Diagenesis/benthic flux settings are made in the Benthic tab shown in Figure 1. The nutrient benthic flux computational options are set using the Modify Parameters button in the Benthic Flux frame.

Figure 1  Water Quality Tab: Benthic.

Clicking the button brings up the form shown in Figure 2. The top frame, Benthic Nutrient Flux Method is the option that controls EFDC's benthic flux approach. If the nutrient mass fluxes are to be specified, either as constants or variable in time and space, then the diagenesis tabs are not used and consequently disabled. If the Full Diagenesis Model (DiToro & Fitzpatrick, 1993) option is selected then the three diagenesis tabs are available to allow the user to specify the diagenesis parameters.

Figure 2  Sediment nutrient flux – Sediment Diagenesis Options and Parameters.

Figure 3 shows one of the diagenesis tabs for defining the diagenesis parameters. The best way to initialize all of the diagenesis parameters is to use the Load Settings button. This will read an existing WQSD3D.INP file from another project and initialize the settings for the current project with those from the loaded project. After the user initializes the parameters they can modify the settings during the model development stages. The diagenesis values from the Chesapeake Bay ICM application (Cerco & Cole, 1995) provide a good starting point for diagenesis model parameterization.

Figure 3  Sediment Diagenesis: Diagenesis – Options.

In addition to the diagenesis kinetic parameters, the sediment bed diagenesis initial concentrations also need to be specified. This can be accomplished by applying measured data for each parameter using the Spatially Varying IC's button. When pressed, the form shown in Figure 4 is displayed. For each of the required parameters, the user can interpolate the data onto the model. Each nutrient reaction class, i.e. G1 (most reactive), G2 and G3 (least reactive or inert) must be separately specified. The Operator can be used to factor or otherwise modify the interpolated field or a previously defined IC field. The data can be interpolated for the entire model in a single operation or using only selected cells by specifying a Poly File.

The user can initialize the spatial field to a set of constants using the Initialize to Constants button. It should be noted that the sediment diagenesis bed is not linked in any way to the sediment transport sub-model bed definition, scour or deposition processes.

Figure 4  Sediment Diagenesis: setting the initial conditions.

The diagenesis kinetic parameters can be divided into zones. Figure 5 provides access to setting the zones and assigning the zone specific parameters. The maximum number of zones needed is set by entering the appropriate number in the "# of Zones" field. To edit a specific zone, the user should scroll to the desired zone using the up/down arrow control.

The zones and the zone specific parameters can be viewed and editing using the ViewPlan by selecting the View Option Diagenesis, then checking the Show Zone option. If the Enable Edit is checked, then RMC'ing on a cell allows the user to edit the cell's corresponding diagenesis zone's kinetic parameters. The cell's diagenesis zone assignments can be edited using the Property Copy function.

Figure 5  Sediment Diagenesis: Diagenesis kinetic zones.

Rooted Macrophytes

If the user wished to implement the Rooted Plant and Epiphyte Model (RPEM) the Use button should be selected as shown in Figure1. The Modify button in the Rooted Macrophytes frame allows the user to set various constants associated with RPEM as shown in Figure 6.

The RPEM: General tab allows the user to enable or disable a variety of combinations for RPEM, including enabling simulation of rooted plants or epiphytes; enabling epiphytes growing on rooted plants; enabling RPEM – Water Column Nutrient Interaction; enabling RPEM – Sediment Diagenesis Interaction.
For details on the theory behind this sub-model, please refer to "A Generic Rooted Aquatic Plant and Epiphyte Algae Sub-Model for EFDC" (Hamrick, 2006).

Figure 6  RPEM: General.

The Initial Conditions tab is shown Figure 7. This tab allows the user set various approaches for the RPEM such as: Constant IC's, Spatially varying IC's - WQRPEMSIC.INP, and Spatially varying IC's - WQRPEMRST.INP. These latter two options allow user to input a variable carbon biomasses rather than setting them as constant values. Clicking on any of the buttons for setting shoot, root, epiphyte or detritus carbon ICs will bring up a form as shown in Figure 8. Using this form the user may import a polyfile or datafile for the IC.

Figure 7  RPEM: Initial Conditions.

Figure 8  RPEM: Initial Conditions: Shoot Carbon

The Root, Shoot & Detritus tab sets growth and respiration rates amongst other parameters for shoots, roots and detritus as shown in Figure 9.

Figure 9  RPEM: Root, Shoot and Detritus.

Root and Shoot temperatures may be set in the R & S Temperature tab as shown in Figure 10.

Figure 10  RPEM: Root &Shoot Temperature.

Constants for epiphyte growth respiration, light limitation, temperature effects for growth and respiration may be set in the Epiphyte tab as shown in Figure 11.

Figure 11  RPEM: Epiphytes.