GMS 7.

0 TUTORIALS
MT3DMS – Grid Approach

1 Introduction
This tutorial describes how to perform an MT3DMS simulation within GMS. An
MT3DMS model can be constructed in GMS using one of two approaches: the
conceptual model approach or the grid approach. With the conceptual model approach,
the sources/sinks and zones in the model are defined with GIS objects and automatically
assigned to the grid. With the grid approach, values are manually assigned to the grid.
While the conceptual model approach is generally preferable for large, complicated
models, simple models can be easily constructed using the grid approach. The grid
approach is described in this tutorial.

1.1 Contents

1 Introduction..................................................................................................................... 1-1
1.1 Contents ................................................................................................................... 1-1
1.2 Outline...................................................................................................................... 1-2
1.3 Required Modules/Interfaces ................................................................................... 1-2
2 Description of Problem................................................................................................... 2-2
3 Getting Started ................................................................................................................ 3-3
4 The Flow Model............................................................................................................... 4-3
5 Building the Transport Model ....................................................................................... 5-4
5.1 Initializing the Simulation........................................................................................ 5-4
5.2 The Basic Transport Package................................................................................... 5-4
5.3 The Advection Package............................................................................................ 5-6
5.4 The Dispersion Package........................................................................................... 5-6
5.5 The Source/Sink Mixing Package ............................................................................ 5-7
5.6 Saving the Simulation and Running MT3DMS ....................................................... 5-7
5.7 Changing the Contouring Options ........................................................................... 5-7
5.8 Setting Up an Animation.......................................................................................... 5-7
5.9 Calculating the Mass of the Contaminant ................................................................ 5-8

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6 Conclusion ....................................................................................................................... 6-9

1.2 Outline
This is what you will do:

1. Open a MODFLOW simulation and run MODFLOW.

2. Initialize MT3D and enter the data for several MT3D packages.

3. Run MT3D and read the solution.

4. Set up an animation to visualize the solution.

5. Calculate the mass of the contaminant.

1.3 Required Modules/Interfaces

You will need the following components enabled to complete this tutorial:

• Grid

• MODFLOW

• MT3DMS

You can see if these components are enabled by selecting the Help | Register command.

2 Description of Problem
The problem to be solved in this tutorial is shown in Figure 1. This problem corresponds
to the sixth sample problem ("Two-Dimensional Transport in a Heterogeneous Aquifer")
described in the MT3DMS documentation. The problem consists of a low K zone inside
a larger zone. The sides of the region are no flow boundaries. The top and bottom are
constant head boundaries that cause the flow to move from the top to the bottom of the
region. An injection well with a specified concentration provides the source of the
contaminants. A pumping well serves to withdraw contaminated water migrating from
the injection well. A steady state flow solution will be computed and a transient transport
simulation will be performed over a one year period.

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Constant head boundary (H=250 m) (flow model)

No mass flux boundary (transport model)

INJECTION WELL
Q = 0.001 m3/s
C = 57.87 ppm

Hyd. Cond. =
1.474x10-7m/s
LOW K ZONE

No flow boundary No flow boundary

(flow model) DY = 2000 m PUMPING WELL (flow model)
No mass flux Q = -0.0189 m3/s No mass flux
boundary boundary
(transport model) (transport model)
Number of rows = 40
Number of columns = 32
Aquifer thickness = 10 m
K = 1.474x10-4 m/s
Porosity = 0.3
Longitudinal dispersivity = 20 m
Dispersivity ratio = 0.2
Simulation time = 1.0 yr

DX = 1600 m
Constant head boundary (H = 36.25 m)

Figure 1. Sample Flow and Transport Problem.

3 Getting Started
Let’s 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.

4 The Flow Model

Before setting up the MT3DMS simulation, we must first have a MODFLOW simulation.
The MODFLOW solution will be used as the flow field for the transport simulation. In
the interest of time, we will read in a previously created MODFLOW simulation.

