Questions Abount MOZART-MOSAIC in WRF-Chem

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twgl...@ncsu.edu

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Feb 26, 2018, 3:51:55 PM2/26/18
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Hello,


   I’m currently working on an air quality/climate change project that is focused on Africa to span the period of 2000-2017. I’m interested in using the WRF-Chem MOZART-MOSAIC/VBS aqueous chemistry option ( chem_opt = 202) for my simulations but I had a few questions about this option. 

 

1)     Is this option coupled to both aerosol direct and indirect effects as well as the Greenhouse effects of O3 within the model ?

2)     Are there any WRF physics options or other chemistry options that this chemical mechanism is not compatible with?

3)     Are there any limitations that would make this option a bad choice for the scope and length of simulation I’m doing other than the computational efficiency?

4)   I noticed that sea-salt emissions for MOSAIC have been disabled in the WRFv9.1.1. version. Sea-salt aerosols are important in chemistry-climate studies so are there any work arounds to turn them on? I can't use the GOCART aerosols because I need nitrate, ammonium, and SOA in my study.

5) Is there currently any way to generate fire emission for use with the plume rise calculations and aircraft emissions using the NCAR emission processing utilities?

6) Is there any way to easily output the dry/wet deposition fluxes, natural emissions (Dust, Sea-Salt, and Biogenic VOCs), and AOD at 550 nm using this option?

Thanks,

Tim Glotfelty

Gabriele Pfister

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Feb 28, 2018, 11:58:19 AM2/28/18
to twgl...@ncsu.edu, wrf-chem
Hi Tim, 

yes, chem_opt =202 does consider aerosol direct and indirect effects and you can look at the User's Guide on our website for recommended settings and compatibility.
Also on the website you can download the fire_emiss tool that you can use to create wrffirechemi* files for use with the plumerise code. We do not have a public tool for aircraft emissions. 
​The MOSAIC aerosol scheme has been implemented by PNNL and not our team. As far as I know, seas_opt=2 has been taken out because of the problem with the code. You should, however, be able to use seas_opt=1. ​

Outputting deposition fluxes, natural emissions, AOD (or rather extinction factor) is possible. Look through the registry.chem to see all the field
​ name​
s. E.g. biogenic isoprene emissions are defined as:
state    real  ebio_iso       ij      misc        1         -      rh        "EBIO_ISO"         "Actual biog emiss"  "mol km^-2 hr^-1"
The h indicates that it should be output to the history file. Alternatively you can also control output during runtime using the
​​
iofields_filename
​option in namelist.input. 

In summary, yes chem_opt=202 is a suited option if you need to consider all these processes. However, be aware that your intention of simulating 17 years with WRF-Chem is a huge computational undertaking and you will create very large volumes of output. 

Gabriele
--
================================
Gabriele Pfister
Atmospheric Chemistry Observations & Modeling
National Center for Atmospheric Research
Email: pfi...@ucar.edu
Phone: +1 303 497 2915
Web: https://staff.ucar.edu/users/pfister

Mary Barth

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Mar 1, 2018, 1:17:25 PM3/1/18
to twgl...@ncsu.edu, wrf-...@ucar.edu, Jerome Fast

Hello Tim,

Just to follow up on Gabi's response, and your questions.

1) Yes, chem_opt = 202 is appropriate for examining aerosol-radiation and aerosol-cloud interactions. As part of this, you would set aer_rad_feedback = 1 (and aer_op_opt > 0). This ensures that WRF-Chem predicted aerosols affect the radiation calculation in either RRTMG or Goddard shortwave scheme -- this is explained in the WRF-Chem Users Guide. However, I suggest confirming that the radiation code is also using the predicted O3 from WRF-Chem. I am not positive that this is the case.

2) With respect to your questions regarding what chem_opt=202 is or is not compatible with, I suggest following the guidance of our Users Guide at https://www2.acom.ucar.edu/wrf-chem, and if you have a specific question, to ask that.

3) As Gabi said, you are proposing a very large run with lots of output. In addition, the cloud chemistry could possibly slow the computation somewhat/significantly (I'm not sure how much). If you were conducting shorter runs, I would suggest skipping the cloud chemistry, but I think the sulfate production would be important for your proposed project.

