Thanks for posting your revised SpecDef file. This is a good start, but you want to do more than just comment out species that are not shared between the two mechanisms - whenever possible, you want to calculate cb05e51_ae6 species that aren’t present in cb6r3m_ae7 from species that are.
For the aerosol species, please see my earlier post and use lines 196 - 350 from our example SpecDef_racm_ae6_aq_derived_from_cb6r3m_ae7_kmtbr.txt file to calculate ae6 species from ae7 species. For example, this line "AALK1J ,ug m-3 ,AAVB1J*0.16, AE7 to AE6 Mapping " means that the ae6 species AALK1J can be estimated by multiplying the ae7 species AAVB1J with 0.16 whereas using your current version of the file, you’d not have any AALK1J values in your BC file so CMAQ would initialize this species to 0.
For the gas phase species mapping, I am not an expert, but I know that that you’d want to estimate the organic nitrate species in cb05e51 (NTRALK, NTRCN, NTROH, NTRI, NTRCNOH, NTRPX, and NTRM) from the organic nitrate species in cb6r3m (NTR1, NTR2, and INTR), and you’d also want to define the cb05e51 species PAR as sum of the cb6r3m species PAR, PRPA, KET, ACET, and BENZENE since the four latter species were split out from PAR in the transition from cb5 to cb6. Here is how you might do this - again, I am no expert in chemical mechanisms, and I’d ask others to weigh in and correct me. Specifically, while I do know that in the past we had summed NTRALK and NTRCN to get NTR1 when going from cb05e51 to cb6r3, summed NTROH, NTRI, NTRCNOH, and NTRPX to get NTR2 when going from cb05e51 to cb6r3, and mapped NTRM to INTR, I do not know if the even split I’m suggesting below is appropriate to disaggregate these species from cb6r3 to cb05e51.
PAR ,ppmv ,PAR+PRPA+KET+ACET, CB6R3 to CB05e51 Mapping
NTRALK ,ppmv ,0.5 * NTR1, CB6R3 to CB05e51 Mapping
NTRCN ,ppmv ,0.5 * NTR1, CB6R3 to CB05e51 Mapping
NTROH ,ppmv ,0.25 * NTR2, CB6R3 to CB05e51 Mapping
NTRI ,ppmv ,0.25 * NTR2, CB6R3 to CB05e51 Mapping
NTRCNOH ,ppmv ,0.25 * NTR2, CB6R3 to CB05e51 Mapping
NTRPX ,ppmv ,0.25 * NTR2, CB6R3 to CB05e51 Mapping
NTRM ,ppmv ,INTR, CB6R3 to CB05e51 Mapping
I will respond to your other question in a separate post below.