Steps Simple Model using ModelMuse

1/ Step 1 - Generating the Grid

The model is a quasi-3-D model with three simulated layers and two nonsimulated confining beds. The model has 15
rows and columns. The cells are square with sides that are 5000 feet long.
Start ModelMuse and select Create new MODFLOW model and click the Next button. Change the MODFLOW
version to MODFLOW-2005. Fill in a description of the model and specify "Not Applicable" for the projection. Then
click the Next button again.
Enter the grid data shown in the illustration below including selecting MODFLOW-2005 as the MODFLOW version
and click Finish.

The model is a quasi-3-D model in which some layers are not simulated. To specify the layers that are not
simulated, select Model|MODFLOW Layer Groups. If the names of the layers are too long to be fully displayed, it
may be helpful to widen the area in which the layer names are displayed by clicking down just to the right of the
list of layers and drag to make the list wider. Select the upper confining bed and change it from Confined to Non-
simulated. Do the same for the lower confining bed. The middle and bottom aquifers are confined but the upper
aquifer is unconfined so change it from Confined to Convertible. Click OK to close the dialog box.
Finally, change the length units of the model from meters to feet by selecting Model|MODFLOW Options...,
changing to the Options tab and changing the length units. If desired, it is also possible to specify the information
on the Description tab.

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2/ Step 2 - Aquifer Properties
The only aquifer properties that need to be specified are the horizontal and vertical hydraulic conductivities as
shown in the table below. The horizontal hydraulic conductivity only needs to be simulated for the simulated
layers. The vertical hydraulic conductivity needs to specified in both the simulated and nonsimulated layers.
Layer Kx Kz
Upper Aquifer 0.001 1
Upper Confining Bed 1e-6

Middle Aquifer 0.0001 1

Lower Confining Bed 5e-7
Lower Aquifer 0.0002 1

To illustrate different methods of assigning properties, objects will be used to assign Kx whereas a formula will be
used to assign Kz. First confirm that the selected layer is the top layer. One way to do that is to move the cursor
over the red Selection cube on the top view of the model. The selected layer will be displayed on the Status bar.

Next select Object|Create|Rectangle and click twice on the top view of the model to create a rectangle that
completely encloses the grid. The Object Properties dialog box will appear. Change the name of the object to
"Upper_Aquifer_Kx." Examine the formulas for the Higher Z coordinate and Lower Z coordinate and verify that
they are "Model_Top" and "Upper_Aquifer_Bottom." Select the Data Sets tab, expand "Required|Hydrology" and
check the check box next to "Kx." Change the formula for the Kx data set to "0.001" and click the OK button.
Next change the selected layer to layer 3 (the middle aquifer). One way to do that is to click twice beneath the red
square on the Selection cube on the top view of the model to move the selected layer down. You will need to click
twice to move the selected layer down two layers from layer 1 to layer 3. Create another rectangle object that
completely surrounds the grid. In the Object Properties dialog box, change the name of the object to
"Middle_Aquifer_Kx." Examine the formulas for the Higher Z coordinate and Lower Z coordinate and verify that
they are "Upper_Confining_Bed_Bottom" and "Middle_Aquifer_Bottom." These formulas mean that the top of the
object is at the top of layer 3 and the bottom of the object is at the bottom of layer 3. On the Data Sets tab, check
the check box for the Kx data set and leave the formula for the Kx data set to "0.0001" and click the OK button.
Repeat this process again to assign Kx a value of 0.0002 in layer 5. (Be sure to change the selected layer to the
bottom layer before creating the object used to specify Kx for the bottom layer.)
To define different values of Kz for each layer, select Data|Edit Data Sets... Expand "Required|Hydrology" and
select Kz. The default formula for the Kz data set is "Kx / 10." Click the Edit formula button to display the Formula
Editor. Expand "Functions|Logical" and double click on [Link] formula will change to "CaseR(Index,
Real_Result1, Real_Result2, ...)." In the formula, double-click on "Index" to select it. In the list of formulas, close
"Logical" and expand "Grid." Then double click on "Layer." The formula should now be "CaseR(Layer, Real_Result1,
Real_Result2, ...)." Type in the values of Kz for each layer so that the formula becomes "CaseR(Layer, 1., 1e-6, 1.,
5e-7, 1.)." This formula will assign a different value to Kz for each layer. Kz in layers 1, 3, and 5 will be assigned a
value of 1; Kz in layer 2 will be assigned a value of 1e-6; and Kz in layer 4 will be assigned a value of 5e-7. Click OK
to close the Formula Editor. Then click Apply to make the change in the Data Sets dialog box and then click Close..

