NOx and NH3 of the FCHIST

Ammonium aerosol is simulated in a very simplified manner (in the default) primarily to keep track of the deposition of nitrogen to the land model. It is called 'NH4'. Nitrate aerosols are not simulated in CESM2.1.3.

Click to expand...

Danny Leung said:

Hi wrunyu-

1. If you have a chemical tracer X (for your case X = NOy) in the molar mixing ratio with a unit of mol X / mol air, you can first convert it to the mass mixing ratio by
X (kg X / kg air) = X (mol X / mol air) * molarmass_X (kg X/mol X) / molarmass_air (kg air/mol air)
where molarmass_air = 28.96 g air / mol air is a typical value.
One you have X (kg X / kg air) as mass mixing ratio, you can convert X to mass concentration (μg X / m3 air) by
X (μg X / m3 air) = X (kg X / kg air) * density_air (kg air / m3 air) * 10^9 (μg X / kg X)
where density_air can be obtained by using history outputs of temperature and pressure with the ideal gas law, or alternatively you can directly output air density (RHO_CLUBB) as a CAM history variable.

2. Right, to my knowledge there are no simulations of the ammonium and nitrate aerosols in the default CAM-Chem. You will need to download the source code for a version of CAM-Chem coupled with the MOSAIC and then run your simulation again. See instruction on this page: Use MOSAIC scheme in CESM/CAM-chem - CAM-Chem - wiki.ucar.edu

Hope this helps!
Danny

Click to expand...

rrbuchholz said:

Hi wrunyu,

Danny answered your questions well. He is correct about the default aerosol simulation - some expanded information from Louisa Emmons:


Best,
Rebecca

Click to expand...

nusbaume said:

Hi Runyu,

I am moving your post to the CAM-Chem forum, as they will be the group who can most likely answer your questions.

Hope that helps, and have a good weekend!

Jesse

Click to expand...

Danny Leung said:

Hi wrunyu-

1. If you have a chemical tracer X (for your case X = NOy) in the molar mixing ratio with a unit of mol X / mol air, you can first convert it to the mass mixing ratio by
X (kg X / kg air) = X (mol X / mol air) * molarmass_X (kg X/mol X) / molarmass_air (kg air/mol air)
where molarmass_air = 28.96 g air / mol air is a typical value.
One you have X (kg X / kg air) as mass mixing ratio, you can convert X to mass concentration (μg X / m3 air) by
X (μg X / m3 air) = X (kg X / kg air) * density_air (kg air / m3 air) * 10^9 (μg X / kg X)
where density_air can be obtained by using history outputs of temperature and pressure with the ideal gas law, or alternatively you can directly output air density (RHO_CLUBB) as a CAM history variable.

2. Right, to my knowledge there are no simulations of the ammonium and nitrate aerosols in the default CAM-Chem. You will need to download the source code for a version of CAM-Chem coupled with the MOSAIC and then run your simulation again. See instruction on this page: Use MOSAIC scheme in CESM/CAM-chem - CAM-Chem - wiki.ucar.edu

Hope this helps!
Danny

Click to expand...

wrunyu said:

Hi Rebecca
Thank you very much for your reply. I would like to ask: can the MOSAIC coupling with CAM-Chem be realized in the CESM 2.1.3 model? Have a nice day!

Regards,
Runyu

Click to expand...

wrunyu said:

Hi Danny,

I tried to follow the web page steps to download. Because of the network settings, I can't use the code “git clone GitHub - ESCOMP/CAM: Community Atmosphere Model -b zz_cam6_3_018_mosaic0.3 your_mosaic_directory”. I manually downloaded it from the webpage and extracted it to “/home/wrunyu2023/cesm2.1.3/components/cam”. When I run the code “. /manage_externals/checkout_externals” the output appears as shown below. I didn't know how to fix it, so I built the FCHIST case directly. But I run the code “. /case.build”, an error was reported.I checked the error reported in atm.bldlog: ImportError: cannot import name get_standard_makefile_args.I would very much like to seek your help.If you have a solution for this, I would appreciate it.

