Build a 3D Lake Model with Sigma Zed (Level 2 Step-by-Step Guidance)

1  Introduction

Lake Washington is a large freshwater lake adjacent to the city of Seattle and the largest in King County. It is a ribbon lake, 35 km long and surface area of approximately 88 km2. Mercer Island lies at the southern end of the lake. The main inflows are from the Sammamish River in the north and Cedar River in the south. The outflow is to via a ship canal at Puget Sound in the west with discharge of approximately 7 m3/s.

The bathymetry of Lake Washington shows that it is a deep, narrow, glacial trough with steeply sloping sides and approximately 65 m deep at its deepest point . These morphologic features are highly suitable for application of the SGZ model.

This tutorial document will guide you how to setup Sigma Zed model by using the EFDC_Explorer (EE). It will cover preparation of the necessary input files for the EFDC model and visualization of the output by using the EFDC_Explorer (EE) Software.

The data used for this tutorial are from Lake Washington. All files for this tutorial are found in Lake Washington model downloadable from the EE website.

Before going to each session, let’s us first introduce about the main form of EE User Interface in order to better understand our explanation hereafter. Figure 1 is the main form of EFDC_Explorer or EE User Interface. Functioning for individual icons are described as following;

Figure 1  EFDC Explorer Main Form.


2  Import Grid

This session will guide you to import the grid into EFDC_Explorer. With a complicated grid such as this the grid generation software CVLGrid has been used. Lake Washington in Washington state, the USA will be chosen as an example of building a 3D Lake Model with Sigma Zed in EE.

The gird generation process includes following steps:

  1. Open EE
  2. Click Generate New Model icon as  on the main menu of EE interface. Then Generate EFDC Model frame appears shown in Figure 2.
  3. Select CVLGrid in the Grid Type. The user click Browse button to select grid file name as "LW Grid.cvl" as shown in Figure 2. Note that EE also supports importing a variety of grid formats with option Import Grid shown in Figure 3.

Figure 2  Generate EFDC Model form.

Figure 3  Import grid options.

    4. Click Generate button and finish. A dialog will pop up to show the gird information (see Figure 4).

Figure 4  Newly created grid information.

    5. Save the model by select this button  and create a new directory as shown in Figure 5.

Figure 5  New model saved.

3  Assigning the Initial Conditions

This section will guide you how to assign the initial conditions such as the bathymetry, water level and bottom roughness.

Figure 6  Assigning the Initial Conditions.

3.1  Assigning the Initial Bottom Conditions

  1. Select the Domain/Initial Conditions & Bottom Roughness tab and click the Assign button. A form will displayed as shown in Figure 7.
  2. in the Data File to text box browse to the bathymetry file XXXXX. This bathymetry file is simply a general x,y, z format.
  3. In this case, we choose Modify Options is Interpolate Data in cell and Interpolate Data meaning that it will take the surround data points to interpolate for the cells where there is no data.
  4. Note that Poly File is the area to assign the bathymetry data. There are few modify options for users to assign the data.
  5. Click the Apply button to take the effect before hitting the Done button.

Figure 7  Assigning model bathymetry.

3.2  Assigning the Depth/Water Surface Elevations

The next step is to assign the initial depth or water surface elevations. There are two options for setting the surface water elevation that are Use Constant and Use Point Measurements/Gridded Data. In this case we will use the former option.

  1. Click Assign button, select Use Constant: to assign a flat water surface elevation. Enter "6.5" as the number enter in the Operator or Constant box as shown in Figure 8.
  2. Click Apply button then click Done button to finish.

Figure 8  Assigning water surface elevation.

3.3  Assigning the Bottom Roughness (Z0)

  1. Click the Assign button in the Bottom Roughness (Z0) box (Figure 6).
  2. Check Use Constant and enter the roughness value to 0.02.
  3. Click the Apply button before hitting the Done button. (Figure 9)

Figure 9  Assigning bottom roughness.

4  Assigning the Boundary Conditions

This next step is to prepare for the boundary conditions and assign these to the model grid. In this model there are seven flow boundaries, all but one of which are rivers flowing into Lake Washington. The Lock BC is an outflow. Figure 10 shows flow boundaries of the model.

Figure 10  Inflow and outflow of Lake Washington.

4.1         Preparing the Flow Boundary.

  1. Select the Domain/Boundary Conditions. (See Figure 11).
  2. Click to the E button  which is next to Flow to edit the flow boundary. (Figure 12)
  3. Entering the Number of Series into the box (in this case, enter 7)
  4. Give a Tittle for associated time series.
  5. Copy and Paste the time series data into the workspace. (See Figure 13 ).

