From 6c7bb73d1d864ba192c3ace3ee30b3a6da7f6372 Mon Sep 17 00:00:00 2001
From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
Date: Fri, 14 Mar 2025 10:15:20 +0100
Subject: [PATCH 01/14] renv 1.1.2

---
 renv/activate.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/renv/activate.R b/renv/activate.R
index 13923c562..c9f594259 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.1.0"
+  version <- "1.1.2"
   attr(version, "sha") <- NULL
 
   # the project directory

From 415f5081c4c82c5691b9883b701d9ba44c55c2c9 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Mon, 5 May 2025 09:08:44 +0200
Subject: [PATCH 02/14] bugfix missing files 80_optimization

---
 modules/80_optimization/lp_nlp_apr17/preloop.gms     | 9 +++++++++
 modules/80_optimization/lp_nlp_apr17/realization.gms | 1 +
 modules/80_optimization/nlp_par/preloop.gms          | 9 +++++++++
 modules/80_optimization/nlp_par/realization.gms      | 1 +
 4 files changed, 20 insertions(+)
 create mode 100644 modules/80_optimization/lp_nlp_apr17/preloop.gms
 create mode 100644 modules/80_optimization/nlp_par/preloop.gms

diff --git a/modules/80_optimization/lp_nlp_apr17/preloop.gms b/modules/80_optimization/lp_nlp_apr17/preloop.gms
new file mode 100644
index 000000000..115c631cc
--- /dev/null
+++ b/modules/80_optimization/lp_nlp_apr17/preloop.gms
@@ -0,0 +1,9 @@
+*** |  (C) 2008-2025 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
+
+File optfile /conopt4.opt/;
+
diff --git a/modules/80_optimization/lp_nlp_apr17/realization.gms b/modules/80_optimization/lp_nlp_apr17/realization.gms
index 1ca3296af..2de255020 100644
--- a/modules/80_optimization/lp_nlp_apr17/realization.gms
+++ b/modules/80_optimization/lp_nlp_apr17/realization.gms
@@ -22,5 +22,6 @@
 *####################### R SECTION START (PHASES) ##############################
 $Ifi "%phase%" == "declarations" $include "./modules/80_optimization/lp_nlp_apr17/declarations.gms"
 $Ifi "%phase%" == "input" $include "./modules/80_optimization/lp_nlp_apr17/input.gms"
+$Ifi "%phase%" == "preloop" $include "./modules/80_optimization/lp_nlp_apr17/preloop.gms"
 $Ifi "%phase%" == "solve" $include "./modules/80_optimization/lp_nlp_apr17/solve.gms"
 *######################## R SECTION END (PHASES) ###############################
diff --git a/modules/80_optimization/nlp_par/preloop.gms b/modules/80_optimization/nlp_par/preloop.gms
new file mode 100644
index 000000000..115c631cc
--- /dev/null
+++ b/modules/80_optimization/nlp_par/preloop.gms
@@ -0,0 +1,9 @@
+*** |  (C) 2008-2025 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
+
+File optfile /conopt4.opt/;
+
diff --git a/modules/80_optimization/nlp_par/realization.gms b/modules/80_optimization/nlp_par/realization.gms
index 85345eb91..397caff86 100644
--- a/modules/80_optimization/nlp_par/realization.gms
+++ b/modules/80_optimization/nlp_par/realization.gms
@@ -18,5 +18,6 @@
 *####################### R SECTION START (PHASES) ##############################
 $Ifi "%phase%" == "declarations" $include "./modules/80_optimization/nlp_par/declarations.gms"
 $Ifi "%phase%" == "input" $include "./modules/80_optimization/nlp_par/input.gms"
+$Ifi "%phase%" == "preloop" $include "./modules/80_optimization/nlp_par/preloop.gms"
 $Ifi "%phase%" == "solve" $include "./modules/80_optimization/nlp_par/solve.gms"
 *######################## R SECTION END (PHASES) ###############################

From c99c1a877885c2442356660b09e05b7a19f59e16 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Mon, 5 May 2025 22:28:37 +0200
Subject: [PATCH 03/14] bugfix BII + updates ScenarioMIP

---
 config/scenario_config.csv                    |  2 +-
 modules/44_biodiversity/bii_target/sets.gms   | 10 ++-
 modules/44_biodiversity/bv_btc_mar21/sets.gms | 10 ++-
 scripts/start/projects/project_ScenarioMIP.R  | 86 ++++++++++++++-----
 4 files changed, 82 insertions(+), 26 deletions(-)

diff --git a/config/scenario_config.csv b/config/scenario_config.csv
index 8e0390f65..4c613c49a 100755
--- a/config/scenario_config.csv
+++ b/config/scenario_config.csv
@@ -4,7 +4,7 @@ gms$c09_pop_scenario;;;;SSP1;SSP2;SSP3;SSP4;SSP5;SSP1;SSP1;SSP1;SSP1;SSP1;SSP1;S
 gms$c09_gdp_scenario;;;;SSP1;SSP2;SSP3;SSP4;SSP5;SSP1;SDP_EI;SDP_RC;SDP_MC;SSP1;SSP1;SSP2;SSP3;SSP5;;;;;;;;;;;;;;;;;;;;
 gms$c09_pal_scenario;;;;SSP1;SSP2;SSP3;SSP4;SSP5;SSP1;SSP2;SSP1;SSP1;SSP1;;;;;;;;;;;;;;;;;;;;;;;;
 gms$c14_yields_scenario;cc;nocc;nocc_hist;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
-gms$c15_food_scenario;;;;SSP1;SSP2;SSP3;SSP4;SSP5;SSP1;SSP2;SSP1;SSP1;SSP1;;;;;;;;;;;;;;;;;;;;;;;;
+gms$c15_food_scenario;;;;SSP1;SSP2;SSP3;SSP4;SSP5;SSP1;SSP2;SSP1;SSP1;SSP2;;;;;;;;;;;;;;;;;;;;;;;;
 gms$s15_rumdairy_scp_substitution;;;;0;0;0;0;0;0;0.5;0;0;0;;;;;;;;;;;;;;;;;;;;;;;;
 gms$s15_food_subst_functional_form;;;;1;1;1;1;1;;2;;;;;;;;;;;;;;;;;;;;;;;;;;;
 gms$s15_food_substitution_start;;;;;;;;;;2025;;;;;;;;;;;;;;;;;;;;;;;;;;;
diff --git a/modules/44_biodiversity/bii_target/sets.gms b/modules/44_biodiversity/bii_target/sets.gms
index dfd525875..87712f439 100644
--- a/modules/44_biodiversity/bii_target/sets.gms
+++ b/modules/44_biodiversity/bii_target/sets.gms
@@ -19,10 +19,16 @@ sets
   ac_to_bii_class_secd(ac,bii_class_secd) Mapping between forest ageclasses and bii coefficent land cover classes 
   / (ac0,ac5,ac10,ac15,ac20,ac25,ac30)    . (secd_young)
     (ac35,ac40,ac45,ac50,ac55,ac60,
-       ac65,ac70,ac75,ac80,ac85,ac90,
+     ac65,ac70,ac75,ac80,ac85,ac90,
      ac95,ac100,ac105,ac110,ac115,
      ac120,ac125,ac130,ac135,ac140,
-     ac145,ac150,ac155,acx)         . (secd_mature) /
+     ac145,ac150,ac155,ac160,ac165,
+     ac170,ac175,ac180,ac185,ac190,
+     ac195,ac200,ac205,ac210,ac215,
+     ac220,ac225,ac230,ac235,ac240,
+     ac245,ac250,ac255,ac260,ac265,
+     ac270,ac275,ac280,ac285,ac290,
+     ac295,ac300,acx)                      . (secd_mature) /
   
