodiversity/bii_target/presolve.gms b/modules/44_biodiversity/bii_target/presolve.gms
index c5d6f8dd08..288cd7de62 100644
--- a/modules/44_biodiversity/bii_target/presolve.gms
+++ b/modules/44_biodiversity/bii_target/presolve.gms
@@ -13,7 +13,7 @@ loop(i,
       v44_bii_missing.fx(i,biome44) = 0;
     else
       v44_bii.l(i,biome44) = 
-        sum((cell(i,j),landcover44,potnatveg), vm_bv.l(j,landcover44,potnatveg) * f44_rr_layer(j) * i44_biome_share(j,biome44))
+        sum((cell(i,j),landcover44,potnatveg), vm_bv.l(j,landcover44,potnatveg) * i44_biome_share(j,biome44))
         / i44_biome_area_reg(i,biome44);
     );
   );

From 0a68dcf2bc779de952c8b6d96cc8733f3169ff8b Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 12:51:17 +0100
Subject: [PATCH 09/11] bugfix

---
 scripts/start/test_runs.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/scripts/start/test_runs.R b/scripts/start/test_runs.R
index d61b2133c6..e1c67aa543 100644
--- a/scripts/start/test_runs.R
+++ b/scripts/start/test_runs.R
@@ -75,24 +75,28 @@ codeCheck <- FALSE
 
 ### Business-as-usual
 cfg <- fsecScenario(scenario = "c_BAU")
+cfg$force_replace <- TRUE
 cfg$results_folder <- "output/:title:"
 cfg$results_folder_highres <- "output"
 start_run(cfg = cfg, codeCheck = codeCheck)
 
 ### NatureSparing
 cfg <- fsecScenario(scenario = "b_NatureSparing")
+cfg$force_replace <- TRUE
 cfg$results_folder <- "output/:title:"
 cfg$results_folder_highres <- "output"
 start_run(cfg = cfg, codeCheck = codeCheck)
 
 ### LandscapeElements
 cfg <- fsecScenario(scenario = "a_LandscapeElements")
+cfg$force_replace <- TRUE
 cfg$results_folder <- "output/:title:"
 cfg$results_folder_highres <- "output"
 start_run(cfg = cfg, codeCheck = codeCheck)
 
 ### FSDP Scenario
 cfg <- fsecScenario(scenario = "e_FSDP")
+cfg$force_replace <- TRUE
 cfg$results_folder <- "output/:title:"
 cfg$results_folder_highres <- "output"
 start_run(cfg = cfg, codeCheck = codeCheck)

From fb8fe706d4d095051e775f30b3b80424e5a51b69 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Sat, 14 Dec 2024 19:37:29 +0100
Subject: [PATCH 10/11] lock_timeout

---
 CHANGELOG.md                                    | 2 +-
 scripts/start/projects/project_FSEC_Scenarios.R | 2 +-
 scripts/start_functions.R                       | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 65e1c7fa0f..62acae1b54 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 -
 
 ### added
--
+- **start_scripts** added `lock_timeout` as option to `start_run` function
 
 ### removed
 -
diff --git a/scripts/start/projects/project_FSEC_Scenarios.R b/scripts/start/projects/project_FSEC_Scenarios.R
index 6ef4c15a87..2d54116ae0 100644
--- a/scripts/start/projects/project_FSEC_Scenarios.R
+++ b/scripts/start/projects/project_FSEC_Scenarios.R
@@ -39,5 +39,5 @@ for (scenarioName in c(
 
     # Start runs
     cfg <- fsecScenario(scenario = scenarioName)
-    start_run(cfg = cfg, codeCheck = codeCheck)
+    start_run(cfg = cfg, codeCheck = codeCheck, lock_timeout = 6)
 }
diff --git a/scripts/start_functions.R b/scripts/start_functions.R
index af8da9ddb1..dc616e690e 100644
--- a/scripts/start_functions.R
+++ b/scripts/start_functions.R
@@ -202,7 +202,7 @@ download_and_update <- function(cfg) {
 }
 
 
-start_run <- function(cfg, scenario = NULL, codeCheck = TRUE, lock_model = TRUE) {
+start_run <- function(cfg, scenario = NULL, codeCheck = TRUE, lock_model = TRUE, lock_timeout = 1) {
 
   timePrepareStart <- Sys.time()
 
@@ -222,7 +222,7 @@ start_run <- function(cfg, scenario = NULL, codeCheck = TRUE, lock_model = TRUE)
   withr::defer(setwd(maindir))
 
   if(lock_model) {
-    lock_id <- gms::model_lock(timeout1 = 1)
+    lock_id <- gms::model_lock(timeout1 = lock_timeout)
     withr::defer(gms::model_unlock(lock_id))
   }
 

From 72dffb6448e0d1fc6378276a564a78edd087de1e Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Fri, 20 Dec 2024 14:04:35 +0100
Subject: [PATCH 11/11] increase R package versions

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c96ed5b726..77156ed8ae 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,14 +21,14 @@ Imports:
     m4fsdp,
     madrat,
     magclass (>= 6.14.0),
-    magpie4 (>= 2.15.8),
+    magpie4 (>= 2.16.1),
     MagpieNCGains,
     magpiesets (>= 0.46.1),
     mip,
     mrcommons,
     patchwork,
     piamenv (>= 0.5.5),
-    piamInterfaces (>= 0.37.1),
+    piamInterfaces (>= 0.40.3),
     piamutils,
     quitte,
     raster,