Error in running mozbc with cam-chem data for MOZART-GOCART (112)

[Naser Mohammadzadeh]

Hello,

I successfully run mozbc for RACM-MADE-VBS (108) using CAM-CHEM data. But when I want to run for MOZART-GOCART(112) (with mapping provided on the website "MOZCART.inp"), it shows this error in the terminal: 

 in module_mozart_lib ...

And the main error in the output file (MOZCART.out) is :

 NetCDF: Variable not found                                                    
 
 fail to process netCDF file...

I wonder why RACM is running successfully, but MOZART-GOCART shows an error.

I would appreciate if you help me

Thank you

Naser

[Mary Barth]

Hi Naser,

That error usually means that the variable name (chemical species) that you are requesting is not in the CAM-Chem output file. You could check the CAM-Chem data using ncdump -h command and compare to the species mapping list in the mozbc input file. 

- Mary

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

Mary Barth 

Senior Scientist   

phone: 303-497-8186    email: bar...@ucar.edu

NSF - National Center for Atmospheric Research

P.O. Box 3000

Boulder, CO 80307

Staff web page

SIMA Web Site

MUSICA Web Site

DC3 Web Site 

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

[Naser Mohammadzadeh]

Dear Mary 

In RACM, I updated chemical species like O3, NO, and NO2 with CAM-CHEM successfully. CAM-CHEM contains all the species I need to update using MOZBC. However, when I changed the mapping from RACM.inp to MOZART.inp, I encountered an error. Do you have any ideas? It is noteworthy that my domain and resolution are changed from RACM (9km) to MOZART(18km). Don't you think this causes errors?

If you need additional information, please let me know.

Yours,

Naser

[Naser Mohammadzadeh]

Dear Mary

Hello again

I solved my problem with adding "moz_var_suffix = '' to my MOZART.inp. 

I have another question. please see my available variable in bellow:

spc_map = 'no -> NO', 'o3 -> O3',
          'no2 -> NO2', 'no3 -> NO3', 'nh3 -> NH3', 'hno3 -> HNO3', 'hno4 -> HO2NO2',
          'n2o5 -> N2O5', 'ho -> OH', 'ho2 -> HO2', 'h2o2 -> H2O2',
!          'ch4 -> CH4', 'co -> CO', 'ch3o2 -> CH3O2', 'ch3ooh -> CH3OOH',
          'hcho -> CH2O', 'ch3oh -> CH3OH', 'c2h4 -> C2H4',
          'ald -> CH3CHO', 'ch3cooh -> CH3COOH', 'acet -> CH3COCH3', 'mgly -> CH3COCHO',
!          'paa -> CH3COOOH', 'pan -> PAN', 'mpan -> MPAN', 'macr -> MACR',
          'mvk -> MVK', 'c2h6 -> C2H6', 'c3h6 -> C3H6', 'c3h8 -> C3H8',
!          'c2h5oh -> C2H5OH', 'c10h16 -> C10H16',
!          'onit -> ONIT', 'onitr -> ONITR', 'isopr -> ISOP',
!          'isopn -> ISOPNO3', 'acetol -> HYAC', 'glyald -> GLYALD',
!          'hydrald -> HYDRALD', 'mek -> MEK',
          'bigene -> BIGENE', 'open -> BIGALD', 'bigalk -> BIGALK',
          'tol -> TOLUENE', 'cres -> CRESOL', 'dms -> DMS', 'so2 -> SO2',
!          'BC1 -> .4143*CB1;1.e9', 'BC2 -> .4143*CB2;1.e9',
!          'OC1 -> .4143*OC1;1.e9', 'OC2 -> .4143*OC2;1.e9',
!          'SEAS_1 -> 2.*SA1;1.e9', 'SEAS_2 -> 2.*SA2;1.e9',
!          'SEAS_3 -> 2.*SA3;1.e9', 'SEAS_4 -> 2.*SA4;1.e9'
!          'DUST_1 -> 1.1738*[DUST1];1.e9', 'DUST_2 -> .939*[DUST2];1.e9',
!          'DUST_3 -> .2348*[DUST2]+.939*[DUST3];1.e9',
!          'DUST_4 -> .2348*[DUST3]+.5869*[DUST4];1.e9', 'DUST_5 -> .5869*[DUST4];1.e9'

As you can see, when I activate the "!" item for some variables, I will be faced with in module_mozart_lib ... .

For example,  we don't have CB1, CB2, OC1, OC2 ...... in CAM-CHEM and WACCM. Do you know any other variable to update for OC, EC, SEAS, DUST ...?

Do you get my question?

Thank you

I am looking forward to your answer.

