v. 8.

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GMS 8.0 Tutorial

MODFLOW Generating Data from Solids

Using solid models to represent complex stratigraphy with MODFLOW

Objectives
Learn the steps necessary to convert solid models to MODFLOW data on a 3D grid. The elevations
associated with the grid are adjusted to match the elevations defined by the solid models. Also, the
material assigned to each grid cell is inherited from the solid that encompasses the cell.

Prerequisite Tutorials

Required Components

Time

None

Sub-surface
Characterization
Grid
Map

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Contents
1
2

Contents ...............................................................................................................................2
Introduction.........................................................................................................................2
2.1
Outline..........................................................................................................................4
3
Getting Started ....................................................................................................................4
4
Reading in the Solids ..........................................................................................................4
5
Boundary Matching Versus Grid Overlay .......................................................................5
5.1
Boundary Matching......................................................................................................5
5.2
Grid Overlay ................................................................................................................5
6
Solids MODFLOW Using Grid Overlay ......................................................................6
6.1
Displaying the 3D Grid ................................................................................................6
6.2
Initializing MODFLOW...............................................................................................6
6.3
Activating Cells............................................................................................................6
6.4
SolidsMODFLOW ...................................................................................................7
6.5
Viewing the Grid..........................................................................................................7
7
Solids MODFLOW Using Boundary Matching ..........................................................8
7.1
Layer Ranges................................................................................................................8
7.2
Assigning Layers to Solids.........................................................................................10
7.3
SolidsMODFLOW .................................................................................................11
8
Viewing the Grid ...............................................................................................................11
9
Thin Cells...........................................................................................................................12
9.1
Assigning Minimum Thickness .................................................................................12
9.2
Top Cell Bias .............................................................................................................12
10 Converting the Conceptual Model...................................................................................13
10.1
Using Materials to Define Hydraulic conductivity ....................................................13
11 Running MODFLOW.......................................................................................................14
12 Solids HUF ....................................................................................................................14
12.1
Selecting the HUF Package........................................................................................15
12.2
Converting the Solids to HUF Data ...........................................................................15
12.3
Viewing the HUF Data...............................................................................................16
12.4
Converting the Conceptual Model .............................................................................16
12.5
Running MODFLOW ................................................................................................17
13 Conclusion .........................................................................................................................17

Introduction
Complex stratigraphy can be difficult to simulate in MODFLOW models. MODFLOW
uses a structured grid that requires that each grid layer be continuous throughout the
model domain. This makes it difficult to explicitly represent common features such as
pinchouts and embedded seams in a MODFLOW model.
Solid models can be used to represent arbitrarily complex stratigraphy. Figure 1 shows a
cross section through a solid model where different stratigraphic units pinchout.
Designing a MODFLOW compatible grid for this type of stratigraphy is very difficult.

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Figure 1.

Cross-section through a solid model.

In this tutorial we will cover the steps necessary to convert solid models, like the one in
Figure 1, to MODFLOW data. The elevations associated with the finite-difference grid
will be adjusted to match the elevations defined by the solid models. Also, the material
assigned to each grid cell will be inherited from the solid that encompasses the cell.
Figure 2 shows a MODFLOW compatible grid of the cross section shown in Figure 1.

Figure 2.

Finite difference grid with elevations and materials inherited from the solid
model.

One of the main benefits of using solid models to define stratigraphy for MODFLOW
models is that it provides a grid-independent definition of the layer elevations that can be
used to immediately re-create the MODFLOW grid geometry after any change to the grid
resolution.
Solid models of stratigraphy can easily be created in GMS using the horizons
approach. The tutorial entitled Stratigraphy Modeling Horizons and Solids explains
how to create solid models using GMS.

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2.1

MODFLOW Generating Data From Solids

Outline
This is what you will do:
1. Open a file containing solids data.
2. Use the Solids MODFLOW command using the Grid Overlay option.
3. Assign grid layers to the solids
4. Use the Solids MODFLOW command using the Boundary Matching option.
5. Fix problems associated with thin cells.
6. Convert the conceptual model to MODFLOW and run MODFLOW.
7. Convert the solids to HUF data.
8. Convert the conceptual model again and run MODFLOW.

