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
- 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.

|
Figure 26. GoPhast start-up
dialog box. |
- 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.

|
Figure 27. Initial Grid dialog
box. |
- The GoPhast main window will appear (fig. 28).

|
Figure 28. Initial appearance of
GoPhast main window in Example 1. |
Phast Options
- 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.

|
Figure 29. Top section of the
Title and Units dialog box showing the title for example 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.
- 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
|
- 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.

|
Figure 30. Grid options dialog
box showing selection of just the X
Chemistry dimensions. |
Data Sets
- 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
|

|
Figure 31. Data Sets dialog box
showing specifications of the
aquifer properties |
- 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.
- 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).

|
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.
 |
Figure 33. Drawing a line
near the left side of the top view
of the model. |
- 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.

|
Figure 34. Object Properties
dialog box showing how to set up the
specified head boundary for the left side of the model. |
- 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.
- 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).

|
Figure 35. Three dimensional
view of model showing object on left
side of model. |
- 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.

|
Figure 36. Drawing a line to
represent a specified head boundary on
the right side of the top view of the model. |
Initial Head
- 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).

|
Figure 37. Data Sets dialog box
showing how to set up a gradient in
initial head. |
- 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
- 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.
- 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.

|
Figure 38. Solution Method
dialog boxes showing how to set up the
solution method for example 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.

|
Figure 39. Time Control dialog
box showing how to set up the time
control for example 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
- 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.

|
Figure 40. Main window showing
the grid being colored by the
Initial_Head data set. |
- 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.)