SMS:ADCIRC Tutorial

Objectives

This lesson will teach you how to prepare a mesh for analysis and run a solution for ADCIRC. It will cover preparation of the necessary input files for the ADCIRCcirculation model and visualization of the output. You will start by reading in a coastline file and then a SHOALS file.

The data used for this tutorial are from Shinnecock Bay off of Long Island in New York. All files for this tutorial are found in ADCIRC Data Files directory.

Prerequisites	Requirements	Time
Overview Tutorial	ADCIRC Map Module Mesh Module Scatter Module LeProvost Tidal Database	60–90 minutes

1 Reading in a Coastline File

For this tutorial, you will first read in a coastline file, which has already been set up for you. This sample coastline will form the boundary for your mesh. To set up your coverage for ADCIRC and open the coastline file:

1. Change the coverage type to ADCIRC by right-clicking on default coverage, selecting Type, and choosing ADCIRC (in the models subcategory).
2. Select File | Open.
3. Select the file shin.cst in the Data Files Folder for this tutorial and click the Open button.

Coastline files include lists of two-dimensional polylines that may be closed or open. The open polylines are converted to Feature Arcs and are interpreted as open sections of coastline. Closed polylines are converted to arcs and are assigned the attributes of islands.

1.1 Defining the Domain

We need to assign a boundary type to the coastline arc, and then we can define the region to be modeled. To do this:

1. Make sure you are in the Map module, if not already selected.
2. Choose the Select Feature Arc tool from the Toolbox and click on the coastline arc to select it.
3. Select Feature Objects | Define Domain.
4. Select the Semi-circular option and click OK.
5. Frame the display.

A semi-circular arc is created to define the region.

1.2 Assigning Boundary Types

Boundary types for arcs are specified in the Map module. Boundary types are prescribed by setting attributes to Feature Arcs. To set the boundary types:

1. Choose the Select Feature Arc tool from the Toolbox.
2. Double-click the arc representing the ocean boundary, shown in Figure 1. In the ADCIRC Arc / Nodestring Attributes dialog, assign this arc to be of type Ocean.
3. Click the OK button to close the dialog.

Figure 1 Feature Arcs after boundary types have been assigned.

2 Editing the Coastline File

Now that the coastline file has been read in and a corresponding map object created, several modifications must be made to the data before the SHOALS file is read in. Since the SHOALS file is in UTM coordinates, zone 18(78W to 72 W northern Hemisphere), the data should also be set to those coordinates. In order to do this the display projection must be set to same global projection. To convert the display coordinates:

1. Choose Edit | Project….
2. In the Current Projection dialog that appears, toggle on Global projection. Set the zone to 18 ( 78W to 72W – Northern Hemisphere) and the datum as NAD 27.
3. Click OK.
4. Ensure that the vertical units is set to Meters.
5. Click the OK button to exit the dialog.

Next, to set the Map object coordinates:

1. Right-click on the "default coverage" map object and select Projection (floating)... "Floating" indicates that the projection has not been set previously.
2. Repeat steps 2–4 above.

The coastline data has now been converted from a local projection to a global projection of UTM coordinates with zone 18 (78w to 72W—Northern Hemisphere) and Datum set at NAD27.

3 Reading in a SHOALS File

You will now read in a SHOALS file, shin.pts, which contains data at various locations along the coastline and throughout the region you are modeling.

1. Choose File | Open.
2. Select the file shin.pts.
3. In the Open File Format dialog, toggle on Use Import Wizard and click OK.

The File Import Wizard dialog will open, allowing you to specify how the data will be read into SMS. For Step 1 of the dialog, the first line in the File preview box is the file header. The next line shows the name of each respective column of data. In this case, the file has three data columns. The first column is the XCoordinate, the second column is the YCoordinate, and the third column is the depth/bathymetry.

• Click the Next > button to move on to Step 2 of the File Import Wizard.

