Merge pull request #770 from pascal-sauer/develop

MAgPIE release 4.9.1

.Rprofile

@@ -1,4 +1,4 @@
-# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+# |  (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

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.9.0",
+  "version": "4.9.1",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -123,5 +123,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2024-12-05"
+  "publication_date": "2025-01-28"
 }

CHANGELOG.md

@@ -3,9 +3,25 @@
 All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+
+## [4.9.1] - 2025-01-28
+
+### changed
+- **scripts** peatland rewetting now automatically considered in `extra/runSEALSallocation.R`
+
+### added
+- **scripts** added start script for land-based mitigation and biodiversity conservation paper
+- **scripts** release number can be passed as an argument to test_runs.R to tag as release
+- **start_scripts** added `lock_timeout` as option to `start_run` function
+
+### fixed
+- **44_biodiversity** bugfix i44_biome_share, code cleanup, added scaling of `q44_bii`
+
+
 ## [4.9.0] - 2024-12-05
 
 ### changed
+- **scripts** changed EL2 Deep Dive c30_bioen_water switch to all and added sensitivity for paper revision
 - **35_natveg** revised age-class initialization of secondary forest
 - **38_factor_costs** updated use of USDA cost shares
 - **config** changed default input data to use 2017USD
@@ -1051,7 +1067,8 @@ This release version is focussed on consistency between the MAgPIE setup and the
 First open source release of the framework. See [MAgPIE 4.0 paper](https://doi.org/10.5194/gmd-12-1299-2019) for more information.
 
 
-[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.9.0...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.9.1...develop
+[4.9.1]: https://github.com/magpiemodel/magpie/compare/v4.9.0...v4.9.1
 [4.9.0]: https://github.com/magpiemodel/magpie/compare/v4.8.2...v4.9.0
 [4.8.2]: https://github.com/magpiemodel/magpie/compare/v4.8.1...v4.8.2
 [4.8.1]: https://github.com/magpiemodel/magpie/compare/v4.8.0...v4.8.1

CITATION.cff

@@ -156,8 +156,8 @@ abstract: The *Model of Agricultural Production and its Impact on the Environmen
   exogenously given population in 10 food energy categories, based on regional diets.
   Future trends in food demand are derived from a cross-country regression analysis,
   based on future scenarios on GDP and population growth.
-version: 4.9.0
-date-released: 2024-12-05
+version: 4.9.1
+date-released: 2025-01-28
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

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,

README.md

@@ -24,8 +24,8 @@ https://www.pik-potsdam.de/research/projects/activities/land-use-modelling/magpi
 A framework description paper has been published in
 Geoscientific Model Development (GMD): https://doi.org/10.5194/gmd-12-1299-2019
 
-The model documentation for version 4.9.0 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.9.0/
+The model documentation for version 4.9.1 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.9.1/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -43,7 +43,7 @@ The Coding Etiquette explains also the naming conventions and other
 structural characteristics.
 
 ## COPYRIGHT
-Copyright 2008-2022 Potsdam Institute for Climate Impact Research (PIK)
+Copyright 2008-2025 Potsdam Institute for Climate Impact Research (PIK)
 
 ## LICENSE
 This program is free software: you can redistribute it and/or modify
@@ -226,7 +226,7 @@ magpie@pik-potsdam.de
 Please contact magpie@pik-potsdam.de
 
 ## CITATION
-See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.9.0/#how-to-cite) in the model documentation for information how to cite the model.
+See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.9.1/#how-to-cite) in the model documentation for information how to cite the model.
 
 ## AUTHORS
 See list of authors in CITATION.cff

config/default.cfg

@@ -1,4 +1,4 @@
-# |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+# |  (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
@@ -25,7 +25,7 @@ cfg$model <- "main.gms"   #def = "main.gms"
 cfg$input <- c(regional    = "rev4.116_h12_magpie.tgz",
                cellular    = "rev4.116_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz",
                validation  = "rev4.116_h12_validation.tgz",
-               additional  = "additional_data_rev4.59.tgz",
+               additional  = "additional_data_rev4.60.tgz",
                calibration = "calibration_H12_27Sep24.tgz")
 
 # NOTE: It is recommended to recalibrate the model when changing cellular input data
@@ -97,18 +97,18 @@ cfg$calib_accuracy_landconversion_cost <- 0.01         # def = 0.01
 # What is the maximum number of iterations if the precision goal is not reached?
 cfg$calib_maxiter_landconversion_cost <- 40           # def = 40
 # Restart from existing calibration factors (TRUE or FALSE)
-cfg$restart_landconversion_cost <- TRUE           # def = TRUE
+cfg$restart_landconversion_cost <- FALSE           # def = FALSE
 # Number of lowpass filter iterations applied on calibration factors
 # for time steps 1995-2015
-cfg$lowpass_filter_landconversion_cost <- 5        # def= 5
+cfg$lowpass_filter_landconversion_cost <- 1        # def= 1
 # Set upper limit for cropland calibration factor
 cfg$cost_calib_max_landconversion_cost <- 3         # def= 3
 # Set lower limit for cropland calibration factor
 cfg$cost_calib_min_landconversion_cost <- 0.05            # def= 0.05
 # Selection type of calibration factors.
 # If FALSE, calibration factors from the last iteration are used.
 # If TRUE, calibration factors from the iteration with the lowest divergence are used.
-cfg$best_calib_landconversion_cost <- TRUE     # def = TRUE
+cfg$best_calib_landconversion_cost <- FALSE     # def = FALSE
 