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3/ Step 3 - Time
The model has a single, steady-state stress period with a length of 86400 seconds. To specify it,
select Model|MODFLOW Time... In the dialog box, set the Starting time to 0, the Ending time to 86400 and
the Max first time step length to 86400. Together, the length of the stress period, the maximum length of the first
time step, and the time step multiplier control the number of time steps in the stress period. Click OK to close the
dialog box. If you would prefer to set the number of time steps rather than the length of the first time step, click
the cell in the table for Max first time step length. Then click the "F()" button that appears in that cell to display
the Time Step Length Calculator.

4/ Step 4 - Specified-Head Boundary

Four boundary condition packages are used in this model, the CHD, DRN, RCH, and WEL packages. To activate
them, select Model|MODFLOW Packages and Programs. Then expand Boundary conditions and each of the items
beneath it. Locate the check boxes for each of the packages and check them. Then click OK to close the dialog box.
There is a specified-head boundary with a head of 0.0 in the first column of the model. It is present in both the
upper and middle aquifers but not the lower aquifer. (It also is not present in the confining bed because the
confining bed is not simulated.) Select Object|Create|Polyline and then create a polyline on the top view of the
model through column 1 for the full length of the model (row 1 to row 15). Double click to end creating the polyline.
It doesn't matter if the object goes past the end of the model or doesn't go completely through the first or last cell.
Change the formula for the Higher Z coordinate and Lower Z coordinate to "Model_Top" and
"Middle_Aquifer_Bottom" respectively. These will cause the object to extend vertically from the top of layer 1 to
the bottom of layer 3. Go to the MODFLOW Features tab and check the check box for the CHD package. Enter
a Starting time of 0, and Ending time of 86400, and a Starting head and an Ending head of 0. (Note that when
entering times, you can select times for the start and end of the stress periods from the drop-down list in the cells
for the times.) If the starting and ending heads were different, the specified head at the end of each time step
between the starting time and the ending time would be determined by linear interpolation between the starting
head at the starting time and the ending head at the ending time. Click OK to close the Object Properties dialog
box.
To check that the specified heads were assigned correctly, select Data|Data Visualization|Color Grid... and
set the Data set or boundary condition to "CHD Starting Head." (It is found under "Boundary Conditions,
Observations, and Other Features|MODFLOW CHD|CHD Starting Head." Click the Apply button. Then change the
selected layer and verify that the specified heads are assigned only in layers 1 and 3. (They are not assigned to
layer 2 because layer 2 is not simulated.)
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5/ Step 5 - Recharge
The model has a uniform recharge rate of 3e-8 ft/s. On the top view of the model with the top layer selected, create
a Rectangle object that completely surrounds the grid. In the Object Properties dialog box, switch to
the MODFLOW Features tab and check the check box for the RCH package. Enter a Starting time of 0, an Ending
time of 86400 and a Recharge rate of 3E-8. Click OK to close the dialog box.