Figure 11  Assigning Flow Boundary Conditions.

Figure 12  Editing the Boundary Time Series.

    6. Click to the Current button  to view the current time series. If there are a number of layers then check Sum Layers to show total flow. (See Figure 13).

Figure 13  Flow Time Series Plot.

    7. Change up/downward this  button to edit other time series.

    8. Click OK to finish editing the boundary time series.

4.2         Preparing Temperature Boundary.

  1. Select the Domain/Boundary Conditions. (See Figure 14).
  2. Click to the E buttonwhich is next to Temperature to edit the flow boundary. (Figure 14)
  3. Enter the Number of Series (Type 3) (See Figure 15)
  4. Give a Tittle for associated time series.
  5. Copy and Paste the time series data into the workspace. (See Figure 15 ).

Figure 14  Assigning Temperature Boundary Conditions.

Figure 15  Editing the Boundary Time Series.

6. Click to the Current button  to view the current time series. (See Figure 16).

Figure 16  Editing the Boundary Time Series.

4.2         Preparing Wind Boundary.

  1. Select the Domain/Boundary Conditions. (See Figure 17 ).
  2. Click to the E button which is next to Winds to edit the boundary. (See Figure 17)
  3. Enter the Number of Series (Type 1) (See Figure 18)
  4. Give a Tittle for associated time series.

Figure 17  Assigning Winds Boundary Conditions.

Figure 18  Editing the Boundary Time Series.

Figure 19  Editing Wind Station Parameters.

Figure 20  Wind Rose.

4.3         Preparing Atmospheric Boundary.

  1. Select the Domain/Boundary Conditions.
  2. Click to the E button which is next to Atmospheric to edit the boundary. (See Figure 21)
  3. Enter the Number of Series (Type 1) (See Figure 22)
  4. Give a Tittle for associated time series.

Figure 21  Assigning Atmospheric Boundary.

Figure 22  Editing the Boundary Time Series.

Figure 23  Editing ATM Station Parameters.

Figure 24  Viewing ATM Data.

4.4         Assigning Time Series to the Boundary Location Cells.

When all required boundary time series are prepared. You have to assign those boundary time series into the model cells.

4.4.1      Assigning flow boundary

In order to assign the flow boundary, the following steps should be taken

1. Click to the 2D Planview icon  on the main form (See Figure 1 ).

2. Choose Boundary C’s in the Viewing Opt’s .

3. Check Enable Edit and Show Grid (See Figure 25).

4. In order to know locations of cells assigned flow BC, the user should load the labels file (BC Location.dat). Go to "Display Options" in the top menu of 2D ViewPlan then go to "Annotations", next load the label file as shown in Figure 26 and Figure 27.

Figure 25  Assigning Boundary Condition Cells.

Figure 26  Loading Label File.

Figure 27  Labels Displayed

5. Zoom in to each label location then Right-Mouse-Click on the inflow/outflow location cell/ choose New (See Figure 28).

7. Select boundary types. It is dependent on your current boundary type to choose the suitable boundary type. In this case, we have 1 flow boundary so we choose number 1 (See Figure 30).

8. Select the associated with this inflow boundary time series. (See Figure 31). then click OK to complete.

Figure 28  Right-Mouse-Click on the inflow cell.

Figure 29  Enter Boundary Group ID.

Figure 30  Select the Boundary Types.

Figure 31  Assign the Corresponding Time Series.

9. The boundary cells might have multiple cells to present the real river width. In order to assign the next cell as inflow cell, you need to come back to step 5 and Right-mouse Click to that cell and choose Add to Adjacent. The inflow is now divided to the number of assigned cells. (See Figure 32).

Figure 32  Assign the more boundary cells.

4.3.2      Assigning temperature boundary

Temperature boundary associated with flow boundary, in this case there two temperature boundary, one is associated with Cedar River inflow and the other is related to Sammamish River inflow. The following steps should be taken:

  1. Click to the 2D ViewPlan icon  on the main form (See Figure 1).
  2. Choose Boundary C’s in the Viewing Opt’s .
  3. Enable Edit grid by checking to
  4. Right-mouse Click on the inflow location cell/ choose Edit (See Figure 33).
  5. Select temperature timeseries corresponding to inflow boundary (ID), for example temperature table 0831 belongs to Cedar River Inflow (See Figure 34).
  6. Click OK button to finish.

Figure 33  Right-Mouse-Click on the inflow cell.

Figure 34  Assign Temperature Boundary.

