Example 1

Example 1 is described beginning on page 85 of the PHAST documentation (Parkhurst and others, 2004).  The flow and transport data file itself begins on page 88.  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\ex1\ex1.trans.dat.  To follow this example, the user should open this file in a text editor.  For the most part, the various data sets will be specified in the same order in which they appear in the original input file.  The one exception will be the grid.  It will be specified before anything else.

Creating the Grid

  1. Start GoPhast by double-clicking on its icon.  The start-up dialog box shown in figure 26 will appear.  If it is not already selected, select Create a new model.  Then click the Next button.
GoPhast start-up dialog box.
Figure 26. GoPhast start-up dialog box.
  1. The initial grid dialog box will appear.  Fill it in as illustrated in figure 27 and click the Finish button.  This will create the grid illustrated in figure 28.
Initial Grid dialog box.
Figure 27. Initial Grid dialog box.
  1. The GoPhast main window will appear (fig. 28).
Initial appearance of GoPhast main window in Example 1.
Figure 28. Initial appearance of GoPhast main window in Example 1.

Phast Options

  1. Next, select PHAST Options|Title and Units…  With ex1.trans.dat in a text editor, copy the title section to the clipboard and paste it into the Title section of the Title and Units dialog box (fig. 29).  The title can be edited to remove the blank spaces, “#”and quote characters at the beginnings of the lines.  If desired, a different title of the user’s choice can be specified.  The dialog box can be resized so that more of the title is visible.  Click OK to close the dialog box.
Top section of the Title and Units dialog box showing the title for example 1.
Figure 29. Top section of the Title and Units dialog box showing the title for example 1.
  1. The next steps are to activate steady flow and solute transport.  To do so, select PHAST Options|Steady Flow... and check the Steady Flow check box.  Then click OK and select PHAST Options|Chemistry Options… and check the Use solute transport check box.  Click OK to close the dialog box.
  2. Next change some of the default units.  Select PHAST Options|Title and Units… again and this time specify the units as follows.  (Those that are not listed can be ignored.)  Click OK to close the dialog box.
Item
Units
time
sec
horizontal grid units
cm
vertical grid units
cm
head units
cm
hydraulic_conductivity units
cm/s
specific_storage
1/cm
dispersivity
cm
  1. The grid is one-dimensional so the model will be more efficient if the chemistry dimension is specified as X.  Select PHAST Options|Grid Options… and change the chemistry dimensions to just X (fig. 30).  Click OK to close the dialog box.
Grid options dialog box showing selection of just the X Chemistry dimensions.
Figure 30. Grid options dialog box showing selection of just the X Chemistry dimensions.

Data Sets

  1. The aquifer properties are constant so it is possible to use the default formulas for the data sets to specify those properties (fig. 31).  Select Data|Edit Data sets... to edit the data sets.  The default formulas should be as follows.  When they have been entered, click OK to close the dialog box.


Data Set
Default Formula
Kx
0.12
Ky
0.12
Kz
0.12
porosity
0.1
specific storage
0
longitudinal_dispersivity
0.1
horizontal_transverse_dispersivity
0.1
vertical_transverse_dispersivity
0.1


Data Sets dialog box showing specifications of the aquifer properties
Figure 31. Data Sets dialog box showing specifications of the aquifer properties
  1. This model does not use a free surface.  Select PHAST Options|Free Surface… and verify that a free surface is not used.  Click OK to close the dialog box.

Boundary Conditions

There are two specified head boundaries.  One is on the left end of the model and the other is on the right.  The one on the left has a head of 1 and an associated solution with an index of 2 from time 0 to time 60.  For the rest of the duration of the model, it has an associated solution with an index of 1.  The boundary on the right side has a head of 0.0 and an associated solution of 1.  

  1. First zoom in on the left side of the model by selecting View|Zoom In and then clicking on the left side of the top view of the model (fig. 32).
Appearance of model in example 1 after zooming in on the left side of the top view of the model.
Figure 32. Appearance of model in example 1 after zooming in on the left side of the top view of the model.

The next step is to create the boundary condition on the left side of the model.  Select Object|Create Straight Line.  Click on the top view of the model and then click again so as to draw a line near the left end of the model (fig. 33). Double-click or push the Enter key on the keyboard to finish drawing the line.

Drawing a line near the left side of the top view of the model.
Figure 33.  Drawing a line near the left side of the top view of the model.
  1. At this point the Object Properties dialog box will appear.  On the Properties tab, check the Nodes radio button.  Then change to the Boundary Conditions tab and select the Specified head radio button.  Change the Number of times (near the bottom left) to 2.  Then fill in the table for the specified head boundary condition as illustrated in figure 34.  This specified head boundary will have a head of 1 for the duration of the model but its associated solution will change from 2 to 1 after 60 seconds.  The value for head only needs to be specified once.
Object Properties dialog box showing how to set up the specified head boundary for the left side of the model.
Figure 34. Object Properties dialog box showing how to set up the specified head boundary for the left side of the model.
  1. Click the OK button.  A warning message will appear.  Read the message and click the No button.  Then on the Properties tab, check the Set values of intersected nodes check box. Also check that the Higher Z coordinate is 1 and the lower Z coordinate is 0.  This means that the line is a vertical surface with a top of 1 and a bottom of 0. Click the OK button again.  That completes setting up the specified head boundary for the left side of the model.
  2. Click with the mouse on the 3D view of the model and drag with the mouse button held down to rotate the 3D view.  Note that on the left side there is a black rectangle representing the 3D vertical surface (fig. 35).
Three dimensional view of model showing object on left side of model.
Figure 35. Three dimensional view of model showing object on left side of model.
  1. The next step is to create the specified head boundary on the right side of the model (fig. 36).  Select View|GoTo...  and change to the Element tab.  Uncheck the check boxes for Front and Side.  Change Column to 60 and click the OK button.  The right end of the model should now be visible in the top view of the model.  Again select Object|Create Straight Line and draw a line on the right side of the top view of the model. Again select the Nodes radio button and check the Set values of intersected nodes check box.  On the Boundary Conditions tab, select a specified head boundary and set the head to 0 for time 0 and the associated solution to 1.  Click the OK button.  This specified head boundary will have a head of 0 for the duration of the model and an associated solution of 1.  
Drawing a line to represent a specified head boundary on the right side of the top view of the model.
Figure 36. Drawing a line to represent a specified head boundary on the right side of the top view of the model.

