Disclaimer

This is just a tutorial created to assist the execution of the Model of Emissions of Gases and Aerosols from Nature (MEGAN) model. Please visit the developer site for more information: https://bai.ess.uci.edu/megan/

Reference: https://gmd.copernicus.org/articles/5/1471/2012/

The tutorial is developed for academic purposes in support of the UKM-YSD Chair in Climate Change grant (ZF-2020-001)

Downloading data and codes

Download required files as provided:

Basic:

MEGAN source code
Tutorial input files
Run scripts

Getting the device environment ready

Download Ubuntu 20.04 LTS from the Microsoft Store or https://ubuntu.com/wsl

Follow the instructions here to install the required Windows Subsytem and restart the machine, as per the instructions on

https://docs.microsoft.com/en-us/windows/wsl/install-on-server

Download MobaXTerm for Windows

https://mobaxterm.mobatek.net

Download gedit for Windows

https://gedit.en.uptodown.com/windows

Moving files to the Linux environment

Locate the Ubuntu folder in your machine (AppData\Local\Packages\CanonicalGroupLimited.UbuntuonWindows_79rhkp1fndgsc)

Enter to the home directory and create a folder called "MEGAN"

Example: (replace the username according to your account)

C:\Users\Chelg\AppData\Local\Packages\CanonicalGroupLimited.UbuntuonWindows_79rhkp1fndgsc\LocalState\rootfs\home\maggieooi\MEGAN

Move MEGANv2.10_beta.tar.gz and Tutorial1 into .../home/user/MEGAN

Setting up WSL Ubuntu environment

Enter to the WSL Ubuntu

Open your MobaXTerm and double-click on WSL

Installing necessary functions

Type commands below and key in password when prompted

sudo apt-get update
sudo apt install ncview
sudo apt install csh

Extracting the files

Check files permissions

Some basic LINUX commands:

pwd         - present working directory
ls          - listing files in folder
ls -lah     - listing files in folder with all details (a) in human readable form (h)
cd          - change directory
cd MEGAN    - enter MEGAN directory

Change file access status

chmod             - change mode of access (**r**ead,**w**rite,e**x**ecute); level: 7 (rwe), 5 (r-e), 4 (r--); 
                    user: user, group, others                  
chmod 700         - change mode of access to 700 (only admin can rwe)
chmod 755         - change mode of access to 755 (admin can rwe, groups and other can read and execute)
chmod 755 *       - change mode recursively (applies 700 for all the files)
chmod -R 755 *    - change mode recursively (applies 700 for all the files and files inside folders)
ls -lah

Move files into the MEGAN folder

mv MEGANv2.10_beta.tar.gz MEGAN
mv Tutorial1.zip MEGAN

Untar and unzip files ending with .tar.gz

In MEGAN directory:

cd ~/MEGAN
ls
tar -zxvf MEGANv2.10_beta.tar.gz
ls -lah
ls -lah MEGANv2.10
cd ../
unzip Tutorial1.zip
ls -lah
ls -lah Tutorial1

Running MEGAN

Understanding MEGAN codes

in MEGAN/MEGANv2.10

|-bin         : execution files (txt2ioapi, met2mgn, emproc, mgn2mech)
|-src         : source codes
|-work        : script executed (txt2ioapi, met2mgn, emproc, mgn2mech csh files)
|-Input       : input files (EF, PFT, LAI csv files)
|-Output      : output files
|-setcase.csh : setting the environment variables

Preparation

Correction of bin/mgn2mech link

cd bin
ls -l
ln -sf ../src/MGN2MECH/mgn2mech .
ls -l

Copy tutorial input files into MEGANv2.10 folder

cd ~/MEGAN/Tutorial1/Input
ls
cp * ../../MEGANv2.10/Input

Copy tutorial script files into MEGANv2.10 folder

cd ~/MEGAN/Tutorial1
ls
cp *csh ../MEGANv2.10
cd ../MEGANv2.10
ls -lah
ls -lah Input

Setting environmental variables setcase.csh

cd MEGAN/MEGANv2.10
cat setcase.csh     - printout file on screen
pwd
vi setcase.csh      - edit `MGNHOME` directory

In vi/vim editor:

Enter i for edit mode; Esc to exit edit mode

Enter :w to save change; ZZ to save change and exit; :q! to exit without saving

Execution

txt2ioapi: Convert the text files into the I/O API files

./run.txt2ioapi.v210.csh

Input files: EF210_mSEA_d01.csv, LAI210_mSEA_d01.csv, PFT210_mSEA_d01.csv

Output files: EFMAPS.mSEA.d01.ncf, LAIS46.mSEA.d01.ncf, PFTS16.mSEA.d01.ncf

Output logfile: log.txt2ioapi.d01.txt

met2mgn: Convert meteorological files (WRF/MCIP output) into I/O API files

./run.met2mgn.v210.2016352.csh

Input files: METCRO2D_d01_2016325, METCRO3D_d01_2016325, METDOT3D_d01_2016325

Output files: MET.MEGAN.2016325.d01.ncf

Output logfile: log.met2mgn.2016325.d01.txt

emproc: MEGAN emission processing files

./run.emproc.v210.2016352.csh

Input files: Output files from txt2ioapi and met2mgn

Output files: ER.mSEA.2016325.d01.ncf

Logfiles: log.emproc.2016325.d01.txt

mgn2mech: MEGAN output speciated to specified chemical mechanism

./run.mgn2mech.v210.2016352.csh

Input files: ER.mSEA.2016325.d01.ncf

Output files: MEGANv2.10.mSEA.CB05.2016325.d01.ncf

Logfiles: log.run.CB05.2016325.d01.txt

magooi / MEGAN2.10