Marine Ecosystem Dynamics Modeling Laboratory

Model System

The Satilla River estuarine water quality management model system includes 5 major components: 1) the meso-scale meteorological model (MM5); 2) the hydrodynamic model (FVCOM); 3) the water quality model, 4) the suspended sediment model; and 5) the computer interface GUI system. The linkage of these models is illustrated in the schmatic figure shown below.

MM5 is the 5th generation mesoscale weather model developed by NCAR/Penn State (Dudhia et al 2003) for community use. This model features non-hydrostatic dynamics, terrain-following sigma-coordinate, variable domain and spatial resolution, multiple grid nesting, 4-D data assimilation, several planetary boundary layer (PBL) modules to represent turbulent mixing over the ground and ocean, and user-friendly access platforms (Grell et al 1994). MM5 uses NCAR/NCEP or ETA weather model fields as initial and boundary conditions with two-way nesting capability, and can provide continuous hindcasts and 5-day forecasts. The detailed description of the present configuration of MM5 for the South Atlantic Bight and Georgia coast is given in Meterological Model.

FVCOM is a recently developed prognostic, unstructured grid, finite-volume, free-surface, 3-D primitive equation coastal ocean circulation model (Chen et al 2003). In common with other coastal models, FVCOM uses the modified Mellor and Yamada level 2.5 (MY-2.5) and Smagorinsky turbulent closure schemes for vertical and horizontal mixing, respectively (Mellor and Yamada 1982; Galperin et al 1988; Smagorinsky 1963) and a sigma coordinate to follow bottom topography. Unlike existing coastal finite-difference and finite-element models, FVCOM is solved numerically by flux calculation in the integral form of the governing equations over an unstructured triangular grid. This approach combines the best features of finite-element methods (grid flexibility) and finite-difference methods (numerical efficiency and code simplicity) and provides a much better numerical representation of momentum, mass, salt, and heat conservation. FVCOM includes a mass conservative wet/dry point treatment technique to simulate the flooding/drying process over the coasal-estuarine-tidal and creek-intertidal marsh complex. This technique is also capable of predicting the flooding area due to storm surges over the land along the coast. A 3-D Lagrangian particle tracking program is incorporated into FVCOM, which can be used to trace fluid particles, fish larvae, and toxic contaminant tracers. The ability of FVCOM to accurately solve scalar conservation equations in addition to the topological flexibility provided by unstructured meshes and the simplicity of the coding structure makes FVCOM ideally suited for interdisciplinary application for coastal oceans, estuaries, and lakes.

The suspended sediment model is a simple 3-D passive tracer equation with inclusion of sinking, sedimentation, and resuspension processes. The sediment flux at the bottom is specified as the difference of resuspension via sedimentation. No feedback on the fluid motion and flocculation and deflocculation processes are considered in the resuspension process. The model is coded with the same finite-volume approach that is used to calculate the tracer concentration in FVCOM. This model can be run either together with FVCOM or offline with the input of 3-D flow field and turbulence mixing.

WQ is a water quality model modified from the EPA water quality analysis simulation program (called WASP) by including the benthic flux from sediment resuspension via sedimentation processes (Amborse et al., 1995, Zheng, 2001). This is a typical eutrophication model consisting of eight water quality state variables: (1) ammonia (NH3); (2) nitrate and nitrite (NO2 and NO3); (3) inorganic phosphorus (OPO4); (4) organic nitrogen (ON); (5) organic phosphorus (OP); (6)phytoplankton (PHYT); (7)carbonaceous biochemical oxygen demand (CBOD); and (8) dissolved oxygen (DO). The benthic and sediment suspension processes are incorporated into the water model by adding a benthic layer and a sediment pool on the bed of the estuary. This biological/chemical model incorporates a basic transformation process including photosynthesis, uptake, respiration, nitrification, denitrification, benthic flux, sediment suspension, and external loads, etc.  The modified water quality model was developed based on the characteristics of biological and chemical processes in Georgia estuaries, with the help of biologists at the University of Georgia, Skidaway Institution of Oceanography, and Enironmental Protection Agency (EPA) in Athens. The key references include Ambrose et al. (1993), Di Toro et al. (1971), Thomann et al. (1974), Di Toro and Matystik (1980), Di Toro and Connolly (1980), and Thomann and Fitzpatrick (1982), and Di Toro and Fitzpatrick (1993). 

The computer GUI interface software includes: 1) an operational control interface for model runs; 2) user’s selected environmental evaluation tool, and 3) visualization and graphic package. The control interface provides managers and users with direct access on configuration of model runs for various needs regarding the management. The environmental evaluation tool allows users to investigate the impact of point or non-point tracers (nutrients, organic maters, or others) on the estuarine environment for selected time and locations. Visualization and graphics package enables managers to view the distribution and variation of water temperature, salinity, currents, DO, nutrients, phytoplankton, and other organic matters on any selected area or cross- and along-river transects. The system is operated on a 2-CPU Linux workstation. Some functions included in that system are shown on this website.

Posted on January 16, 2014