I am using CMAQ 5.4 with ISAM for source apportionment. I used BIES for inline biogenic emissions but in the output, I am noticing that the biogenic emissions are very small. I am tracking POM in my ISAM control file for the biogenic tag. I am not sure if I should be tracking other species like SOC, POM and SOM. I am attaching my species definition file that I am using for combine, I am also adding a screenshot of the species available in the ACONC file.
There are no PM emissions from BEIS. Since POM represents primary (i.e. emitted) OM, there should be no POM contribution from BEIS. You’re likely interested in the contribution of biogenic VOC from BEIS to secondary OM, so you would want to make sure that your post-processing of ISAM outputs includes all SOM species.
In addition, there have been a number of updates to ISAM since CMAQv5.4 was released. For ISAM applications, we recommend the use of the latest code available on the CMAQv5.5+ branch.
Thank you for the clarification. That makes sense.
I’ve updated my species definition file to track POM, SOM, POC, and SOC (attached below)
I’ve already completed a 10-year CMAQ-ISAM simulation using CMAQv5.4+, so unfortunately re-running everything with CMAQv5.5+ isn’t feasible at this point. However, I’ll take note of the improvements and consider using the latest branch for future work.
looking at your new SpecDef file, you are double counting a portion of total OM when you compute PM2.5 mass for your different tags. Specifically, by including not only POM and SOM (which should be included) but also POC and SOC, you’re counting the OC (carbonaceous) portion of OM twice.
For example, CMAQ species ASQTJ represents secondary organic aerosol mass resulting from the oxidation of sesqueterpenes (see a schematic of the ae7 module here) and contains both carbon and non-carbon mass. The carbon mass for this species can be calculated from the known OM:OC ratio of 1.52. When OC (the carbon portion of total OM) is computed, each OM species is divided my its OM:OC ratio to yield the carbon portion. Therefore, when computing total PM2.5, including both OM and OC will lead to double counting the carbon portion of total OM.
The reason the standard CMAQ SpecDef file includes both OM and OC is that they serve different purposes - OM is one of the species to be included when computing total PM2.5 mass (like in your case), and OC is the portion of OM that is actually observed through standard network measurement techniques so it is used in model evaluation.