1. Select the Open button .

2. Locate and open the directory entitled tutfiles\mt3dgrid.

3. Open the file entitled [Link].

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Now we’ll save our project under a new name. Since we’re changing the name, we will
run MODFLOW to compute solution files with the new name. Otherwise, when MT3D
runs it will look for solution files with the new name and not find any.

4. Select the File | Save As command.

5. Locate and open the directory entitled tutfiles\mt3dgrid

6. Save the project with the name [Link].

7. Select the 3D Grid Data folder from the Project Explorer.

8. From the MODFLOW menu, select the Run MODFLOW command.

9. When it finishes running, select the Close button.

5 Building the Transport Model

Now that we have a flow solution, we are ready to set up the MT3DMS transport
simulation. Like MODFLOW, MT3DMS is structured in a modular fashion and uses a
series of packages as input. Consequently, the GMS interface to MT3DMS is similar to
the interface to MODFLOW and we will follow a similar sequence of steps to enter the
input data.

5.1 Initializing the Simulation

First, we will initialize the MT3DMS simulation.

1. Select the Edit | Model Interfaces command.

2. Turn on the MT3D | RT3D | SEAM3D under Models to use in project.

3. Select the OK button.

4. Select the MT3D | New Simulation command.

5.2 The Basic Transport Package

The MT3DMS Basic Transport package is always required and it defines basic
information such as stress periods, active/inactive regions, and starting concentration
values.

Species
Since MT3DMS is a multi-species model, we need to define the number of species and
name each species. We will use one species named “tracer."

1. Select the Define Species button.

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2. Select the New button.

3. Change the name of the species to tracer.

4. Select the OK button.

Packages
Next, we will select which packages we wish to use.

1. Select the Packages button.

2. Turn on the following packages:

• Advection Package

• Dispersion Package

• Source/Sink Mixing Package

3. Select the OK button.

Stress Periods
The next step is to set up the stress periods. The flow simulation was steady state but the
transport simulation will be transient. We will run the simulation for a one year time
period. To do this we will use a single stress period (since the input values are constant)
and allow MT3DMS to determine the appropriate transport step size.

1. Select the Stress Periods button.

2. Change the Length field to 365.

3. Make sure the value in the Trans. step size is 0.0. A value of zero signifies that
MT3DMS will automatically compute the appropriate transport step size.

4. Select the OK button to exit the Stress Periods dialog.

Output Control
Next, we will specify the output options.

1. Select the Output Control button.

2. Select the Print or save at specified interval option.

3. Change the specified interval to 10. This will output a solution at every tenth
transport step.

4. Select the OK button to exit the Output Control dialog.

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ICBUND Array
The ICBUND array is similar to the IBOUND array in MODFLOW. The ICBUND array
is used to designate active transport cells (ICBUND>0), inactive transport cells
(ICBUND=0), and constant concentration cells (ICBUND<0). For our problem, all of
the cells are active, therefore, no changes are necessary.

Starting Concentration Array

The starting concentration array defines the initial condition for the contaminant
concentration. In our problem, the starting concentrations are all zero and the default is
adequate.

HTOP and Thickness Arrays

MT3DMS uses the HTOP array and a thickness array to determine the layer geometry.
However, the values for these arrays are determined by GMS automatically from the
MODFLOW layer data and no input is necessary.

Porosity Array
Finally, we will define the porosity for the cells. Our problem has a constant porosity of
0.3. This is the default value in GMS so no changes need to be made.

This completes the definition of the Basic Transport package data.

1. Select the OK button to exit the Basic Transport Package dialog.

5.3 The Advection Package

The next step is to enter the data for the Advection package. We want to use the Third
Order TVD scheme (ULTIMATE) solution scheme. This is the default, so we don’t need
to do anything.

5.4 The Dispersion Package

Next, we will enter the data for the Dispersion package.

