Parameter for model in AMET_species_list.R (AMET)

AMET
1

I want to know what is PM_MOD_SPEC parameter.
I guess it is one of the model parameters (PM2.5 mass) but I could not find any information in CMAQ result.
AERO_4 "obs, unit, model, unit, output"
Where can I get the information about the parameter?

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2

Good question. PM_MOD_SPEC is a variable species that is actually defined in the AQ_matching.R script. This is the part of the AQ_matching.R script that defines PM_MOD_SPEC:

########################################################

Check which PM names being used in combine file.

Ignored if ncdf4 R library is not installed.

########################################################
PM_MOD_SPEC ← “ATOTIJ”
PM_FRM_MOD_SPEC ← “ATOTIJ_FRM”
PM10_MOD_SPEC ← “ATOTIJK”

if(require(ncdf4)) {
if (Sys.getenv(“WRITE_SITEX”) == “T”) {
M3_FILE ← Sys.getenv(“CONC_FILE_1”)
if (file.exists(M3_FILE)) {
m3_file_in ← nc_open(M3_FILE)
var_list ← ncatt_get(m3_file_in,0,“VAR-LIST”)
var_list ← var_list$value
if(var_list != 0 ) {
vars ← strsplit(var_list," +")
if (“PMIJ” %in% vars[[1]]) {
PM_MOD_SPEC ← “PMIJ”
PM_FRM_MOD_SPEC ← “PMIJ_FRM”
PM10_MOD_SPEC ← “PM10”
}
}
}
}
}
##########################################################

Perhaps you can see already, but in AMETv1.5 PM_MOD_SPEC, by default, is set to the species ATOTIJ. Similarly, PM_FRM_MOD_SPEC is set to ATOTIJ_FRM, and PM10_MOD_SPEC is set to ATOTIJK. The reason that these species are not simply hardcoded in the AQ_species_list.input file is because, for a time, there was a transition in the name being used to in combine to define those species. So, the AQ_matching.R script checks to see what PM species name is being used in the combine file and makes sure the same name is used when creating the site compare run scripts. Eventually, I plan to remove this part of the code, as few people would be using combine files that have the older PM species names. But, for now, I have left the code in there.

If you wanted, you could modify the AQ_species_list.input file and hard-code the PM species names to whatever name is being used in your combine files. However, if you’re not running into an error, you can simply leave the code unmodified. But to answer your question, by default the PM_MOD_SPEC is ATOTIJ in AMETv1.5. You can confirm this by looking at the site compare run scripts generated by AMET. The only reason it would be different is if the name is different in your combine file.

Let me know if that helps, and if you have any other questions.

Wyat

3

  1. ATOTIJ is Total PM Aggregates and what are the differences between ATOTIJ and PM25_TOT?
    Definition in combine:
    PM25_TOT ,ug/m3 ,ATOTI[0]*PM25AT[3]+ATOTJ[0]*PM25AC[3]+ATOTK[0]*PM25CO[3]

  2. What is the exact meaning of PM25AT (PM25 Aitken mode species of mass?)?

  3. Why do they use ATOTIJ instead of PM25_TOT or PM25_FRM in AMET for PM2.5 mass?

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4

ATOTIJ is the total PM2.5 mass that is the sum of the i (Aitken) and j (accumulation) modes in CMAQ, while PM25_TOT is the total PM2.5 mass that consists of only those particles less than 2.5 microns from all three modes (i, j, and k).

So, ATOTIJ can contain some particles that are greater than 2.5 microns (in the tail of the j mode), but can miss some particles from the k (course) mode that are less than 2.5 microns. PM25_TOT looks at all three modes and applies factors (e.g., PM25AT) to each mode to include all particles less than 2.5 microns. So, it can clip large particles from the tail of the j mode but also include smaller particles from the tail of the k mode.

Historically, only the sum of the i and j modes was available in CMAQ to represent PM2.5 mass. Later on, the ability to cut the modes at 2.5 microns was added to CMAQ. So, the use of ATOTIJ is somewhat based on history. Technically, PM25_TOT is a better representation of the method that some networks, like CSN and IMPROVE, use to measure PM2.5, but there are additional considerations when deciding which value to use (e.g., continuity with previous analyses).

Wyat

1 Like