From the theory manual summary: The Modular Aquatic Simulation System in Two Dimensions (MASS2) is a two-dimensional, depth-averaged hydrodynamic and transport model. The model simulates time varying distributions of depth-averaged velocities, water surface elevations, and water quality constituents. MASS2 is applicable to a wide variety of environmental analyses of rivers and estuaries where vertical variations in the water column are negligible or unimportant. MASS2 uses a boundary-fitted, orthogonal, curvilinear computational mesh. A key feature is the use of multiple computational mesh blocks. Multiple blocks allow MASS2 to be applied to complex domains. Blocks can be connected to each other with cells having a one-to-one or one-to-many correspondence. This allows the use of a high-density mesh where detailed results are needed and coarser meshes elsewhere. MASS2 is designed to simulate a range of river and estuarine flow and water quality problems. MASS2 can simulate a wide variety of hydrodynamic conditions, including supercritical flow and hydraulic jumps. MASS2 can also be used to simulate the fate and transport of water quality parameters. Any number of conservative or decaying scalar quantities (e.g., salinity, radionuclides) may be simulated simultaneously with hydrodynamics or using precomputed hydrodynamics. In addition, MASS2 has the ability to simulate some special water quality parameters: total dissolved gas, temperature, and suspended sediment. The equations of mass, momentum, and species conservation are discretized using the finite-volume method and solved using iterative solution procedures. The coupling of the momentum and mass conservation (continuity) equations is achieved using a variation of the SIMPLE algorithm extended to shallow-water flows. MASS2 is coded in standard Fortran90 and has been compiled on a variety of operating systems including Linux, Windows, and Mac OS X. Features and capabilities of MASS2 include the following: Fully-conservative formulation of the governing equations that allows for shock-capturing Unsteady simulation including time-marching to a steady-state Multi-block, orthogonal curvilinear computational grid to allow for simulation of complex channels and islands Implicit finite-volume discretization on a staggered grid Iterative solution methods Parallel processing using Global Arrays (GA) and message passing interface (MPI) Supercritical flows including hydraulic jumps Wetting and drying Temperature simulation through solution of the thermal energy equation Total dissolved gas transport including a temperature-dependent equation of state Species and contaminant transport Non-conservative transport processes such as surface heat exchange, surface gas exchange, sediment-contaminant interaction Suspended sediment transport \item Bed evolution including erosion and deposition Sediment-contaminant interaction using partition coefficients Spatially-distributed coefficients (roughness, eddy viscosity, species diffusion) Input and model control using text files Restart from previous simulation results Transport-only model using previously computed hydrodynamics MASS2 has been developed over the last 20 years. It is currently being used on DOE projects that require MASS2 to be open source. Hence, the authors would like to distribute MASS2 in source form.