 # Settings for NPI/NDC recalculation
 # * (TRUE): NPI/NDC recalculation will be performed
@@ -612,7 +612,7 @@ cfg$gms$s21_trade_tariff_startyear <- 2025
 # * end year of fadeout if s21_trade_tariff_fadeout = 1 # def = 2050
 cfg$gms$s21_trade_tariff_targetyear <- 2050
 
-# * Minimum trade margin for forestry products (USD17MER per tDM) 
+# * Minimum trade margin for forestry products (USD17MER per tDM)
 # * (inflated from default originally in USD05 using USD05 --> USD17 inflation rate:1.23)
 cfg$gms$s21_min_trade_margin_forestry <- 62   # def = 50 * 1.23
 
@@ -760,8 +760,8 @@ cfg$gms$s29_treecover_scenario_start <- 2025   # def = 2025
 cfg$gms$s29_treecover_scenario_target <- 2050   # def = 2050
 # * Penalty for violation of treecover target before scenario start (USD17MER per ha)
 # * (inflated from default originally in USD05 using USD05 --> USD17 inflation rate:1.23)
-cfg$gms$s29_treecover_penalty_before <- 0   # def = 0 
-# * Penalty for violation of treecover target after scenario start (USD17MER per ha) 
+cfg$gms$s29_treecover_penalty_before <- 0   # def = 0
+# * Penalty for violation of treecover target after scenario start (USD17MER per ha)
 # * (inflated from default originally in USD05 using USD05 --> USD17 inflation rate: 1.23)
 cfg$gms$s29_treecover_penalty <- 6150   # def = 5000 * 1.23
 # * Tree cover establishment cost (USD17MER per ha)
@@ -1733,13 +1733,13 @@ cfg$gms$policy_countries58  <- all_iso_countries
 cfg$gms$s58_rewetting_exo <- 0   # def = 0
 # * Switch for exogenous peatland rewetting for all other countries (0=off, 1=on)
 cfg$gms$s58_rewetting_exo_noselect <- 0   # def = 0
-# * The following default values for exogenous peatland rewetting are based on the 
+# * The following default values for exogenous peatland rewetting are based on the
 # * Nature Restoration Law (NRL): 30 % by 2030, 40% by 2040, 50% by 2050
 # * Start year for exogenous peatland rewetting
 cfg$gms$s58_rewet_exo_start_year <- 2030   # def = 2030
 # * Target year for exogenous peatland rewetting
 cfg$gms$s58_rewet_exo_target_year <- 2050   # def = 2050
-# * Start value for exogenous peatland rewetting as share of drained peatland in reference period 
+# * Start value for exogenous peatland rewetting as share of drained peatland in reference period
 cfg$gms$s58_rewet_exo_start_value <- 0.3   # def = 0.3
 # * Target value for exogenous peatland rewetting as share of drained peatland in reference period
 cfg$gms$s58_rewet_exo_target_value <- 0.5   # def = 0.5
@@ -1907,9 +1907,9 @@ cfg$gms$c60_biodem_level <- 1                     # def = 1
 cfg$gms$s60_2ndgen_bioenergy_dem_min <- 1       # def = 1
 
 # * t DM-based first generation bioenergy subsidy (USD17MER per ton)
-# * The subsidy can simulate a perfectly elastic demand for bioenergy from the energy sector and should be used as a 
-# * default floor price that avoids the wastage of ethanal or oils in case that the demand for byproducts 
-# * (oilcake and brewers grains) exceeds the demand for these secondary products. As such, it also avoids unrealistic 
+# * The subsidy can simulate a perfectly elastic demand for bioenergy from the energy sector and should be used as a
+# * default floor price that avoids the wastage of ethanal or oils in case that the demand for byproducts
+# * (oilcake and brewers grains) exceeds the demand for these secondary products. As such, it also avoids unrealistic
 # * price fluctuations connected to the inelastic demand for couple products.
 # * (1stgen_priced_dec18):    c60_bioenergy_subsidy is applied constant over historic and model horizon, c60_bioenergy_subsidy_fix_SSP2 has no effect
 # * (1st2ndgen_priced_feb24): c60_bioenergy_subsidy_fix_SSP2 is applied constant to historic time steps (up until sm_fix_SSP2).

config/projects/scenario_config_el2.csv

@@ -17,6 +17,7 @@ gms$s15_exo_brans;0;0;0
 gms$s15_exo_scp;1;1;1
 gms$s15_exo_alcohol;1;1;1
 gms$s15_alc_scen;0;0;0
+gms$c30_bioen_water;all;all;all
 gms$factor_costs;sticky_labor;sticky_labor;sticky_labor
 gms$c70_feed_scen;ssp1;ssp2;ssp2
 input['cellular'];rev4.116EL2_h12_c6a7458f_cellularmagpie_c200_IPSL-CM6A-LR-ssp370_lpjml-8e6c5eb1.tgz;;

config/projects/scenario_config_miti_consv.csv

@@ -0,0 +1,3 @@
+;MitiConsv;MitiConsv-NoBuff
+gms$s56_buffer_aff;0.2;0
+input['calibration'];calibration_rev16_MitiConsv_22Jan25.tgz;calibration_rev16_MitiConsv_22Jan25.tgz

core/calculations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

core/declarations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

core/load_gdx.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

core/macros.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

core/sets.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

main.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/09_drivers/aug17/declarations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/09_drivers/aug17/input.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/09_drivers/aug17/preloop.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/09_drivers/aug17/realization.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/09_drivers/aug17/sets.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/09_drivers/module.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/declarations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/equations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/input.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/postsolve.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/presolve.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/realization.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/scaling.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/sets.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/landmatrix_dec18/start.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/10_land/module.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/11_costs/default/declarations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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

modules/11_costs/default/equations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2024 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (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