Does aerosol cation species ANAK not exist in cb6_ae6

I am checking the species information at CMAQ/AE_cb6r3_ae6_aq.nml at master · USEPA/CMAQ · GitHub and do not see the coarse mode representation of aerosol cation NA - ANAI and ANAJ with molecular weight of 23 g/mol are listed there though. I do see another species ASEACAT of slightly different molecular weight (23.5 g/mol) but which may be a part of coarse PM. For some other species like Cl, species of all three modes are listed (ACLI, ACLJ, ACLK - all with molecular weight 35.5 g/mol). This must be based on research, but I just wanted to make sure I understand the reason behind it.

Yes, you are correct that CMAQ does not consider sodium ions explicitly in the particle coarse mode. Instead, the effect of sodium on the coarse-mode is treated as a weighted combination Sea Spray, Soil, and Anthropogenic Coarse-mode particle emissions. You can view these weight fractions in AERO_DATA (CMAQ/AERO_DATA.F at master · USEPA/CMAQ · GitHub) lines 524-526. These are also fractions that you could use to post-process output concentrations or deposition fluxes of Sea Spray, Soil, and Anthropogenic Coarse particles to get the coarse-mode sodium.

Thanks @Ben_Murphy for pointing me to the AERO_DATA.F file in Github. It was very useful. I wanted to ask you if the same species fraction information in AERO_DATA.F is also used for user-supplied BCs. For example, if I supply just ANA species as a boundary condition to CMAQ runs, will CMAQ use the same fractions in AERO_DATA.F to divide ANA from BC into ANAI and ANAJ?

You’re most welcome. No, unfortunately the BCs are not set up to do this automatically. However, you can do it manually at this point quite easily. If you look in the AE namelist (e.g. AE_saprc07tic_ae7i_aq.nml) there are two columns (cols 5 and 6) for specifying BC mapping. Here you can point ANAI and ANAJ to ‘ANA’ and set the BC_FAC to the value you prefer. The -1 for most species just instructs CMAQ to try to map each model species to a BC file variable of the same name.

Thanks @Ben_Murphy. I was curious how CMAQ would distribute BC/IC species by default if no change was made to AERO_DATA.F; for example how species ANA from BC/IC would be distributed to ANAI, ANAJ (and whether to ASEACAT also?)?

I think I understand your question, and ANA would not be distributed to ANAI or ANAJ without being specifically mapped manually. For BCs and ICs, CMAQ is looking for exact name matches. THe only exception is for mapping ALVOO1 to APOC. ASEACAT is likewise only mapped to ASEACAT by default. Any other mapping for ASEACAT will need to be specified manually.

Does this answer your question?

Thanks @Ben_Murphy - I had been thinking CMAQ will automatically allocate BC/IC species to their respective I,J and K mode species, but clearly I was not thinking correctly. Has it always been like this, or the very old versions of CMAQ did allocate, say, BC/IC ANH4 to ANH4I, ANH4J and ANH4K using its internal rule? This is in context of using BC/IC from non-CMAQ source, like a global model, which only has ANH4.

To my knowledge, it has always been the case that allocation to I, J, and K modes had to be done manually. Perhaps if the BCON or ICON tools were run, they may have mapped these, but I’m not sure. I’m looping in @hogrefe.christian and @barronh who may have more insight.

I agree with @Ben_Murphy .To my knowledge, it was always left to the user to split up aerosols from a non-CMAQ source to the appropriate CMAQ aerosol modes using the information available to them. Since ICON / BCON did not and do not directly support such generalized species mapping, users have to use other tools to accomplish this. Step 3 in the BCON tutorial provides an example of how to use combine to map between different CMAQ mechanisms, but something similar could be done to define the translation from the non-CMAQ species to the CMAQ mechanism species.

Thanks @Ben_Murphy and @hogrefe.christian. Recently, I have adapted the tutorial for BC/IC generation from H-CMAQ to map global model species to I,J,K CMAQ species. In my test runs from months ago, I only mapped species to species and had problems with low PM on Western US. Thanks - I am clear now on what should be done!

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Does CMAQ make assumptions on the aerosol diameter distrubutions (and even cutoffs) for Aitken, Accumulation and Coarse modes of aerosol species? I am curious how one could map the following four MOZART-2 species of different diameters to CMAQ modal species based on diameter size:

Hi @skunwar,
Yes CMAQ does make assumptions about the aerosol cutoffs, but the translation these species is pretty straightforward. I would map SA1 and SA2 to ANAJ and ACLJ. For SA3 and SA4, you can map the Cl mass to ACLK. You can map the NA mass to ASEACAT, but I would check to make sure there aren’t other sea spray cations you want to map there as well (e.g. MG, K, or Ca).

Thanks @Ben_Murphy ! I assume it would be fine to roughly allocate:

seasalt with 0.01um < diameter < 0.1um to Aitken mode (I) species,
seasalt with 0.1um < diameter < 1um to Accumulation mode (J) species, and
seasalt with diameter > 1um to Coarse mode (K) species

and likewise for dust species with four bins of different diameters?

Sure, you can do that, if you know the fraction in each of those sections. I assume you have diameter and number (and perhaps other moments) available to make that determination?

At this point, I see from their publication that 'distributions of four sizes of dust (0.05–0.5, 0.5–1.25, 1.25–2.5, and 2.5–5.0 μm) ’ exist but do not see other info like mean, variance.

Hi again,

Just to circle back, I would do as you say and put the 1st and 2nd bins in Accumulation and the 3rd and 4th bins in Coarse. Certainly you could adjust this to test the sensitivity of your results to this assumption; that would possibly be a good idea if you have time.


Thanks. I have another question about BC species which I believe is related to this thread, so did not start a new one: I have sulfate and nitrate aerosol species saved from the global model but not ammonium aerosol (not saved) to set as BCs for CMAQ. By default, then, CMAQ would set ammonium aerosol species modes (I,J,K) BC to a very small positive number. I was wondering if this absence of user-specified ammonium aerosol species (while sulfate and nitrate are present) could skew the aerosol chemistry somehow, assuming most of sulfate and nitrate aerosols are ammonium sulfate and ammonium nitrate?