v. 10.

GMS 10.0 Tutorial

MODFLOW – Grid Approach
Build a MODFLOW model on a 3D grid

Objectives
The grid approach to MODFLOW pre-processing is described in this tutorial. In most cases, the
conceptual model approach is more powerful than the grid approach. However, the grid approach is
useful for simple problems or academic exercises where cell-by-cell editing is necessary.

Prerequisite Tutorials Required Components Time

 None  Grid Module  35-55 minutes
 MODFLOW

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 1 Introduction ......................................................................................................................... 2
1.1 Outline .......................................................................................................................... 3
2 Description of Problem ....................................................................................................... 3
3 Getting Started .................................................................................................................... 4
4 Units ..................................................................................................................................... 4
5 Creating the Grid ................................................................................................................ 5
6 Creating the MODFLOW Simulation ............................................................................... 5
6.1 The Global Package ..................................................................................................... 5
7 Assigning IBOUND Values Directly to Cells .................................................................... 7
7.1 Viewing the Left Column ............................................................................................. 8
7.2 Selecting the Cells ........................................................................................................ 8
7.3 Changing the IBOUND Value ...................................................................................... 8
7.4 Checking the Values ..................................................................................................... 9
8 The LPF Package ................................................................................................................ 9
8.1 Layer Types .................................................................................................................. 9
8.2 Layer Parameters .......................................................................................................... 9
8.3 Top Layer ..................................................................................................................... 9
8.4 Middle Layer .............................................................................................................. 10
8.5 Bottom Layer.............................................................................................................. 10
9 The Recharge Package ...................................................................................................... 11
10 The Drain Package ............................................................................................................ 11
10.1 Selecting the Cells ...................................................................................................... 11
10.2 Assigning the Drains .................................................................................................. 12
11 The Well Package .............................................................................................................. 13
11.1 Top Layer Wells ......................................................................................................... 13
11.2 Middle Layer Wells .................................................................................................... 14
11.3 Bottom Layer Well ..................................................................................................... 15
12 Checking the Simulation ................................................................................................... 16
13 Saving the Simulation ....................................................................................................... 17
14 Running MODFLOW ....................................................................................................... 17
15 Viewing the Solution ......................................................................................................... 17
15.1 Changing Layers......................................................................................................... 17
15.2 Color Fill Contours..................................................................................................... 18
15.3 Color Legend .............................................................................................................. 18
16 Zone Budget ....................................................................................................................... 18
16.1 Assigning Zone Budget Ids ........................................................................................ 18
16.2 Viewing the Zone Budget Report ............................................................................... 19
17 Conclusion.......................................................................................................................... 19

1 Introduction
Two approaches can be used to construct a MODFLOW simulation in GMS: the grid
approach and the conceptual model approach. The grid approach involves working
directly with the 3D grid and applying sources/sinks and other model parameters on a
cell-by-cell basis. The conceptual model approach involves using the GIS tools in the
Map module to develop a conceptual model of the site being modeled. The data in the
conceptual model are then copied to the grid.

The grid approach to MODFLOW pre-processing is described in this tutorial. In most

cases, the conceptual model approach is more efficient than the grid approach. However,
the grid approach is useful for simple problems or academic exercises where cell-by-cell

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editing is necessary. It is not necessary to complete this tutorial before beginning the first
and second “MODFLOW – Conceptual Model Approach” tutorials.

1.1 Outline
Here are the steps of this tutorial:

1. Create a 3D grid.

2. Set up a MODFLOW simulation.

3. Check the simulation and run MODFLOW.

4. Assign zone budgets and view the report.

2 Description of Problem
The problem that this tutorial will be solving is shown in Figure 1. This problem is a
modified version of the sample problem described near the end of the MODFLOW
Reference Manual. Three aquifers will be simulated using three layers in the
computational grid. The grid covers a square region measuring 75000 feet by 75000 feet.
The grid will consist of 15 rows and 15 columns, each cell measuring 5000 feet by 5000
feet in plan view. For simplicity, the elevation of the top and bottom of each layer will be
flat. The hydraulic conductivity values shown are for the horizontal direction. For the
vertical direction, the tutorial will use some fraction of the horizontal hydraulic
conductivity.

