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
- 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.
- 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.
- 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
|
- 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
- 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.
- 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.

|
Figure 41. Creating a rectangle
object in GoPhast. |
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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
|
- 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
- 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.

|
Figure 42. Object Properties
dialog box. Specified Head boundary
condition. |
- Now color the grid (Data|Color Grid…) with the
specified head. The left end of the model should be specified
head cells.
- 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.
- 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.
- 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.

|
Figure 43. Location of the
specified concentration boundary. The
grid has been colored by the specified head solution. |
PHAST Options
- 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
|
- 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
|
- Set the time control to a time step size of 10
and ending time of 400 (PHAST Options|Time Control…).
- 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.