Build a 3D Coastal Model (Level 2 Step-by-Step Guidance)


1. Introduction

This tutorial document will provide a guideline on how to set up a coastal hydrodynamic model by using the EFDC_Explorer 10 (EE10). It will cover the preparation of the necessary input files for the EFDC model and visualization of the output by using the EFDC_Explorer (EE10) Software.

The data used for this tutorial are from Tra_Khuc Estuary in Vietnam. All files for this tutorial are found in Data folder downloadable from the EEMS Website.

Before going to each session, let us first introduce the EE main form in order to better understand our explanation hereafter. Figure 1 is the main form of EFDC_Explorer or EE User Interface. The functions of individual icons are described in Model Control Form.


Figure 1.  EFDC_Explorer main form.

2. Create a New Grid

This section will provide guidelines on how to create a new simple gird with EFDC_Explorer. For a complicated grid, users are recommended to use specialized grid generation software such as CVLGrid.

Tra_Khuc Estuary in Quang Ngai province, Vietnam is chosen as the example of building a 3D coastal model in EE10.

The gird generation process includes the following steps:

1.Open EE

2.Click on icon New Model on the main menu of EE interface.

3. In Grid Tool, select Import Grid from Files and click Import Grids button. Users should choose Grid type as CVL Grid and then click Browse button to select the grid file name as "Tra_Khuc.cvl" in Grid folder as shown in Figure 2. On the other hand, EE also supports users to import various formats of grid files with the option Grid type.


Figure 2. Import grid file.

4. Set UTM Zone is 49 and then click OK to load the grid in Figure 3.


Figure 3. Load grid file.

5. Save the model by selecting this button  and create a new directory as shown in Figure 4


Figure 4 New model saved.

3. Assigning the Initial Conditions

This section will show how to assign the initial conditions such as the bathymetry, water level.


Figure 5 Assigning initial conditions.

3.1 Assigning the Bathymetry

  1. Right mouse click (RMC) on Bathymetry in Model Control tab. A popup Bathymetry tab will appear as presented in Figure 6, click Assign button.

Figure 6 Initial bathymetry.

2. The Apply Cell Properties via Polygons: Bottom Elevation form appears, select options Only grid cells inside polygons, Scatter (XYZ) data, Centroid Interp as a polyline file is used to define the area to assign the bathymetry data.

3. For Polygon Files, users should click Add File button to browse the file "Domain.p2d" in Bathymetry folder Figure 7 and Figure 8.

Figure 7 Apply Cell Properties via Polygons: Bottom Elevation form.

Figure 8 Add polygon file.

4. In this example, Scatter (XYZ) data is recommended to select to set the data values for bathymetry.  In Scatter Data Files, users should click  Add File to browse to the bathymetry data named "Bathymetry.dat" in the Bathymetry folder as shown in Figure 9.

Figure 9. Adding bathymetry data file.

5. There are a number of options for users to modify the assigned. In this case, users can select Centroid Interpolation in the Interpolation Options. Click Apply Defined Conditions to apply all the settings before. A pop-up message will appear to inform the modified cell information, click OK (Figure 10).


Figure 10.  Results of assigning the bathymetric condition.

Note that you can also obtain the bathymetry data from the online source. See the page (Online Download Data Feature in EEMS10)

3.2 Assigning the Depth/Water Surface Elevations

The next steps show the way to assign the initial depth or water surface elevations. 

  1. RMC on Water Depth/Elevation in Model Control tab. A popup Water Depth/Surface Elevation tab will appear as presented in Figure 11, click Assign Elevation button.

Figure 11.  Assign initial water surface elevation.

2. A polyline file is used to define the area to assign the bathymetry data. In Grid Options, select option Only grid cells inside polygons. In Polygon Files, users should click Add File button to browse the file "Domain.p2d" in Bathymetry folder. (Figure 12).

Figure 12 Add polygon file to assign water surface elevations. 

3.  In this example, Scatter(XYZ) data is recommended to select to set the data values for water surface elevations.  In Scatter Data Files, users should click  Add File to browse to the water elevation data named "IC_WSEL.dat" in the Boundaries folder as shown in Figure 13.

Figure 13 Add water surface elevation data.

4. There are a number of options for users to modify the assigned. In this case, users can select Centroid Interpolation (Figure 14) in the Interpolation Options.

5. Next, click Apply Defined Conditions to apply all the settings before. A pop-up message will appear to inform the modified cell information, click OK (shown as Figure 14).

Figure 14. Results of assigning the water surface elevations.