6/ Step 6 - Wells
The next step is to specify the wells. There are 12 wells on layer 1, 2 wells on layer 3 and 1 well on layer 5. Make
sure the selected layer is layer 1. Select Object|Create|Point and click on column 8 row 9 in the top view of
the model to create the first well. (The column and row of the cell beneath the cursor are displayed on the status
bar.) In the Object Properties dialog box, go to the MODFLOW Features tab and check the check box for the WEL
package. Change the Pumping rate interpretation from Calculated to Direct. Enter a Starting time of 0, an Ending
time of 86400 and a Pumping rate of -5. (Negative rates mean that water is being pumped out of the aquifer.)
Click OK to close the dialog box. To check that the well pumping rate has been assigned correctly, color the
grid with the well pumping rate.
It would be possible to specify the rest of the wells on layer 1 in the same way but because all these wells are
identical, there is an easier way. Select Object|Edit|Add Point Sections . Then click on each of the cells that
should be a well in the top layer. When you are done, your model should look similar to the figure below. All twelve
of these wells are defined by a single object composed of 12 separate points.

Wells in layer 1.
Now make layer 3 the selected layer. We will need two identical wells on this layer. To make them, we will first
create one of the wells. Then we will copy it to the clipboard. Next, we will then move the well to another location
and then paste the original well from the clipboard to the grid to recreate the well at the original location.
Select Object|Create|Point and click on in column 6, row 4 to make another well. It will have the same times
and pumping rate as the others. Select Edit|Copy to copy the object to the clipboard. Select Object|Select
Objects and drag the well object on column 6, row 4 to column 12, row 6. To drag the well object, click down
on it, drag it with the mouse button held down and then release the mouse when you reach the correct location.
Select Edit|Paste to paste the object on the clipboard back into column 6, row 4.
Finally make layer 5 the selected layer. Select Object|Create|Point and click on in column 11, row 5 to make
another well. It will have the same times and pumping rate as the others. Change the selected layer and on each
layer check that the wells are in the right places. There should be 12 wells on layer 1, 2 wells on layer 3 and 1 well
on layer 5.
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7/ Step 7 - Drains
The drains could be created in much the same way as the wells. However, this is time consuming. Instead open
the file [Link] (Ex. mine in the "Hydrogeology\ExampleModelMuse\Examples\Example2\Txt" folder)

In a text editor, select all the text in the file and copy it to the clipboard. Then go back to ModelMuse and
select Edit|Paste. The objects in [Link] define the drains required for the model.

8/ Step 8 - Solver
This model uses the SIP solver. To use it select Model|MODFLOW Packages and Programs. Expand the Solvers and
check the radio button for the SIP package. Change MXITER to 50, IPCALC to 0, and WSEED to 0.001. Then
click OK to close the dialog box.

9/ Step 9 - Save the Model

Select File|Save , select a name for your ModelMuse file, and save it.

10/ Step 10 - Running the Model

To verify that MODFLOW is installed, select Model|Program Locations. If it isn't, the edit box where it should be
specified will be colored red. If it isn't installed, you can click on the URL above the edit box to open a web browser
and navigate to the MODFLOW-2005 page. You can then download and install it. If it is installed but not at the
location specified in the dialog box, click the button next to the edit box, navigate to where it is installed and select
it.
To run the model, select File|Export|MODFLOW-2005 Input Files . Select the name of the name file to export
and the model will be exported. The rest of the files for the model will have the same name as the name file except
that the file extension will be changed. By default, the file name will be the same as the ModelMuse file name with
the extension changed to ."nam."
ModelMonitor will display the percent discrepancy in the model as the model runs. The model should finish almost
immediately. Close ModelMonitor. Then close the listing file and the command line (DOS) window.

11/ Step 11 - Viewing Model Results

To see the heads calculated by MODFLOW, select File|Import|Model Results... In the Open file dialog box, the file
containing the heads will already be selected. Click Open to select it. In the Select Model Results to Import dialog
box, click OK. The grid will be colored with the heads for the single stress period. If desired, you can turn off coloring
the grid with the model results and instead view contour lines of the results. You specify the contours in
the Contour Data pane of the Data Visualization dialog box. In the Contour Data pane, the data set for the heads
will be named "Head_P1_S1." You will find it under "Data Sets|Optional|Model Results|3D Data."
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