At last week's group meeting, I discussed the difference between 2 of CMAQ's output files: ACONC and CONC.
CONC = instantaneous pollutant concentration at each output timestep (each hour)
ACONC = average pollutant concentration for each model hour (average throughout hour)
The CONC file automatically includes all pollutants at all vertical model layers, whereas the pollutants and vertical layers in the ACONC are set by the user in the CCTM run script. In general, use ACONC for comparison with ground-based measurements and CONC for comparison with satellite data.
Overall, I found that ACONC and CONC concentrations compare very well over both the CONUS and GL domains for secondary (formed in atmosphere) pollutants. A much bigger difference is seen between ACONC and CONC for primary (directly emitted) pollutants. This difference is expected - subhourly variations in wind speed and other meteorological factors will affect the local concentrations of primary pollutants emitted from point sources (e.g. SO2, CO) much more that the concentrations of the more well-mixed secondary pollutants (e.g. O3, ASO4).
Nothing earth-shattering, but might be helpful to someone running CMAQ for the first time.
Steve