4. Assigning the Boundary Conditions

The main aim of this section is to show how to prepare for the boundary conditions and assign it to the model cell configuration. In this coastal case, there are two flow boundaries; one is river discharge from the upstream and the other is tidal level. Thus, users should prepare two time series of inflow and tidal level boundaries for this particular case. In order to set a boundary time series the steps outlined below should be taken.

4.1 Preparing the Flow Boundary.

1.In Model Control, users should click on External Forcing Data tab, then RMC on Flow and select Add New Data Series (see Figure 15).

Figure 15.  Assigning flow boundary conditions.

2. In order to add new boundary data series, click Add New button and type the series name as "River". LMC on Import data from files by selecting this button  and click Import Series as shown Figure 16.

 

Figure 16. Add new boundary data series.

3. For ASCII Data Import, users should browse to "BC_Inflow.dat" file in the Boundaries folder and click Open to import file. Check the Date Format as EE DAT or WQ Data and Header Rows to Skip as 13 before clicking OK ( illustrated in Figure 17).

Figure 17. Import flow boundary.

4. Users can select which layer they want to assign value in the Import Data tab. In this example, please check -1 to assign the same value for all layers and click OK. (Figure 18).

5. A pop-up window will appear to inform that data is imported successfully and click OK.



Figure 18.  Import data.

6. To view the data series plot, users could check View Series button in the toolbar.

Figure 19. View data time series plot.

7. The time series plot will be shown as Figure 20. EE10 also supports users to edit, export the time series plot. Please check the toolbar and the user guide for more functions.

Figure 20 Time series plot.


4.2 Preparing the Tidal Level Boundary.

  1. RMC on Water Level and select Add New Data Series Figure 21.

Figure 21 Preparing the tidal level boundary.

2. Click on Add New to insert a new data series and name it as "Tides" in Series Name. Browse to the "BC_Water Level.dat" file in Boundaries folder and click Open to import data file (shown Figure 22).

Figure 22 Import water level time series.

3. Check the Data Format as EE DAT or WQ Data and select Header Rows to Skip as 1 before clicking OK. Then, users should enter -1 to assign the same values for all layers ( See Figure 23). After clicking OK, a pop-up message will appear to inform that data was imported. 

Figure 23. Selected the data format to import.

4. Select View Series as this button  to visualize the data time series. 

Figure 24.  Water elevation time series plot.


4.3 Assigning Time Series to the Boundary Location Cells.

When all required boundary time series are prepared the next step is to assign those boundary time series to the model cells.

4.3.1 Assigning the Flow Boundary

In order to assign the flow boundary, the following steps should be taken. Figure 25 shows the location of inflow and tidal level at the open boundary for the Tra_Khuc model case.

  1. Click to the 2DH View icon  on the main form.
  2. In View Layer Control, turn on the Model Grid layer and turn on the editing mode of the Boundaries Layer by clicking the pencil icon shown as Figure 25.


Figure 25.  Locations of inflow and open tidal boundaries.

3. Click on Selection Tool  in the main toolbar  and then select Line Crossing


Figure 26. Line crossing.

4. Use line crossing to select all the cells at the inflow boundary location in Figure 26.  Then, RMC on a selected cell and choose Add New Boundary Group (see Figure 27).

Figure 27. Add a new inflow boundary group.


5. Enter the inflow boundary group as "River" and select boundary group type as "Flow Boundary".

Figure 28. Set up inflow boundary.


6. For flow boundary conditions, check the flow table as "River" and set it for all by click All button. A pop-up message will show to inform that 17 cells have been changed, then click OK.

Figure 29. Assign boundary conditions for all selected cells.

7. The inflow boundary is now assigned to all selected cells as shown in Figure 30.

Figure 30. Upstream boundary cells assigned.

4.3.2 Assigning Tides Boundary

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

1.Click to the 2DH View icon  on the main form.

2. In View Layer Control, turn on the Model Grid layer and turn on the editing model of the Boundaries Layer by clicking the pencil icon  shown as Figure 25.

3. Clicking on Selection Tool in the main toolbar  and then select Inside Polygon as Figure 31.

Figure 31. Select inside polygon.

4. Draw a polygon that can cover all the cells at the tides boundary location in Figure 32

Figure 32 Draw a polygon to assign tides boundary.


5. To assign the tides boundary group, users should RMC on a selected cell and click Add New Boundary Group.

Figure 33.  Add new tides boundary group.


6. Enter the Boundary Group Name "Ocean" and select the appropriate boundary type. In this case, the river flows to the east, so choose " East Open Boundary".