   biome44 biomes
   / AA1,AA2,AA4,AA7,AA8,AA10,AA11,AA14,AN11,AT1,AT2,AT7,AT8,AT9,AT10,AT12,AT13,AT14,IM1,
diff --git a/modules/44_biodiversity/bv_btc_mar21/sets.gms b/modules/44_biodiversity/bv_btc_mar21/sets.gms
index 2b8b68d73..9e02784e6 100644
--- a/modules/44_biodiversity/bv_btc_mar21/sets.gms
+++ b/modules/44_biodiversity/bv_btc_mar21/sets.gms
@@ -19,9 +19,15 @@ sets
   ac_to_bii_class_secd(ac,bii_class_secd) Mapping between forest ageclasses and bii coefficent land cover classes 
   / (ac0,ac5,ac10,ac15,ac20,ac25,ac30)    . (secd_young)
     (ac35,ac40,ac45,ac50,ac55,ac60,
-       ac65,ac70,ac75,ac80,ac85,ac90,
+     ac65,ac70,ac75,ac80,ac85,ac90,
      ac95,ac100,ac105,ac110,ac115,
      ac120,ac125,ac130,ac135,ac140,
-     ac145,ac150,ac155,acx)         . (secd_mature) /
+     ac145,ac150,ac155,ac160,ac165,
+     ac170,ac175,ac180,ac185,ac190,
+     ac195,ac200,ac205,ac210,ac215,
+     ac220,ac225,ac230,ac235,ac240,
+     ac245,ac250,ac255,ac260,ac265,
+     ac270,ac275,ac280,ac285,ac290,
+     ac295,ac300,acx)                      . (secd_mature) /
   
 ;
diff --git a/scripts/start/projects/project_ScenarioMIP.R b/scripts/start/projects/project_ScenarioMIP.R
index c985a8a82..735f265bd 100644
--- a/scripts/start/projects/project_ScenarioMIP.R
+++ b/scripts/start/projects/project_ScenarioMIP.R
@@ -30,7 +30,7 @@ cfg$force_replace <- TRUE
 .title <- function(cfg, ...) return(paste(cfg$info$flag, sep="_",...))
 
 #download default input data
-cfg$input[["report_coupling"]] <- "SMIPv04_report_coupling.tgz"
+cfg$input[["report_coupling"]] <- "SMIPv06_report_coupling.tgz"
 download_and_update(cfg)
 
 cfg$gms$c56_pollutant_prices <- "coupling"
@@ -47,8 +47,8 @@ cfg$gms$s32_annual_aff_limit <- 0.03
 cfg$title <- .title(cfg, "H-SSP3-rollBack")
 cfg <- setScenario(cfg,c("SSP3","NPI-revert","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2150"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-H-SSP3-rollBack-def-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-H-SSP3-rollBack-def-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-H-SSP3-rollBack-def-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-H-SSP3-rollBack-def-rem-7.mif"
 cfg$gms$c15_food_scenario <- "SSP2"
 cfg$gms$s32_npi_ndc_reversal <- 2030
 cfg$gms$s35_npi_ndc_reversal <- 2030
@@ -62,8 +62,8 @@ start_run(cfg, codeCheck = FALSE)
 cfg$title <- .title(cfg, "M-SSP2-NPi2025")
 cfg <- setScenario(cfg,c("SSP2","NPI","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2150"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-M-SSP2-NPi2025-def-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-M-SSP2-NPi2025-def-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-M-SSP2-NPi2025-def-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-M-SSP2-NPi2025-def-rem-7.mif"
 cfg$gms$s29_treecover_target <- 0
 cfg$gms$s44_bii_target <- 0
 cfg$gms$s59_scm_target <- 0
@@ -74,8 +74,8 @@ start_run(cfg, codeCheck = FALSE)
 cfg$title <- .title(cfg, "ML-SSP2-PkBudg1500")
 cfg <- setScenario(cfg,c("SSP2","NPI","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2040"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-ML-SSP2-PkBudg1500-def-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-ML-SSP2-PkBudg1500-def-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-ML-SSP2-EcPrice310-var-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-ML-SSP2-EcPrice310-var-rem-7.mif"
 cfg$gms$s29_treecover_target <- 0
 cfg$gms$s44_bii_target <- 0
 cfg$gms$s59_scm_target <- 0
@@ -86,8 +86,8 @@ start_run(cfg, codeCheck = FALSE)
 cfg$title <- .title(cfg, "L-SSP2-PkBudg1000")
 cfg <- setScenario(cfg,c("SSP2","NDC","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-L-SSP2-PkBudg1000-def-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-L-SSP2-PkBudg1000-def-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
 cfg$gms$s29_treecover_scenario_start <- 2030
 cfg$gms$s29_treecover_target <- 0.01
 cfg$gms$s44_bii_target <- 0
@@ -100,8 +100,8 @@ start_run(cfg, codeCheck = FALSE)
 cfg$title <- .title(cfg, "VLHO-SSP2-EcBudg400")
 cfg <- setScenario(cfg,c("SSP2","NPI","AR-plant","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-VLHO-SSP2-EcBudg400-var_plantation-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-VLHO-SSP2-EcBudg400-var_plantation-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-VLHO-SSP2-EcPrice1250-var-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLHO-SSP2-EcPrice1250-var-rem-7.mif"
 cfg$gms$s29_treecover_scenario_start <- 2030
 cfg$gms$s29_treecover_target <- 0.02
 cfg$gms$s44_bii_target <- 0
@@ -114,11 +114,11 @@ start_run(cfg, codeCheck = FALSE)
 cfg$title <- .title(cfg, "VLLO-SSP1-PkBudg650")
 cfg <- setScenario(cfg,c("VLLO","NDC","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-VLLO-SSP1-PkBudg650-def-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-VLLO-SSP1-PkBudg650-def-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPrice500-def-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPrice500-def-rem-7.mif"
 cfg$gms$s29_treecover_scenario_start <- 2025
 cfg$gms$s29_treecover_target <- 0.02
-cfg$gms$s44_bii_target <- 0.77
+cfg$gms$s44_bii_target <- 0.76
 cfg$gms$s59_scm_scenario_start <- 2025
 cfg$gms$s59_scm_target <- 0.2
 cfg$gms$c60_1stgen_biodem <- "const2030"
@@ -130,8 +130,8 @@ start_run(cfg, codeCheck = FALSE)
 cfg$title <- .title(cfg, "H-SSP3-NPi2025")
 cfg <- setScenario(cfg,c("SSP3","NPI","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2150"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-M-SSP3-NPi2025-var-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-M-SSP3-NPi2025-var-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-M-SSP3-NPi2025-def-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-M-SSP3-NPi2025-def-rem-7.mif"
 cfg$gms$c15_food_scenario <- "SSP2"
 cfg$gms$s29_treecover_target <- 0
 cfg$gms$s44_bii_target <- 0
@@ -139,12 +139,56 @@ cfg$gms$s59_scm_target <- 0
 cfg$gms$c60_1stgen_biodem <- "const2030"
 start_run(cfg, codeCheck = FALSE)
 
