Update documentation.

scripts/start/prepare_and_run.R

@@ -737,6 +737,9 @@ run <- function(start_subsequent_runs = TRUE) {
 
   #====================== Subsequent runs ===========================
   if (start_subsequent_runs) {
+    # Note: step 1. and 2. below write to the same .RData file but are usually executed by different runs.
+    # Step 1. is usually only executed by BASE runs, step 2 by every run that preceeds another run.
+    
     # 1. Save the path to the fulldata.gdx of the current run to the cfg files 
     # of the runs that use it as 'input_bau.gdx'
 

tutorials/4_RunningREMINDandMAgPIE.md

 Running REMIND and MAgPIE in coupled mode
 ================
 David Klein (<dklein@pik-potsdam.de>)
-16 February, 2020
+27 April, 2020
+
+- [Running REMIND and MAgPIE in coupled mode](#running-remind-and-magpie-in-coupled-mode)
+- [How to start coupled runs](#how-to-start-coupled-runs)
+    + [Clone the models](#clone-the-models)
+    + [Switch to relevant branchs](#switch-to-relevant-branchs)
+    + [Create snapshot of R libraries](#create-snapshot-of-r-libraries)
+    + [Activate snapshot for REMIND and MAgPIE](#activate-snapshot-for-remind-and-magpie)
+    + [Configure start_bundle_coupled.R](#configure-start-bundle-coupledr)
+    + [Configure the scenario_config_coupled.csv of your choice](#configure-the-scenario-config-coupledcsv-of-your-choice)
+    + [Perform test start before actually submitting runs](#perform-test-start-before-actually-submitting-runs)
+    + [After checking that coupling scripts finds all gdxes and mifs start runs](#after-checking-that-coupling-scripts-finds-all-gdxes-and-mifs-start-runs)
+- [Technical concept](#technical-concept)
+    + [Dynamic](#dynamic)
+    + [Static](#static)
+    
+# How to start coupled runs
 
 ### Clone the models
 
@@ -50,14 +66,6 @@ See comments in the head section of the file. Most importantly you need to provi
 By default these are (A) `scenario_config_coupled_SSPSDP.csv` and (B) `scenario_config_SSPSDP.csv`. A provides some extra information
 for coupled runs (e.g. which run should be started). All other settings are taken from B. Thus every scenario in A must also be present in B.
 
-### Use the latest GAMS version
-
-This step is optional. If you want to use the latest GAMS version type this into the same command line you will start the runs from:
-
-```bash
-module load gams/30.2.0
-```
-
 ### Perform test start before actually submitting runs
 
 ```bash
@@ -68,4 +76,25 @@ Rscript start_bundle_coupled.R test
 
 ```bash
 Rscript start_bundle_coupled.R
-```
+```
\ No newline at end of file
+
+# Technical concept
+
+Two components: a dynamic (models solve iteratively and exchange data), a static (exogenous assumptions derived from the other model, update manually from time to time).
+
+### Dynamic
+
+* bioenergy demand, GHG prices from REMIND to MAgPIE (technical: getReprotData in magpie/startfunctions.R)
+* bioenergy prices, GHG emissions from MAgPIE to REMIND (technical: getReportData in remind/scripts/start/prepare_and_run.R)
+
+### Static
+
+* bioenergy supply curves in REMIND derived from MAgPIE (vignette remulator package, MAgPIE emulator description)
+* CO2 MAC: currently deactivated due to negligible differences in CO2 LUC emissions across RCPs
+* CH4/N2O MAC (on in standaline, off in coupled because abatement is part of MAgPIE)
+* GHG emission baselines for SSPs/RCPs (fixed for standalone runs, updated in coupled runs)
+* total agricultural production costs (fixed for standalone and coupled)
+
+### The coupling scripts
+
+* at the end: generate combined reporting file by binding REMIND and MAgPIE mifs together
\ No newline at end of file