Chapter 13. Examples and Lessons Previous Page Next Page

13.1 Lesson 1, Conservative Solute Tracer Simulation (Revised)

This tutorial will step through the tasks necessary to create a one dimensional, constant source conservative solute tracer simulation. The following table presents the input parameters in this tutorial.

Parameter Value Units
Aquifer Length 100 meter
Grid Spacing 1 meter
Starting Time 1 day
Ending Time 10 day
Output Timestep 1.0 day
Longitudinal Dispersitivity 1.0 meter
Transverse Dispersitivity 0.1 meter
Effective Diffusion 0.0 sq.meter/day
Constant Inlet Concentration 10.0 mg/l
Effective Porosity 0.5 cu.meter/cu.meter
Pore Water Velocity 2.0 meter/day

Roughly speaking, conducting this BUGS SCRATCHPAD simulation can be divided into 10 steps:

  1. Starting the Program
  2. Defining the Grid Mesh
  3. Adding the Conservative Solute
  4. Creating the Boundary Condition "Reaction"
  5. Creating the Reaction Systems
  6. Assigning Reaction Systems to Nodes
  7. Setting the Hydraulic Flow Conditions
  8. Saving the Simulation Project File.
  9. Running the Simulation
  10. Viewing Results

These steps are described below:


    To start BUGS SCRATCHPAD, either double click on the program icon (Windows 3.1) or select BUGS SCRATCHPAD from the Start Menu -> Programs -> BUGS SCRATCHPAD program group (Windows '95).

    After loading, BUGS SCRATCHPAD presents the main window. The program is ready to accept input for a new simulation.

    [Main BUGS Scratchpad Window]

  2. Define the Aquifer Grid Mesh.

    The first thing to is to define the size and shape of the aquifer mesh. This is done from the Aquifer Parameters window. To bring up this window select Aquifer Properties from the Window menu.

    [Selecting <STRONG>Aquifer Properties</STRONG> from the <STRONG>Window</STRONG> menu.]

    The Aquifer Parameters window will appear. The grid mesh spacing is 1.0 meters, which is the same as the default (the dX field). However, the number of nodes in the X direction needs to be changed to 100 (the X field). This will result in an aquifer length of 100 meters. (100 nodes spaced 1 meter apart).

    [Aquifer Paramters window]

    Also notice, the Time group, this is where the starting and ending times for the simulation are entered. Also, the Step field refers the timestep in which results are recorded. (The default is for recording the results every 1 time unit.) Since the default values are the same used for this tutorial, they do not need to be modified.

    The Default System will be explained later below.

    Close the Aquifer Parameters window.

  3. Add the Conservative Solute

    The next step is to add the Conservative Solute. This will be done from the Parameters window. To display the Parameters window, select Parameters from the Window window.

    [Selecting <STRONG>Paramters</STRONG> from the <STRONG>Window</STRONG> menu.]

    The Parameters window will appear.

    [Initial Parameters Window]

    Parameters represent many things in a BUGS SCRATCHPAD simulation. They can represent system defined data such as porosity, hydraulic head, as well as user defined solutes and sorbed species. They are grouped together as "Parameters" for the convenience of providing a uniform method to enter simulation initial values.

    The first thing to do is add the conservative solute. This will be a user defined parameter. To add the parameter, click on the Add button.

    [Add Button]

    The New Parameter dialog box will appear. Enter "O2" as the name for the new parameter (conservative solute) and click the OK button.

    [Add New Parameter Dialog]

    The Parameters window will change to the following.

    [Parameters Window]

    The default parameter type for a user parameter is an Immobile parameter (sorbed species). This needs to be changed to a Mobile parameter (mobile solute species). To change the new parameter from a Immobile to a Mobile parameter, first make sure that "O2" is selected in the list box, then check the Mobile Parameter checkbox.

    [Mobile Paramter Checkbox]

    The Parameters window expands to show some additional data entry fields for a mobile parameter (solute species).

    [Parameters Window for a Mobile Solute]

    Al, At, and D* are the longitudinal dispersitivity, transverse dispersitivity, and effective diffusion coefficients respectively. Change the default values of the longitudinal and transverse dispersitivity to 1.0 and 0.1 respectively. The effect of diffusion is ignored in this simulation.

    [Entered Diffusion Properties]

    Close the Parameters window.

  4. Create the Boundary Condition "Reaction"

    Next, it is necessary to create the constant source boundary condition. In BUGS SCRATCHPAD, boundary conditions are entered a bit differently than in traditional groundwater modeling programs. BUGS SCRATCHPAD represents boundary conditions using Reactions. The primary way BUGS SCRATCHPAD manipulates the values of parameters in a simulation is through Reactions, therefore it makes sense to describe a constant source boundary condition through a Reaction. This opens the door to many possibilities with specialized boundary conditions. For example, BUGS SCRATCHPAD provides a Reaction that is dependent upon the simulation time, thus a timed pulsing nutrient injection well boundary condition can be represented by a reaction almost as easily as a constant source can be, as in this simulation.