+#L-SSP2-PkBudg1000 - varBII72
+cfg$title <- .title(cfg, "L-SSP2-PkBudg1000_varBIItarget72")
+cfg <- setScenario(cfg,c("SSP2","NDC","AR-natveg","nocc_hist"))
+cfg$gms$c56_mute_ghgprices_until <- "y2030"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
+cfg$gms$s29_treecover_scenario_start <- 2030
+cfg$gms$s29_treecover_target <- 0.01
+cfg$gms$s44_bii_target <- 0.72
+cfg$gms$s59_scm_scenario_start <- 2030
+cfg$gms$s59_scm_target <- 0.1
+cfg$gms$c60_1stgen_biodem <- "const2030"
+start_run(cfg, codeCheck = FALSE)
+
+#L-SSP2-PkBudg1000 - varBII74
+cfg$title <- .title(cfg, "L-SSP2-PkBudg1000_varBIItarget74")
+cfg <- setScenario(cfg,c("SSP2","NDC","AR-natveg","nocc_hist"))
+cfg$gms$c56_mute_ghgprices_until <- "y2030"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
+cfg$gms$s29_treecover_scenario_start <- 2030
+cfg$gms$s29_treecover_target <- 0.01
+cfg$gms$s44_bii_target <- 0.74
+cfg$gms$s59_scm_scenario_start <- 2030
+cfg$gms$s59_scm_target <- 0.1
+cfg$gms$c60_1stgen_biodem <- "const2030"
+start_run(cfg, codeCheck = FALSE)
+
+#L-SSP2-PkBudg1000 - nobii decrease
+cfg$title <- .title(cfg, "L-SSP2-PkBudg1000_varBIInodecrease")
+cfg <- setScenario(cfg,c("SSP2","NDC","AR-natveg","nocc_hist"))
+cfg$gms$c56_mute_ghgprices_until <- "y2030"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
+cfg$gms$s29_treecover_scenario_start <- 2030
+cfg$gms$s29_treecover_target <- 0.01
+cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 0
+cfg$gms$s59_scm_scenario_start <- 2030
+cfg$gms$s59_scm_target <- 0.1
+cfg$gms$c60_1stgen_biodem <- "const2030"
+start_run(cfg, codeCheck = FALSE)
+cfg$gms$c44_bii_decrease <- 1
+
 #VLHO-SSP2-EcBudg400-ARnatveg
 cfg$title <- .title(cfg, "VLHO-SSP2-EcBudg400-ARnatveg")
 cfg <- setScenario(cfg,c("SSP2","NPI","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-VLHO-SSP2-EcBudg400-var_plantation-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-VLHO-SSP2-EcBudg400-var_plantation-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-VLHO-SSP2-EcBudg400-var_natveg-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLHO-SSP2-EcBudg400-var_natveg-rem-7.mif"
 cfg$gms$s29_treecover_scenario_start <- 2030
 cfg$gms$s29_treecover_target <- 0.02
 cfg$gms$s44_bii_target <- 0
@@ -157,11 +201,11 @@ start_run(cfg, codeCheck = FALSE)
 cfg$title <- .title(cfg, "VLLO-SSP1-PkBudg650-noAnnualAffLimit")
 cfg <- setScenario(cfg,c("VLLO","NDC","AR-natveg","nocc_hist"))
 cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv04-VLLO-SSP1-PkBudg650-def-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv04-VLLO-SSP1-PkBudg650-def-rem-7.mif"
+cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPrice500-def-rem-7.mif"
+cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPrice500-def-rem-7.mif"
 cfg$gms$s29_treecover_scenario_start <- 2025
 cfg$gms$s29_treecover_target <- 0.02
-cfg$gms$s44_bii_target <- 0.77
+cfg$gms$s44_bii_target <- 0.76
 cfg$gms$s59_scm_scenario_start <- 2025
 cfg$gms$s59_scm_target <- 0.2
 cfg$gms$c60_1stgen_biodem <- "const2030"

From 3a7339de7327d1a68e441739af07868059429fb7 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Tue, 6 May 2025 14:42:58 +0200
Subject: [PATCH 04/14] changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0dfdf833a..be3bee5ba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 ### fixed
 - **18_residues** fixed equation for cluster level production of crop residues in flexreg_apr16 realization
+- **44_biodiversity** expanded age-classes from 150 to 300 years in line with `ac` set. This bugfix is crucial for the BII indicator.
 
 
 ## [4.10.0] - 2025-04-03

From 511c4299c01eb4cce37f42abe58acb600ca28716 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Tue, 6 May 2025 14:52:53 +0200
Subject: [PATCH 05/14] changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be3bee5ba..bbe2025a8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **default.cfg** input data upgraded from rev4.117 to rev4.118, default for bioenergy demand and GHG prices changed from R32M46 to R34M410, `rcp4p5` used for SSP2-NPi2025 in line with MAGICC climate outcome and REMIND assumptions.
 - **default.cfg** changed running magpie by default with optfile for specified solver settings (Tol_Optimality)
 - **script/start/test_runs.R** Test runs adjusted based on availability from coupled runs for R34M410. 
+- **scenario_config.csv** SSP2 food system assumptions for ScenarioMIP VLLO to avoid sudden jump of calorie intake after 2025
 
 ### added
 - **default.cfg** added option to set Tol_Optimality (GAMS solver setting) to a certain value (GAMS-default 1e-7, new MAgPIE-default 1e-8)

From 2f70400aeae07eeae4b410e5369ac34f01e75bd6 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Thu, 8 May 2025 10:36:06 +0200
Subject: [PATCH 06/14] update SceanrioMIP start script

---
 scripts/start/projects/project_ScenarioMIP.R | 69 +++++++-------------
 1 file changed, 22 insertions(+), 47 deletions(-)

diff --git a/scripts/start/projects/project_ScenarioMIP.R b/scripts/start/projects/project_ScenarioMIP.R
index 735f265bd..2c6d98007 100644
--- a/scripts/start/projects/project_ScenarioMIP.R
+++ b/scripts/start/projects/project_ScenarioMIP.R
@@ -21,7 +21,8 @@ source("scripts/start_functions.R")
 source("config/default.cfg")
 
