Merge pull request #3 from magpiemodel/develop

Develop
magpiemodel · Mar 3, 2020 · b862d2d · b862d2d
2 parents d341612 + d0f990e
commit b862d2d
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diff --git a/.Rprofile b/.Rprofile
@@ -11,6 +11,8 @@ if(file.exists("~/.Rprofile")) source("~/.Rprofile")
 # to the model output folder. Otherwise, the run itself will again use the
 # default library set!
 
-# snapshot <- "/p/projects/rd3mod/R/libraries/snapshots/dec2016"
-# if(file.exists(snapshot)) .libPaths(snapshot)
-
+# snapshot <- "/p/projects/rd3mod/R/libraries/snapshots/2019_02_28"
+# if(file.exists(snapshot)) {
+# cat("Set libPaths to",snapshot,"\n")
+# .libPaths(snapshot)
+# }
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,3 @@
+# Handle line endings automatically for files detected as text
+# and leave all files detected as binary untouched.
+* text=auto
diff --git a/README.md b/README.md
@@ -30,10 +30,13 @@ model source code via the R package goxygen
 package and run the main function (goxygen) in the main folder of the model.
 The resulting documentation can be found in the folder "doc".
 
+Please find a set of tutorials here https://github.com/magpiemodel/tutorials. 
+This guide will give you a brief technical introduction in how to install, run and use the model
+and how to analyse the model output.
+
 Please pay attentions to the MAgPIE Coding Etiquette when you modify the code.
-The Coding Etiquette you find at
-https://redmine.pik-potsdam.de/projects/pik-model-operations/wiki/Coding_Etiquette
-The Coding Etiquette explains also the used name conventions and other
+The Coding Etiquette you find at the beginning of the documentation mentioned above.
+The Coding Etiquette explains also the naming conventions and other
 structural characteristics.
 
 ## COPYRIGHT
@@ -88,8 +91,6 @@ Under Windows you need to install Rtools
 (https://cran.r-project.org/bin/windows/Rtools/) and to add it to the PATH
 variable. After that you can run the following lines of code:
 
-After that all packages can be installed via `install.packages`
-
 ```
 pkgs <- c("gdxrrw",
           "ggplot2",

diff --git a/config/default.cfg b/config/default.cfg
@@ -23,8 +23,11 @@ cfg$model <- "main.gms"   #def = "main.gms"
 
 # which input data sets should be used?
 
-cfg$input <- c("magpie4.1_default_apr19.tgz", "additional_data_rev3.68.tgz",
-               "isimip_rcp-IPSL_CM5A_LR-rcp2p6-co2_rev38_c200_690d3718e151be1b450b394c1064b1c5.tgz")
+cfg$input <- c("isimip_rcp-IPSL_CM5A_LR-rcp2p6-co2_rev42_c200_690d3718e151be1b450b394c1064b1c5.tgz",
+               "rev4.42_690d3718e151be1b450b394c1064b1c5_magpie.tgz",
+               "rev4.42_690d3718e151be1b450b394c1064b1c5_validation.tgz",
+               "calibration_H12_c200_26Feb20.tgz",
+               "additional_data_rev3.77.tgz")
 
 #a list of repositories (please pay attention to the list format!) in which the
 #files should be searched for. Files will be searched in all repositories until
@@ -124,6 +127,9 @@ cfg$gms$c12_interest_rate <- "medium"          # def = "medium"
 # ***---------------------    13_tc    -----------------------------------------
 # * (endo_jun18): endogenous technological change with full cost accounting and
 # *               stepwise updated crop area information
+# * (exo): exogenous technological change (removes non-linearities from the model);
+# *			requires an existing model run with endo tc for generating the input file
+# * 		f13_tau_scenario.csv
 cfg$gms$tc <- "endo_jun18"              # def = endo_jun18
 
 # * tc cost scenario: low, medium or high
@@ -169,9 +175,67 @@ cfg$gms$s15_elastic_demand <- 1            # def =1
 # *            OTHER: "PB" (planetary boundaries)
 cfg$gms$c15_food_scenario <- "SSP2"        # def = SSP2
 
-# * ruminant meat share scenario
+# * Temporal development of ruminant meat share within the livestock food product
+# * group (applied before food demand model is executed)
