If you examine your new CTM_LOG file, you’ll see that adding setenv CTM_EMLAYS 1 solved all these types of warnings
Bad argument LAY1= 29
>>--->> WARNING in subroutine GET_EMIS:INTERPX
Bad window dimension(s)
M3WARN: DTBUF 0:02:30 Jan. 14, 2020 (2020014:000230)
>>--->> WARNING in subroutine GET_EMIS on PE 001
Could not read NO2 from EMIS_1
M3WARN: DTBUF 0:02:30 Jan. 14, 2020 (2020014:000230)
that were present in your original log file. The reason you saw these warnings (and the reason no emissions could be read from your EMIS_1 file) was that you set CTM_PT3DEMIS to N in your run script, but did not provide a 3D emissions file, only a single layer emission file. This is not an expected setup in CMAQv52 where the assumption is that you provide an offline 3D emissions file if CTM_PT3DEMIS is set to N and a combination of a 2D gridded emission file and stack emission / stack group files for inline point source plume rise calculations if CTM_PT3DEMIS is set to Y. Put differently, based on your run script settings, the code was expecting a 3D gridded emissions file and failed to read emissions when you provided a 2D gridded emissions file. Adding setenv CTM_EMLAYS 1 solved this by telling the code that your gridded emissions file only has one layer despite setting CTM_PT3DEMIS to N. You could also have solved this issue by setting CTM_PT3DEMIS to Y, specifying EMISfile in the second portion of the if/then block below, and setting NPTGRPS to 0.
if ( $CTM_PT3DEMIS == 'N' ) then
#> Offline 3d emissions file name
set EMISfile = emis_mole_all_\${YYYYMMDD}_cb6_bench.nc
else
set EMISfile = emis_mole_all_${YYYYMMDD}_cb6_bench.nc #> Surface emissions
setenv NPTGRPS 0 #> Number of elevated source groups
endif
As a side comment, it likely is not appropriate for most cases to add all of your emissions to the first model layer, without considering plume rise for point sources either offline or within CMAQ. You may want to reconsider your emissions processing approach.
The crash in aqchem you are now seeing is triggered by NaN values likely originating after reading in your emissions. If you examine your new CTM_LOG file, you see the following:
Maximum eddy diffusivity of: 345.54 (m**2/sec)
at col, row, layer: 2, 64, 4
corresponding to a free tropospheric wind shear of: 4.65772E-03 (/sec),
a bulk Richardson Number of: -34.532 ,
and pot. temps. in layer and layer+1: 266.07 263.37
after VDIFF G NaN A NaN N NaN
after COUPLE_WR G NaN A NaN N NaN
These reported NaN values likely originate from missing and/or bad values in your emissions input file, and then cause the CCTM calculations to fail. To solve this issue, you will need to examine your emission input files for bad (very large negative or positive) values.