The second step of the File Import Wizard allows you to change other specifications as you read in the SHOALS file.

• Click the Finish button.

Figure 2 shows the plot of the points read in from the shin.ptsfile.(If the scatter set does not appear at first, make sure that Points is toggled on in the display options under Scatter).

Once the scatter set is read in, we must set its projection. To do this:

1. Right-click on the shin scatter set in the project explorer, and click on projection.
2. In the Object Projection dialog, the projection will already be set to UTM since the Display Projection is currently set to UTM. Click OK to exit the dialog.

Figure 2 Display of shin.pts.

4 Shallow Wavelength Functions

The next step before you build your finite-element mesh is to create several functions for creating the finite element mesh. For this tutorial, the mesh will be generated according to the wavelength at each node. Large elements will be created in regions of long wavelengths. Conversely, smaller elements are needed closer to the shore to correctly model the smaller wavelengths.

To create this shallow wavelength function from the bathymetric data:

1. In the Scatter module, select Data | Dataset Toolbox.
2. In the Dataset Toolbox dialog, select the Wavelength and Celerity tool in the Coastal section. This enables the wavelength options on the dialog.
3. Make sure the options for creating a Wavelength and Celerity function are checked. Leave the period at 20 seconds and enter a name “20 sec” in the Output dataset names edit field.
4. Click the Compute button to create the datasets and the Done button to close the

dialog. Two functions are created: celerity and wavelength at each node using the shallow water wavelength equation. The celerity is calculated as:

• $Celerity=(Gravity*Nodal\,Elevation)^{0.5}$

The wavelength is calculated as:

• $Wavelength=Period*Celerity\,$

5 Creating Size Functions

Now that you have created the wavelength function, you must make a few more conversions before you are ready to create your mesh. A size function is a multiple that guides the size of elements to be created in SMS. Any dataset may be used for this purpose. If you were to generate your mesh using the original wavelength function alone, you would get a decent mesh to work with, but we want a mesh whose density radiates out from a point in the inlet. This allows you to get more accurate results in the inlet where we are most concerned with the outcome of the ADCIRCrun. Therefore, we will now need to create a size function based on the wavelength to attain this end. The final size function you use for modeling applications varies and is found through trial and error to give a nicely formed mesh. This example illustrates one method of building a size function.

5.1 Finding the Central Point for the Mesh

Since the mesh will be generated in a radial fashion, the distance from a central point must be found. The first step is to locate the central point and then use the Data Calculator to compute the distances of all points from this center point. To do this:

1. Still in the Scatterpoint module, zoom in to the area of the inlet shown in

Figure 3 with the Zoom tool until your screen looks like Figure 4.

1. Click on one of scatterpoints in the middle of the inlet using the Select Scatterpoints tool. Make note of this point’s X and Y coordinates in the Edit Window at the top of the screen.
2. Frame the data by clicking the Frame tool in the Toolbox.

Figure 3 Inlet location to zoom in on.

Figure 4 Choose a center point.

For now, turn off the scatterpoint display. However, you may turn it back on at any time during the tutorial if you so desire. To turn off the visibility of the shin.pts data, deselect the box next to the shin dataset in the Project Explorer.

You are now ready to proceed. We will use the Data Calculator to compute new datasets by performing operations with scalar values and existing datasets. The Data Calculator will be used to create the size function.

5.2 Distance Function

For consistency, we will use the (x,y) location of (712768.675, 4523969.712) as the center scatterpoint for our mesh.

1. Select Data | Data Calculator…. This brings up the Dataset Toolbox, with the data calculator active.
2. Click the sqrt(x) button.
3. In the Expression field, using the keyboard replace “??”so the expression looks like:

   • sqrt((d4 - 712768)^2 + (d5 - 4523950)^2)

   This expression takes the x and y locations of each scatter point, which correspond to the “d4” and “d5” datasets respectively, and computes its distance to the point designated as the mesh center.

