The program CCTM is the CMAQ chemistry-transport model, the Eulerian air quality model component of CMAQ. Typically run last in the sequence of the CMAQ programs, CCTM uses input data produced by all of the other CMAQ programs and from an emissions model, such as SMOKE. CCTM produces multiple output files for each simulation. The basic CCTM outputs include instantaneous and average hourly concentration files, wet and dry deposition files, and visibility estimates. Other CCTM outputs can include diagnostic aerosol and cloud files, hourly plume-in-grid files, and processes analysis files.

CCTM contains several science configurations for simulating transport, chemistry, and deposition. All of the science configuration options, including the chemical mechanism, in CCTM are set when compiling the executable. The model grid and vertical layer structure for CCTM are set at execution. The important distinction between selecting the science configuration and the model grid/layer configuration is that CCTM does not need to be recompiled when changing model grids/layers but does need to be recompiled when new science options are invoked.

Optional output files are created when their associated optional processes are invoked in CCTM.