Flow into the system is due to infiltration from precipitation and is defined as recharge in
the input. Flow out of the system is due to buried drain tubes, discharging wells (not
shown on the diagram), and a lake, which is represented by a constant head boundary on
the left. Starting heads will be set equal to zero, and a steady state solution will be
computed.

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Recharge = 0.0009 m/d

Const Head = 0 m
in column 1 of
layers 1 & 2 Drain

Unconfined
Confined
Confined

Layer 1: K = 15 m/d, top elev. = 60 m, bot elev. = -45 m

Layer 2: K = 0.9 m/d, top elev. = -45 m, bot elev. = -120 m
Layer 3: K = 2 m/d, top elev. = -120 m, bot elev. = -215 m

Figure 1 Sample problem to be solved

3 Getting Started
Do as follows to get started:

1. If necessary, launch GMS.

2. If GMS is already running, select the File | New command to ensure that the
program settings are restored to their default state.

4 Units
At this point, it is possible to define the units used in the model. The units that are
chosen will be applied to edit fields in the GMS interface to remind us of the proper units
for each parameter.

1. Select the Edit | Units command.

2. For Length, click the “…” Button next to the length field.

3. In the Display Projection dialog, set the units for both horizontal and vertical to
“Meters.”

4. Click OK.

5. For Time, enter “d” (for days). Ignore the other units (they are not used for flow
simulations).

6. Select the OK button to exit the Units dialog.

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5 Creating the Grid

The first step in solving the problem is to create the 3D finite difference grid.

1. In the Project Explorer, right-click on the empty space and then, from the pop-up
menu, select the New | 3D Grid command.

2. In the section entitled X-dimension, enter “22860” for the Length value, and “15”
for the Number cells value.

3. In the section entitled Y-dimension, enter “22860” for the Length value, and “15”
for the Number cells value.

4. In the section entitled Z-dimension, enter “3” for the Number cells value.

Later, the user will enter the top and bottom elevations for each layer of the grid. Thus,
the thickness of the cells in the z directions entered here will not affect the MODFLOW
computations.

5. Select the OK button.

The grid should appear in the window in plan view. A simplified representation of the
grid should also appear in the Mini-Grid Toolbar.

Figure 2 Mini-Grid toolbar

6 Creating the MODFLOW Simulation

The next step in setting up the model is to initialize the MODFLOW simulation.

1. In the Project Explorer, right-click on “grid” .

2. From the pop-up menu, select the New MODFLOW command.

The MODFLOW Global/Basic Package dialog will appear.

6.1 The Global Package

The input to MODFLOW is subdivided into packages. Some of the packages are optional
and some are required. One of the required packages is the Global package.

Packages
First, select the packages.

1. Select the Packages button.

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The MODFLOW Packages dialog will appear. It is used to specify which of the packages
will be used to set up the model. The Basic package is always used, and, therefore, it
cannot be turned off. To select the other packages, do as follows:

2. In the Optional packages section, turn on the Drain (DRN1), Recharge (RCH1),
and Well (WEL1) options.

3. In the Solver section, select the Stongly Impl. Proc. (SIP1) package.

4. Select the OK button to exit the MODFLOW Packages dialog.

The IBOUND Array

The next step is to set up the IBOUND array. The IBOUND array is used to designate
each cell as either active (IBOUND>0), inactive (IBOUND=0), or constant head
(IBOUND<0). For this problem, all cells will be active, except for the first two layers in
the leftmost column, which will be designated as constant head.

1. In the MODFLOW Global/Basic Package dialog, select the IBOUND button.

The IBOUND Array dialog displays the values of the IBOUND array in a spreadsheet-
like fashion, one layer at a time. The edit field in the upper left corner of the dialog can
be used to change the current layer. For this problem, all of the values in the array need
to be greater than zero, except for the left column of the top two layers, which should be
less than zero. By default, the values in the array should already be greater than zero.
Therefore, changing the values for the constant head cells is all that needs to be done.
This can be accomplished by entering a value of -1 for each of the thirty constant head
cells. However, there is another way to edit the IBOUND array that is much simpler for
this case. This method will be described later in the tutorial. For now, leave all of the
cells active.