 # create additional information to describe the runs
-cfg$info$flag <- "SMIP61"
+cfg$info$flag <- "SMIP63"
+cfg$qos <- "standby_dayMax"
 
 cfg$results_folder <- "output/:title:"
 cfg$force_replace <- TRUE
@@ -54,6 +55,8 @@ cfg$gms$s32_npi_ndc_reversal <- 2030
 cfg$gms$s35_npi_ndc_reversal <- 2030
 cfg$gms$s29_treecover_target <- 0
 cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 1
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_target <- 0
 cfg$gms$c60_1stgen_biodem <- "const2030"
 start_run(cfg, codeCheck = FALSE)
@@ -66,6 +69,8 @@ cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-M-SSP2-NPi2025-d
 cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-M-SSP2-NPi2025-def-rem-7.mif"
 cfg$gms$s29_treecover_target <- 0
 cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 1
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_target <- 0
 cfg$gms$c60_1stgen_biodem <- "const2030"
 start_run(cfg, codeCheck = FALSE)
@@ -78,6 +83,8 @@ cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-ML-SSP2-EcPrice3
 cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-ML-SSP2-EcPrice310-var-rem-7.mif"
 cfg$gms$s29_treecover_target <- 0
 cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 1
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_target <- 0
 cfg$gms$c60_1stgen_biodem <- "const2030"
 start_run(cfg, codeCheck = FALSE)
@@ -91,6 +98,8 @@ cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPric
 cfg$gms$s29_treecover_scenario_start <- 2030
 cfg$gms$s29_treecover_target <- 0.01
 cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 0
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_scenario_start <- 2030
 cfg$gms$s59_scm_target <- 0.1
 cfg$gms$c60_1stgen_biodem <- "const2030"
@@ -105,6 +114,8 @@ cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLHO-SSP2-EcP
 cfg$gms$s29_treecover_scenario_start <- 2030
 cfg$gms$s29_treecover_target <- 0.02
 cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 0
+cfg$gms$s44_start_year <- 2050
 cfg$gms$s59_scm_scenario_start <- 2030
 cfg$gms$s59_scm_target <- 0.2
 cfg$gms$c60_1stgen_biodem <- "const2030"
@@ -118,7 +129,9 @@ cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPric
 cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPrice500-def-rem-7.mif"
 cfg$gms$s29_treecover_scenario_start <- 2025
 cfg$gms$s29_treecover_target <- 0.02
-cfg$gms$s44_bii_target <- 0.76
+cfg$gms$s44_bii_target <- 0.7
+cfg$gms$c44_bii_decrease <- 0
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_scenario_start <- 2025
 cfg$gms$s59_scm_target <- 0.2
 cfg$gms$c60_1stgen_biodem <- "const2030"
@@ -135,54 +148,12 @@ cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-M-SSP3-NPi202
 cfg$gms$c15_food_scenario <- "SSP2"
 cfg$gms$s29_treecover_target <- 0
 cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 1
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_target <- 0
 cfg$gms$c60_1stgen_biodem <- "const2030"
 start_run(cfg, codeCheck = FALSE)
 
-#L-SSP2-PkBudg1000 - varBII72
-cfg$title <- .title(cfg, "L-SSP2-PkBudg1000_varBIItarget72")
-cfg <- setScenario(cfg,c("SSP2","NDC","AR-natveg","nocc_hist"))
-cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
-cfg$gms$s29_treecover_scenario_start <- 2030
-cfg$gms$s29_treecover_target <- 0.01
-cfg$gms$s44_bii_target <- 0.72
-cfg$gms$s59_scm_scenario_start <- 2030
-cfg$gms$s59_scm_target <- 0.1
-cfg$gms$c60_1stgen_biodem <- "const2030"
-start_run(cfg, codeCheck = FALSE)
-
-#L-SSP2-PkBudg1000 - varBII74
-cfg$title <- .title(cfg, "L-SSP2-PkBudg1000_varBIItarget74")
-cfg <- setScenario(cfg,c("SSP2","NDC","AR-natveg","nocc_hist"))
-cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
-cfg$gms$s29_treecover_scenario_start <- 2030
-cfg$gms$s29_treecover_target <- 0.01
-cfg$gms$s44_bii_target <- 0.74
-cfg$gms$s59_scm_scenario_start <- 2030
-cfg$gms$s59_scm_target <- 0.1
-cfg$gms$c60_1stgen_biodem <- "const2030"
-start_run(cfg, codeCheck = FALSE)
-
-#L-SSP2-PkBudg1000 - nobii decrease
-cfg$title <- .title(cfg, "L-SSP2-PkBudg1000_varBIInodecrease")
-cfg <- setScenario(cfg,c("SSP2","NDC","AR-natveg","nocc_hist"))
-cfg$gms$c56_mute_ghgprices_until <- "y2030"
-cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
-cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-L-SSP2-PkPrice400-var-rem-7.mif"
-cfg$gms$s29_treecover_scenario_start <- 2030
-cfg$gms$s29_treecover_target <- 0.01
-cfg$gms$s44_bii_target <- 0
-cfg$gms$c44_bii_decrease <- 0
-cfg$gms$s59_scm_scenario_start <- 2030
-cfg$gms$s59_scm_target <- 0.1
-cfg$gms$c60_1stgen_biodem <- "const2030"
-start_run(cfg, codeCheck = FALSE)
-cfg$gms$c44_bii_decrease <- 1
-
 #VLHO-SSP2-EcBudg400-ARnatveg
 cfg$title <- .title(cfg, "VLHO-SSP2-EcBudg400-ARnatveg")
 cfg <- setScenario(cfg,c("SSP2","NPI","AR-natveg","nocc_hist"))
@@ -192,6 +163,8 @@ cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLHO-SSP2-EcB
 cfg$gms$s29_treecover_scenario_start <- 2030
 cfg$gms$s29_treecover_target <- 0.02
 cfg$gms$s44_bii_target <- 0
+cfg$gms$c44_bii_decrease <- 1
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_scenario_start <- 2030
 cfg$gms$s59_scm_target <- 0.2
 cfg$gms$c60_1stgen_biodem <- "const2030"
@@ -205,7 +178,9 @@ cfg$path_to_report_ghgprices <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPric
 cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLLO-SSP1-PkPrice500-def-rem-7.mif"
 cfg$gms$s29_treecover_scenario_start <- 2025
 cfg$gms$s29_treecover_target <- 0.02
-cfg$gms$s44_bii_target <- 0.76
+cfg$gms$s44_bii_target <- 0.7
+cfg$gms$c44_bii_decrease <- 0
+cfg$gms$s44_start_year <- 2030
 cfg$gms$s59_scm_scenario_start <- 2025
 cfg$gms$s59_scm_target <- 0.2
 cfg$gms$c60_1stgen_biodem <- "const2030"

From 559896ed4169da9a5b1b74d3d9458a210dcd81d7 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Thu, 8 May 2025 10:44:20 +0200
Subject: [PATCH 07/14] magpie4 version increase

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e91f4d21a..daedf343b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,7 +21,7 @@ Imports:
     m4fsdp,
     madrat,
     magclass (>= 6.14.0),
-    magpie4 (>= 2.22.1),
+    magpie4 (>= 2.22.9),
     MagpieNCGains,
     magpiesets (>= 0.46.1),
     mip,

