Example 2


Example 2 is described beginning on page 91 of the PHAST documentation (Parkhurst and others, 2004).  The flow and transport data file itself is reproduced beginning on page 94.  If PHAST is installed on a Windows computer at the default location, this file can be found at

C:\Program Files\USGS\phast-1.1\examples\ex2\ex2.trans.dat.

Initial Set Up

  1. Start GoPhast by double-clicking its icon.  The start-up dialog box will appear.  If it is not already selected, select Create a new model.  Click the Next button.
  2. The initial grid dialog box will appear.  The grid in this example is too complex to create through this dialog box so click the Do not create initial grid button.  The grid will be created in a different way.
  3. In the main GoPhast window select PHAST Options|Title and Units… Copy the title from ex2.trans.dat to the clipboard and paste it in the title section or enter an appropriate title.  Assign the following units.  Then click the OK button to close the dialog box.
Data Set
Units
Time units
days
Horizontal grid units
meters
Vertical grid units
meters
Head units
meters
Hydraulic conductivity units
meters/day
Specific storage units
1/meters
Dispersivity units
meters
  1. Activate solute transport by selecting PHAST Options|Chemistry Options… and checking the Use solute transport check box.  Uncheck all the other check boxes except for Use kinetics and click the OK button.

Create the Grid with Objects

  1. The next step is to define the grid.  In this case, objects will be used to define where the grid should be and the grid element sizes.  (See “Using Objects to Specify the Grid” on p. 17.)  The grid should be 100 m long in the X direction, 20.5 m wide in the Y direction and 12.5 m high in the Z direction.  The elements will be 4 m long in the X direction.  The first row of elements will be 0.5 m wide in the Y direction.  The rest will be 1 m wide in the Y direction.  The first layer will be 0.5 m high in the Z direction.  The rest will be 1 m high in the Z direction.  The default view of the top view is zoomed out too far to draw an object of this size conveniently.  Therefore select View|Zoom In and click on the top view until the size of the top view is appropriate.  It is possible to use the menu items View|Go To… or View|Pan to position the top view so that the origin is included in the top view.
  2. Select Object|Create Rectangle and click on the top view of the model to create a rectangle whose opposite corners are close to (0, 0) and (100, 20.5) (fig. 41).  The locations do not need to be precise because they will be edited later.
Creating a rectangle object in GoPhast.
Figure 41. Creating a rectangle object in GoPhast.
  1. Change the name of the object to “Domain_Outline” in the “Object Properties Dialog Box” (p. 49), check the Use to set grid element size checkbox, set the Grid element size to 4.  Switch to the Vertices tab.  On the Vertices tab, set the corners of the rectangle to be at (0, 0), (100, 0), (100, 20.5), (0, 20.5) and (0, 0).  (The last vertex is a duplicate of the first one so that the object will be a closed polygon.)  This object will be used to define the horizontal extent of the grid and set the size of grid elements in the X direction to 4 meters.  However, more needs to be done to define the grid.  Click OK to close the dialog box.
  2. It will be easier to see the gird on the front and side views of the model if the vertical exaggeration is decreased.  Change the vertical exaggeration from 20 to 1.  (Select View|Vertical Exaggeration… and enter “1”.)  Then on the front view of the model zoom in and draw a line object from approximately (-1, 0.5) to (-1, 12.5).  In the Object Properties dialog box, change its name to “Z_Discretization”, check the Use to set grid element size checkbox, and set the Grid element size to 1.  On the Vertices tab, edit the position of the vertices so that the Z-coordinates are exactly 0.5 and 12.5.  This object will help define the vertical extent of the grid and set the height of the layers to 1 m.  Click OK to close the dialog box.
  3. Draw another line object on the front view from about (-2, 0) to (-2, 0.5).  In the Object Properties dialog box, change its name to “Z_Discretization_Bot_Layer”, check the Use to set grid element size checkbox, and set the Grid element size to 0.5.  On the Vertices tab, edit the position of the vertices so that the Z-coordinates are exactly 0 and 0.5.  This object will define the position of the bottom layer of the grid.  Click OK to close the dialog box.
  4. Draw another line object on the top view.  It should extend from approximately (105, 0) to (105, 0.5).  In the Object Properties dialog box, change its name to “Y_Discretization_First_Row”, check the Use to set grid element size checkbox, and set the Grid element size to 0.5.  On the Vertices tab, edit the position of the vertices so that the Y-coordinates are exactly 0 and 0.5.  This object sets the width of the first row in the Y direction.  Click OK to close the dialog box.
  5. Draw another line object on the top view.  It should extend from approximately (110, 0) to (110, 20.5).  In the Object Properties dialog box, change its name to “YDensity” check the Use to set grid element size checkbox, set the Grid element size to 1.  On the Vertices tab, edit the position of the vertices so that the Y-coordinates extend at least from 0 to 20.5.  This object defines the width of the rows in the Y direction.  Because it is not a polygon, and it is on the top view of the model, it does not define the location of the grid but only the grid element size.  (Polylines on the front view of the model do define the vertical extent of the grid.  This object overlaps in the Y direction with the previous object (step 10).  They both set the grid element size but because the previous object sets a smaller value, the previous object wins out.  Click OK to close the dialog box.
  6. There are now a sufficient number of objects to define the desired grid.  Choose Grid|Generate Grid... and click the OK button to create the grid.  Note that the first row and bottom layer are smaller than the others.  They are smaller than the other rows and layers because the “Z_Discretization_Bot_Layer” (step 9) and “Y_Discretization_First_Row” (step 1) objects specified smaller element sizes than the “Z_Discretization” (step 8) and “YDensity” (step 11) objects respectively.  Also note that all the elements are longer in the X direction than in the Y direction.  This is because the “YDensity” object (step 11) specified a smaller element size than the “Domain_Outline” (step 7) object.