4) I am not sure about the sea-salt emissions being disabled in MOSAIC for WRFV3.9.1.1. You could confirm this with Jerome Fast and/or by looking at the code. Plus, there's nothing stopping you from modifying the code to be sure it is working okay.

5) See Gabi's answer for the fire emission question.

We can create aircraft emissions (Barth et al., 2012). Attached is the preprocessor that I have for the aircraft emissions along with a README file. The preprocessor code is in IDL. I hope that is not a problem. I hope to upload this preprocessor code to our web page soon. For Barth et al., 2012, we used aircraft emissions from Baughcum 1999, which may be outdated. I know there are also other aircraft emission datasets available. Let me know if you need to get an aircraft emissions inventory.

Regards,

Mary

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Mary Barth                                Phone:  303-497-8186
Senior Scientist                          email: bar...@ucar.edu

National Center for Atmospheric Research                        
P.O. Box 3000                  
Boulder, CO 80307           

https://staff.ucar.edu/users/barthm  
DC3 Web Site:  http://www2.acom.ucar.edu/dc3/
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aircraft_preprocessor_files.tar

Timothy Glotfelty

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Apr 4, 2018, 11:54:20 AM4/4/18
to Mary Barth, wrf-...@ucar.edu
Hi Mary and Gabriele,

   Thank you both for the information it has been most helpful in trying to set up a test run!  I haven't got around to trying the aircraft processor yet since I'm not experienced at IDL but I will give it a try some time soon. 

   Just to let you know it turns out the MOSAIC sea-salt emissions are functional and therefore it must have been an error in the WRF-Chem users guide or some sort of miss communication.

   I did have an issue/question about the fire emissions though. I wasn't sure if this was by accident or design but when I was using the MOZART biomass burning emissions option (biomass_burn_opt  = 3) none of the aerosol emissions from FINN were being read into the model for use in the MOSAIC aerosol module. I double checked the code and it looks like in order to use biomass burning aerosols with MOZART and MOSAIC you need to use biomass_burn_opt  = 2 for MOZCART. This isn't really clear in the official WRF-Chem User's guide and it's not corrected in the option 202 user's guide you pointed me to because it says that they never tested the plumerise code in conjunction with option 202. However, from my testing and the code it appears that the plumerise code is compatible with the option 202 as long as  biomass_burn_opt  = 2. So I guess my question is whether this is an oversight with the User's Guide or a bug with the code?


   I'm also having some trouble with the lightning NOx parameterization as well. Since my domain is over Africa I'm trying to use the prescribed IC:CG ratios since option 2 only works for the U.S,. but the model will hang after it completes the first time step. If I switch the option to 2 or 3 the model runs successfully but all output for lighting NOx is zero. I've attached the physics and chemistry portion of my namelist. Is there anything that is not set correctly?


&physics
 mp_physics                          = 10,     5,     5,
 ra_lw_physics                       = 4,     4,     4,
 ra_sw_physics                       = 4,     4,     4,
 radt                                = 30,    30,    30,
 sf_sfclay_physics                   = 5,     1,     1,
 sf_surface_physics                  = 4,     2,     2,
 bl_pbl_physics                      = 5,     1,     1,
 bldt                                = 0,     0,     0,
 cu_physics                          = 5,     1,     0,
 cudt                                = 5,     5,     5,
 icloud                              = 1,
 cu_rad_feedback                     = .true.,.true.,.false.,
 num_soil_layers                     = 4,
 num_land_cat                        = 21,
 sf_urban_physics                    = 0,     0,     0,
 sst_update                          = 1,
 tmn_update                          = 1,
 sst_skin                            = 1,
 bucket_mm                           = 1000.0,
 bucket_J                            = 1.e9
 sf_lake_physics                     = 1,
 aer_opt                             = 1,
 progn                               = 1,
 lightning_option                    = 11,
  iccg_method                         = 3,
 iccg_prescribed_num                 = 3,
 iccg_prescribed_den                 = 1,
 cellcount_method                    = 1,
 lightning_start_seconds             = 600,
 flashrate_factor                    = 60.,
 cldtop_adjustment                   = 0,
 /