4. In the Output dataset name field, enter the name of “distance” for the dataset and click the Compute button.

5.3 Initial Size Function

1. Highlight the “20 sec_Wavelength” dataset and click the Add to Expression button. You now should see the letter and number “d2” in the Expression field.
2. In the Expression field, make the equation look like “d2*7”.
3. Enter the name “size” for this dataset in the Output dataset name area and click the Compute button. This creates a function of 7 times the wavelength.

5.4 Scale Function

The last separate function before computing the final size function will be a scale factor out from the center point. It will take on the following format:

• scale = (distance/max distance)^0.5

This scale function will range between 0 and 1, 0 being at the center point and 1 at the farthest point from the center of the mesh. This will allow the mesh to radiate out in density from the middle of the inlet. Taking the square root of the scale factor forces the elements to grow larger more quickly as one moves away from the center. To compute this function:

1. Highlight the “distance” function in the Datasets window and click the Dataset Info... button. Notice that the Maximum value is 65607.9.
2. Click the X in the corner of the dialog window to close the info dialog.
3. Enter “sqrt(d6 / 65607.9)” in the Expression field. This assumes that d6 is the distance function.
4. Enter the name “scale” and click the Compute button.

5.5 Final Size Function

You are now ready to create the final size function that your mesh will be based on.

1. Click the max(x,y) button.
2. Replace “??,??” so the equation reads “max(50, (d7*d8))”. This will multiply the scale factor (which varies from very small by the center of the domain up to one at the edges) by the size (which is seven times that of the wavelength). The result will be a value that varies from very small to seven times that of the wavelength that is truncated to a minimum size of 50 meters to prevent infinitely small elements from being created around the mesh center.
3. Enter the name “radial size” in the Result field and click the Compute button. The data calculator gives you many options for building the size function. The size function created in this tutorial was created through several steps. This was done to show the many possibilities that exist for defining the size function, and ultimately for defining the finite element mesh. Other options that could be used for this or other meshes include:

• Use the wavelength multiplied by a scale factor (without using distance).
• Don’t take the square root of the scale factor for a denser mesh.
• Use a value other than 50 meters as the minimum size for a denser mesh in the channel, etc.

5.6 Smooth Size Function

The final step in creating a size function is to smooth the size function. Smoothing modifies the size function so the size function values do not change too quickly. Size functions that change too quickly can create poor transitions in element size.

1. In the Dataset Toolbox, select Smooth datasets from the tool list on the left..
2. Select the scatter dataset named “radial size”.
3. Change the Element area change limit to 0.5. This will modify the size function so the elements created by the size function are at most twice as big or half as small as their adjacent elements.
4. Enter the name “radial size smoothed 0.5” and click the Compute button.
5. Click Done to exit the Dataset Toolbox.(Note: If desired, the differences between the dataset “radial size” and “radial size smoothed 0.5” can be visualized by using the data calculator to subtract “radial size” from “radial size smoothed 0.5” and contouring the resulting dataset.)

6 Creating Polygons

A polygon is defined by a closed loop of Feature Arcs and can consist of a single Feature Arc or multiple Feature Arcs, as long as a closed loop is formed. For initial mesh generation, polygons are a means for defining the mesh domain.

6.1 Building Polygons

To create polygons from the arcs on the screen:

1. Switch to the Map module.
2. Make sure that no arcs are currently selected.
3. Select Feature Objects | Build Polygons. Now a polygon has been created out of all the arcs.

6.2 Polygon Attributes

Next, each polygon (this case only has one) must be assigned proper attributes.

1. Choose the Select Feature Polygon tool from the Toolbox and click inside the polygon.
2. Select Feature Objects | Attributes. (Double-clicking inside the polygon will perform this same step.) The 2D Mesh Polygon Properties dialog will open.

