The root cause is not AQCHEM. From your log file:
After INITSCEN : Gas 4.242E-01 | Aer 9.471E+01 | Non 2.637E-03
This shows the sum of species concentrations for gas-phase, aerosols, and nonreactives, respectively, after reading in the initial conditions. The first science process is VDIFF, which includes emissions. After this process, your log file says:
After VDIFF : Gas 4.205E-01 | Aer NaN | Non 2.650E-03
This indicates aerosols already contains NaN, or Not a Number.
Check to be sure there are no errors (missing data, NaNs, or infinity values) in your emissions file.
Also, I notice that your emissions file has 7 layers. That ought to work, but most of our testing with gridded emissions files over the past few years has involved files that have only one layer. You might try using the IOAPI tool M3XTRACT to extract layer 1 from the file, and rerun. If that solves the problem, let us know, since this would indicate there is a bug that should be fixed.
This thread may also be helpful.