Getting Started
Lets get started.
1. If necessary, launch GMS. If GMS is already running, select the File | New
command to ensure that the program settings are restored to their default state.

Reading in the Solids

First, we will read in a file containing a set of solids for the site we are modeling.
1. Select the Open button

2. Locate and open the directory entitled tutfiles\MODFLOW\sol2mf.

3. Open the file named start.gpr.
You should see cross-sections in the main GMS window that show the stratigraphy for
this site.
There are five different solids in this project file. There are two main units labeled
upper_aquifer (green) and lower_aquifer (red). Inside of upper_aquifer there are two
silty-clay (blue) units, and between upper_aquifer and lower_aquifer there is a clay
(yellow) unit.

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Boundary Matching Versus Grid Overlay

There are two options when doing Solids MODFLOW, the Boundary Matching option
and the Grid Overlay option. These options are illustrated in the following figure.

Solids

Grid
Boundary Matching

Grid Overlay

Figure 3.

5.1

Solids MODFLOW options illustrated. Side view shown.

Boundary Matching
With the Boundary Matching option, the top and bottom of the grid are deformed to
match the tops and bottoms of the solids. The interior grid layers are also deformed to
match the boundaries of the solids. The grid cell materials are set to match the material of
the solid that the grid cell center is located in.
This option results in a close fit between the grid and the solids, but it can result in thin
cells which can cause stability problems or dry cell issues when running MODFLOW.
This option requires that you determine which grid layers should be associated with
which solids.

5.2

Grid Overlay
With the Grid Overlay option, the top and bottom of the grid are deformed to match the
tops and bottoms of the solids. The interior grid layer boundaries are deformed to be
evenly spaced between the top and bottom of the grid using a simple linear interpolation.

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The interior grid layers are not changed to match the solid boundaries. As with the
boundary matching option, the grid cell materials are set to match the material of the
solid that the grid cell center is located in.
This option does not result in as close a fit between the grid and the solids as the
boundary matching option, but may avoid the thin cell problems associated with the
Boundary Matching option. This option does not require you to assign grid layer ranges
to each solid.

Solids MODFLOW Using Grid Overlay

We will first examine the Grid Overlay option. With this option, all that is needed are a
set of solids and a grid in the same location.

6.1

Displaying the 3D Grid

The grid was read in as part of the project, but the display of the grid cells was turned off.
Lets turn on the display of the grid.
1. In the Project Explorer turn on the 3D Grid Data folder

You should now see the 3D grid.

6.2

Initializing MODFLOW
We must initialize MODFLOW before we can execute the Solids MODFLOW menu
command.
1. If necessary expand the 3D Grid Data folder
on the plus symbol next to the item.

the Project Explorer by clicking

underneath the 3D Grid Data folder and select

2. Right-click on the grid item
the New MODFLOW command.
3. Select the Starting Heads button.
4. Select the Constant Grid button.
5. Enter a value of 250.0 and select OK to exit the dialog.
6. Click OK to exit the dialog.

6.3

Activating Cells
We need to inactivate the cells outside our model domain.
1. In the Project Explorer select the Map Data folder

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2. Select the Feature Objects | Activate Cells in Coverage(s) menu command.

6.4

SolidsMODFLOW
1. In the Project Explorer select the Solid Data folder

2. Select the Solids | Solids MODFLOW menu command.

3. Make sure that the Grid Overlay option is selected and select OK to execute the
Solids MODFLOW menu command.
The Solids MODFLOW command may take a few seconds to a few minutes to
complete depending on the speed of your computer. When done, the 3D grid should
appear to be deformed to match the top and bottom of the solids.

6.5

Viewing the Grid

Lets examine the grid.
1. Select the Display Options button
2. Select the

3D Grid Data item on the left.

3. Turn on Cell faces.

4. Click OK.
Notice the solid cross sections are now mostly obscured from view by the grid, but you
can still see them poking out in places. If you look closely you can see that the top of the
grid matches the top of the solid cross sections quite well. The grid and cross sections
should appear as shown in Figure 4.