&chem
 kemit                               = 1,
 chem_opt                            = 202,
 bioemdt                             = 30,
 photdt                              = 30,
 chemdt                              = 10,
 io_style_emissions                  = 1,
 emiss_opt                           = 10,          0,
 emiss_opt_vol                       = 0,          0,
 emiss_ash_hgt                       = 20000.,
 chem_in_opt                         = 1,          0,
 phot_opt                            = 1,          0,
 gas_drydep_opt                      = 1,          1,
 aer_drydep_opt                      = 1,          1,
 bio_emiss_opt                       = 3,          0,
 ne_area                             = 400,
 depo_fact                           = 0.25,
 dust_opt                            = 3,
 dmsemis_opt                         = 0,
 seas_opt                            = 2,
 gas_bc_opt                          = 1,          0,
 gas_ic_opt                          = 1,          0,
 aer_bc_opt                          = 1,          0,
 aer_ic_opt                          = 1,          0,
 gaschem_onoff                       = 1,          0,
 aerchem_onoff                       = 1,          0,
 wetscav_onoff                       = 1,          0,
 cldchem_onoff                       = 1,          0,
 vertmix_onoff                       = 1,          0,
 chem_conv_tr                        = 1,          0,
 conv_tr_wetscav                     = 1,          0,
 conv_tr_aqchem                      = 1,          0,
 biomass_burn_opt                    = 2,          0,
 plumerisefire_frq                   = 30,         0,
 have_bcs_chem                       = .true., .false., .false.,
 aer_ra_feedback                     = 1,
 aer_op_opt                          = 1,
 opt_pars_out                        = 1,
 lnox_opt                            = 1,
 N_IC                                = 125.,
 N_CG                                = 125.,
 diagnostic_chem                     = 0,
 /

Thanks,
Tim

Mary Barth

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Apr 4, 2018, 12:35:42 PM4/4/18
to Timothy Glotfelty, wrf-...@ucar.edu

Tim,

Here is one thing to check  which is posted on the wrfchem-ltng discussion email  https://groups.google.com/a/ucar.edu/forum/?hl=en#!forum/wrf-chem-lightning

Check to see if the lightning start time and time step works smoothly with the meteorology time step. We've added a correction to the logic that is implemented in the upcoming WRFV4.0.

I do not know the biomass burning emissions as well and will let someone else answer that question.

Mary

Timothy Glotfelty

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Apr 4, 2018, 3:56:44 PM4/4/18
to Mary Barth, wrf-...@ucar.edu
Mary,

   Thanks for the information. I was able to get the lightning NOx parameterization running. It was a combination of what was mentioned in that post and also because I did not set the lightning_dt variable in the namelist.

   In the User's guide it says that the lightning_dt variable defaults to the model time step but in my case it was defaulting to zero. Once I set it to the model time step in the namelist and made the other changes it was able to work just fine.

Thanks,
Tim 

Gabriele Pfister

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Apr 4, 2018, 4:29:44 PM4/4/18
to twgl...@ncsu.edu, Mary Barth, wrf-chem, Christoph Knote, Alma Hodzic Roux
Tim,

thanks for your note on the fire emissions. MOZART-MOZAIC fire emission aerosols are considered when using biomass_burn_opt = 2 (BIOMASSB_MOZC). This needs to be updated in the User Guides. 

Gabriele
--
================================
Gabriele Pfister, Deputy Director
Atmospheric Chemistry Observations & Modeling
National Center for Atmospheric Research

Timothy Glotfelty

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Apr 19, 2018, 5:02:05 PM4/19/18
to Mary Barth, wrf-...@ucar.edu

Hi Mary,

     I was able to test the aircraft emission processor and it looks as though it worked. I was able to generate aircraft emissions of NO, SO2, and CO from the RCP and EDGAR emissions inventories. 

     One thing I might suggest is to include some directions in the README or any other documentation that the user needs to set  hemi = -1 on line 201 of  01.prepemis.pro if they are doing a domain in the southern hemisphere. This gave me a little bit of trouble at first.