Figure 34 Set up tides boundary.

7. Select level data time series that created earlier, "Tides" as shown in Figure 35. Next, click All button to assign tides to all cells. The number of changed cells will be informed and click OK.

 

Figure 35 Assign tide flow boundary.

8. The tides open boundary is now assigned for all selected cells. 

Figure 36. Tides boundary cells are assigned.

5. Hydrodynamics Settings

  1. Back to the main tab, select Windows in the toolbar and click to Model Control, or select Model | Show Active Model from the main menu.

Figure 37.  Use the Windows option to return to the Model control tab.

2. In Modules sub-main tab, click + to expand Hydrodynamics tab, all sub-tabs of Hydrodynamics will be shown as Figure 38. The users need to RMC on each sub-tab to adjust option settings.

.

Figure 38.  Hydrodynamic options setup.

3. Set Roughness

RMC on Roughness. A popup Bottom Roughness tab will appear as presented Figure 39, click Assign button.

Figure 39.  Assign bottom roughness. 

For Grid Options, select option Only grid cells inside polygons. In Polygon Files, users should click Add File button to browse the file "Domain.p2d" in the Bathymetry folder. (Figure 40

Figure 40. Load polygon file.

Select Scatter (XYZ) data to set the data values for the bottom roughness.  In Scatter Data Files, users should click  Add File to browse to the bottom roughness data named "IC_Bot_Roughness.dat" in the Boundaries folder as shown in Figure 41.

Figure 41. Load bottom roughness data. 

There are a number of options for users to modify the assigned. In this case, users can select Centroid Interpolation (Figure 42) in the Interpolation Options.

Then, click Apply Defined Conditions to apply all the settings before. A pop-up message will appear to inform the modified cell information, click OK (shown as Figure 42).


Figure 42. Results of assigning bottom roughness.


4. Setting Wetting and Drying

In order to optimize simulation time, the EFDC model can be set so that dry cells are ignored with Shallow Water Options frame. In this case, users should set this condition as Figure 43.


Figure 43.  Wetting and Drying setting for the model.


5. Setting Turbulence

RMC on Turbulence sub-tab, in the Turbulence Options, select Turbulent Diffusion to set turbulence diffusion. Select options as "Smagorinsky" and click OK.


Figure 44.  Turbulence Diffusion Settings.

6. Setting Vertical Layers

The hydrodynamic model is ready for running a test now. Normally a model is run for one vertical layer for initial calibration. It is also possible to add more vertical layers by the following steps:

  1. RMC on Grid in the Model Grid.
  2. Select Standard Sigma
  3. Enter the number of vertical layers into the box (# Layers). For Tra_Khuc case, set vertical layers to 5 layers and then click OK to save the setting.


Figure 45. Setting the vertical layers.

7. Model Timing

The final step is to set the model simulation time and model time steps.

  1. In the Timing / Linkage, RMC on Timing. Enter the duration of starting/ ending the simulation. Note that the boundaries time series should be always covered in this simulation duration period. Otherwise, the model will not able to run.

Figure 46.  Setting the model run time.


2. RMC to Linkages and select the EFDC_Explorer Linkage tab to set the frequency of the output of the EFDC results. Setting this to 15 minutes means that EFDC will save the output every 15 minutes for the display of the model results in the EE. (Figure 47). Click OK. Note that, the smaller output frequency will create a larger output file.


Figure 47.  Setting Linkage Output Frequency.

8. Running EFDC+

Back to the main form, click this button to run the model. Browse to the EFDC+ executable file and select the updated executable file.  Click Run EFDC+ button to run.

Figure 48.  Run EFDC settings.


If all steps before are followed correctly, the model will start running and then MS-DOS Window will show the model simulation as seen in Figure 49.

Figure 49.  Running EFDC Window.

Note

Note that users can hit any characters on the keyboard to pause the simulation and check the model results. If they want to exit the simulation hit the same key if they want to continue running then hit any other key.

9. Visualizing the Model Output

This session will show how to view the model simulation results.In general, users can access the main form to click 2DH View button  to view the model simulation results.

  1. In Layer Control, click Add button to add a New EFDC View Layer . The users should see the 2DH View Options window with Primary Group and Parameter to display.

Figure 50. Parameter visualization. 

2. Figure 51 is an example of showing the vector and magnitude velocity field results. Similarly, EE10 is able to support the visualization of other model parameters. 

Figure 51. Velocity vector visualization.

Please refer to the “EFDC_Explorer User’s Manual” for more information on EE capabilities.