From bb001022cd75f043b93a2078d0e3a7b572f743c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zolt=C3=A1n=20BARCZA?= Date: Tue, 22 Jan 2019 14:11:08 +0100 Subject: [PATCH] Update README.org --- README.org | 20 +++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/README.org b/README.org index 690c40c..32879a8 100644 --- a/README.org +++ b/README.org @@ -67,11 +67,24 @@ In this example the C:\model directory will contain the following files: - hhs_2013-2016.mtc43 - meteorology input file for the normal simulation - CO2_from1961.txt - CO_{2} file for the normal simulation +In the followings we will demonstrate the usability of RBBGCMuso with the hhs example dataset. If you have your own model input data set, you might need to change the commands accordingly. + +---------- +#+begin_note +*Important note on file naming convention* + +We propose to use the following filename convention for the INI files. For practical reasons, name your spinup INI file as something_s.ini, and the normal INI file as something_n.ini where something is arbitrary (note the s and n convention). It is not obligatory, but if you do not follow this convention then you have to generate the settings variable +manually with the setupMuso command. However, if you do follow this convention, then RBBGCMuSo will automatically recognize your spinup and normal INI file name and content, so the work will be much easier. (See help of setupMuso command in R). +In our example s.ini and n.ini follows this convention, so by default RBBGCMuso will use these files for spinup and normal run, repsectively. +#+end_note +---------- + + *** Running the model Now as we have a complete set of input data, we are ready to run the model. You can run the model in spinup model, in normal mode, or in both phases (including the so-called transient run; see the Biome-BGCMuSo User's Guide). Using the runMuso functcion (that is part of RBBGCMuso) you will be able to execute the the model in both spinup or normal phase, and you can also simplify the execution of both phases consecutively. Note that runMuso is the same as the obsolete calibMuso function. -In order to execute the simulation, first you have to set the working directory in R so that RBBGCMuso will find the model and the input files: +In order to execute the simulation, first you have to set the working directory in R so that RBBGCMuso will find the model and the input files. In our example this is as follows: #+BEGIN_SRC R :eval no setwd("c:/model") @@ -85,13 +98,14 @@ In order to run the model as it is provided simply use the following command in runMuso(skipSpinup = FALSE) #+END_SRC -Note that by default runMuso skips the spinup simulation (in order to speed up the model execution), but in our case we do not yet have the result of the spinup run (the so-called endpoint file), so spinup simulation is obligatory. This is performed with the skipSpinup=FALSE parameter. +Note that by default runMuso skips the spinup simulation (in order to speed up the model execution), but in our case we do not yet have the result of the spinup run (the so-called endpoint file), so spinup simulation is obligatory. This is performed with the skipSpinup=FALSE parameter. Note that according to the naming convention described above the model will use s.ini and n.ini for spinup and normal phase, repsectivelt. It means that the 3rd ini file is not used in this case. -If the simulation is successful, the results can be found in the C:\model directory. Two files were created with .log extension that contain some information about the spinup and the normal phase. The hhs.endpoint file is the result of the spinup (and optional transient) run, and can be considered as initial conditions for the normal run.( Here we have to note that now runMuso can be called without the skipSpinup parameter which means that the simulation will be restricted to the normal phase only.) The results of the simulation (carbon fluxes, state variables, whatever was set by the user in the DAILY_OUTPUT block of the normal INI file) are available in the file hegyhatsal.dayout. Note that annual output was not requested in this case. +If the simulation is successful, the results can be found in the C:\model directory. In our example two files were created with .log extension that contain some information about the spinup and the normal phase. The hhs.endpoint file is the result of the spinup (and optional transient) run, and can be considered as initial conditions for the normal run. (Here we have to note that now runMuso can be called without the skipSpinup parameter which means that the simulation will be restricted to the normal phase only.) The results of the simulation (carbon fluxes, state variables, whatever was set by the user in the DAILY_OUTPUT block of the normal INI file) are available in the file hegyhatsal.dayout. Note that annual output was not requested in this case. Also note that in the hhs example file set binary daily output is created and further processed by RBBGCMuso. *** Visualization of the model output + *** Perform Quick experiments