Data Sets

  1. Select Data|Edit Data Sets… and enter the follow for the default formulas.  Leave the “Data Sets Dialog Box” (p. 39) open.
Data Set
Default Formula
Kx
2
Ky
2
Kz
2
Porosity
0.1
Specific_Storage
0
Longitudinal_Dispersivity
1.5
Horizontal_Transverse_Dispersivity
0.45
Vertical_Transverse_Dispersivity
0.15
Chemistry_Initial_Solution
1
Chemistry_Initial_Kinetics
1
  1. The next step is to set the initial heads.  The heads will vary uniformly from 1 on the left to 0 on the right.  Select the row for Initial_Head.  Note that the Use PHAST interpolation for all cells check box becomes enabled.  Check this check box.  Leave the interpolation direction set to X.  Set Distance 1 and Distance 2 to 0 and 100 respectively.  Set Value 1 to 1 and Value 2 to 0.  Click OK to close the dialog box.

Boundary Conditions

  1. The next step is to define the specified head boundaries.  On the side view of the model, draw a polygon completely surrounding the grid. In the Object Properties dialog box, select the Nodes radio button. Set the name of the object to “Left_Specified_Head_Boundary”, and check the Set values of intersected nodes check box. Set Associated third dimension formulas to one.  Leave X-coordinate set at 0.  On the Boundary Conditions tab, select a specified head boundary.  Change the type of solution to specified solution.  In the table enter a value of 1 for both Head and Specified solution (fig. 42).  Click OK to close the dialog box.
Object Properties dialog box. Specified Head boundary condition.
Figure 42. Object Properties dialog box. Specified Head boundary condition.
  1. Now color the grid (Data|Color Grid…) with the specified head.  The left end of the model should be specified head cells.
  2. Right-click on the side view of the model and select Hide from the popup menu to hide the previous object.  (The object must be selected.)  Hiding an object does not deactivate it; it just makes the working area less cluttered.  On the side view of the model, draw another polygon completely surrounding the grid. In the Object Properties dialog box, select the Nodes radio button. Set its name to “Right_Specified_Head_Boundary”.  Check the Set values of intersected nodes check box.  Set Associated third dimension formulas to one.  Set X-coordinate to 100.  On the Boundary Conditions tab, select a specified head boundary.  Leave the type of solution at associated solution.  In the table enter a value of 0 for Head and 1 for associated solution.  Click OK to close the dialog box.  Now both the left and right ends of the model should be specified head boundaries.
  3. Hide all the objects created so far by selecting Object|Show or Hide Objects…  Then in the dialog box, uncheck the check box for All Objects.  If desired, click Close to close the dialog box.
  4. The next step is to create a specified concentration boundary on the left end of the model.  On the side view of the model, draw another polygon.  This should enclose only part of the grid.  It should extend from approximately (Y’, Z) = (15, 10) to (21, 13) (fig. 43).  In the Object Properties dialog box, select the Nodes radio button.  Set its name to “Specified_Concentation_Boundary”.  Check the Set values of enclosed nodes check box.  Set Associated third dimension formulas to one.  Leave the X-coordinate set to 0.  On the Boundary Conditions tab, select a specified head boundary.  Change the type of solution to specified solution.  In the table enter a value of 1 for Head and 2 for Specified solution.  Click OK to close the dialog box.  Now color the grid with the Specified_Head_Solution (fig. 43).  The left end of the model should be specified head cells.  The cells with a specified head solution of 1 will be colored red and those with a specified head solution of 0 will be colored blue.
Location of the specified concentration boundary. The grid has been colored by the specified head solution.
Figure 43. Location of the specified concentration boundary. The grid has been colored by the specified head solution.

PHAST Options

  1. Set the following options for the solution method (PHAST Options|Solution Method…).
Solution Option
State
Solver
Iterative
Use cross dispersion
unchecked
Space Differencing
0.5
Time Differencing
0.5
Tolerance
1e-14
  1. Set the following options for print frequency (PHAST Options|Print Frequency…).
Print Frequency Option
Value
HDF chemistry
400 days
Velocities
400 days
XYZ chemistry
400 days
XYZ heads
400 days
XYZ velocities
400 days
  1. Set the time control to a time step size of 10 and ending time of 400 (PHAST Options|Time Control…).
  2. Save the project by selecting File|Save.  Then run the model in the same way as in example 1 except that the file name should be ex2.trans.dat and the other files should come from the ex2 folder.