6.3 Assigning the Meshing Type

1. Select Scalar Paving Density as the Mesh Type.
2. Click the Scatter Options... button below the Mesh Type.
3. In the Interpolation dialog, in the dataset tree under Scatter Set To Interpolate From, make sure the “radial size smoothed 0.5” function is highlighted.
4. In the Extrapolation section, set the Single Value to 50.
5. Turn on the Truncate values option and set the Min to 50 and the Max to 5000.
6. Click the OK button to return to the 2D Mesh Polygon Properties dialog.

6.4 Assigning the Bathymetry Type

Next, the bathymetry type is selected. In this case the imported bathymetry is in the form of a scatter set. 1. Select Scatter Set as the Bathymetry Type. 2. Click the Scatter Options... button below the Bathymetry Type option. 3. In the Interpolation dialog, highlight Z under Scatter Set To Interpolate From, leave the Single Value at 0.000, and make sure the Truncate values option is turned off. 4. Click the OK button.

6.5 Assigning the Polygon Type

1. Make sure the Polygon Type is set to Ocean. 2. Click the OK button to close the 2D Mesh Polygon Properties dialog.

7 Creating the Mesh

Once the polygon attributes are set, the mesh can be generated automatically based on the options that were selected. To generate the mesh:

1. Select Feature Objects | Map &narr; 2D Mesh.
2. Turn off the toggle for Copy coverage before meshing and click OK.

7.1 Mesh Display Options

After SMS has completed generation of the mesh, you should be able to view the bathymetry, nodes, and elements. To set the display:

1. Switch to the Mesh module.
2. Select Display | Display Options... or select the macro from the Toolbox.
3. Make sure the Nodes and Contours are turned off and the Elements are turned on.
4. Click the OK button to close the Display Options dialog.

Figure 5 View of elements after automatic mesh generation.

Figure 5 shows the final mesh. Notice how the elements are smaller closer to the coast and within the inlet. Once the mesh has been created and refined, final preparations must be done in order to run ADCIRC. These items are renumbering of the mesh nodes and saving the grid.

7.2 Minimizing Mesh Bandwidth

Before running ADCIRC, the mesh nodes must be renumbered to minimize the bandwidth of the mesh. This allows the ADCIRC model to run efficiently. SMS has done this automatically as the mesh was generated. However, if you edit the mesh, you would need to renumber again. To do this:

1. Select the Select Nodestring tool from the Toolbox and select the nodestring along the ocean boundary.
2. Select Nodestrings | Renumber Nodestrings.

The nodes have now been renumbered for the entire mesh starting with those along the ocean boundary.

8 Building the ADCIRC Control File

The control file specifies values corresponding to different parameters for ADCIRCruns.

These parameters include specifications for tidal forcing, selection of terms to include, hot start options, model timing, numerical settings, and output control. In order for ADCIRC to run properly, the mesh must be converted to Latitude/Longitude coordinates.

8.1 Converting Back to Lat/Lon

The model control expects the coordinates to be in latitude/longitude. The initial conversion was made to UTM coordinates for the meshing. The size function was calculated in meters, so the mesh could not be created while the coordinates were in degrees without performing more conversions (i.e. degrees ↔ meters). To convert back to Geographic coordinates:

1. Right-click on the mesh object in the Project Explorer.
2. Select Reproject. In the New Projection side, Click on Set Projection and set the projection to Geographic and leave the datum as NAD 27.
3. Make sure the Vertical units are in Meters.
4. Click the OK button.
5. To change the Display Projection to Geographic lat/lon as well, right-click on the mesh object in the Project Explorer and select Work in Object Projection. (Note that this is an optional step and does not affect the settings of the model, just our view of the model).

8.2 Main Model Control Screen

Before we set the model control, we need to make sure that SMS points to the right location of the LeProvost tidal database, as SMS will need to accessthe database at some point in the model control. To do this:

1. Select Edit | Preferences and click on the File Locations tab.
2. In the Other Files section of the dialog, set the LeProvost tidal database to point to the location where the LeProvost tidal database files are strored. They may be found in the Data Files folder of this tutorial.