Yours,

Naser

[Mary Barth]

Naser,

Are you using MOZCART.inp for option 112 or MOZART.inp? I think MOZCART.inp, but I want to be sure.

And you said you used RACM.inp for option 108 but shouldn't it be RACMSORG.inp?

Nevertheless, what may be the issue is that the MOZCART.inp file is expecting bulk aerosol information from CAM-chem but your CAM-chem file has output for the modal aerosol model (MAM) constituents. My recommendation is that you check the species in each of the ! lines using the ncdump -h command. For example,

ncdump -h cam-chem-output.nc | more

will list all the variables in the cam-chem-output file, and 

ncdump -h cam-chem-output.nc | grep CB

will list all the lines with "CB" in it. If nothing is returned then CB1 is not in the CAM-chem output file. 

You could also look for organic carbon aerosol by typing:

ncdump -h cam-chem-output.nc | grep "a02"

If the CAM-chem output has MAM aerosols then this command will list all the aerosol species in the a02 mode. And organic carbon would be one of them. 

Same thing with C10H16 which may now be called MTERP or APINENE. (sorry I don't have a CAM-chem output file to look at).

I will also check to see if there is an updated MOZCART.inp file available.

Cheers,
Mary

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

Mary Barth 

Senior Scientist   

phone: 303-497-8186    email: bar...@ucar.edu

NSF - National Center for Atmospheric Research

P.O. Box 3000

Boulder, CO 80307

Staff web page

SIMA Web Site

MUSICA Web Site

DC3 Web Site 

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

[Mary Barth]

Hello Naser,

We found a mozbc input file that maps from CAM-chem (or WACCM) using MAM4 aerosol scheme and T1 chemistry to WRF-Chem T1_MOZCART (chem_opt = 114). It is attached. 

If you prefer using MOZCART (chem_opt=112) then you will need to make a change. 

For MOZCART gas species replace:  

'tol -> TOLUENE', 'benzene -> BENZENE', 'xylenes ->XYLENES',  

with  

'tol -> TOLUENE+BENZENE+XYLENES',  

There is a document on the web that describes mapping between gas-phase mechanisms and mapping for the MAM4 aerosol scheme. It should also help you with any further modifications.

Good luck,

Mary

[Mary Barth]

Hi again,

Use this version of MOZCART_T1.inp. It has the c10h16 mapping in it.

- Mary

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

Mary Barth 

Senior Scientist   

phone: 303-497-8186    email: bar...@ucar.edu

NSF - National Center for Atmospheric Research

P.O. Box 3000

Boulder, CO 80307

Staff web page

SIMA Web Site

MUSICA Web Site

DC3 Web Site 

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

[Naser Mohammadzadeh]

Dear Mary

Hi

 I am very glad to contact with you.

First of all, I apologize for my typo. You are right. I use MOZCART (112) (MOZART_GOCART) instead of MOZART.

Regarding RACM, I always use RACM-MADE-VBS (108) and use RACM.inp. Did I choose the right mapping for 108?

In the case of aerosol parameters like SO4, NO3, NH4, SOA, and POA, there is no mapping in the RACM.inp file that I used. You can see my RACM.inp below.

Do you have any new mapping for the RACM-MADE-VBS (108) scheme?

Finally, thank you for your kindness in sending me the new version of MOZCART_T1.

spc_map = 'co -> CO',
          'o3 -> O3',
          'so2 -> SO2',
          'no -> NO',
          'no2 -> NO2',
          'h2o2 -> H2O2',
          'no3 -> NO3',
          'n2o5 -> N2O5',
          'hno3 -> HNO3',
          'nh3 -> NH3',
          'hcho -> CH2O',
          'pan -> PAN',
          'tpan -> MPAN',
          'tol -> .75*TOLUENE',
          'xyl -> .25*TOLUENE',
          'hno4 -> HO2NO2',
          'eth -> C2H6',
          'hc3 -> C3H8',
          'hc5 -> BIGALK',
          'iso -> ISOP',
          'macr -> MACR',
!          'ald -> GLYALD+CH3CHO',
          'ket -> CH3COCH3',
          'gly -> GLYOXAL',
          'mgly -> CH3COCHO',
          'hket -> HYAC',
          'csl -> CRESOL',
          'ete -> C2H4',    
          'olt -> C3H6+MVK+0.5*BIGENE',
          'oli -> .5*BIGENE',

!          'paa -> CH3COOOH',

!          'onit -> ONIT+ONITR',
          'ora2 -> CH3COOH',
!          'op1 -> CH3OOH',
!          'op2 -> C2H5OOH+ALKOOH+MEKOOH',
          'ch4 -> CH4',
!          'sulf -> SO4;0.30173e6'
/  

Thank you very much

Naser