Double counting NH3 emissions when using NH3 Bidi flux in CMAQ

I am turning the ‘ammonia bi-directional flux’ on within the CMAQv5.3.2 runscript environment variable setenv CTM_ABFLUX Y and feeding in FEST-C input files:

setenv E2C_SOIL ${INPDIR}/toCMAQ_festc1.4_epic/
setenv E2C_CHEM ${INPDIR}/toCMAQ_festc1.4_epic/us1_2016_cmaq12km_time${YYYYMMDD}.nc
setenv E2C_LU ${INPDIR}/beld4_camq12km_2011_4CMAQioapi.ncf

There is also another option in the runscript that I switched on to subtract fertilizer NH3 from emissions because it will be handled by the BiDi calculation: setenv CTM_BIDI_FERT_NH3 Y.

From what I understand, in the SMOKE emission files, the ‘ag’ sector is one sector that includes NH3 emissions from fertilizers and livestock; there may be other industrial sources of NH3 as well. Does not doing setenv CTM_BIDI_FERT_NH3 Y in CMAQ runscript nullify all NH3 emissions coming from the merged 2D SMOKE emissions (using mrggrd to merge all 2D emission sector files) fed to CMAQ? From what I understand, I should only make the SMOKE fertilizer NH3 emissions zero if I am separately feeding FEST-C daily files, but not sure how I can do that. I am just trying to make sure I am not double counting NH3 emissions in CMAQ!

Fertilizer emissions should not be double counted as long as your emissions file contains the variable NH3_FERT (emissions from fertilizers) and NH3 (the total NH3 emissions from all sectors). When bidirectional NH3 is selected and setenv CTM_BIDI_FERT_NH3 Y the NH3_FERT variable from the emissions file is subtracted from the total NH3 emissions. If you do not have the NH3_FERT variable, then you should get an error when these flags are selected.