The chemical mechanism I used in CMAQv5.4 is cb6r5m_ae7_aq, and I found that there are two pathways for the formation of SOA. One is SOAcld (AORGC) generated from glyoxal and methyl glyoxal through OH radical oxidation in the cloud water in subroutine aqchem . The other is SOA generated by the gas-particle partitioning of VOCs in subroutine orgaer. I want to know if CMAQ takes into account the SOA generated during the reactions on the surface of aerosol particles? If so, which module is responsible for calculating this type of SOA?
Yes CMAQ accounts for cloud (aqueous - aqchem) chemistry and the formation of SOA on aerosol particle surfaces (heterogeneous - orgaer) as you stated (via partitioning). Formation of SOA on aerosol particles from surface chemistry is encoded in AEROSOL_CHEMISTRY.F. Note that the formation of IEPOX and MAE SOA species depends on a parameterized reactive uptake parameter (gamma) that takes into consideration aqueous-aerosol chemistry - but most species in AEROSOL_CHEMISTRY.F have a fixed gamma. All heterogeneous rate expressions depend on surface area.
Hope this helps clarify, let me know if you have any further questions!