Figure 4.

Grid and solid cross-sections after Solids MODFLOW using grid

overlay.

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Lets look at the grid from the side.

.

5. Select the Ortho Mode button

6. In the Project Explorer, click on the 3D Grid Data folder

7. Select the Select Cells tool

8. Select a cell somewhere near the middle of the grid.

9. Select the Front View button

The solid cross sections are in front of the grid row we are viewing.
10. In the Project Explorer, turn off the Solid Data folder
11. In the Mini Grid toolbar, use the arrow buttons
different rows.

.
to view the grid along

The grid at row 14 should appear as shown in Figure 5 below.

Figure 5.

Grid row after Solids MODFLOW using grid overlay.

At this point we could continue to develop the MODFLOW model, but before doing that
well take a look at the Solids MODFLOW Boundary Matching option.

Solids MODFLOW Using Boundary Matching

The boundary matching option results in a close fit between the solid boundaries and the
grid layer, but it requires a bit more work on your part.

7.1

Layer Ranges
Before we can convert the solids to MODFLOW data using the Boundary Matching
option we must assign a layer range to each of the solids. The layer range represents the
consecutive sequence of layer numbers in the MODFLOW grid that are to coincide with
the solid model. A sample set of layer range assignments is shown in Figure 6(a). The
example in Figure 6 is a case where each solid is continuous through the model domain

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and there are no pinchouts. Each of the solids is given a layer range defined by a
beginning and ending grid layer number. The resulting MODFLOW grid is shown in
Figure 6(b).

A. Layers 1-2
B. Layer 3-5
C. Layers 6-7
(a)

(b)
Figure 6.

(a) A set of simple solids with grid layer assignments.

(b) The MODFLOW grid resulting from the layer assignments.

A more complex case with pinchouts is illustrated in Figure 7(a). Solid A is given the
layer range 1-4, and the enclosed pinchout (solid B) is given the layer range 2-2. The set
of grid layers within the defined range that are actually overlapped by the solid may
change from location to location. The layer range represents the set of grid layers
potentially overlapped by the solid anywhere in the model domain. For example, on the
left side of the problem shown in Figure 7(a), solid A covers grid layers 1, 2, 3 and 4. On
the right side of the model, solid A is associated with grid layers 1, 3 and 4 since the
enclosed solid (solid B) is associated with layer 2. Likewise, Solid C is associated with
grid layers 5 and 6 on the left side of the model but only with layer 6 on the right side of
the model where solid D is associated with layer 5. The resulting MODFLOW grid is
shown in Figure 7(b).

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A. Layers 1-4
B. Layers 2-2

D. Layers 5-5

C. Layers 5-6
(a)

1
2
3
4
5
6
(b)
Figure 7.

(a) Grid layer assignments for a set of solids with pinchouts.

(b) The MODFLOW grid resulting from the layer assignments.

When assigning layer ranges to solids, care must be taken to define associations that are
topologically sound. For example, since solid B in Figure 7(a) is enclosed by solid A,
solid B could not be assigned a layer range that is outside the layer range of solid A.

7.2

Assigning Layers to Solids

Now we are ready to assign the grid layers to the solids.
The figure below is a cross section through our site. Notice that we must have a
minimum of five grid layers in order to represent all of the layers present in this crosssection. In this case the upper_aquifer (green) will be assigned to layers 1-3. The siltyclay (blue) will be assigned to layer 2. The clay (yellow) will be assigned to layer 4, and
the lower_aquifer (red) will be assigned layers 4-5.

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Figure 8.

Cross-section through the model domain.

1. In the Project Explorer expand the Solid Data folder

if necessary.

in the Project Explorer. For the

2. Double click on upper_aquifer 1 solid
Begin layer, enter 1 and for the End layer, enter 3. Click OK.
3. Repeat this process on the remaining solids, entering the values shown in the
following table.

7.3

upper_aquifer 1

lower_aquifer 2

clay 3

silty-clay 4

silty-clay 5

Begin layer

End layer

SolidsMODFLOW
1. Select the Solids | Solids MODFLOW menu command.
2. Select the Boundary Matching option and select OK.
The Solids MODFLOW command may take a few seconds to a few minutes to
complete depending on the speed of your computer.