2. Select the OK button to exit the IBOUND Array dialog.

Top and Bottom Elevations

The next step is to set up the top and bottom elevation arrays.

1. Select the Top Elevation button.

2. In the Top Elevation dialog, make sure the Layer is “1.”

3. Select the Constant  Layer button.

4. In the Layer Value dialog, enter a value of “60,” and select the OK button.

5. Select the OK button to leave the Top Elevation dialog.

GMS forces the top of a layer to be at the same location as the bottom of the layer above.
Thus, it is only necessary to enter the bottom elevations of all the layers now and the tops
of the layers will be set automatically.

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6. Select the Bottom Elevation button.

7. In the Bottom Elevation dialog, make sure the Layer is “1.”

8. Select the Constant  Layer button.

9. In the Layer Value dialog, enter a value of “-45,” and select the OK button.

10. In the Bottom Elevation dialog, change the Layer to “2.”

11. Select the Constant  Layer button.

12. In the Layer Value dialog, enter a value of “-120,” and select the OK button.

13. In the Bottom Elevation dialog, change the Layer to “3.”

14. Select the Constant  Layer button.

15. In the Layer Value dialog, enter a value of “-215,” and select the OK button.

16. Select the OK button to exit the Bottom Elevation dialog.

17. Select the OK button to exit the MODFLOW Global/Basic Package dialog

Starting Heads
The Starting Heads array is used to establish an initial head value when performing a
transient simulation. Since the user is computing a steady state simulation, the initial
head for each cell shouldn't make a difference in the final solution. However, the closer
the starting head values are to the final head values, the more quickly MODFLOW will
converge to a solution. Furthermore, for certain types of layers, if the starting head
values are too low, MODFLOW may interpret the cells as being dry. For the problem at
hand, the initial values are set to 60 because the Starting heads equal grid top elevation
toggle is turned on.

The Starting Heads array is also used to establish the head values associated with
constant head cells. For this problem, the constant head values should be zero. Since all
of the starting head values are already 60 by default, it will be necessary to make these
changes later in the tutorial.

7 Assigning IBOUND Values Directly to Cells

As mentioned above, the IBOUND values can be entered through the IBOUND Array
dialog. In some cases, it is easier to assign values directly to cells. This can be
accomplished using the Cell Properties command. Before using the command, it is
necessary to first select the cells in the leftmost column of the top two layers.

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7.1 Viewing the Left Column

To simplify the selection of the cells, the user will change the display so that he or she is
viewing the leftmost layer.

1. Choose the Side View button.

The grid appears very thin. To make things easier, increase the Z magnification so that
the grid appears stretched in the vertical direction:

2. Select the Display Options button.

3. In the Display Options dialog, change the Z magnification to “15.”

4. Select the OK button.

7.2 Selecting the Cells

Do the following to select the cells:

1. Choose the Select Cells tool.

2. Change the column to “1” in the Mini-Grid Toolbar and hit the TAB key.

Notice that the user is now viewing column number one (the leftmost column).

3. Drag a box around all of the cells in the top two layers of the grid.

7.3 Changing the IBOUND Value

To edit the IBOUND value:

1. Right-click on one of the selected cells.

2. Select the Properties command.

3. In the 3D Grid Cell Properties dialog, change the IBOUND option to “Specified
head.”

4. Change the Starting head to “0.0.”

5. Select the OK button to exit the 3D Grid Cell Properties dialog.

6. Select the Plan View button .

Notice that a symbol is displayed in the cells that were edited, indicating that the cells
are constant head cells.

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7.4 Checking the Values

To ensure that the IBOUND values were entered correctly:

1. Select the MODFLOW | Global Options command.

2. In the MODFLOW Global/Basic Package dialog, select the IBOUND button.

3. Choose the up arrow to the right of the layer field in the upper left corner of the
dialog to cycle through the layers.

Notice that the leftmost column of cells in the top two layers both have a value of -1.
Most of the MODFLOW input data can be edited in GMS using either a spreadsheet
dialog such as this, or by selecting a set of cells and entering a value directly, whichever
is most convenient.

