Exercise 3: Generating MEGAN biogenics to use along with the other emissions
for the Souteastern Asia domain.
Purpose: To familiarize the user with the use of biogenic emissions in a WRF-Chem simulation.
- After completing tutorial exercise 2, change your directory to (or stay in the directory) WRFV3/test/em_real and set the the following options
in your namelist.input file. Start with changing from GOCART simple chemistry option to the GOCART-RACM_KPP
aerosol option (chem_opt=301). Keep the simulation run time at 7 days starting at
00 UTC on 16 September 2012. Be sure that the chemical time step is no longer 1 hour as that is needed just for the simple GOCART
scheme (exercise 2) and now the chemistry should be updated with the meteorology time step. Include biogenic emissions by
setting the bio_emiss_opt in the chemistry namelist to turn on the Geunther biogenic emissions (bio_emiss_opt=1).
And finally, dust, sea salt, DMS, and biomass burning will stil be included so keep
those options turned on.
- With the updated namelist.input file you can now run real.exe.
Examine the wrfinput data file. Do you see still the GOCART background fields in the wrfinput_d01 file?
- With the input and boundary conditions files built you can now run wrf.exe.
mpirun -np 4 ./wrf.exe
It will probably take approximately 5 minutes to finish the simulation on your computer.
- When finished, examine results of the simulation.
Does the isoprene (iso) data show up in your wrfout file and does it look like places where plants should be located?
- Save the wrfout output file(s) by copying to a different file name or directory. You will needs these files to compare
the results with the simulation produced later in this exercise.
- Now the biogenic emissions will be changed from the Geunther scheme to MEGAN. The program is a separate utility developed at
NCAR/ACD so it needs to remain separate from WRF. Start by making a MEGAN biogenic emissions
directory at the same level as the WRFV3 directory
cd ../../..
mkdir MEGAN
cd MEGAN
- Now untar the MEGAN biogenic emissions program into the new directory and move down into the megan_code directory.
tar -zxf
/CODE/MEGAN/megan_tutorial.tar.gz
cd MEGAN/megan_code
- The code should already be compiled. If you need to compile the MEGAN code, then follow the directions in Appendix C of
the User's Guide.
- Edit the megan_bio_emiss.inp input file to set the WRF and megan_data directory path.
Keep in mind that the MEGAN data files are
large and each person can use the same files. Therefore, your megan_data directory might be in /DATA instead of inside your MEGAN directory.
- Run the megan executable (step 7 in Appendix C). To complete the run you will need about 10 Gb of memory so don't try running the program on a small PC.
./megan_bio_emiss < megan_bio_emiss.inp >& run.out
Examine the run.out log file for any error messages. You
should see the following message at the end of a successful run.
Finished megan2 bio emiss dataset shr200121_30sec.nc
map_megan2_emissions: Before write_bioemiss
map_megan2_emissions: After write_bioemiss
map_megan2_emissions: 3 cached grid(s)
(No, there is not a nice ending statement at this time.)
- Verify that the biogenic emissions data exists in the MEGAN directory and that the fields appear
correct. It is easist to use a netCDF data file viewer (e.g., ncview) to quickly examine your biogenic emissions data. Does it look like it matches
your domain (SE Asia)? Does it have 12 months of data for leaf area index (MLAI), etc.
- Next change the chemistry namelist options for bio_emiss_opt from Geunther to MEGAN biogenics (ne_area also needs to be set when MEGAN is used).
Also turn on the time_control namelist options for the auxiliary input port 6 (e.g., io_form_auxinput6 (2 = netCDF, 0 = off)) in the namelist.input file as
the MEGAN biogenic scheme needs to read in the land use and leaf area index data. (Recall that the Geunther scheme uses the landuse information already contained in the WRF
input file.)
As a helpful reminder, the auxiliary input ports are defined as:
auxinput_5 -> Anthropogenic emissions
auxinput_6 -> Biogenic emissions (BEIS, MEGAN)
auxinput_7 -> Surface biomass burning fields
auxinput_8 -> GOCART background fields
auxinput_12 -> Chemistry initial fields
auxinput_13 -> Volcanic ash emissions
auxinput_14 -> Aircraft emissions
auxinput_15 -> Green House Gas emissions
- With the updated namelist.input file you can now run real.exe.
Examine the wrfinput data file. Do you see the GOCART background fields in the wrfinput_d01 file? Are the biogenic emissions (e.g., MLAI) included as well?
- With the input and boundary conditions files built you can now turn off the biogenic emissions/GOCART background auxiiliary input and run wrf.exe.
mpirun -np 4 ./wrf.exe
It will probably take approximately 10 minutes to finish the simulation on your computer.
- Once again, when finished you should examine results of your simulation. Do you see a message starting with
"calculate MEGAN emissions at " in the log file? Does the isoprene (iso) data show up in your wrfout file and does it look like places where plants should be located?
- Compare the results of the MEGAN biogenic simulation with the earlier simulation results.
Do the isoprene (iso) data show up in both simulatiosn wrfout files? Does the isoprene fields look like places where plants
should be located, but have different concentrations? How does this impact the surface ozone concentration at the end of the simulation?
This concludes WRF-Chem Souteastern Asia domain tutorial exercise 3.
To compare solutions, download desired files from here.
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