I want to get the concentrations of some PM2.5 species like Si, Fe and Al. But they are not calculated in SpecDef_cb6r3_ae7_aq.txt. I find ASIJ, AALJ and AFEJ in the CMAQ ACONC, so can I use ASIJ*PM25AC to get the concentration of PM25_SI? Do they have the coarse concentration (such as ASIK)?
yes, you are exactly correct that if you are interested in PM2.5 Si, Fe, etc., you would multiply ASIJ, AFEJ, etc. from the ACONC file with PM25AC from the APMDIAG file (as an aside, it seems you are working with CMAQv5.3.3 or older - starting in CMAQv5.4, you could actually obtain PM2.5 Si, Fe, etc. directly from the AELMO output file as variables PM25_SI, PM25_FE, etc. with no need for extra computations).
CMAQ does not keep track of speciated coarse mode concentrations for these species. Depending on the source type (e.g. anthropogenic PM10 emission inventories, CMAQ windblown dust, etc.), their mass is included in the bulk ACORS and/or ASOIL coarse mode species.