4. Select the OK button to exit the IBOUND Array dialog.

5. Select the OK button to exit the MODFLOW Global/Basic Package dialog.

8 The LPF Package

The next step in setting up the model is to enter the data for the Layer Property Flow
(LPF) package. The LPF package computes the conductance between each of the grid
cells and sets up the finite difference equations for the cell-to-cell flow.

To enter the LPF data:

1. Select the MODFLOW | LPF – Layer Property Flow command.

8.1 Layer Types

The options in the Layer Data section of the LPF Package dialog are used to define the
layer type and hydraulic conductivity data for each layer. This problem has three layers.
The top layer is unconfined, and the bottom two layers are confined. The default layer
type in GMS is “convertible,” which means the layer can be confined or unconfined.
Thus, it isn’t necessary to change the layer types.

8.2 Layer Parameters

The buttons in the Layer Data section of the dialog are for entering the parameters
necessary for computing the cell-to-cell conductances. MODFLOW requires a set of
parameters for each layer depending on the layer type.

8.3 Top Layer

First, enter the data for the top layer:

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1. Select the Horizontal Hydraulic Conductivity button.

2. In the Horizontal Hydraulic Conductivity dialog, select the Constant  Layer

button.

3. In the Layer Value dialog, enter a value of “15” and click OK.

4. Select the OK button to exit the Horizontal Hydraulic Conductivity dialog.

5. Select the Vertical Anisotropy button.

6. In the Vertical Anisotropy dialog, select the Constant  Layer button.

7. In the Layer Value dialog, enter a value of “10” and click OK.

8. Select the OK button to exit the Vertical Anisotropy dialog.

8.4 Middle Layer

Next, enter the data for the middle layer:

1. Select the up arrow to the right of the layer edit field in the Layer Data section to
switch to layer “2.”

2. Using the Constant  Layer button, enter the following values for layer 2:
Parameter Value
Horizontal Hydraulic Conductivity 0.9 m/d
Vertical Anisotropy 5

8.5 Bottom Layer

Now enter the data for the bottom layer:

1. Switch to layer 3 and, using the Constant  Layer button, enter the following
values:
Parameter Value
Horizontal Hydraulic Conductivity 2 m/d
Vertical Anisotropy 5

This completes the data entry for the LPF Package dialog.

2. Select the OK button to exit the LPF Package dialog.

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9 The Recharge Package

Next, it is necessary to enter the data for the Recharge package. The Recharge package is
used to simulate recharge to an aquifer due to rainfall and infiltration. To enter the
recharge data, do the following:

1. Select the MODFLOW | Optional Packages | RCH – Recharge command.

2. In the MODFLOW Recharge Package dialog, select the Constant  Array

button.

3. In the Grid Value dialog, enter a value of “0.0009,” and click OK.

4. Select the OK button to exit the MODFLOW Recharge Package dialog.

10 The Drain Package

The next step is to define the row of drains in the top layer of the model. To define the
drains, first select the cells where the drains will be located, and then select the Point
Sources/Sinks command.

10.1 Selecting the Cells

The drains are located in the top layer (layer 1). Since this is the current layer, it isn’t
necessary to change the view.

First, select the cells on columns 2-10 of row 8. To select the cells, do the following:

1. Choose the Select Cells tool.

2. Notice that as the user moves the cursor across the grid, the ijk indices of the cell
beneath the cursor are displayed in the Edit Window at the bottom of the screen,
as shown in Figure 3.

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Figure 3 IJK indices of cell under cursor

3. Select the cell at i=8, j=2, k=1.

4. Hold down the Shift key to invoke the multi-select mode and select the cells on
columns 3-10 of the same row as the cell that was already selected (Figure 4).

Z
X

Figure 4 Cells to be selected

10.2 Assigning the Drains

To assign drains to the cells:

1. Right-click in the graphics window on the selected cells, and from the pop-up
menu select the Sources/Sinks command.

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2. Select Drain from the list on the left.

3. Select the Add BC button. This adds a new instance of a drain to each of the
selected cells.

At this point, the user must enter an elevation and a conductance for the selected drains.
The drains all have the same conductance but the elevations are not all the same.

