Two types of vertical coordinates are available in CMAQ version 4.4. For hydrostatic conditions, the time-dependent hydrostatic sigma-pressure vertical coordinate system can be used in the MM5 meteorological model. This coordinate system can also be used for non-hydrostatic conditions, such cases as nested-grid simulations, where the nested grids are too small to make the same hydrostatic assumptions used in the coarser grids of the model. The other vertical coordinate system is the time-independent reference non-hydrostatic sigma-pressure vertical coordinate system, which is used for non-hydrostatic simulations in the MM5 meteorological model.

Resolving the surface boundary layer requires high resolution near the surface for meteorological simulations. To determine mass exchange between the boundary layer and free troposphere, good resolution near the boundary layer top is preferable. In addition, different cloud parameterization may perform differently depending on the layering structure. Layer definitions should be appropriate for the topographic features of the simulation domain. Aerodynamic resistance, which influences dry deposition velocities, is a function of layer thickness and the boundary layer stability. For emissions processing, the layer thickness affects the plume rise from major stacks. The vertical extent of the emission effects is determined by the thickness of the lowest model layer for the CCTM. Although a six-layer vertical grid definition is provided with the tutorial simulation examples, there is no recommendation that it be used for regulatory applications.

In the early versions of CMAQ (pre version 4.5), Fortran include files defined the vertical layer configuration. The VGRD.EXT and COORD.EXT files contained a parameter and data statements, respectively, for defining the number of layers and sigma coordinates of the vertical layer structure to be used for CMAQ. CMAQ used these include files during compilation to build executables hard-wired with the chosen vertical layers. Starting with version 4.5, CMAQ began to use a dynamic vertical layer configuration, similar to the dynamic horizontal grid, which is specified at execution rather than at compilation. The dynamic vertical layers forgo the need to recompile CMAQ each time the user changes the vertical layer configuration between simulations.