From 5cc8469500af45f4be87c8a852089c6b11556726 Mon Sep 17 00:00:00 2001
From: florianh <humpenoeder@pik-potsdam.de>
Date: Thu, 8 May 2025 10:54:16 +0200
Subject: [PATCH 08/14] update SceanrioMIP start script

---
 scripts/start/projects/project_ScenarioMIP.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/start/projects/project_ScenarioMIP.R b/scripts/start/projects/project_ScenarioMIP.R
index 2c6d98007..df82bac0e 100644
--- a/scripts/start/projects/project_ScenarioMIP.R
+++ b/scripts/start/projects/project_ScenarioMIP.R
@@ -163,8 +163,8 @@ cfg$path_to_report_bioenergy    <- "input/REMIND_generic_C_SMIPv06-VLHO-SSP2-EcB
 cfg$gms$s29_treecover_scenario_start <- 2030
 cfg$gms$s29_treecover_target <- 0.02
 cfg$gms$s44_bii_target <- 0
-cfg$gms$c44_bii_decrease <- 1
-cfg$gms$s44_start_year <- 2030
+cfg$gms$c44_bii_decrease <- 0
+cfg$gms$s44_start_year <- 2050
 cfg$gms$s59_scm_scenario_start <- 2030
 cfg$gms$s59_scm_target <- 0.2
 cfg$gms$c60_1stgen_biodem <- "const2030"

From 3d379dbaf9d99ddf70c44629dd47b7d0075019eb Mon Sep 17 00:00:00 2001
From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
Date: Mon, 12 May 2025 10:22:00 +0200
Subject: [PATCH 09/14] request 24h

---
 scripts/slurmOutput.yml | 8 ++++----
 scripts/slurmStart.yml  | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/scripts/slurmOutput.yml b/scripts/slurmOutput.yml
index d3e35abe5..55d858c99 100644
--- a/scripts/slurmOutput.yml
+++ b/scripts/slurmOutput.yml
@@ -1,5 +1,5 @@
 slurmjobs:
-  SLURM standby: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --wrap=\"Rscript %SCRIPT\" --qos=standby --mem-per-cpu=5G --cpus-per-task=3"
-  SLURM standby highMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=standby --time=24:00:00 --mem-per-cpu=5G --cpus-per-task=16"
-  SLURM priority: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --time=200 --wrap=\"Rscript %SCRIPT\" --qos=priority --mem-per-cpu=5G --cpus-per-task=3"
-  SLURM priority highMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=priority --time=24:00:00  --mem-per-cpu=5G --cpus-per-task=16"
+  SLURM standby:          "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --mem-per-cpu=5G --cpus-per-task=3 --qos=standby --time=200"
+  SLURM standby highMem:  "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --mem-per-cpu=5G --cpus-per-task=16 --qos=standby --time=24:00:00"
+  SLURM priority:         "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --mem-per-cpu=5G --cpus-per-task=3 --qos=priority --time=200"
+  SLURM priority highMem: "sbatch --job-name=scripts-output --output=logs/out-%NAME-%j.out --error=logs/out-%NAME-%j.err --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --mem-per-cpu=5G --cpus-per-task=16 --qos=priority --time=24:00:00"
diff --git a/scripts/slurmStart.yml b/scripts/slurmStart.yml
index 264a8c341..ceb2776b5 100644
--- a/scripts/slurmStart.yml
+++ b/scripts/slurmStart.yml
@@ -1,4 +1,4 @@
 slurmjobs:
-  SLURM priority: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=priority --cpus-per-task=3"
-  SLURM standby: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=standby --cpus-per-task=3 --time=24:00:00"
-  SLURM medium: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --qos=medium --cpus-per-task=3"
+  SLURM priority: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --cpus-per-task=3 --time=24:00:00 --qos=priority"
+  SLURM standby:  "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --cpus-per-task=3 --time=24:00:00 --qos=standby"
+  SLURM medium:   "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --cpus-per-task=3 --time=24:00:00 --qos=medium"

From f38c89c4a1a5e8ca6f8cffa80c916e5eb0649e50 Mon Sep 17 00:00:00 2001
From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
Date: Mon, 12 May 2025 10:56:53 +0200
Subject: [PATCH 10/14] set --time in sh scripts

---
 config/default.cfg                                  |  9 +++------
 scripts/run_submit/submit_priority.sh               |  1 +
 scripts/run_submit/submit_priority_highMem.sh       |  1 +
 scripts/run_submit/submit_short.sh                  |  1 +
 scripts/run_submit/submit_short_highMem.sh          |  1 +
 scripts/run_submit/submit_standby.sh                |  1 +
 scripts/run_submit/submit_standby_dayMax.sh         | 11 -----------
 scripts/run_submit/submit_standby_highMem.sh        |  1 +
 scripts/run_submit/submit_standby_highMem_dayMax.sh | 11 -----------
 scripts/slurmStart.yml                              |  2 +-
 10 files changed, 10 insertions(+), 29 deletions(-)
 delete mode 100644 scripts/run_submit/submit_standby_dayMax.sh
 delete mode 100644 scripts/run_submit/submit_standby_highMem_dayMax.sh

diff --git a/config/default.cfg b/config/default.cfg
index 7776f0afb..dd496ae55 100644
--- a/config/default.cfg
+++ b/config/default.cfg
@@ -2212,14 +2212,11 @@ cfg$sequential <- NA
 # *   options:   short  (24h max, 3 CPUs, no preemption)
 # *              short_highMem (same as short but with 16 CPUs and 80GB of memory)
 # *              medium (1 week max, 3 CPUs, no preemption)
-# *              priority (immediate start, 3 CPUs, but slots limited to 5 in parallel)
+# *              priority (immediate start, 24h max, 3 CPUs, but slots limited to 5 in parallel)
 # *              priority_highMem (same as priority but with 16 CPUs and 80GB of memory)
-# *              standby (1 week max, 3 CPUs, preemption possible)
-# *              standby_dayMax (24h max, 3 CPUs, preemption possible)
-# *              standby_highMem_dayMax (same as standby_dayMax but with 16 CPUs and 80GB of memory)
+# *              standby (24h max, 3 CPUs, preemption possible)
 # *              standby_highMem (same as standby but with 16 CPUs and 80GB of memory)
-# *              NULL (educated guess of best option based
-# *                    available resources)
+# *              NULL (educated guess of best option based on available resources)
 cfg$qos <- NULL               # def = NULL
 
