Since the model infrastructure was designed to promote modularity,. CMAQ requires new executables for each suite of science configuration options for all programs except MCIP. There are too many combinations of the various chemical mechanisms, horizontal and vertical transport schemes, cloud routines, and chemistry solvers in the CMAQ science configuration to include in a single executable. The burden of recompiling CMAQ each time the science configuration changes is offset by the flexibility to add new science to the model or simply to switch between different configurations. This point about modularity is most pertinent to the CCTM, although there are configuration options that must be selected when compiling the other CMAQ programs.

In addition to compile-time configuration options with CMAQ, there are also execution-time configuration options. The horizontal domain configuration and the vertical coordinate are dynamic features in CMAQ that are independent of the executable. In other words, a user can employ a single executable for a simulation that uses any of the supported map projections or grid definitions, without having to recompile the code. Distinctions between which CMAQ options must be selected at compilation versus at execution are described in Chapter 5.

As the chemistry-transport model component of CMAQ, the CCTM is the final program to be run in the CMAQ modeling sequence. The four other main programs prepare input data for the CCTM. Before describing each of the CMAQ programs (Section 1.2.4), we present a conceptual formulation of CMAQ and Eulerian air quality modeling to provide a framework for understanding the purposes and relationships of the various programs to each other and to the overall system.

Eulerian chemistry-transport models use coupled ordinary differential equations to solve the changes in concentration of pollutants throughout a three-dimensional grid that is fixed relative to a selected map projection. The changes in concentration in each grid cell are affected by the following processes:

Mathematically, these processes relate to the concentration change in each grid cell through the continuity equation, which is presented in simplified form below:

δC/δt = Adv + Diff + R_c + E_c - S_c

In CMAQ, the advection and emissions terms are calculated based on input files generated by the meteorology and emissions models, respectively; the diffusion, chemical transformation, and loss process terms are calculated within the CCTM.

The Eulerian representation of the modeling domain is a series of contiguous grid cells that form a limited-area box on a subset of the globe, so the domain lateral boundary must define advection into the modeling grid. CMAQ currently accounts for advection into the domain only from the horizontal (i.e., lateral) boundaries, assuming there is no exchange through the top boundary of the domain. These spatial boundary conditions are estimated in CMAQ using the boundary conditions preprocessor, BCON. As a temporal boundary condition, the first time step of a model simulation is estimated in CMAQ using the initial conditions preprocessor, ICON. To model solar radiation, which provides the energy source for photolysis reactions, the program JPROC calculates clear-sky photolysis rates at various latitude bands and hours based on sun angles. Output from these CMAQ programs is used with output files from the emissions and meteorology models and other CMAQ preprocessors to form the required data for running the CCTM.