A useful poster on Atlantis processes in the Chesapeake Bay model (by Tom Ihde and others)
Here is a very useful table listing all (or at least most) processes in Chesapeake Bay Atlantis Model (zoom in!).
The reference is:
Ihde, T. F., I. C. Kaplan, E. A. Fulton, I. A. Gray, M. Hasan, D. Bruce, W. Slacum, and H. M. Townsend. 2016. Design and parameterization of the Chesapeake Bay Atlantis Model: A spatially explicit end-to-end ecosystem model. U.S. Dept. of Commer., NOAA. NOAA Technical Memorandum NMFS-F/SPO-166, 145 p.