Regards,
Runyu

Click to expand...

rrbuchholz said:

Hi wrunyu,


I believe the branch is only available on that specific tag of the model (CESM Version 2.0). There are some hard-coded aspects that would need to be updated in more recent versions.

Best,
Rebecca

Click to expand...

Danny Leung said:

Hi Runyu-
I think as Rebecca said, you cannot just copy the source code of the cam component to your CESM2.1.3 to replace your cam; there will be some software engineering needed because of the MOSAIC and because of the version differences (this CAM6.3.018 tag is closer to a CESM2.2 tag).
Danny

Click to expand...

wrunyu said:

Hi Rebecca,

After a week of hard work I've managed to get ./case.build in cesm2.2.0.. But now I have a new problem:

See log file for details: /home/wrunyu2023/cesm/scratch/tfFCnudged/run/cesm.log.54982.250314-215436
Submit job case.st_archive
Starting job script case.st_archive
st_archive starting
moving /home/wrunyu2023/cesm/scratch/tfFCnudged/run/cpl.log.54982.250314-215436 to /home/wrunyu2023/cesm/archive/tfFCnudged/logs/cpl.log.54982.250314-215436
moving /home/wrunyu2023/cesm/scratch/tfFCnudged/run/cesm.log.54982.250314-215436 to /home/wrunyu2023/cesm/archive/tfFCnudged/logs/cesm.log.54982.250314-215436
moving /home/wrunyu2023/cesm/scratch/tfFCnudged/run/atm.log.54982.250314-215436 to /home/wrunyu2023/cesm/archive/tfFCnudged/logs/atm.log.54982.250314-215436
Cannot find a tfFCnudged.cpl*.r.*.nc file in directory /home/wrunyu2023/cesm/scratch/tfFCnudged/run
Archiving history files for cam (atm)
Archiving history files for clm (lnd)
Archiving history files for cice (ice)
Archiving history files for docn (ocn)
Archiving history files for mosart (rof)
Archiving history files for drv (cpl)
Archiving history files for dart (esp)
st_archive completed
Submitted job case.run with id None
Submitted job case.st_archive with id None

In cesm.log.54982.250314-215436:
Opened existing file
/home/wrunyu2023/cesm/inputdata/atm/cam/chem/trop_mozart/ub/clim_p_trop.nc
79
ERROR: FLDLST: 23 errors found, see log
ERROR: FLDLST: 23 errors found, see log
ERROR: FLDLST: 23 errors found, see log
······
Abort(1001) on node 363 (rank 363 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1001) - process 363

I checked clim_p_trop.nc and the resolution is 2.5×2.5 while I set it to 0.9×1.25:./create_newcase --case case --mach=test --res f09_f09_mg17 --compset FCnudged --run-unsupported. But my nc file was indeed downloaded from the official website.I would like to know what you have to offer.
Have a nice day!

Regards,
Runyu

Click to expand...

wrunyu said:

Hi Danny,

I really appreciate the ideas you've provided.I've managed to get ./case.build in cesm2.2.0.The code I used to build the case :./create_newcase --case case --mach=test --res f09_f09_mg17 --compset FCnudged --run-unsupported.But I ran into a new problem after the model was submitted.View attachment 6544
In cesm.log.54982.250314-215436:
Opened existing file
/home/wrunyu2023/cesm/inputdata/atm/cam/chem/trop_mozart/ub/clim_p_trop.nc
79
ERROR: FLDLST: 23 errors found, see log
ERROR: FLDLST: 23 errors found, see log
ERROR: FLDLST: 23 errors found, see log
······
Abort(1001) on node 363 (rank 363 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1001) - process 363

I checked clim_p_trop.nc and the resolution is 2.5×2.5 while I set it to 0.9×1.25.But my nc file was indeed downloaded from the official website.I would like to know what you have to offer.Have a nice day!

Regards,
Runyu

Click to expand...