    To create the reaction to represent the constant source boundary, select Reactions from the Window menu.

    [Selecting <STRONG>Reactions</STRONG> from the <STRONG>Window</STRONG> menu.]

    Since this as a new simulation, no receptions have been defined yet. BUGS SCRATCHPAD immediately prompts for a new reaction name.

    [New Reaction Dialog Prompt]

    Enter "Constant Source" for the name of the reaction and press the OK button.

    [Entering Reaction Name]

    BUGS SCRATCHPAD displays the Reactions window with the "Constant Source" reaction highlighted in the list box.

    [Initial Reactions Window]

    Since the Type tab in the Reactions window is already activated, the window displays the available types of reactions. The default is Standard Equilibrium. The type of reaction used to represent a constant source is the Equality Equilibrium reaction. This type of reaction is the simplest of all reactions that BUGS SCRATCHPAD provides. It simply adjusts the value of a parameter to the set value at every timestep (just what a constant source does).

    To select the Equality Equilibrium, click on the Equality in the Equilibrium group.

    [Selecting Equality Equilibrium Reaction]

    Now to show the window to describe the details of this constant source reaction, click the Rate tab.

    [Rate Tab]

    This reaction allows the user to specify that a parameter will be adjusted to equal a value defined by a linear combination of all the available parameters at that node. However, this simulation is only interested in a constant value, so this extra ability will be ignored for now. The only two data values that need to be entered are the dependent parameter (O2) and the value to set the dependent parameter to (10).

    In the Depndt. combo box, select "O2".

    [Selecting O2]

    In the Coefficient. field, enter "10".

    [Entering Constant Source Value]

    Notice that BUGS SCRATCHPAD echoes the equality reaction equation as it is being built in the window below the Coefficient. field. (O2 = 10).

    [Reaction Window for an Equality Reaction]

    This is all that needs to be done with this window, the Systems tab will not be used at this time. Reaction Systems are explained below.

    Close the Reactions window.

  5. Create the Reaction Systems

    Reaction Systems are the means by which the user tells BUGS SCRATCHPAD which reactions occur at which nodes in an aquifer simulation. They allow the user to group different sets of reactions and name the set of reactions. Then the user tells BUGS SCRATCHPAD that this collection of reactions occurs at a particular region in the aquifer. A Reaction can belong to any number of Reaction Systems but only one Reaction System can occur at any one node.

    This particular simulation requires two Reaction Systems. One for the boundary condition, and one for the remainder of the aquifer.

    To bring up the Reaction Systems window, select Reaction Systems from the Window menu.

    [Selecting <STRONG>Reaction Systems</STRONG> from the <STRONG>Window</STRONG> menu.]

    Since this as a new simulation, no Reaction Systems have been defined yet. BUGS SCRATCHPAD immediately prompts for a new Reaction System name.

    [New Reaction System Name]

    Enter "Boundary Condition" for the new Reaction System name and press the OK button.

    [Entering New Reaction System Name]

    BUGS SCRATCHPAD displays the Reaction Systems window with the "Boundary Condition" Reaction System highlighted in the list box.

    [Reaction Ssytems Window]

    Notice that the "Constant Source" Reaction is also displayed in the Not Included list. This means that "Constant Source" is not included in the "Boundary Condition" Reaction System. This needs to be changed. To include the "Constant Source" Reaction in the "Boundary Condition" Reaction System, first click on "Constant Source" in the Not Included list ("Boundary Condition is already selected) and click on the [>] button. The reaction now appears in the Included list.

    [Reaction Ssytems Window]

    The "Boundary Condition" Reaction System will be placed at the inlet node, as described later. Now it is necessary to define the Reaction System that will represent the remainder of the aquifer. Since this is a conservative tracer simulation, the second reaction system will contain now reactions, but it still must be defined anyway.

    Click on the Add button to bring up the New Reaction System Dialog. Enter "Interior" for the name of the new Reaction System and press the OK button.

    [Reaction Ssytems Window]

    The "Interior" Reaction System will reside at every node in the aquifer except for the inlet. Therefore it will become the Default System (so that each node does not have to be specifically assigned this reaction system). Check the Use This Reaction System as Default checkbox at the bottom of the Reaction Systems window.

    [Reaction Ssytems Window]

    Close the Reaction Systems window.

  6. Assign Reaction Systems to Nodes

    The next step is to tell BUGS SCRATCHPAD where the reaction systems are located in the aquifer. This is done through the Nodes window.

    To bring up the Nodes window, select Nodes from the Window menu.