 # *   options:   constant, halving2050, mixed
-cfg$gms$c15_rumscen <- "mixed"             # def = mixed
+cfg$gms$c15_rum_share <- "mixed"             # def = mixed
+
+# * Stronger ruminant fadeout in India
+# *   options:  0 (=off), 1 (=on)
+cfg$gms$s15_rum_share_fadeout_india_strong <- 1             # def = 1
+
+# * Milk share fadeout in India within the livestock food product
+# * group (applied before food demand model is executed)
+# *   options:  0 (=off), 1 (=on)
+cfg$gms$s15_milk_share_fadeout_india <- 1             # def = 1
+
+# * Exogenous food substitution scenarios including functional forms, targets
+# * and transition periods (applied after food demand model is executed)
+# *   options:   constant,
+# *              lin_zero_10_50, lin_zero_20_50, lin_zero_20_30,
+# *              lin_50pc_10_50_extend90, lin_75pc_10_50_extend90, lin_80pc_20_50, lin_80pc_20_50_extend95, lin_90pc_20_50_extend95,
+# *              lin_99-98-90pc_20_50-60-100
+cfg$gms$c15_rumscen <- "constant"                         # def = constant
+cfg$gms$c15_fishscen <- "constant"                        # def = constant
+cfg$gms$c15_alcscen <- "constant"                         # def = constant
+cfg$gms$c15_livescen <- "constant"                        # def = constant
+
+
+# * target year for transition to exogenous scenarios
+# * only active for exogenous scenario switches that are set to 1
+# * currently available: waste (s15_exo_waste) and EAT Lancet diets (s15_exo_diet)
+# *   options:   y2030, y2050
+cfg$gms$c15_exo_scen_targetyear <- "y2050"   # def = y2050
+
+
+# * switch for transition to food waste scenarios
+# * (1):      transition towards exogenous food waste target
+# * (0):      regression-based estimation of food waste
+cfg$gms$s15_exo_waste <- 0               # def = 0
+
+# * scenario target for the ratio between food demand and intake
+# * only activated if s15_exo_waste is set to 1
+# *   options: scalars >1
+# * (1.1):  corresponds to 10% food waste ~ quarter waste of HIC
+# * (1.2):  corresponds to 20% food waste ~ half waste of HIC
+cfg$gms$s15_waste_scen <- 1.2          # def = 1.2
+
+
+# * switch for transition to EAT Lancet diet scenarios
+# * (1):      transition towards exogenous diets and food demand
+# * (0):      regression-based estimation of diets and food demand
+cfg$gms$s15_exo_diet <- 0               # def = 0
+
+# * exogenous calorie scenario (EAT Lancet diet scenarios)
+# * only activated if s15_exo_diet is set to 1
+# *   options:   healthy_BMI, 2100kcal, 2500kcal
+cfg$gms$c15_kcal_scen <- "healthy_BMI"       # def = healthy_BMI
+
+# * exogenous food-specific diet scenario (EAT Lancet diet scenarios)
+# * only activated if s15_exo_diet is set to 1
+# *   options:   BMK, FLX, PSC, VEG, VGN, FLX_hmilk, FLX_hredmeat
+cfg$gms$c15_EAT_scen <- "FLX"                # def = FLX
+
 
 # ***---------------------    16_demand    -------------------------------------
 # * (sector_may15): default for flexible regions
@@ -200,6 +264,7 @@ cfg$gms$processing <- "substitution_dec18"        # def = substitution_dec18
 # ***---------------------    21_trade    --------------------------------------
 # * (free_apr16):       free trade without restrictions
 # * (off):              no trade at all
+# * (exo):              exogenously prescribed trade
 # * (selfsuff_reduced): self-sufficiency based trade with trade costs related
 # *                     to exports
 cfg$gms$trade <- "selfsuff_reduced"             # def = selfsuff_reduced
@@ -237,17 +302,18 @@ cfg$gms$s31_fac_req_past  <- 1             # def = 1
 
 # ***---------------------    32_forestry    -----------------------------------
 # * (static_sep16) :     static forestry sector
-# * (affore_vegc_dec16): static forestry sector + afforestation
-cfg$gms$forestry  <- "affore_vegc_dec16"              # def = affore_vegc_dec16
