Using the Transport Module

The Transport Module uses the Particle Tracking Module particle paths to simulate ammonium and nitrate plumes originating from the potential septic tank locations traveling toward the water bodies. This module also calculates the inflow mass from the septic tanks into the groundwater and the amount of mass removed by denitrification.

Data Inputs

Once you are satisfied with the Particle Tracking Module’s data outputs, it is time to move on to the Transport Module. Access the [ArcNLET.pyt] ArcGIS Python Toolbox and the ArcNLET-Py ArcGIS Pro toolsets within, as described in Section 3.6.

Figure 5‑57: The ArcNLET-Py Python Toolset and Transport Module in the Catalog Pane.

1. Double-click the [4 Transport] module, and the Transport Python toolset opens in the [Geoprocessing Pane].

   1. Take a moment to review the data inputs, outputs, options, and parameters. Please remember that data inputs and outputs marked with a red asterisk [*] are required for the geoprocessing operation.

   2. Click the drop-down arrow next to [Options] and [Parameters] to expose the choices.

2. Consideration of NH4

   1. Default option: [Unchecked Box].

3. Data inputs:

   1. Input the source locations (point).

      1. Lakeshore Example input vector point: [PotentialSepticTankLocations.shp]

   2. Input the water bodies (polygon).

      1. Lakeshore Example input water body polygons: [water bodies.shp]

   3. Input the particle paths (polyline).

4. Transport Module output polyline: [demo_path.shp]

Figure 5‑58: The Transport Module in the Geoprocessing Pane.

5. There are several options for selecting data for a geoprocessing tool in ArcGIS Pro. If you are unfamiliar with ArcGIS Pro geoprocessing tools, please use the following URL to learn how to use geoprocessing tools. URL: https://pro.arcgis.com/en/pro-app/latest/help/analysis/geoprocessing/basics/run-geoprocessing-tools.htm

6. Use the [Map], [Catalog View], [Catalog Pane], or [Folder Icon] to select the necessary data inputs.

   1. If you have the data from the Lakeshore example in a [Map] in your ArcGIS Pro Project file and the [Geoprocessing Pane] open, you can drag and drop the necessary inputs or select the files from the drop-down menu for each of the input fields.

Figure 5‑59: Selecting Transport Module data inputs in the Map View.

2. If you have the data from the Lakeshore example open in a [Catalog Pane] or [Catalog View] and the [Geoprocessing Pane] open, then you can drag and drop the necessary inputs.

Figure 5‑60: Selecting the Transport Module inputs by dragging and dropping from the Catalog View.

3. You can also click the [Folder Icon] next to each field to select the data inputs using the Windows File Explorer. To use this method, you must use the Windows File Explorer to navigate to the […\lakeshore_example\lakeshore_example] and […\LakeshoreExampleOutputs_2023_09_28] folder to select each data input and click [OK].

Figure 5‑61: Selecting Transport Module inputs from the Windows File Explorer.

Data Outputs and Parameters

Storing your files in an organized and appropriately named manner is good practice when selecting locations for data outputs. Earlier in this exercise, we used the Windows File Explorer or ArcGIS Pro [Catalog Pane] to create a new folder titled [LakeshoreExampleOutputs_YYYY_MM_DD]. The folder stores the output raster images.

1. If you need to create a new file folder in ArcGIS Pro, use the [Catalog Pane], right-click on the folder […\lakeshore_example\lakeshore_example], hover over the option [New] in the submenu, and click [Folder].

Figure 5‑62: The Lakeshore example output folders in the Windows File Explorer.

2. Select the necessary data output by clicking the [Folder Icon] next to the [Output Plumes of NO3 (raster)] field in the [Geoprocessing Pane].

   1. The Windows File Explorer opens, and in the left pane under [Project], click the drop-down arrows to expand the [Folders] and ArcGIS Pro home folder.

   2. Select the [lakeshore_example\lakeshore_example] folders.

   3. Click the output folder, created in step 1 above, to store the output raster in the Transport Module. The file path and name for the output [Output Plumes of NO3 (raster)] for this example is: […LakeshoreExampleOutputs_2023_09_28\demo_plumes]

   4. Type the name of the raster output into the [Name] field with no file extension and click [OK].

   5. The ArcNLET-Py ArcGIS Pro Python toolset automatically assigns the correct file types, and if you enter a file type, a warning is triggered.

   6. Please note that when typing the data output into the provided field in the [Geoprocessing Pane], the outputs are automatically stored in the folder with the [Input Particle Paths (polyline)].

3. Data output:

   1. The Output plumes of nitrate (NO3) raster.

      1. Lakeshore Example output raster: [demo_plumes]

4. The Options are related to the Domenico Robbins solution type for two-dimensional (2-D) denitrification (decay).

   1. Solution type.

      1. Default option: [DomenicoRobbinsSSDecay2D]

   2. Plume warping control point spacing [Cells].

      1. Default value: [48]

   3. Plume warping method.

      1. Default methods: [Polyorder2]

   4. Threshold Concentration [M/L3].

      1. Default value: [0.000001]

   5. Post-processing.

      1. Default value: [Medium]

   6. Domenico Bdy.

      1. You must select: [Specified Z]

5. The Parameters are related to the septic tank size, the nitrogen mass going into the septic tank for a specific timeframe, and the width of the septic tank.