 # How should log information be treated?
diff --git a/scripts/run_submit/submit_priority.sh b/scripts/run_submit/submit_priority.sh
index b23c5bd67..60d00a38e 100644
--- a/scripts/run_submit/submit_priority.sh
+++ b/scripts/run_submit/submit_priority.sh
@@ -6,5 +6,6 @@
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=3
 #SBATCH --mem-per-cpu=5G
+#SBATCH --time=24:00:00
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_priority_highMem.sh b/scripts/run_submit/submit_priority_highMem.sh
index feae97160..cf749a944 100644
--- a/scripts/run_submit/submit_priority_highMem.sh
+++ b/scripts/run_submit/submit_priority_highMem.sh
@@ -6,5 +6,6 @@
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=16
 #SBATCH --mem-per-cpu=5G
+#SBATCH --time=24:00:00
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_short.sh b/scripts/run_submit/submit_short.sh
index 433ed3308..9092201c6 100644
--- a/scripts/run_submit/submit_short.sh
+++ b/scripts/run_submit/submit_short.sh
@@ -6,5 +6,6 @@
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=3
 #SBATCH --mem-per-cpu=5G
+#SBATCH --time=24:00:00
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_short_highMem.sh b/scripts/run_submit/submit_short_highMem.sh
index cf8f9669a..37be642e5 100644
--- a/scripts/run_submit/submit_short_highMem.sh
+++ b/scripts/run_submit/submit_short_highMem.sh
@@ -6,6 +6,7 @@
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=16
 #SBATCH --mem-per-cpu=5G
+#SBATCH --time=24:00:00
 
 Rscript submit.R
 
diff --git a/scripts/run_submit/submit_standby.sh b/scripts/run_submit/submit_standby.sh
index e3ab2dd5b..aa6b3673d 100644
--- a/scripts/run_submit/submit_standby.sh
+++ b/scripts/run_submit/submit_standby.sh
@@ -6,5 +6,6 @@
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=3
 #SBATCH --mem-per-cpu=5G
+#SBATCH --time=24:00:00
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_standby_dayMax.sh b/scripts/run_submit/submit_standby_dayMax.sh
deleted file mode 100644
index aa6b3673d..000000000
--- a/scripts/run_submit/submit_standby_dayMax.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-#SBATCH --qos=standby
-#SBATCH --job-name=mag-run
-#SBATCH --output=slurm.log
-#SBATCH --mail-type=END,FAIL
-#SBATCH --cpus-per-task=3
-#SBATCH --mem-per-cpu=5G
-#SBATCH --time=24:00:00
-
-Rscript submit.R
diff --git a/scripts/run_submit/submit_standby_highMem.sh b/scripts/run_submit/submit_standby_highMem.sh
index 4791ed844..674bc10f5 100644
--- a/scripts/run_submit/submit_standby_highMem.sh
+++ b/scripts/run_submit/submit_standby_highMem.sh
@@ -6,5 +6,6 @@
 #SBATCH --mail-type=END,FAIL
 #SBATCH --cpus-per-task=16
 #SBATCH --mem-per-cpu=5G
+#SBATCH --time=24:00:00
 
 Rscript submit.R
diff --git a/scripts/run_submit/submit_standby_highMem_dayMax.sh b/scripts/run_submit/submit_standby_highMem_dayMax.sh
deleted file mode 100644
index 674bc10f5..000000000
--- a/scripts/run_submit/submit_standby_highMem_dayMax.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-#SBATCH --qos=standby
-#SBATCH --job-name=mag-run
-#SBATCH --output=slurm.log
-#SBATCH --mail-type=END,FAIL
-#SBATCH --cpus-per-task=16
-#SBATCH --mem-per-cpu=5G
-#SBATCH --time=24:00:00
-
-Rscript submit.R
diff --git a/scripts/slurmStart.yml b/scripts/slurmStart.yml
index ceb2776b5..581079547 100644
--- a/scripts/slurmStart.yml
+++ b/scripts/slurmStart.yml
@@ -1,4 +1,4 @@
 slurmjobs:
   SLURM priority: "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --cpus-per-task=3 --time=24:00:00 --qos=priority"
   SLURM standby:  "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --cpus-per-task=3 --time=24:00:00 --qos=standby"
-  SLURM medium:   "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --cpus-per-task=3 --time=24:00:00 --qos=medium"
+  SLURM medium:   "sbatch --job-name=%NAME --output=logs/%NAME-%j.out --mail-type=END,FAIL --wrap=\"Rscript %SCRIPT\" --cpus-per-task=3 --qos=medium"

From 3d5daaafa5c9ffc8d420541338c2f5b71b063862 Mon Sep 17 00:00:00 2001
From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
Date: Mon, 12 May 2025 11:18:58 +0200
Subject: [PATCH 11/14] replace dayMax scripts

---
 CHANGELOG.md                                                 | 1 +
 scripts/output/extra/highres.R                               | 2 +-
 scripts/projects/fsec.R                                      | 2 +-
 scripts/start/projects/paper_peatlandTax.R                   | 2 +-
 scripts/start/projects/project_ABCDR.R                       | 2 +-
 scripts/start/projects/project_EAT2p0.R                      | 2 +-
 scripts/start/projects/project_EAT2p0_DeepDive.R             | 2 +-
 scripts/start/projects/project_EAT2p0_DeepDive_Sensitivity.R | 2 +-
 scripts/start/projects/project_ScenarioMIP.R                 | 2 +-
 scripts/start/projects/project_WetHorizons.R                 | 2 +-
 10 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bbe2025a8..64542ccff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **default.cfg** changed running magpie by default with optfile for specified solver settings (Tol_Optimality)
 - **script/start/test_runs.R** Test runs adjusted based on availability from coupled runs for R34M410. 
 - **scenario_config.csv** SSP2 food system assumptions for ScenarioMIP VLLO to avoid sudden jump of calorie intake after 2025
+- **scripts** request 24h for SLURM jobs (except for medium which still requests 7 days)
 
 ### added
 - **default.cfg** added option to set Tol_Optimality (GAMS solver setting) to a certain value (GAMS-default 1e-7, new MAgPIE-default 1e-8)
diff --git a/scripts/output/extra/highres.R b/scripts/output/extra/highres.R
index 3e515ef7b..074dfd2d1 100644
--- a/scripts/output/extra/highres.R
+++ b/scripts/output/extra/highres.R
@@ -104,7 +104,7 @@ highres <- function(cfg = cfg, res = "c1000", tc = NULL) {
   cfg$gms$s_use_gdx   <- 0
 
   #max resources for parallel runs
-  cfg$qos <- "standby_highMem_dayMax"
+  cfg$qos <- "standby_highMem"
 
   # set force download to FALSE
   # otherwise data is download again when calling start_run(), which overwrites
diff --git a/scripts/projects/fsec.R b/scripts/projects/fsec.R
index f57b6da79..6a72a0e00 100644
--- a/scripts/projects/fsec.R
+++ b/scripts/projects/fsec.R
@@ -214,7 +214,7 @@ fsecScenario <- function(scenario) {
   # general
   cfg$title       <- paste(v, scenario, sep = "")
   cfg$recalibrate <- FALSE
-  cfg$qos         <- "standby_highMem_dayMax"
+  cfg$qos         <- "standby_highMem"
   cfg$output      <- c("extra/highres",
                        "extra/disaggregation",
                        "projects/FSEC_nitrogenPollution",
diff --git a/scripts/start/projects/paper_peatlandTax.R b/scripts/start/projects/paper_peatlandTax.R
index 35579248a..593b86621 100644
--- a/scripts/start/projects/paper_peatlandTax.R
+++ b/scripts/start/projects/paper_peatlandTax.R
@@ -29,7 +29,7 @@ cfg$results_folder <- "output/:title:"
 cfg$results_folder_highres <- "output"
 cfg$force_replace <- TRUE
 cfg$force_download <- FALSE
-cfg$qos <- "standby_dayMax"
+cfg$qos <- "standby"
 
