There are multiple chemical mechanisms available with the CMAQ system. Each chemical mechanism has a corresponding “Species Definition” file that prescribes how model output variables should be combined to predict different gas, particle and deposition species. When you download the CMAQ code for version 5.2 or later, these definition files are automatically included under the subdirectory “CCTM/src/MECHS”. Within each of the listed mechanism folders, you will find files “SpecDef_MECH_NAME.txt” and “SpecDef_dep_MECH_NAME.txt” that contain a long list of species definitions and corresponding documentation. For example, to find out how to calculate PM2.5 using the CB05e51_ae6 mechanism, open the file “SpecDef_cb05e51_ae6_aq.txt” and read the documentation on PM2.5 calculations. The species definition file will indicate which species should be included in PM2.5 (for example: sulfate, ammonium, and organic carbon) as well as factors to obtain the fraction of each CMAQ size distribution mode that corresponds to 2.5 micron (diameter) and smaller particles. Similar information is available for calculating PM10 and PM1. These species definition files are designed to be used with the combine utility to extract model variables that can be matched to observed quantities from specific monitoring networks. Within the combine run script you will need to set the environment variable SPECIES_DEF to the path of the appropriate species definition file, e.g.,
setenv SPECIES_DEF ${CMAQ_HOME}/CCTM/src/MECHS/cb6r3_ae6_aq/SpecDef_cb6r3_ae6_aq.txt