4. In the MODFLOW Sources/Sinks dialog, enter the following values for the
elevations and conductances of the drains:
ID Elevation Conductance
107 0 7430
108 0 7430
109 3 7430
110 6 7430
111 9 7430
112 15 7430
113 20 7430
114 27 7430
115 30 7430

5. Select the OK button.

6. Unselect the cells by clicking anywhere outside the grid.

11 The Well Package

Next, the user will define several wells by selecting the cells where the wells are located
and using the Point Sources/Sinks command.

11.1 Top Layer Wells

Most of the wells are in the top layer but some are in the middle and bottom layers.
Define the wells in the top layers first:

1. While holding down the Ctrl key, select the cells shown in Figure 5.

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row col lay

Constant Head Cells (i) (j) (k)
9 8 1
9 10 1
Drain Cells 9 12 1
9 14 1
11 8 1
11 10 1
11 12 1
11 14 1
Select these cells
13 8 1
Y 13 10 1
13 12 1
Z
X 13 14 1

Figure 5. Cells to be selected on top layer.

2. Right-click on one of the selected cells and select the Sources/Sinks command.

3. In the MODFLOW Sources/Sinks dialog, select Wells from the list on the left.

4. Select the Add BC button.

5. Enter a Flow value of “-12230” for all the wells (a negative value signifies
extraction).

6. Select the OK button.

7. Unselect the cells by clicking anywhere outside the grid.

11.2 Middle Layer Wells

Next, the user will define some wells on the middle layer. First, it is necessary to view
the middle layer.

1. Select the Up arrow in the Mini-Grid Toolbar to view layer 2.

To select the cells:

2. While holding down the Ctrl key, select the cells are shown in Figure 6.

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Constant Head Cells

Select these cells

row col lay
(i) (j) (k)
4 6 2
6 12 2

Z
X

Figure 6. Cells to be selected on middle layer.

3. Right-click on one of the selected cells and select the Sources/Sinks command.

4. In the MODFLOW Sources/Sinks dialog, select Wells from the list on the left.

5. Select the Add BC button.

6. Enter a Flow value of “-12230” for both wells.

7. Select the OK button.

8. Unselect the cells by clicking anywhere outside the grid.

11.3 Bottom Layer Well

Finally, the user will define a single well on the bottom layer. Do the following to view
the bottom layer:

1. Select the Up arrow in the Mini-Grid Toolbar to view layer 3.

2. Select the cell as shown in Figure 7.

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Select this cell row col lay

(i) (j) (k)
5 11 3

Z
X

Figure 7 Cell to be selected on bottom layer

3. Right-click on the selected cell and select the Sources/Sinks command.

4. In the MODFLOW Sources/Sinks dialog, select Wells from the list on the left.

5. Select the Add BC button.

6. Enter a Flow value of “-0.15.”

7. Select the OK button.

8. Unselect the cell by clicking anywhere outside the grid.

Now that all of the wells have been defined, it is possible to go back to the top layer.

9. Select the down arrow twice in the Mini-Grid Toolbar to view layer 1.

12 Checking the Simulation

At this point, the user has completely defined the MODFLOW data and is ready to run
the simulation. However, before saving the simulation and running MODFLOW, the user
should run the MODFLOW Model Checker and check for errors. Because of the
significant amount of data required for a MODFLOW simulation, it is often easy to omit
some of the required data or to define inconsistent or incompatible options and
parameters. Such errors will either cause MODFLOW to crash or to generate an
erroneous solution. The purpose of the Model Checker is to analyze the input data
currently defined for a MODFLOW simulation and report any obvious errors or potential
problems. Running the Model Checker successfully does not guarantee that a solution
will be correct. It simply serves as an initial check on the input data and can save a
considerable amount of time that would otherwise be lost tracking down input errors.

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Do the following to run the Model Checker:

1. Select the MODFLOW | Check Simulation command.

2. In the Model Checker dialog, select the Run Check button.

A list of messages is shown for each of the MODFLOW input packages. If the user has
done everything correctly, the packages should have no errors. When an error exists, if
the user selects or highlights the error, when appropriate, GMS selects the cells or layers
associated with the problem.

3. Select the Done button to exit the Model Checker.

13 Saving the Simulation

Now the user is ready to save the simulation and run MODFLOW.