5  Setup Grid Layers (Sigma Zed)

  1. In the EE main form, click to Domain Tab then click Grid (See Figure 35).
  2. Choose SGZ: Specified Bot Layer.
  3. Enter the number of water layer. In this case # of Layers is 55 then press enter button on the keyboard (See Figure 35).
  4. Click Set SGZ Layering, the form will appear as shown in Figure 36.
  5. Put KMin = 2 then click OK button.
  6. Cells information will be updated as shown in Figure 37.

Figure 35  Assign Temperature Boundary.

Figure 36  SGZ Layering Options Form.

Figure 37  SGZ Layering Options Information.

6  Activate Modules

When the user click Activate Modules tab, a list of modules will be displayed for selecting. Check on box of Activate Temperature as shown in Figure 38. After that the Temperature tab will be turned on (See Figure 38). Click Temperature tab, a form will appear as shown in Figure 39

  • General & Data Sub-tab

Click Assign button to assign initial condition for temperature. In the appeared form, the user set values as shown in Figure 40 then click Apply and Done button to finish.

Figure 38  Activate Modules.

Figure 39  Temperature Module Form.

Figure 40  Assigning Initial Temperature Form.

  • Surface Heat Exchange

Figure 41  Surface Heat Exchange Settings.

  • Bed Heat and Ice Option

Figure 42  Bed Heat & Ice Options Settings.


7  Model Timing

After above sessions, you are almost having a hydrodynamic model. This part will guide you how to setup the model simulation time and model time steps.

  1. Step 1: Select Timing/ Linkage and Model Run Timing (See Figure 43)
  2. Enter Duration of starting/ ending the simulation. Note that the boundaries time series should be always covered this simulation duration period. Otherwise the model will not run.

Figure 43  Model Run Time.

Table 2  Model Run Time Explanation.



Time of Start (days)

Julian starting date (an automate conversion to Gregorian date is there)

# Reference Periods

Total simulation time (an automate conversion to Gregorian date is there)

Duration of Reference Period (hours)

Reference period

Time Step (second)

Delta T

Safety Factor

0<Safety Factor < 1 to active the Dynamic time step

# Ramp-Up Loops

Number of initial interaction to hold the time step to a  constant during ramp-up

Maximum dH/dT

If >0 then it is an additional criteria to determine the dynamic time step.

Beginning Date/Time

The base date of all data and simulation period.

3. Select the EFDC_Explorer Linkage to set the EFDC Results to EFDC_Explorer Frequency. 60 minutes mean that the EE will store the output in every 60 minute for displaying the model results in the EE. (See Figure 44). Note that, smaller output frequency will cause larger output file.

Figure 44  Setting Linkage Output Frequency.

8  Hydrodynamic Model Setup

This session will guide you how to set the hydrodynamic model. Since the EFDC model is applied the Wet and Dry condition to optimize the simulation time. Thus, we should set for this condition as following:

  1. Step 1: Select Hydrodynamics/ Wetting & Drying box
  2. Step 2: Set Flag is equal to -99.
  3. Step 3: Entering the Wet/Dry Depth. Remember that the wet depth should always greater than the Dry depth. (Figure 45).
  4. The user can go to the Modify button to adjust the calibration hydraulic parameters there (Figure 46).
  5. Save the model project.

Figure 45  Hydrodynamic Model Setup.

Figure 46  HMD Modify Form.

9  Running EFDC

  1. Select the Setting icon  on the main form to browse to the EFDC Executable file. (Figure 47).

Figure 47  Browse to the EFDC Executable File.

2. Step 2: Select the Run EFDC icon to on the main form and click the Run EFDC_DSI button to run the model (Figure 48).

Figure 48  Run EFDC Setting.


If everything are setting well, the model will start running and you will see the MS-DOS Window appear to shown the model results as see in Figure 49. Note that you can hit any characters on the key-broad to pause the simulation and check the model results. If you want to exit the simulation hit the same key, if you want to continue run then hit any other key.

Figure 49  Running EFDC Window.

10  View the Model Calibration Plots

Go to Model Analysis Tab, select Model Calibration as shown in Figure 50. Click Define/Edit button to fill the Time Series Comparison form as Figure 51 then click OK button to finish.

After that click Plots button, a form of plot generation options appears for the user (See Figure 52). if the user check on two boxes, the EE will automatically generate plots and ASCII data file and they are stored in #calib_plots folder. The user can stop the process by press Esc button on the keyboard during automatic generation.

Otherwise the EE generate plot one by one.

Time Series Comparison and Vertical Profile Comparisons plots shown in Figure 53 and 54.

Figure 50  Model Calibration Window.

Figure 51  Time Series Comparison Form.

Figure 52  Calibration Plot Generation Options.

Figure 53  Time Series Comparison Plot.

Figure 54  Vertical Profile Comparison Plot.