To set up the model control for ADCIRC:

1. Select ADCIRC | Model Control.
2. In the General tab, turn on the following options under Terms in the center of the dialog: Finite Amplitude Terms, Wetting/Drying, Advective Terms, and Time Derivative Terms.
3. Click the Options... button below the Wetting/Drying option.
4. Make sure the following values are entered in the Wetting/Drying Parameters dialog:
   • Minimum Water Depth................................. 0.05
   • Minimum Velocity for Wetting..................... 0.02
5. Click OK to return to the Model Control dialog.
6. Enter a value of 3.0 for the Lateral Viscosity in the Generalized Properties section on the right side of the dialog.
7. Change the Bottom Stress/Friction method to Constant Quadratic and set the Friction coefficient to 0.005.

8.3 Time Control

Next, values for the Timing must be set. To set these values:

1. Click on the Timing tab.
2. Set the following values:
   • Ramp function value: 1.0 days. (This is a time period for the model to ramp from no circulation to full tidal amplitude. This enhances stability. The results from these calculations do not match physical reality and are normally not even saved.
   • Time Step: 2.0 seconds
   • Run Time: 1.5 days (Normal simulations last for several days up to a full lunar month. This is set to 36 hours just to get past the ramp time and show a tidal cycle.)

8.4 Output Files

ADCIRC will generate two global output files, water-surface elevation and velocity. To set the time for the two files:

1. Click on the Files tab.
2. In the Output Files Created by Adcirc section scroll down to Elevation Time Series (Global) and turn the Output checkbox on.
3. Make sure the Start (day) is set to 1.0 and set the End (day) to 1.5 and the Frequency (min) to 30.
4. Repeat steps 2 and 3 for the Velocity Time Series (Global).

8.5 Tidal Forces

For this run of ADCIRC, tidal forcing will be used. To define the tidal constituents that ADCIRC will apply at the ocean boundaries:

1. Click on the Tidal/Harmonics tab.
2. Check the Use forcing constituents and Use potential constituents boxes in the Tidal Constituents section.
3. Click the New button next to the checkboxes.
4. In the New Constituent dialog, make sure the LeProvost constituent database is selected. Select the K1, M2, N2, O1, and S2 constituents in the Constituents section.
5. Set the Starting Day as 0.0 hours on February 1, 2000 (Hour: 0.0, Day: 1, Month: 2, and Year: 2000). This is the date from which the tides will start.
6. Click the OK button to return to the ADCIRC Model Control dialog. SMS takes each constituent, extracts the values it needs from the LeProvost constituent database, and places them into the spreadsheet in the lower left corner. The amplitude and phase values may then be adjusted for each node. If a message appears indicating that SMS cannot find one of the constituent files, click OK and find the file. The file should be located with the tutorial files.
7. Click the OK button to exit the ADCIRC Model Control dialog.

8.6 Saving the Mesh and Control Files

To save the mesh and control files:

1. Select File | Save New Project…
2. Enter the name shinfinal.sms and click the Save button.

9 Running ADCIRC

You are now ready to run ADCIRC. Presently, ADCIRC uses a specific naming convention for its input and output files. Therefore, before ADCIRC can start, the basic input files must be present in the working directory, which SMS takes care of automatically. SMS makes a copy of the active mesh file and names it fort.14, then makes a copy of the model control information file and names it fort.15. To run ADCIRC:

1. Select ADCIRC | Model Control.
2. Select the General Tab. Name your project "test" in the Project title: and Run ID: "test" as well. Press OK.
3. Select ADCIRC | Run ADCIRC.
4. If the name of the ADCIRC executable does not appear, click the folder icon , locate the ADCIRC executable, and click OK.