Viewing the Grid

See how our grid has changed. Your view should look something like that shown in
Figure 9.

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Figure 9.

Row 30 of grid after Solids MODFLOW using boundary matching.

1. Notice that the second layer has both silty-clay (blue) and upper_aquifer (green)
materials assigned to it.
2. Use the arrow buttons

to view the grid along different rows.

3. Select the Side View button

4. Use the arrow buttons

different columns.

in the Mini-Grid Display to view the grid along

Thin Cells
The purpose of the Boundary Matching option for the Solids MODFLOW command is
to ensure that each upper and lower boundary defined by the solid model is precisely
matched by a layer boundary in the MODFLOW grid. As a result of this approach thin
cells often occur where solids pinchout. Notice the thin cells that you get on the edges of
the clay (yellow) and silty-clay (blue) solids in Figure 9. If you want to limit the effect of
the thin cells in your model grid you can set a target minimum thickness for each of the
solids.

9.1

Assigning Minimum Thickness

Now we will use the Target minimum thickness to limit the thin cells in our model.
1. Double click on the upper aquifer 1 solid

in the Project Explorer.

2. Change the Target min. cell thickness to 20 and select OK to exit the dialog.
3. Repeat these steps for all of the remaining solids.

9.2

Top Cell Bias

Another problem that may be encountered using the Boundary Matching option is that
the cells in the top layer of the grid may also be too thin and subject to wetting and
drying. To ensure that the top layer of your grid is sufficiently thick you can use the Top
cell bias option.

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1. Double-click on the upper_aquifer 1 solid

in the Project Explorer.

2. Change the option next to Use top cell bias to Yes and select OK to exit the
dialog.
3. Select the Solids | Solids MODFLOW menu command.
4. Select OK to execute the Solids MODFLOW menu command.

Figure 10.

Row 30 of the model grid using target minimum thickness and top cell bias.

Your grid should now look similar to Figure 10. Notice the top row is thicker, and the
thin cells in the yellow and blue areas are now thicker.

10

Converting the Conceptual Model

We can now finish developing the MODFLOW model. In the interest of time, the
conceptual model has already been built and was read in when we read in the project file.
For more information on conceptual models, refer to the MODFLOW Conceptual
Model Approach tutorial.
1. In the Project Explorer select the Map Data folder
2. Select the Plan View button

3. Select the Feature Objects | Map MODFLOW menu command.

4. Ensure the All applicable coverages option is selected and select OK.

10.1

Using Materials to Define Hydraulic conductivity

Now we need to set the option for MODFLOW to use the material assigned to the grid
cell to define the hydraulic conductivity for the cell.
1. Select the MODFLOW | LPF Package menu command.
2. Select the Use Material IDs option in the Layer property entry method section of
the dialog.

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3. Select the Material Properties button in the Layer data section of the dialog.
4. Select each material in the list and enter the values for the properties shown in
the table below.
Horizontal k

Vert. anisotropy
(Kh / Kv)

upper_aqufier

15.0

3.0

lower_aquifer

30.0

3.0

clay

0.5

3.0

silty-clay

1.0

3.0

5. Select OK twice to exit both dialogs.

11

Running MODFLOW
We are now ready to run MODFLOW. First, we must save our MODFLOW simulation.
1. Select the File | Save As menu command.
2. Save the project with the name run1_lpf.gpr.
3. Select the MODFLOW | Run MODFLOW menu command.
4. When MODFLOW has finished running, select the Close button.
MODFLOW solution will automatically be read in.
5. Select the Display Options button
6. Select the

The

3D Grid Data item on the left.

7. Turn off the Cell faces option and select OK to exit the dialog.
You should now see the head contours on the grid. Cycle through the layers to see how
the head contours change within the different layers. You can also switch into side view
to see the contours on the rows or columns.