Initial Head

  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 Data|Edit Data Sets…  Select the row for Initial Head.  Note that the Use PHAST-style 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 12 respectively.  Set Value 1 to 1 and Value 2 to 0 (fig. 37).
Data Sets dialog box showing how to set up a gradient in initial head.
Figure 37. Data Sets dialog box showing how to set up a gradient in initial head.
  1. The next step is to set the initial conditions for chemistry.  The solution, surface and kinetics will all have an initial index of 1. With the Data Sets dialog box still visible, set the formula for Chemistry_Initial_Solution, Chemistry_Initial_Surface, and Chemistry_Initial_Kinetics each to 1. Click the OK button.

More PHAST Options

  1. To deactivate the other chemistry options, select PHAST Options|Chemistry Options… and uncheck the check boxes for Use equilibrium phases, Use exchange, Use gas phases, and Use solid solution.  Leave the other three check boxes checked.  Click OK to close the dialog box.  Then select Data|Edit Data Sets… again.  Note that the data for Chemistry_Initial_Equilibrium_Phases, Chemistry_Initial_Exchange, Chemistry_Initial_Gas_Phase, and Chemistry_Initial_Solid_Solutions are all now in italics with a light gray background indicating that they are not being used.  Click OK to close the dialog box.
  2. The next step is to set up the solution method.  Select PHAST Options|Solution Method…  Click the Direct radio button and set the space differencing and time differencing both to 0.5 (fig. 38).  Click OK to close the dialog box.
Solution Method dialog boxes showing how to set up the solution method for example 1.
Figure 38. Solution Method dialog boxes showing how to set up the solution method for example 1.
  1. The model has a duration of 120 seconds with time steps lasting 0.4 seconds.  Select PHAST Options|Time Control… and set the time step length to 0.4 and the ending time to 120 (fig. 39).  Click OK to close the dialog box.
Time Control dialog box showing how to set up the time control for example 1.
Figure 39. Time Control dialog box showing how to set up the time control for example 1.
  1. The final step in setting up the model is to set up the print frequency.  Select PHAST Options|Print Frequency… The units of all the items that will be changed are seconds.  For time 0 set HDF chemistry to 10 seconds and XYZ chemistry to 0 seconds.  (The frequency edit box for HDF chemistry is initially disabled because the default unit is “end”.  Changing the units to seconds will enable the frequency edit box.)  Click the Add button to add another time at which to specify the print frequency.  Resize the dialog box to completely show the new column.  In the new column set the time to 60.  Also set Force chemistry print to 60 seconds, Velocities to 60 seconds and XYZ chemistry to 60 seconds.  Note that HDF chemistry for time = 60 has a value of 10 seconds.  This value was copied from the previous time when the Add button was clicked.  Click OK to close the dialog box.  Select File|Save to save the model.

Visualizing Data

  1. The model is now ready to run.  However, before running it, it is worthwhile to color the grid with some of the data sets to make sure the data have been applied properly.  Select Data|Color Grid… and select the Initial_Head data set.  Click the OK button.  The model should appear similar to figure 40.  Try using the selection cube for the side view of the model to change the selected column progressively from 1 to 61.  The color displayed on the side view should change from red to blue.  (See “The Selection Cubes” on page 13.)  If the mouse cursor is over a colored cell or element on the top view of the model, the value of the data set for the colored element or cell will be displayed in the third panel of the status bar along with an explanation of how the value was assigned.  It is possible to color the grid using the Specified_Head_Solution data set at time 0 and time 60.
Main window showing the grid being colored by the Initial_Head data set.
Figure 40. Main window showing the grid being colored by the Initial_Head data set.
  1. Now that the model has been set up, it is possible to run it.  Select File|Export PHAST Input File.  In the Save File dialog box, save the file as ex1.trans.dat.  Then copy phast.dat and ex1.chem.dat from the examples distributed with PHAST to the location where ex1.trans.dat was saved.  Open up a command prompt and change the directory to the location where ex1.trans.dat was saved.  (On Windows, an easy way to do this is to type “cd” in the command prompt window and then drag the directory from Windows Explorer.  The directory name will be copied into the command prompt window.  Then push the Enter button on the keyboard.)  Run PHAST by typing Phast ex1 in the command prompt window.  When it is finished running, Model Viewer (Hsieh and Winston, 2002) can be used to display the results.  (The capability of displaying PHAST results in Model Viewer was added by Scott R. Charlton.)