Environment variable settings about biogenic emissions in CMAQ


Can someone help me to explain the following settings in details to run CMAQ with inline biogenic emissions (e.g. MEGAN3.2)?

USE_MEGAN_LAI | F (default)
MGN_ONLN_DEP | F (default)
CTM_MGEMDIAG | F (default)

The first option, USE_MEGAN_LAI is available if users would like to use their own LAIv input. This is currently configured to work with the 8-daily LAIv from the MEGAN preprocessor. If you don’t want to bother making this file then you can leave it set to False, in which case values from the MCIP files will be used.

MGN_ONLN_DEP is a hidden/experimental option for calculating the contribution from online deposition to the nitrogen reservoir in BDSNP. Enabling it will produce unreasonable soil NO emissions. This option will be improved in a future release.

The next two are for BEIS and not MEGAN. The last one is about marine gas emissions.


In addition, you can also view a list of BEIS and MEGAN online biogenic emission configuration options along with a short description of each option in Appendix A of the users guide.

Out of curiosity, did you see the MGN_ONLN_DEP option specified in any run script or by examining the code? As noted by @willison.jeff , this is not an option recommended for any applications with the current code. In my recollection, it was therefore not included in any of the example CCTM run scripts distributed in the CMAQ github repository, and as you noted its default value in the code is F.

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Hi Jeff and Christian,

I wanted to express my gratitude for your response and explanation. I understand that using the option of MGN_ONLN_DEP is not recommended.

As per your comments above, if we set USE_MEGAN_LAI to False, the model will use values from the MCIP files. However, it’s important to note that MCIP only provides LAI and not LAIv, which is actually used in the calculation of biogenic VOC emissions. Therefore, we need to ensure that we have a reliable source for LAIv values if we choose to use MCIP for LAI.

We have developed the 8-daily LAIv for our nested model domains, and we would like to use our own LAIv input. Additionally, we believe that using the BDSNP algorithm for soil NO emissions will provide more reasonable results. We have all the necessary files for this module.

In light of this, I plan to set the following environment variables in my CMAQ run script:


if ($CTM_BIOGEMIS_MG == ‘Y’) then
setenv MEGAN_LAI = /path-to-file/LAI.nc

Could you kindly let me know if this is the correct approach?

Thank you very much for your time and assistance.

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Hi Feng,

these settings look correct to me if you’d like to use your own LAI files, but I don’t have first hand experience with it.

This looks right. Please let me know if you encounter any problems.

Thank you for raising the issue of MCIP files without LAIv. I think I need to add a check so that MCIP LAI gets converted to LAIv if using NOAH.

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Hi Christian and Jeff,

Thank you both for confirming the settings for using our own LAIv files. I am happy to report that the updated settings have allowed the CMAQ to run successfully.