 # support function to create standardized title
 .title <- function(cfg, ...)
diff --git a/scripts/start/projects/project_ABCDR.R b/scripts/start/projects/project_ABCDR.R
index e7c6e9aaf..09cf74a8c 100644
--- a/scripts/start/projects/project_ABCDR.R
+++ b/scripts/start/projects/project_ABCDR.R
@@ -25,7 +25,7 @@ cfg$results_folder <- "output/:title:"
 cfg$force_replace <- TRUE
 cfg$force_download <- FALSE
 
-cfg$qos <- "standby_dayMax"
+cfg$qos <- "standby"
 
 # support function to create standardized title
 .title <- function(cfg, ...) return(paste(cfg$info$flag, sep="_",...))
diff --git a/scripts/start/projects/project_EAT2p0.R b/scripts/start/projects/project_EAT2p0.R
index ee615cdd9..e0d00e1ab 100644
--- a/scripts/start/projects/project_EAT2p0.R
+++ b/scripts/start/projects/project_EAT2p0.R
@@ -27,7 +27,7 @@ cfg$results_folder <- "output/:title::date:"
 cfg$force_download <- TRUE
 
 # Special outputs required for Deep Dive
-cfg$qos <- "standby_highMem_dayMax"
+cfg$qos <- "standby_highMem"
 cfg$output <- c(
   "output_check",
   # "extra/highres", # do manually on last magpie run
diff --git a/scripts/start/projects/project_EAT2p0_DeepDive.R b/scripts/start/projects/project_EAT2p0_DeepDive.R
index b91dfeb51..ecb377d05 100644
--- a/scripts/start/projects/project_EAT2p0_DeepDive.R
+++ b/scripts/start/projects/project_EAT2p0_DeepDive.R
@@ -27,7 +27,7 @@ cfg$results_folder <- "output/:title::date:"
 cfg$force_download <- TRUE
 
 # Special outputs required for Deep Dive
-cfg$qos <- "standby_highMem_dayMax"
+cfg$qos <- "standby_highMem"
 cfg$output <- c(
   "output_check",
   "extra/highres",
diff --git a/scripts/start/projects/project_EAT2p0_DeepDive_Sensitivity.R b/scripts/start/projects/project_EAT2p0_DeepDive_Sensitivity.R
index 30b000592..072b256c7 100644
--- a/scripts/start/projects/project_EAT2p0_DeepDive_Sensitivity.R
+++ b/scripts/start/projects/project_EAT2p0_DeepDive_Sensitivity.R
@@ -27,7 +27,7 @@ cfg$results_folder <- "output/:title::date:"
 cfg$force_download <- TRUE
 
 # Special outputs required for Deep Dive
-cfg$qos <- "standby_highMem_dayMax"
+cfg$qos <- "standby_highMem"
 cfg$output <- c(
   "output_check",
   "extra/disaggregation",
diff --git a/scripts/start/projects/project_ScenarioMIP.R b/scripts/start/projects/project_ScenarioMIP.R
index df82bac0e..acd68cacb 100644
--- a/scripts/start/projects/project_ScenarioMIP.R
+++ b/scripts/start/projects/project_ScenarioMIP.R
@@ -22,7 +22,7 @@ source("config/default.cfg")
 
 # create additional information to describe the runs
 cfg$info$flag <- "SMIP63"
-cfg$qos <- "standby_dayMax"
+cfg$qos <- "standby"
 
 cfg$results_folder <- "output/:title:"
 cfg$force_replace <- TRUE
diff --git a/scripts/start/projects/project_WetHorizons.R b/scripts/start/projects/project_WetHorizons.R
index caf5cdea4..2f43dfa01 100644
--- a/scripts/start/projects/project_WetHorizons.R
+++ b/scripts/start/projects/project_WetHorizons.R
@@ -29,7 +29,7 @@ cfg$results_folder <- "output/:title:"
 cfg$results_folder_highres <- "output"
 cfg$force_replace <- TRUE
 cfg$force_download <- FALSE
-cfg$qos <- "standby_dayMax"
+cfg$qos <- "standby"
 
 # support function to create standardized title
 .title <- function(cfg, ...)

From ad4f2c1e6ca4e2d7aedf3af140e8aea784ddbd73 Mon Sep 17 00:00:00 2001
From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
Date: Thu, 15 May 2025 11:41:18 +0200
Subject: [PATCH 12/14] use magpie4::disaggregateLandConservation

---
 DESCRIPTION                           |  2 +-
 scripts/output/extra/disaggregation.R | 14 +++++++++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index daedf343b..f311e482d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,7 +21,7 @@ Imports:
     m4fsdp,
     madrat,
     magclass (>= 6.14.0),
-    magpie4 (>= 2.22.9),
+    magpie4 (>= 2.24.0),
     MagpieNCGains,
     magpiesets (>= 0.46.1),
     mip,
diff --git a/scripts/output/extra/disaggregation.R b/scripts/output/extra/disaggregation.R
index eac94dfba..270d54328 100644
--- a/scripts/output/extra/disaggregation.R
+++ b/scripts/output/extra/disaggregation.R
@@ -281,7 +281,19 @@ message("Disaggregating conservation land")
 
 land_consv_hr <- NULL
 if (file.exists(wdpa_hr_file)) {
-  land_consv_hr <- .dissagLandConsv(gdx, cfg, map_file, wdpa_hr_file, consv_prio_hr_file)
+  if (file.exists(consv_prio_hr_file)) {
+    conservationPrioHr <- read.magpie(consv_prio_hr_file)
+  } else {
+    warning("Future land conservation used in MAgPIE run but high resolution ",
+            "conservation priority data for disaggregation not found.")
+    conservationPrioHr <- NULL
+  }
+  land_consv_hr <- magpie4::disaggregateLandConservation(gdx, cfg,
+                                                         mapping = readRDS(map_file),
+                                                         wdpaHr = read.magpie(wdpa_hr_file),
+                                                         conservationPrioHr = conservationPrioHr)
+  land_consv_hr2 <- .dissagLandConsv(gdx, cfg, map_file, wdpa_hr_file, consv_prio_hr_file)
+  stopifnot(identical(land_consv_hr, land_consv_hr2))
 
   # Write gridded conservation land
   .writeDisagg(land_consv_hr, land_consv_hr_out_file,

From 45466ea4cfa1460b2b2460963d5efae704620970 Mon Sep 17 00:00:00 2001
From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
Date: Thu, 15 May 2025 14:35:41 +0200
Subject: [PATCH 13/14] remove .dissagLandConsv