      Originally when I tested the aircraft emissions in WRF-Chem the simulation seemed to run successfully. However, when I did a more careful quality check of the results I noticed that the Q2 in my simulation by the second hour and changed significantly. I've attached a screen shot to illustrate what I mean.  The ncview plot on the left is without aircraft emissions and the one on the right is with aircraft emissions. I double checked the QVAPOR variable and it appears unchanged which means whatever is causing this only impacts the diagnostic Q2 variable. I added and then removed only the aircraft emission lines of the namelist several times to make sure that was the only difference between my simulations. I found out it doesn't matter if aircraft_emiss_opt  is set to 1 or 0. The issue is caused by the lines for reading the aircraft emission files:

frames_per_auxinput14               = 1,
auxinput14_inname                   = 'wrfaircraftchemi_d<domain>_<date>',
auxinput14_interval_m               = 60,
io_form_auxinput14                  = 2,


      I've confirmed that this issue occurs multiple times and on two different computer clusters so I don't believe it is a random error. If I allow the simulation to run for multiple hours the Q2 variable will periodically go back to normal and then this strange pattern again. When I have seen issues like this with WRF before it usually indicates a memory corruption where one variable is overwriting the other. I'm not sure how Q2 and aircraft emissions would even be directly related to one another in the model. Any ideas?

Thanks,
Tim



    

Rui Pedro Silva

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May 4, 2021, 12:08:40 PM5/4/21
to wrf-chem, twgl...@ncsu.edu, wrf-...@ucar.edu, Mary Barth
Hello,


I am using WRF-Chem V3.9.1 with the following &chem options:

&chem
 chem_opt = 32, ! CBMZ/MOSAIC 4bins
 chem_in_opt = 1, ! Set as 1 if chemical lateral BC are provided by global model. Data will be read in through aux input port 12
 io_style_emissions = 2, ! date/time specific emissions data files used
 chemdt = 90, ! time step used by chemistry in minutes
 bioemdt = 90, ! update time interval used by biogenic emissions in minutes
 kemit = 1, ! number of vertical levels in the emissions
 photdt = 90, ! update time interval used by photolysis routine in minutes
 phot_opt = 2, ! uses Fast-J photolysis
 emiss_opt = 3, ! uses RADM2-MADE/SORGAM anthropogenic emissions
 gas_drydep_opt = 1, ! includes dry deposition of gas species
 aer_drydep_opt = 1, ! include dry deposition of aerosols
 bio_emiss_opt = 3, ! includes MEGAN biogenic emissions online based upon the weather, land use data. 
 ne_area = 200, ! used by MEGAN biogenic emissions to provide a minimum total number of chemical species used by specified chemistry option.
 emiss_inpt_opt = 101, ! RADM2 emission speciation adapted after reading the data file to follow CBMZ/MOSAIC
 dust_opt = 3, ! includes GOCART dust emissions with AFWA modifications
 seas_opt = 2, ! includes GOCART sea salt emissions
 dmsemis_opt = 0, ! includes GOCART dms emissions from sea surface - need to provide dms reference field
 aer_op_opt = 1, ! aerosol optical properties calculated based upon volume approximation
 opt_pars_out = 1, ! include optical properties in the output
 gas_bc_opt = 16, ! 
 gas_ic_opt = 16, !
 aer_bc_opt = 1, ! 
 aer_ic_opt = 1, ! 
 gaschem_onoff = 1, !
 aerchem_onoff = 1, !
 wetscav_onoff = 1, !
 cldchem_onoff = 1, !
 chem_conv_tr = 1, !
 vertmix_onoff = 1, ! vertical turbulent mixing turned on
 conv_tr_wetscav = 1, ! subgrid convective wet scavenging turned on in the simulation
 conv_tr_aqchem = 1, ! subgrid convective aqueous chemistry turned on in the simulation. Currently linked to MADE modal aerosol options
 have_bcs_chem = .true., ! gets lateral boundary data from wrfbdy data file
 aer_ra_feedback = 1, ! feedback from aerosols to the radiation schemes turned on, see also chem_opt parameter
 /


I am wondering if seas_opt=1 and seas_opt=2 work with MOSAIC, because I don't see any variable regarding sea-salt in my outputs. 

I've checked subroutine mosaic_seasalt_emiss in module_mosaic_driver.F and found this:

print.png
print2.png

It seems that the model is doing the partitioning of sea-salt between different aerosol species that are present in my wrfouts (cl_a01, cl_a02, cl_a03, cl_a04), na_a01, ...). 
Am I correct?

Thank you for your help.

Best regards,
Rui Silva 
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