   1. Source Dimension Y [L]. The DEM is the basis for the length unit. For example, if the DEM uses the units of meters, everything should be in the units of meters.

      1. You must change the value to [12]

   2. Source Dimension Z [L].

      1. Default value: [1.5]

   3. Plume cell size [L].

      1. You must change the value to [0.8]

   4. NO3 Concentration [M/L3].

      1. Default value: [40]

   5. NO3 Dispersity αL [L].

      1. Default value: [2.113]

   6. NO3 Dispersity αTH [L].

      1. Default value: [0.234]

   7. Denitrification Decay Rate [1/T].

      1. Default value: [0.008]

   8. Volume Conversion Factor.

      1. Default value: [1000]

Figure 5‑63: Selecting the data output location from the Windows File Explorer for the Transport Module.

6. Double-check to ensure all red astricts [*] are removed from the [Geoprocessing Pane], indicating that all necessary data inputs and outputs have the correct file type and are accessible.

Figure 5‑64: The Transport Module Data inputs and output in the Geoprocessing Pane.

Execute the Module

1. Once satisfied with the data input and output selections, click [Run] in the [Geoprocessing Pane].

Figure 5‑65: The Run button in the Geoprocessing Pane.

2. The ArcNLET-Py Transport Module begins to process data, and the progress bar appears.

   1. Please note that the runtime can be lengthy depending on the data sets’ file sizes, spatial scale, and raster cell size.

Figure 5‑66: The Progress Bar in the ArcGIS Pro Geoprocessing Pane for the Transport Module.

3. If you feel the process has stalled or frozen, please click [View Details] below the blue progress bar. In the dialog box, click [Messages], then scroll to the bottom to ensure plumes are calculated for each septic tank location. New messages should populate the window until the process is complete.

   1. Your Messages have a number that differs on your machine from the example depending on how many plumes have been processed.

Figure 5‑67: The Messages box showing calculating plumes for OSTDS.

4. ArcGIS Pro indicates the tool is finished with a green notification box at the bottom of the [Geoprocessing Pane]. You may click [View Details] for more information about the process, including data inputs and output(s), start and end times and dates, and a success or failure message.

Figure 5‑68: The green notification box in the ArcGIS Pro Geoprocessing Pane for the Transport. Module.

View and Verify Results

1. If you have your data inputs in an open [Map] in ArcGIS Pro, the data output(s) are automatically added to the [Contents Pane] and the [Map View].

   1. Alternatively, if you do not have your input data in a [Map], nor do you have a [Map View] open in your ArcGIS Pro Project, and you ran the ArcNLET-Py Transport Module from the [Geoprocessing Pane], then your results are accessible via the [Catalog Pane] or [Catalog View] in the output folder [LakeshoreExampleOutputs_YYYY_MM_DD]

Figure 5‑69: The ArcNLET-Py Transport Module outputs in the Catalog Pane.

2. Take a moment to review the outputs to ensure your data has been processed correctly. Your data must be processed correctly because data outputs from the Transport Module are used as inputs in the Load Estimation Module.

   1. Your raster image outputs appear in your [Map View] as a black image with white plumes with the greatest magnitude at each potential septic tank location, and the plume diminishes towards the water bodies. This black-and-white symbology is not an indicator that there is an error. A solid black raster image in a [Map View] in ArcGIS Pro indicated that proper symbology is not set for the raster layer.

      1. Please note that if your raster image outputs have a solid black fill with only null or no-data values, then this is an indicator that there might have been an error processing the data inputs. Please ensure all your data inputs are correct, in an accessible file folder, and are uncorrupted.

   2. Your vector shapefile outputs appear as point features marking your potential septic tank locations.

      1. If the shapefile is empty, then this indicates that there might have been an error processing the data inputs. Please ensure all your data inputs are correct, in an accessible file folder, and are uncorrupted.

3. If you continue having issues processing your data, please [View

   Details] as mentioned in Section 5.9.3 to see if empty datasets were created as outputs. Empty datasets indicate an issue with the input data, or ArcGIS Pro does not have read/write access to input or output file locations.

   1. If you cannot find a solution to the issue, then please submit a [New issue] in the ArcNLET-Py GitHub repository (Issues · ArcNLET-Py/ArcNLET-Py · GitHub) as described in the GitHub instructions at Creating an issue - GitHub Docs.

5‑70: The ArcNLET-Py Transport Module outputs in the Contents Pane and Map.Figure

Figure 5‑71: The ArcNLET-Py Transport Module outputs info points and plumes stylized.

The plumes are shown with the highest magnitude in red, and analyte levels near zero are purple. The water body is shown in blue.