WRF-Chem chemistry output details

[Lin Lu]

Hi, 

I am a relatively new user of WRF-Chem and I am looking for some more detailed understanding of the outputs and schemes in the chem runs.

I would highly appreciate if anyone could direct me towards appropriate literature/documentation for the following queries that I have-

1. Where can I find the details about Chemistry variables in the wrfout output files? e.g. How they are mapped from different the emissions (I am using MOZART+GOCART scheme)

2. In my wrfout fils I see that both 'BC1' and 'OC1' are described as "Hydrophobic Black Carbon" in ug/kg-dryair". Could you help me where to find their mapping details?

3. The first-hour output of wrfout files from chemistry runs show zero concentration of aerosols and other gaseous species. Could anyone explain to me why is that or is my simulation not being reinitialized properly?

Please help me with these queries.

Thanks a lot,

Lin

[Alexander Frie]

Hello Lin,

There's a few things that might help.

1. you can find the species (and emission variables) for a specific chemical mechanism in Registry.chem in the registry folder of the directory where you compiled WRF-CHEM.  If you want to make changes to this file I recommend looking at the WRF (not WRF-chem) manual as it details how the registry files are set up. If you mean Emission's mapping from your inventory I encourage you to look into the WRF-CHEM emissions guide and also look closely at whatever tool you're using to generate emissions as it likely contains some sort of emissions mapping array.  

2.  I think the registry file will provide most of this information for you, but you might have to look into documentation/publications for a specific mechanism depending on the level of detail you require.

3. The basic chemical boundary conditions for WRF-CHEM are non-realistic (sometimes 0) for many species.  One way to get around this is to use the mozbc tool (just google mozbc wrf-chem and you should be able to find it) which will allow you to input chemical boundary conditions from a global model result.  You can also use the chem_input_opt to set initial boundary conditions using an output from a previous model run.

I hope this helps!

Alexander Frie

[Lin Lu]

Dear  Alexander,

Thanks for the helpful information.

I am using mozbc tool for providing Chemical boundary conditions from the MOZART-4 data. I still get zero conc in the first output file.

Would you be able to tell me why could that be ? Or is it something common to WRF-Chem model for all schemes?

Best, 

LiN 

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[Mary Barth]

Hello Lin,

Short-lived species such as OH, HO2 and other radicals are initialized to zero because they will quickly form from the chemistry. Therefore MOZART-4 and CAM-chem output contains longer-lived species. We try to provide for all the needed longer-lived species, but sometimes there may be an omission. If you find there are long-lived species without initial concentrations, check the mozbc log file to see if some error occurred. It could be as simple as a typo in the mozbc input file.

Regards,
Mary

p.s. Thanks Alexander, for being so helpful with these questions.

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[Louisa Emmons]

Hi Lin and all,

We also encourage all users to transition from using MOZART-4 to CAM-chem.  We are no longer running MOZART-4, and will likely remove the MOZART-4 output files from our website in the not too distant future to make room for more years of CAM-chem results.

Only a minor change is required to the namelist to match the new variable names in CAM-chem, but otherwise the output is very similar.  

Please see these webpages for more information:

https://www2.acom.ucar.edu/gcm/cam-chem-output

https://www2.acom.ucar.edu/wrf-chem/wrf-chem-tools-community

thanks,

Louisa

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Louisa Emmons

Atmospheric Chemistry Observations and Modeling (ACOM) Lab

National Center for Atmospheric Research

Boulder CO 80307-3000

emm...@ucar.edu

V: 303-497-1491

[Lin Lu]

Thanks to all for the useful information.

@ Mary  is the short-lived species like aerosols formed after the model is initialized and it's okay to not have the concentrations for those in the first output?

 Is there more information documented about this that I can look into?

Many Thanks,

Lin

[altayeb ragab]

hi experts I am a new user of WRF-chem., I want to know how can I calculate AOD from the output and which software should I use...
chem_opt = 300...
please help me...
kind regards

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Friday, 28 August 2020, 05:44AM +08:00 from Lin Lu linl...@gmail.com:

[Alexander Frie]

Hello Lin,

I believe that there should be species in the first output for most of aerosol species.  You can check your mozbc input file to see what species are being mapped; if a species is mapped it should have concentrations in the first frame of the wrf output.

Also make sure you run mozbc after real.exe and before wrf.exe.  If you run real.exe after mozbc you'll lose your initial boundary conditions.

Cheers,

Alex

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Louisa Emmons

Atmospheric Chemistry Observations and Modeling (ACOM) Lab

National Center for Atmospheric Research

Boulder CO 80307-3000

emm...@ucar.edu

V: 303-497-1491

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[Alexander Frie]

Hello Altayeb,

I believe you can get AOD outputs from WRF-CHEM using the "opt_pars_out" and/or "aer_op_opt" option in namelist.  That said, I would look closer at the user guide to make sure since I don't have direct experience with these options.

Cheers,

Alex

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Louisa Emmons

Atmospheric Chemistry Observations and Modeling (ACOM) Lab

National Center for Atmospheric Research

Boulder CO 80307-3000

emm...@ucar.edu

V: 303-497-1491

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[Gonzalo A. Ferrada]

Altayeb:

The way I calculate AOD is by using the variables named TAUAER1, TAUAER2, TAUAER3 and TAUAER4.

These variables are the aerosol optical depth of each model layer at 300, 400, 600 and 1000 nm, respectively. To calculate the optical depth at another wavelength then you have to calculate the Angstrom exponent following the formula shown in https://en.wikipedia.org/wiki/Angstrom_exponent

E.g. I calculate the total AOD in the column at 550 nm using TAUAER2 and TAUAER3 because the 550 nm wavelength falls between 400 and 600 nm:

angstrom_exponent =  -( log(TAUAER2) - log(TAUAER3) ) / log(400/600) 

AOD550_3D         =  TAUAER2 * ( (400/550) ^ angstrom_exponent )

AOD550_2D         =  sum(AOD550_2D,3)

AOD550_3D is the 3-dimensional AOD where you have an optical depth for each layer of your model. Then, the total column AOD is simply the sum across the third dimension.

If the variables TAUAER<n> are not listed in your model outputs, then you need to modify the registry file for chemistry (Registry/registry.chem)and compile again:

state    real  tauaer1         ikj     misc        1         -      rh       "TAUAER1"               "bin 1 layer optical thickness" "?"

state    real  tauaer2         ikj     misc        1         -      rh       "TAUAER2"               "bin 2 layer optical thickness" "?"

state    real  tauaer3         ikj     misc        1         -      rh       "TAUAER3"               "bin 3 layer optical thickness" "?"

state    real  tauaer4         ikj     misc        1         -      rh       "TAUAER4"               "bin 4 layer optical thickness" "?"

Gonzalo A. Ferrada

Department of Chemical and Biochemical Engineering

Center for Global and Regional Environmental Research

409 Iowa Advanced Technology Laboratories

The University of Iowa

Iowa City, IA 52242