+# * (affore_vegc_dec16): static forestry sector + afforestation #to_be_deleted
+# * (dynamic_oct19): 	static forestry sector + afforestation with detailed age-classes
+cfg$gms$forestry  <- "dynamic_oct19"              # def = dynamic_oct19
 
 # * afforestation planing horizon (years)
-cfg$gms$s32_planing_horizon <- 80                # def = 80
+cfg$gms$s32_planing_horizon <- 50                # def = 50
 
 # Afforestation policy
 # * ("none"): no prescribed afforestation
 # * ("npi"): prescribed afforestation based on NPI policies
 # * ("ndc"): prescribed afforestation based on NPI+NDC policies
-cfg$gms$c32_aff_policy <- "npi"              # def = "none"
+cfg$gms$c32_aff_policy <- "npi"              # def = "npi"
 
 # maximum total global afforestation in Mha (Inf = no constraint)
 cfg$gms$s32_max_aff_area <- Inf              # def = Inf
@@ -266,8 +332,8 @@ cfg$gms$urban   <- "static"                # def = static
 # ***---------------------    35_natveg    --------------------------------------
 # * 35_natveg includes primforest, secdforest and other land
 # * (static):               static natveg land
-# * (dynamic_may18): 		dynamic natveg land
-cfg$gms$natveg  <- "dynamic_may18"           # def = dynamic_may18
+# * (dynamic_oct19): 		dynamic natveg land with detailed age-classes
+cfg$gms$natveg  <- "dynamic_oct19"           # def = dynamic_oct19
 
 # * protected areas (primforest,secdforest,other land)
 # * (WDPA) WDPA IUCN catI+II
@@ -347,10 +413,14 @@ cfg$gms$s42_watdem_nonagr_scenario <- 1      # def = 1
 # * (3): gdp driven increase
 cfg$gms$s42_irrig_eff_scenario <- 1           # def = 1
 
+# * Irrigation efficiency
+# * (Only used if global static value is requested)
+cfg$gms$s42_irrigation_efficiency <- 0.66       # def=0.66
+
 # * Environmental flow protection policy
 # * (off):   no EFP policy
-# * (on):    global EFP policy starting in 2015
-# * (mixed): EFP policy starting in 2015 only in hic regions
+# * (on):    global EFP policy
+# * (mixed): EFP policy only in hic regions
 cfg$gms$c42_env_flow_policy <- "off"             # def = "off"
 
 # * Environmental flow protection scenario
@@ -395,13 +465,14 @@ cfg$gms$climate <- "static"    # def = static
 # * (exoeff_aug16): exogenous nr efficiency
 cfg$gms$nr_soil_budget <- "exoeff_aug16"    # def = exoeff_aug16
 
-# * options: neff55_55_starty1990,neff60_60_starty1990,neff65_70_starty1990,
+# * scenario for nr efficiency on croplands or pastures
+# * options: constant,
+# *          neff55_55_starty1990,neff60_60_starty1990,neff65_70_starty1990,
 # *          neff65_70_starty2010,neff60_60_starty2010,neff55_60_starty2010,
 # *          neff70_75_starty2010,neff75_80_starty2010,neff80_85_starty2010
+# *          neff85_85_starty2010
 cfg$gms$c50_scen_neff <- "neff60_60_starty2010"   # def = neff60_60_starty2010
-# * scenario for animal waste management.
-# * option: "ssp1", "ssp2", "ssp3", "ssp4", "ssp5", "constant", "a1", "a2", "b1","b2"
-cfg$gms$c55_scen_conf <- "ssp2"    # def = ssp2
+cfg$gms$c50_scen_neff_pasture <- "constant"   	  # def = constant
 
 # ***---------------------    51_nitrogen   ------------------------------------
 # * (ipcc2006_sep16): IPCC based nitrogen implementation
@@ -413,6 +484,9 @@ cfg$gms$nitrogen    <- "ipcc2006_sep16"                 # def = ipcc2006_sep16
 # * (off):          carbon calculations deactivated
 cfg$gms$carbon <- "normal_dec17"                       # def = normal_dec17
 
+# * switch for using natveg (0) or plantation (1) growth curves for afforestation
+cfg$gms$s52_forestry_plantation <- 0		# def = 0
+
 # * carbon scenario
 # *   options:   cc  (climate change)
 # *             nocc (no climate change)
@@ -433,16 +507,27 @@ cfg$gms$phosphorus  <- "off"                     # def = off
 # * (off):            deactivated animal waste management
 cfg$gms$awms  <- "ipcc2006_aug16"                     # def = ipcc2006_aug16
 
+# * scenario for animal waste management.