---
 scripts/output/extra/disaggregation.R | 95 ---------------------------
 1 file changed, 95 deletions(-)

diff --git a/scripts/output/extra/disaggregation.R b/scripts/output/extra/disaggregation.R
index 270d54328..ade2a4afe 100644
--- a/scripts/output/extra/disaggregation.R
+++ b/scripts/output/extra/disaggregation.R
@@ -87,99 +87,6 @@ if (length(map_file) > 1) {
   return(area_shr_hr)
 }
 
-.dissagLandConsv <- function(gdx, cfg, map_file, wdpa_hr_file, consv_prio_hr_file) {
-  land_consv_lr <- readGDX(gdx, "pm_land_conservation", react = "silent")
-  land_consv_lr <- dimSums(land_consv_lr, dim=3.2)
-  wdpa_hr <- read.magpie(wdpa_hr_file)
-  map <- readRDS(map_file)
-
-  # create full time series
-  land_consv_hr <- new.magpie(map[, "cell"], getYears(land_consv_lr), getItems(wdpa_hr, dim = 3.2),
-    fill = 0, sets = c("x.y.iso", "year", "data")
-  )
-
-  iso <- readGDX(gdx, "iso")
-  consv_iso <- readGDX(gdx, "policy_countries22")
-  consv_iso <- consv_iso[consv_iso %in% getItems(wdpa_hr, dim = 1.3)]
-  if (length(consv_iso) == 0) {
-    warning("No countries selected in land conservation disaggregation. Results may be erroneous")
-  }
-
-  base_protect_select <- cfg$gms$c22_base_protect
-  base_protect_noselect <- cfg$gms$c22_base_protect_noselect
-
-  if (!all(c(base_protect_select, base_protect_noselect) %in% "none")) {
-
-    if (base_protect_noselect != "none") {
-      land_consv_hr[, getYears(land_consv_hr), ] <- collapseDim(wdpa_hr[, nyears(wdpa_hr), base_protect_noselect], dim = 3.1)
-      land_consv_hr[, getYears(wdpa_hr), ] <- collapseDim(wdpa_hr[, , base_protect_noselect], dim = 3.1)
-    }
-    if (base_protect_select != "none") {
-      land_consv_hr[consv_iso, , ] <- collapseDim(wdpa_hr[consv_iso, nyears(wdpa_hr), base_protect_select], dim = 3.1)
-    } else {
-      land_consv_hr[consv_iso, , ] <- 0
-    }
-  }
-
-  consv_select <- cfg$gms$c22_protect_scenario
-  consv_noselect <- cfg$gms$c22_protect_scenario_noselect
-
-  if (!all(c(consv_select, consv_noselect) %in% "none")) {
-    if (file.exists(consv_prio_hr_file)) {
-      consv_prio_all <- read.magpie(consv_prio_hr_file)
-      consv_prio_hr <- new.magpie(
-        cells_and_regions = map[, "cell"],
-        names = getNames(consv_prio_all, dim = 2), fill = 0,
-        sets = c("x.y.iso", "year", "data")
-      )
-
-      if (consv_noselect != "none") {
-        consv_prio_hr <- collapseDim(consv_prio_all[, , consv_noselect], dim = 3.1)
-      }
-      if (consv_select != "none") {
-        consv_prio_hr[consv_iso, , ] <- collapseDim(consv_prio_all[consv_iso, , consv_select], dim = 3.1)
-      } else {
-        consv_prio_hr[consv_iso, , ] <- 0
-      }
-      # future conservation only pertains to natveg
-      consv_prio_hr[, , c("crop", "past", "forestry", "urban")] <- 0
-      consv_fader <- readGDX(gdx, "p22_conservation_fader", format = "first_found")
-      consv_prio_hr <- consv_prio_hr * consv_fader[, getYears(land_consv_hr), ]
-
-      # add conservation priority areas
-      land_consv_hr <- (land_consv_hr + consv_prio_hr)
-    } else {
-      warning(paste(
-        "Future land conservation used in MAgPIE run but high resolution",
-        "conservation priority data for disaggregation not found."
-      ))
-    }
-  }
-  # Due to internal constraints and compensation (e.g. NDC forest conservation)
-  # the actual land conservation can sometimes be smaller than the land
-  # conservation in the input data (this can especially happen also if
-  # land restoration is switched off). Therefore a scaling is applied here separately
-  # for grassland and natural vegetation
-  natveg <- c("primforest", "secdforest", "other")
-  consv_sum_lr <- mbind(
-    land_consv_lr[, , "past"],
-    setNames(dimSums(land_consv_lr[, , natveg], dim = 3), "natveg")
-  )
-  consv_sum_hr_agg <- mbind(
-    toolAggregate(land_consv_hr[, , "past"], map, from = "cell", to = "cluster"),
-    toolAggregate(setNames(dimSums(land_consv_hr[, , natveg], dim = 3), "natveg"),
-      map,
-      from = "cell", to = "cluster"
-    )
-  )
-  consv_scaling <- consv_sum_lr / consv_sum_hr_agg
-  consv_scaling[is.na(consv_scaling) | is.infinite(consv_scaling)] <- 1
-  consv_scaling <- toolAggregate(consv_scaling, map, from = "cluster", to = "cell")
-  land_consv_hr[, , "past"] <- consv_scaling[, , "past"] * land_consv_hr[, , "past"]
-  land_consv_hr[, , natveg] <- consv_scaling[, , "natveg"] * land_consv_hr[, , natveg]
-  return(land_consv_hr)
-}
-
 .dissagBII <- function(gdx, map_file, dir) {
   # Biodiversity intactness indicator (BII) at cluster level
   bii_lr <- BII(gdx,
@@ -292,8 +199,6 @@ if (file.exists(wdpa_hr_file)) {
                                                          mapping = readRDS(map_file),
                                                          wdpaHr = read.magpie(wdpa_hr_file),
                                                          conservationPrioHr = conservationPrioHr)
-  land_consv_hr2 <- .dissagLandConsv(gdx, cfg, map_file, wdpa_hr_file, consv_prio_hr_file)
-  stopifnot(identical(land_consv_hr, land_consv_hr2))
 
   # Write gridded conservation land
   .writeDisagg(land_consv_hr, land_consv_hr_out_file,

From 382e0016cb0a34872d2c4e6ff89818ad1339a934 Mon Sep 17 00:00:00 2001
From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com>
Date: Fri, 16 May 2025 10:46:19 +0200
Subject: [PATCH 14/14] changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 64542ccff..febce8449 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **script/start/test_runs.R** Test runs adjusted based on availability from coupled runs for R34M410. 
 - **scenario_config.csv** SSP2 food system assumptions for ScenarioMIP VLLO to avoid sudden jump of calorie intake after 2025
 - **scripts** request 24h for SLURM jobs (except for medium which still requests 7 days)
+- **scripts** disaggregation.R moved disaggregateLandConservation function to magpie4
 
 ### added
 - **default.cfg** added option to set Tol_Optimality (GAMS solver setting) to a certain value (GAMS-default 1e-7, new MAgPIE-default 1e-8)