Introduction

The main objective of this training course is to provide users with a basic knowledge of how-to setup a shellfish model and run a solution for Environmental Fluid Dynamics Code Plus (EFDC+). It will cover preparation of the necessary input files for the EFDC+ model and visualization of the output by using the EFDC+ Explorer Modeling System (EEMS). Kobayashi et al. (1997) is used as a case study to illustrate the general process of developing a model from basic to complex. All files for this tutorial are contained in the EEMS website. After this training, users will be able to:

• 1. Set up a basic water quality and shellfish model from input data using EFDC+ Explorer (EE) version 10.2

• 2. Visualize, extract and manage model output by EE

Model Description 

The model is set up to replicate the Kobayashi et al. (1997) data for shellfish growth in interaction with water quality described in the paper "A population dynamics model for the Japanese oyster, Crassostrea gigas". The goal of the project is to better understand the impact of vegetation to the flow in open channel.
The experiment was carried out in a 300x100 m channel as described in Shellfish Farm#Figure 1 below.

Data Summary

All data used in the model including inputs and comparison data are collected from the paper Kobayashi et al. (1997). These data are stored in "Data" folder from the testcase model (TC-12) available on EEMS website.

Environmental Conditions

Time series of mean water temperature, salinity and chlorophyll are shown in Shellfish Farm#Table 1 and Shellfish Farm#Figure 2 below. Water temperature ranged between 8 to 30^oC, while salinity during this period was relatively constant, ranging only between 28.4 to 31.9 ppt.

Step-by-Step Guide for Building Hydrodynamics Model

This chapter will show users how to:

• Generate a new hydrodynamic model

• Assign initial conditions

• Assign BCs.

Generate a New Model

In this exercise, we will generate a new water quality model. This exercise familiarizes users with the basic interface of EE and demonstrates how to build a model from scratch. Double click on the EE10.2 icon on your Desktop or start it from the list of programs to load the model interface. Click on the New Model button to begin generating a new model, as shown in Shellfish Farm#Figure 3.

For this demo, we will generate a Cartesian grid using the following steps. From the Cartesian Grid Generator form,

• (1) Select Grid Options as Generate Uniform Grid;

• (2) Set the dimension of the uniform grid as Figure 3

• (3) In the example, leave the UTM Zone as 0 or any zone;

• (4) After filling in the parameters, click the Generate button to generate the model grid, then click on the Remove Dry button to remove cells outside the polygon. The preview of the generated grid will show in the right panel.

Note: If the grid is not suitable for your purpose, you can modify the grid parameters and click Generate again to re-generate the grid;

• (5) After the grid is generated, click the OK button to close the form and go to model settings.

After the grid is generated, the Model Control form will be displayed as Figure 4. General information about the model will be displayed that includes the model title, area, number of cells, model width, height, and model location coordinates.

In the model interface, click on Save to save the model.

After clicking on the Save button, a Select Directory pop-up will appear to select saving options. Before project files are saved, the grey box is empty. This is where EE project files are listed. The empty gray box shows that no files have been written yet for the study.
There are three save options:

• Full Write can be selected to save all the input files,

• Write All except Time Series Files can be selected to save all input files without the time series.

• Save Profile File Only (EFDC.EE) can be selected for saving if users have only changed formatting options in EE.

In this project, it is recommended to use Full Write option. After choosing this option, click OK to close the form and save the model.

Assign Model Bathymetry

The next step in the model setup is to assign the bathymetry for the model domain. Assigning bathymetry refers to assigning the elevation value to each cell in the model. In this exercise, bottom elevation is a constant value at elevation of -3m (see Shellfish Farm#Figure 6).

Assign Water Surface Elevation

Water surface elevation can be assigned following the import of bathymetry. In this exercise, water depth of the channel is 3m, so assign WSEL equal to 0m.

Assign Boundary Condition Time series Data

From 2DH View, assign Inflow and Outflow BCs as shown in Shellfish Farm#Figure 7 below and set constant value of inflow and outflow BCs are 10 m3/s and (-10 m3/s).

Hydrodynamics Model

From Model Control form,

1. Go to the Modules tab

2. Expand Hydrodynamics sub-tab

3. RMC on Roughness to assign Bottom roughness (Z0) as shown in Figure 8. In this demo, bottom roughness of the model is 0.01

Open

From the Model Control form,

1. Go to the Modules tab

2. Expand Hydrodynamics sub-tab

3. RMC on Shallow Water to enter the Dry Depth and the Wet Depth.

This feature is required with fluctuating water levels that will leave some of the domain dry. For an area with tidal flats, the user should probably enable the wet and dry option. Although it incurs a certain computational overhead, it is necessary to obtain accurate results as it sets the minimum water depth allowed in a point before it is taken out of calculation (Dry Depth), and also the water depth at which the point will be reentered into the calculation (Wet Depth). In this exercise shallow water parameters are set as shown in Figure 9.

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Note: The Wet Depth should always greater than the Dry Depth.

Step-by-step Guide for Building Shellfish Farm Model

From Model Control form, RMC on Modules tab under Model Control form, check on the Salinity, Temperature, Water Quality and Shellfish Farm check-boxes then click the OK button to activate the salinity, temperature, water quality and shellfish farm modules as shown in Figure 10 below.

Salinity Module

Assign Salinity Initial Condition

From Model Control form,

1. RMC on Salinity sub-tab under Modules tab to open Salinity Parameters form

2. Click on Assign button to set salinity IC

3. Under Value to Set frame, set constant value of salinity equal to 30.1 ppt

4. Click on Apply button to assign salinity IC as shown in Figure 11 below.

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Import Salinity Data Series

After assigning salinity IC, from Salinity Parameters form, click on Edit button under Time Series Data frame to import salinity data series as shown in Figure 12 below.

After clicking on the Edit button, Boundary Data Series form will appear for participants to add/modify data series. In Boundary Data Series form, click on the Add New button to add new data series, then select Import Data button to import Salinity series data as below as shown in Shellfish Farm#Figure 13.

In the ASCII Data Import form,

1. browse to the "Data_Salinity.dat" file and select the data format as EE Dat or WQ Data;

2. Modify Import Settings parameters; then

3. click OK to import data series; Import Data form appears to allow the user to select import options from this form

4. click OK to close the form and finish importing data .

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Note: After importing the data series; from Boundary Data Series form, participants can set the data series name by typing in Series Name blank on the top left corner.

Temperature Module

From the Model Control form, RMC on each module sub-tab under the Modules tab; a list of options will appear for the user to select, as shown in Figure 14 below. From this pop-up menu:

• (1) Go to the Settings;

• (2) Assign the Initial Conditions settings