+# * option: "ssp1", "ssp2", "ssp3", "ssp4", "ssp5", "constant", "a1", "a2", "b1","b2",
+#*          "GoodPractice"
+cfg$gms$c55_scen_conf <- "ssp2"    # def = ssp2
+
 # ***---------------------    56_ghg_policy   ----------------------------------
-# * (price_jan19): GHG emission pricing with phase-in over 20 year period and depending on development state
-cfg$gms$ghg_policy  <- "price_jan19"                     # def = price_jan19
+# * (price_jan20): applies pollutant prices to different emission types and calculates the reward for CDR from afforestation
+cfg$gms$ghg_policy  <- "price_jan20"                     # def = price_jan20
+
+# * Switch for scaling GHG price with development state (1=on 0=off)
+cfg$gms$s56_ghgprice_devstate_scaling <- 0 		# def = 0
+
+# * Switch for phasing-in GHG price over a 20 year period  (1=on 0=off)
+cfg$gms$s56_ghgprice_phase_in <- 0 		# def = 0
 
-# * start year of GHG emission pricing phase-in (only used in price_jan19)
+# * start year of GHG emission pricing phase-in (only used if s56_ghgprice_phase_in=1)
 cfg$gms$s56_ghgprice_start <- 2025 		# def = 2025
 
 # * reduction factor for CO2 price (only used in price_jan19)
 # * lowers the economic incentive for CO2 emission reduction (avoided deforestation) and afforestation
-cfg$gms$s56_cprice_red_factor <- 0.5 		# def = 0.5
+cfg$gms$s56_cprice_red_factor <- 1 		# def = 1
 
 # * GHG pollutant price scenario
 # * Available scenarios:
@@ -473,6 +558,20 @@ cfg$gms$s56_cprice_red_factor <- 0.5 		# def = 0.5
 # *     coupling
 cfg$gms$c56_pollutant_prices <- "R2M41-SSP2-NPi"         # def = "R2M41-SSP2-NPi"
 
+# * Switch for C price driven afforestation (1=on 0=off)
+cfg$gms$s56_c_price_induced_aff <- 1
+
+# * C price expectation for afforestation decision-making in years
+# * 0 is myopic behaviour (only C price of current time step)
+# * reflects perfect-foresight if equal to s32_planing_horizon
+# * should not be higher than s32_planing_horizon
+cfg$gms$s56_c_price_exp_aff <- 50 	# def = 50
+
+# * share of carbon credits for afforestation projects pooled in a buffer
+# * Values > 0 will reduced the incentive for c price induced afforestation
+# * a plausible value is 0.2, based on the Gold Standard for afforestation projects
+cfg$gms$s56_buffer_aff <- 0.2 	# def = 0.2
+
 # * Upper limit for CH4 and N2O GHG price (USD05MER per tC)
 # * Limits GHG prices selected in c56_pollutant_prices to the chosen value.
 # * CH4 and N2O GHG prices are limited by default to 1000 USD05MER per tC equivalent,
@@ -482,16 +581,17 @@ cfg$gms$c56_pollutant_prices <- "R2M41-SSP2-NPi"         # def = "R2M41-SSP2-NPi
 cfg$gms$s56_limit_ch4_n2o_price <- 1000   # def = 1000
 
 # * emission policies
-# * options: none, all, ssp_nosoil, all_nosoil
+# * options: none, all, ssp_nosoil, redd+_nosoil, all_nosoil
 # * none:       Not including any GHG sources
 # * ssp_nosoil: Above ground CO2 emis from LUC in natveg; all CH4 and N2O emissions
+# * redd+_nosoil: Above ground CO2 emis from LUC in natveg and forestry; all CH4 and N2O emissions
 # * all_nosoil: Above ground CO2 emis from LUC for all LUs; all CH4 and N2O emissions
 # * all:        CO2 emis from LUC in all LUs; all CH4 and N2O emissions
-cfg$gms$c56_emis_policy <- "ssp_nosoil" 		# def = ssp_nosoil
+cfg$gms$c56_emis_policy <- "redd+_nosoil" 		# def = redd+_nosoil
 
 # * Treatment of negative costs originating from negative co2 emissions
 # * reward negative co2 emissions (-Inf) or not (0)
-# * s56_reward_neg_emis is applied the on emission policy chosen in c56_emis_policy
+# * s56_reward_neg_emis is applied on the emission policy chosen in c56_emis_policy
 # * In case of carbon pricing s56_reward_neg_emis = -Inf results in increase of other land
 # * For runs with afforestation s56_reward_neg_emis should be 0 (default setting)
 cfg$gms$s56_reward_neg_emis <- 0			# def = 0
@@ -618,7 +718,7 @@ cfg$gms$s80_num_nonopt_allowed <- Inf
 
 # * 1: using optfile for specified solver settings
 # * 0: default settings (optfile will be ignored)
-cfg$gms$s80_optfile <- 0
+cfg$gms$s80_optfile <- 1
 
 
 #*******************************END MODULE SETUP********************************
@@ -638,7 +738,7 @@ cfg$logoption <- 2
 # Should output.R generate output?
 # List of output scripts that should be used
 # Available scripts can be found in scripts/output/
-cfg$output <- c("rds_report","validation","interpolation")
+cfg$output <- c("rds_report","validation","disaggregation")
 
 # Set the format for the results folder
 # :date: is a placeholder for the current time stamp (e.g. "results:date:")
@@ -649,7 +749,10 @@ cfg$results_folder <- "output/:title::date:"
 cfg$files2export <- list()
 # Files that should be copied before MAgPIE is started
 cfg$files2export$start <- c("input/info.txt",
-                            "modules/10_land/input/avl_land.cs3",
+                            "modules/10_land/input/avl_land_t_0.5.mz",
+							"modules/14_yields/input/lpj_yields_0.5.mz",
+							"modules/50_nr_soil_budget/input/f50_NitrogenFixationRateNatural_0.5.mz",
+							"modules/50_nr_soil_budget/input/f50_AtmosphericDepositionRates_0.5.mz",
                             "input/spatial_header.rda",
                             "scripts/run_submit/submit.R",
                             "scripts/run_submit/submit.sh",