12

Solids HUF
Now we will use the HUF package in MODFLOW instead of the LPF package to define
the hydraulic properties of the grid cells. This package is designed to represent complex
stratigraphic relationships in a grid independent fashion.
The hydro-stratigraphy is represented using a set of hydrogeologic units. Each unit is
defined by two arrays, one for the top elevation and one for the thickness. The thickness
values can be set to zero in regions of the model where the unit is not present. When
MODFLOW is executed, each cell is compared to the corresponding unit elevation arrays
and equivalent hydraulic properties are assigned to the cell. The figure below shows an
example of HUF units on a MODFLOW grid.
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Figure 11.

12.1

HUF data.

Selecting the HUF Package

First, we need to select the HUF package as our flow package.
1. Select the MODFLOW | Global Options menu command.
2. Select the Packages button.
3. In the Flow Package section of the MODFLOW Packages dialog change the flow
package to Hydrogeologic Unit Flow (HUF).
4. Select OK twice to exit both dialogs.

12.2

Converting the Solids to HUF Data

We are now ready to convert the solids to HUF data. However, when we ran the Solids
MODFLOW command some of the cells were inactivated in layers 4 and 5. We want
those cells to be active for this new model.
1. In the Project Explorer select the Map Data folder

2. Select the Feature Objects | Activate Cells in Coverage(s) menu command.

3. In the Project Explorer select the Solid Data folder

4. Select the Solids | Solids HUF menu command.

5. Turn on the Adjust grid cell elevations toggle.
The MODFLOW top elevation array of the top layer and the bottom elevation
array of the bottom layer are adjusted to match the tops and bottoms of all the
solids. The interior top and bottom elevation arrays are assigned based on the

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proportions entered in the Elevation bias spreadsheet. The entire grid depth for
each grid column is distributed according to the entries in the spreadsheet for each
layer.
6. In the Elevation bias spreadsheet, change the value for layer 1 to 0.4.
7. Select OK to execute the Solids HUF menu command.

12.3

Viewing the HUF Data

To view the HUF data:
1. In the Project Explorer select the 3D Grid Data folder
2. Select the Display Options button

3. Change the Color option under Cell edges to Specified.

4. Switch to the MODFLOW tab.
5. Turn on the Display hydrogeologic units toggle.
6. Select OK to exit the dialog.
7. Select the Select Cells tool

8. Select a cell somewhere near the middle of the grid.

9. Select the Front View button
10. Use the arrow buttons

12.4

to view the grid along different rows.

Converting the Conceptual Model

We need to convert the conceptual model again to ensure that any cells that were inactive
will have the correct boundary conditions.
1. In the Project Explorer select the Map Data folder

2. Switch to plan view by selecting the Plan View button

3. In the Project Explorer right-click on the MODFLOW conceptual model

select Properties from the menu.

and

4. Change the flow package to HUF and select OK to exit the dialog.
5. Select the Feature Objects | Map MODFLOW menu command.
6. Ensure the All applicable coverages option is selected and select OK.

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12.5

MODFLOW Generating Data From Solids

Running MODFLOW
Were now ready to save the project and run MODFLOW.
1. Select the File | Save As menu command.
2. Save the project with the name run1_huf.
3. Select the MODFLOW | Run MODFLOW menu command.
4. When MODFLOW has finished running, select the Close button.
MODFLOW solution will automatically be read in.

The

You should now see the head contours on the grid. You may see some red triangles on
certain grid cells. These cells have gone dry (the water table is below the bottom of the
cell) in this simulation. Cycle through the layers to see how the head contours change
within the different layers. You can also switch into side view to see the contours on the
rows or columns.

13

Conclusion
This concludes the tutorial. Here are some of the key concepts in this tutorial:

Solids can be used to define the MODFLOW layer elevations. They can also be
used to create MODFLOW HUF data.

You must assign layer ranges to the solids before using them to create a layered
grid if using the Solids MODFLOW Boundary Matching option.

You can use a minimum thickness to avoid thin cells. You can also specify a top
cell bias to make the top grid layer thicker.

If you are using solids to define your MODFLOW layer data, you probably want
to use the Material IDs approach to define the hydraulic properties of grid cells
based on their material.

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