1. Select the File | Save As command.

2. Move to the directory titled Tutorials\MODFLOW\modfgrid.

3. Save the project with the name “gridmod.gpr.”

14 Running MODFLOW
It is now possible to run MODFLOW:

1. Select the MODFLOW | Run MODFLOW command.

At this point, MODFLOW is launched in a new window. The super file name is passed
to MODFLOW as a command line argument. MODFLOW opens the file and begins the
simulation. As the simulation proceeds, the user should see some text output in the
window reporting the solution progress.

2. When MODFLOW finishes, select the Close button.

15 Viewing the Solution

GMS reads the solution in automatically when the MODFLOW window is closed. At
this point, the user should see a set of head contours for the top layer. The user may also
see some cells containing a blue triangle symbol. These cells are flooded, meaning the
computed water table is above the top of the cell.

15.1 Changing Layers

Do the following to view the solution on the middle layer:

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1. Select the up arrow in the Mini-Grid Toolbar.

Do the following to view the solution on the bottom layer:

2. Select the up arrow .

Do the following to return to the top layer:

3. Select the down arrow twice.

15.2 Color Fill Contours

It is also possible to display the contours using a color fill option.

1. Select the Display | Contour Options command.

2. In the Dataset Contour Options – 3D Grid – Head dialog, change the Contour
Method to Color Fill.

15.3 Color Legend

Next, display a color legend:

3. In the Dataset Contour Options – 3D Grid – Head dialog, turn on the Legend
option.

4. Select the OK button.

16 Zone Budget
Zone Budget is a program developed by the USGS (Harbaugh 1990) that is used to
compute subregional water budgets for MODFLOW groundwater flow models. GMS has
incorporated a similar flow budget reporting tool. In GMS, the user defines zones by
assigning a Zone Budget ID to cells. Once the zones are defined, a report can be
generated that shows the flow budget for the zone. The report also includes a component
that shows the flow in/out to adjacent zones.

16.1 Assigning Zone Budget Ids

In this model, the user will make each layer into a zone.

1. Choose the Select Cells tool.

2. If necessary, switch to plan view.

3. Be sure to look at the second layer of the 3D grid. Adjust the layer by using the
up or down arrow in the Mini-Grid Toolbar to view layer 2 of the grid.

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4. Drag a box around all of the cells in layer 2 of the grid.

5. Right-click on one of the selected cells.

6. Select the Properties command in the pop-up menu.

7. Enter “2” for the Zone budget ID and select the OK button.

8. Switch to layer 3 of the grid by selecting the down arrow in the Mini-Grid
Toolbar.

9. Repeat steps 4 through 7, except, this time, enter “3” for the Zone budget ID.

16.2 Viewing the Zone Budget Report

It is now possible to view the flow budget for each of the zones.

1. Select the MODFLOW | Flow Budget command.

2. Select the Zones tab.

The user is currently viewing the report for the first zone (the top layer of the grid). The
report is divided into two sections: flow into the zone and flow out of the zone. Every
source/sink that is present in the model is listed in the report with a flow value. In
addition to the sources/sinks, there is a field for the amount of flow that goes between
zones.

3. In the Zone drop-down box select “2.”

The user may also want to view the report for zone 3.

4. When finished, select the OK button to exit the dialog.

17 Conclusion
This concludes the tutorial. Here are the key points of this tutorial:

 It is possible to specify which units are being used and GMS will display the
units next to input fields to help the user input the appropriate value. GMS does
not do any unit conversions for the user.

 The MODFLOW menu is in the 3D Grid module.

 The desired MODFLOW packages for use in the model can be selected by
choosing the MODFLOW | Global Options command and clicking the
Packages button.

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 Most MODFLOW array data can be edited in two ways: via a spreadsheet or by
selecting grid cells and using the MODFLOW | Advanced | Cell Properties
command.

 Wells, drains, etc. can be created and edited by selecting the grid cell(s) and
choosing the MODFLOW | Advanced | Sources/Sinks command or by right-
clicking on a selected cell and selecting the Sources/Sinks command from the
pop up menu.

 The Model Checker can be used to analyze the input data and check for errors.

 A flow budget report can be generated for a sub-region of the model by assigning
Zone budget IDs to the grid and then using the Flow Budget command.

 In Ortho mode, only one row, column, or layer of the 3D grid is visible at a time.

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