    [Selecting <STRONG>Nodes</STRONG> from the <STRONG>Window</STRONG> menu.]

    BUGS SCRATCHPAD will display the Nodes window.

    [Nodes Window]

    The Nodes window provides the interface for the user to tell BUGS SCRATCHPAD which Reaction Systems occur at which nodes in the aquifer. Since constant source the boundary condition occurs only at the aquifer "inlet" (node 1), this well be an easy task. The current node is already set at coordinate (1,1) which will be the inlet node for the aquifer. To change the default Reaction System for this node, select "Boundary Condition" from the System field.

    [Selecting Boundary Condition]

    Since "Interior" is the default Reaction System, the rest of the nodes will use "Interior" as their Reaction System.

    Leave the Nodes window open for the next step.

  7. Set the Hydraulic Flow Conditions.

    The last data entry step is entering data on the flow conditions. The desired pore water velocity is 2.0 m/d. Since the effective porosity is 0.5, this would correspond to a darcy velocity of 1.0 m/d. Since hydraulic conductivity was not given, (nor is it important for this tutorial) we'll assume it to be 1.0 m/d, resulting in a desired head gradient of 1.0 m/m. Now assuming a free outlet condition at the end of the aquifer, and a relative head of 0.0 m; the head at the entry of the aquifer would be 99 m. (Since node coordinates are block centered, the actual distance is 99 m between end nodes for this simulation.)

    Therefore, to set the desired flow conditions, the initial hydraulic heads at both ends of the aquifer should be entered, and BUGS SCRATCHPAD should be notified that both end nodes in the aquifer are Prescribed Head nodes.

    Since the current node is (1,1), it is easy to start there. To notify BUGS SCRATCHPAD that this is a Prescribed Head node, check the Prescribed Head checkbox.

    [Check Prescribed Head in Nodes]

    Next, With Parameter selected to hydraulic head ("H"), enter "99" in the Value field in the Initial Parameter Values group.

    [Setting Initial Hydraulic Head Value]

    Next, BUGS SCRATCHPAD needs to be told that the outlet node is also a prescribed head. Change the coordinates to node (100,1). (A trick is to click on the up arrow in the spin control for X, it will automatically wrap around to the end of the aquifer).

    [Setting Initial Hydraulic Head Value]

    As before, check the Prescribed Head checkbox.

    [Check Prescribed Head in Nodes]

    Now the necessary information for the flow conditions has been entered (The default hydraulic head value at the end node is 0, so there is no need to change it). BUGS SCRATCHPAD will automatically calculate the hydraulic heads and flow field for the remainder of the nodes in the aquifer grid during calculation initialization.

    Close the Nodes window.

  8. Save the Project File

    Before running an aquifer simulation in BUGS SCRATCHPAD, the project file must be saved. To save the file, select Save from the File menu.

    [Selecting <STRONG>Save</STRONG> from the <STRONG>File</STRONG> menu]

    The user will be prompted with the standard windows save dialog. Enter whatever is appropriate for your system and press OK.

    [Saving the Project File]

  9. Run the Simulation

    The next step is to run the simulation, and save the file afterwards. To run the simulation select Simulate from the Run menu.

    [Selecting <STRONG>Simulate</STRONG> from the<STRONG>Run</STRONG> menu]

    BUGS SCRATCHPAD launches a separate calculation program and waits for its termination.


    Save the file by selecting Save from the File menu.

    [Selecting <STRONG>Save</STRONG> from the <STRONG>File</STRONG> menu]

    Now the results of this simulation can be viewed.

  10. Viewing Results

    BUGS SCRATCHPAD provides two primary ways to view results, table output and graphs. The output graphs come in two varieties as well, profile and node. The profile graphs show concentration profiles through the aquifer at a given point in time. The node graphs plot the concentration value over time at a single location within the aquifer.

    To view a profile graph, select Profile Graph from the Window menu.

    [Selecting <STRONG>Profile Graph</STRONG> from the <STRONG>Window</STRONG> menu]

    BUGS SCRATCHPAD displays the Profile Graph in the default configuration.

    [Profile Graph]

    The profile of hydraulic head is not all that interesting, lets look at the conservative solute profile at the ending timestep.

    From the Parameters select "O2" and then un-select "H".

    [Selecting 'O2']

    Now, slide the scroll bar all the way to the right to select the last timestep.

    [Selecting The Last Timestep]

    The Profile Graph is now configured to show the concentration profile at the last timestep.

    [Profile Graph Showing Concentration Profile]

    To review tabular results, select Output from the Window menu. Viewing various results in this window is left for the reader to discover. However, it is worth mentioning that the output grid can be configured by dragging labels around via. Windows Drag and Drop. Poke around a bit to see how it works.

This concludes constant source conservative tracer tutorial, if you have any questions please feel free to contact us at

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Last Updated 04/19/99