The ADCIRC model wrapper appears and gives status for 64800 time steps while the model runs. On a typical desktop machine, this will take around 15 minutes. Once the ADCIRC run has completed, there will be several new files created. SMS copied the shinfinal.grd file (the mesh file saved when the project file was saved) to fort.14 and shinfinal.ctl file to fort.15, the filenames needed by ADCIRC. ADCIRC created the fort.63 (global elevation) and the fort.64 (global velocity) files. There are a couple of other files that hold basic output information, but we will only focus on the elevation and velocity files for the remainder of this tutorial.

When ADCIRC finishes running, click Exit.

10 Importing ADCIRC Global Output Files

Each output file from ADCIRCis imported into SMS as a “Dataset.” There are two types of datasets, scalar and vector. The global elevation file is an example of a scalar dataset, while the global velocity file is a vector dataset. You will import the global elevation file and the global velocity file simultaneously. To do this:

1. Select File | Open.
2. Hold the SHIFT key down and select both the fort.63 and fort.64 files.
3. Click the Open button.
4. Click OK in the Convert to XMDF dialog to convert both solution files.

SMS reads in the files and adds “Water Surface Elevation (63)” and “Velocity (64) mag” as Scalar datasets and “Velocity (64)” as a Vector dataset in the Mesh Data of the Project Explorer.

11 Viewing ADCIRC Output

Once both ADCIRC output files have been imported, the user must decide on how to view the data. The Project Explorer may be used to select the desired Scalar and Vector datasets.

• Activate the “Water Surface Elevation (63)” Scalar dataset by clicking on it in the Project Explorer.

11.1 Scalar Dataset Options

A good way to view the output is to edit the contour display options. To change the contour properties:

1. Select the Display Options macro in the Toolbox.
2. In the 2D Mesh tab, click the All off button to turn off current display options.
3. Turn on the Contours, and Mesh boundary.
4. Under the Contours Options tab, change the Contour Method to Color Fill.
5. For the Number of contours, enter 25.
6. Click OK to exit the dialog box, and SMS will redraw the screen similar to Figure 6 (it will look about the same for the Time step 1 1:00:00).

To view the data at different time steps, select the desired time steps in the Time Steps window. The Time Step value is in hours, minutes and seconds from the start of the ADCIRCrun.

Figure 6 ADCIRCoutput from the “fort.63” file.

11.2 Vector Dataset Options

You can display velocity vectors several different ways. We will first view them displayed at each node, and then on a normalized grid.

Vectors at Each Node

1. Using the Zoom tool , zoom in on the mesh so only the bay area is visible.
2. Select the Display Options macro in the Toolbox.
3. In the Display Options dialog under the 2D Mesh tab, turn on the Vectors toggle.
4. In the Vectors tab, under the Arrows Options section, make sure the Shaft length is set to Define min and max length.
5. Change the Min length to 15 and the Max length to 40.
6. Click the OK button to exit.

The screen should now look similar to that shown in Figure 7. You can now visualize the flow at each node through Shinnecock Bay at this particular time step.

Figure 7 View of velocity vectors at each node.

Vectors on a Normalized Grid

1. Open the Display Options and go to the Vectors tab.
2. Under Vector Display Placement and Filter, change the Display to the on a grid option.
3. For both the x pix and y pix, enter a value of 15 and click the OK button.

This method of displaying vectors is useful when displaying areas with both coarse and refined areas, such as the entire mesh in this case.

12 Film Loop Visualization

In addition to single time steps of contours and vectors, animations can be generated and saved. SMS enables the user to generate and save animations by using the Film Loop.

To create a film loop of the ADCIRC analysis:

1. Select Data | Film Loop.
2. In the Film Loop dialog, click the Next > button.
3. Click the Next > button, then the Finish button.

SMS now starts the film loop, adding one frame at a time. Once the last frame has been added to the loop, an AVI Application will open and the animation will start automatically.

You may continue to experiment with the film loop features if you desire. Click the Close button when finished. The film loop has been saved as sms.avi.

13 Conclusion

This concludes the ADCIRC Analysis tutorial.