Only one hour of data in the results after running the COMBINE program

Hello everyone.
When I use CMAQ’s ‘combine’ tool, the exported data is only for the first hour, and all the data after that are ‘NaN’ as shown in the picture. What is the reason for this? How can I fix it? I also found some errors reported in the log, but I don’t know what the cause is.
I’ve attached my run script and log below, thanks for your reply!
log.txt (20.7 KB)
run_combine.csh (6.5 KB)


Could you please also post the SPEC_CONC file used in your run script? Looking at your log file, you probably commented out some lines from the default file, but that shouldn’t be a problem.

Given that the last species to be processed successfully is ANO3K, I suspect that the program crashes when trying to compute TNO3 because that is the species defined after ANO3K in the default file:

ANO3K ,ug m-3 ,ANO3K[1]
TNO3 ,ug m-3 ,2175.6*(HNO3[1]*DENS[2])+ANO3I[1]+ANO3J[1]+ANO3K[1]

I’m guessing that the problem occurs when reading DENS from METCRO3D since this probably is the first time METCRO3D is referenced in your SPEC_CONC file, but I don’t know why that would be the case. Your METCRO3D starts earlier and has more time steps than your ACONC and APMDIAG files, but that shouldn’t really cause a problem.

Could you please try recompiling combine in debug mode and run the script again to see if you receive a clearer error message?

Yes, you can certainly use ‘combine’ to compute aggregated variables from the ISAM output files SA_ACONC and/or SA_CONC. You will need to create a custom species definition file, using the SPEC_CONC file used for ACONC processing as a template.

Let’s say in your ISAM runs you defined two tags TAG1 and TAG2 and would like to compute total sulfate mass in the Aitken and accumulation modes attributable to these two tags, you could define a new species ‘ASO4IJ_TAGS12’ in your custom species definition file as follows:

ASO4IJ_TAGS12, ug m-3, AOS4I_TAG1[1] + AOS4I_TAG2[1] + AOS4J_TAG1[1] + AOS4J_TAG2[1]

In this example, in your combine run script you would set INFILE1 to the SA_ACONC file containing your ISAM output.

Since every ISAM setup is different, there aren’t any default species definition files for ISAM post-processing. In addition to using combine to aggregate ISAM outputs for further analysis, I’m sure users have used other tools and scripts as well for their analysis of ISAM results, but again, since every setup is different, there isn’t any standard post-processing suite. You could reach out to other ISAM users to see if they can share their post-processing and analysis approaches and tools.

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I agree that the header of the output file you posted is not consistent with the combination of run script and SpecDef file you posted.

Have you verified that the SPEC_CONC file defined in your run script (/home/cmaq/Workspace/gaohb/CMAQ5.3.2/POST/combine/scripts/spec_def_files/SpecDef_${MECH}.txt) to set SPECIES_DEF is the modified version you posted, not the original version defined for regular concentrations?

Could you please also post your full log file?

If you previously used the same name for OUTFILE ($POSTDIR/COMBINE_ACONC_$RUNID_$YYYY$MM.nc) with a different SPECIES_DEF file, you either need to remove it first or use a new name since the variables you’re defining will be different.