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U.S. GEOLOGICAL SURVEY
Scientific Investigations Report 2006–5137

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Appendix A. Detailed instructions for using SNRSS software.

This appendix provides the following information about the Snake River Nitrate Scenario Simulator (SRNSS):

• Description of associated files.
• Initial model settings.
• Creating or selecting datasets.
• Modifying nitrogen loading factors.
• Running the transport model.
• Customizing and viewing the nitrate scenario simulation.

Description of Associated Files

The simulator is packaged in a compressed zip file for faster download. Table A1 lists and describes the files that are included in the zip file.

The readme.txt file provides instructions for installing the SRNSS.

Initial Model Settings

When you start the SRNSS software, it loads the base case run shown in figure A1.

The base case run starts with conditions at the end of the 90-year historical period simulation (approximately year 2000). The predictive base case simulation runs for 30 years with constant hydraulic and nitrogen loading conditions equal to those in year 2000. All datasets you create are based on the base case; the datasets differ only in the distribution of nitrogen loading, which you can scale up or down by applying a multiplication factor to any of the 26 pre-defined zones. All datasets are simulated for the same 30-year predictive period as the base case. You can view the nitrate distribution for each run, as well as the change in nitrate concentration in each cell relative to the base case simulation at the same point in time. All nitrate concentrations are nitrite plus nitrate as nitrogen with nitrite concentrations being negligible in the study area. In figure A1, the concentration colors have been set to show concentrations between 1 and 5 mg/L by a smoothly varying color range (blue-cyan-green-yellow-red). By default, cells with concentrations less than 1 mg/L plot as gray and those with values greater than 5 mg/L plot as red.

Creating or Selecting Datasets

The SRNSS lets you create and manage datasets for the flow and transport model. The options to create, select, and delete datasets are available from the simulator’s File menu (fig. A2).

To Create a Dataset

1. Click File > New Dataset. The New Dataset dialog box displays.
   NOTE: By default, the software incrementally names each new dataset as CASE_# (where # represents an incremented number).
2. From the drop-down list, select the existing dataset on which to base the new dataset.
3. Click OK. The new dataset is created. You must now select that dataset to work with it.

To Select a Dataset

1. Click File > Select Dataset. The Select Dataset dialog box displays, showing the map for the last currently selected dataset (fig. A3).
2. From the drop-down list on the right, select the dataset that you want.
3. Click Select. The dataset is displayed in the simulator (fig. A4).

To Delete a Dataset

WARNING: If you select the Delete Dataset option, the currently loaded dataset is deleted immediately and cannot be recovered.

Click File > Delete Dataset. The dataset is deleted from the simulator.

Modifying Nitrogen Loading Factors

The SRNSS lets you modify the nitrogen loading factors for any or all of the 26 predefined zones of the mid-Snake region. Each zone’s loading factor may range from 0.1 to 5.0. Modifying loading factors lets you create various scenarios to model potential changes in nitrate concentrations throughout the mid-Snake region.

To Modify Nitrogen Load Factors

1. Click Dataset > Edit loading zones…. The Edit Loading Factors dialog box displays (fig. A5).
2. Do one of the following:
   • To assign a value to an individual zone, click the cell for that zone, click Edit Cell Value, and then enter the desired value in the selected cell.
   • To assign a uniform loading value to all zones, enter the value in the text box at the top of the screen, and then click Assign Uniform Value.
3. Click Save. The case is updated with the modified load factors, and you are prompted to run the transport model.

Running the Flow and Transport Model

When you save changes to a dataset’s loading factors, the simulator prompts you to run MODFLOW 2000, which in turn runs the flow and transport model (MOC3D). However, you can run the model at any time.

1. Click Dataset > Run MODFLOW (fig. A6). The Run MODFLOW dialog box displays.
2. Click Yes. MODFLOW 2000 runs the transport model MOC3D in a command window (fig. A7).

The simulations take about 15 minutes to run on a 1.7 GHz Pentium 4 computer. After the MODFLOW simulation is complete, the map display is updated with the new concentration values (fig. A8).

Viewing the Nitrate Scenario Simulation

When the model run completes, the simulator displays the results. You can then simulate potential increases in nitrate concentrations in shallow ground water by selecting time periods ranging from 5 to 30 years. Also, as you move the cursor around the map, note that the status bar at the bottom of the window displays the row-column position of the mouse pointer on the plot. As you hover the mouse pointer over a zone, the status bar displays that zone’s nitrate concentration values for both the selected dataset (CASE_1 in this example) and the base case, as well as the change in concentration between the two cases (fig. A4)

Customizing the Simulator Display

The SRNSS provides several options for customizing and viewing the nitrate scenario simulations resulting from model runs. These options include:

• Showing and hiding the model grid.
• Showing and hiding basemap layers for cities, counties, lakes, roads, and streams.
• Selecting rendering options.
• Zooming and panning.

To Show and Hide the Model Grid and Basemap Layers

You can customize the simulation plot by showing or hiding the model grid and the individual basemap layers. These options are available from the View menu (fig. A9).

To Select Rendering Options

To change the display of nitrate concentration values, select View > Renderer…. The Renderer Properties dialog box lets you select minimum and maximum nitrate concentration values and a color ramp for displaying those concentrations (fig. A10). You also can specify colors in which to display values that fall below or above the defined range. In the example shown in fig. A10, a Spectrum color ramp is selected for data values between 1 and 5 mg/L. Values less than 1 mg/L will display in gray, and values greater than 5 mg/L will display in red. By experimenting with the data range and colors, you can focus on different aspects of the simulation data.

To Zoom and Pan

The plot can be zoomed by selecting the Zoom tool from the toolbar and dragging a rectangle over the area of interest (fig. A11). The plot will then zoom to that extent (fig.  A12). You can pan the view of the simulation either by using the scrollbars on the map or by selecting the Pan tool from the toolbar, holding down the left mouse button, and then dragging the mouse. To return to the full view of the simulation, click the globe button on the toolbar.

To Export a Map Image

The SRNSS software easily allows a user to export an image of the display by selecting File > Export Map (fig.  A13). This saves an image of the display to the computer’s clipboard or temporary memory to be pasted into another application. This tool does not permanently save a copy of the image to the computer disc.

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