1. Select the MT3D | Dispersion Package command.

2. Select the Longitudinal Dispersivity button.

3. Select the Constant ´ Grid option.

4. Enter a value of 20 and click OK.

5. Select the OK button to exit the Longitudinal Dispersivity dialog.

6. Enter a value of 0.2 for the TRPT parameter.

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7. Select the OK button to exit the Dispersion Package dialog.

5.5 The Source/Sink Mixing Package

Finally, we must define the data for the Source/Sink Mixing package. For our problem,
we only have one source/sink: the injection well. To define the source at the injection
well, we need to select the well and assign a concentration.

1. Select the cell containing the injection well (the upper well) by clicking
anywhere in the interior of the cell.

2. Select the MT3D | Point Sources/Sinks command.

3. Toggle on the Well option for Cell 304.

4. Enter a value of 57.87 for the concentration.

5. Select the OK button.

6. Click outside the grid to unselect the cell.

5.6 Saving the Simulation and Running MT3DMS

We are now ready to save the simulation and run MT3DMS.

1. Select the Save button .

2. Select the MT3D | Run MT3D command.

3. When the simulation is finished, select the Close button.

5.7 Changing the Contouring Options

When displaying plume data, the color fill option often provides excellent results.

1. Select Contour Options from the main toolbar.

2. Change the Contour method to Color Fill.

3. Select the OK button.

5.8 Setting Up an Animation

Now we will observe how the solution changes over the one year simulation by
generating an animation. To set up the animation:

1. Select the Display | Animate command.

2. Make sure the Data set option is on and click Next.

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3. Turn on the Display clock option.

4. Select the Use constant interval option and change the Time interval to 36.5.
This will result in 11 frames.

5. Select the Finish button.

You should see some images appear on the screen. These are the frames of the animation
which are being generated.

6. After viewing the animation, select the Stop button to stop the animation.

7. Select the Step button to move the animation one frame at a time.

8. You may wish to experiment with some of the other playback controls. When
you are finished, close the window and return to GMS.

5.9 Calculating the Mass of the Contaminant

Finally, we will calculate the mass of the contaminant in the aquifer at various times
during the simulation.

1. Choose the Select Cells tool .

2. Select the cell containing the well in the lower portion of the model.

3. Select the MT3D | Calculate Mass command.

This dialog allows the user to calculate the mass of a contaminant in the entire model
domain or in the selected cells. The Definition section of the dialog explains the formula
that is used to calculate the mass. Basically, the volume of water in each cell is
calculated and then multiplied by the concentration computed by MT3D. The user must
supply a conversion factor so that the calculated mass will be computed in the correct
units. The Unit conversion factor section shows an example of a conversion factor. The
Concentration range section allows the user to specify a range over which the mass will
be calculated. This is most useful to ignore negative concentrations that result in MT3D
simulations.

4. In the Concentration range section, turn on the Specify range in calculation

toggle.

5. Enter 0.0 for the Min and 9.0 for the Max.

6. In the Unit conversion factor section, enter 0.0283 for the Factor so that the
resulting mass will be in units of grams.

7. Select the Use only selected cells in calculation option near the bottom of the
dialog.

8. Select the Calculate button.

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Notice that the mass values are shown in the spreadsheet on the right side of the dialog.

9. Now select the Use all cells in calculation option.

10. Select the Calculate button again.

You should now see the total mass in the aquifer for each time step of the solution.

11. When you have finished viewing the results select Done to close the dialog

6 Conclusion
This concludes the MT3DMS – Grid Approach tutorial. Here are the things that you
should have learned in this tutorial:

• MT3D is available only if a MODFLOW model is in memory.

• MT3D relies on the MODFLOW solution files, so if you move or rename your
MODFLOW files, you will probably need to regenerate the MODFLOW solution
files so MT3D can find them.

• GMS gives MT3D the top and bottom elevation data it requires for each layer
from the MODFLOW model.

• You can use the Animation Wizard to create an animation in GMS.

• You can calculate the mass of a contaminant in the 3D grid using the MT3D |
Calculate Mass command.

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