Airport Tutorial - Contaminant Transport Modeling

Visual MODFLOW Flex

Integrated Conceptual & Numerical Groundwater Modeling

Airport Tutorial: Numerical Modeling with Transport

The following example is a walk through of creating a numerical model with groundwater flow (using
MODFLOW-2005) and basic contaminant transport (using MT3DMS). The exercise is based on the
well-known Airport example from Visual MODFLOW Classic.

Objectives

Learn how to create a project and create a numerical grid

Become familiar with navigating the GUI and steps for numerical modeling
Learn how to define new property zones and boundary conditions
Define inputs for contaminant transport
Translate the model inputs into MODFLOW and MT3DMS packages
Run MODFLOW-2005 and MT3DMS engines
Understand the results by interpreting heads, drawdown, and concentrations in several views
Check the quality of the model by comparing observed heads to calculated heads, and observed
vs. calculated concentrations

Creating the Project

Launch Visual MODFLOW Flex.
Select FileNewProject. The Create Project dialog will appear.
Type in project Name Airport.
Click Browse button, and navigate to a folder where you wish your projects to be saved, and
click OK.
Define your coordinate system and datum (or just leave the non-cartesian as defaults).
Define the Units frame. For this project, the default units will be fine.
The Create Project dialog should now look as follows

 Click [OK]. The workflow selection screen will appear.

Select "Numerical Modeling" and the Numerical Modeling workflow will load. The first step is to
Define Objectives.

Define Objectives
In this step, you define the objectives of your model and the default parameters.

 The Start Date of the model corresponds to the beginning of the simulation time period. It is
important to define a relevant start date since your field measurements (observed heads and
pumping schedules) will be defined with absolute date measurements, and must lie within the
simulation time period.
Select 1/1/2000 for the Start Date
For this scenario, we will include contaminant transport in the model run. Turn on the check box
beside "Transport Active" (in the right hand side of the window, under Define Modeling
Objectives.
For Sorption select "Linear Isotherm (equilibrium-controlled)". For this tutorial you will not be
simulating any decay or degradation of the contaminant, so the default Reactions setting of No
kinetic reactions will be fine.
Below the Sorption and Reaction settings are two tabs: Species Parameters and Reaction
Parameters. By default, one species (chemical component) is defined for the transport run. For
this example, we will leave the initial concentration (SCONC) as zero, but adjust SP1 (Kd (the
distribution coefficient)
Type: 1E-7 in SP1 [1/(mg/L)] column
You are now finished setting up the flow and transport objectives. Click

(Next Step) to

proceed.
The following "Define Grid" step will appear; at this step, you can import Visual MODFLOW
Classic or MODFLOW data sets, or define a new empty grid.
Click on [Create Grid] to proceed

Creating Grid
At this step, you can specify the dimensions of the Model Domain, and define the number of
rows, columns, and layers for the finite difference grid. Type the following into the Grid Size
section,
Columns: 40
Rows: 40
For Grid Extents, enter 2000 for Xmax and 2000 for Ymax
Under Define Vertical Grid, enter 3 for Number of Layers

Define Layer Elevations

In Visual MODFLOW Flex, you can define the elevations of the tops and bottom of the model
layers. Or you can have varying layer elevations defined from Surface data objects. Surfaces
could be from data objects you imported from Surfer .GRD, ESRI .ASI, .DEM, or from Surfaces
you have created through interpolating XYZ points. In this exercise, you will import 4 surfaces
(from Surfer .GRD files), then use these to define the layer elevations.
File/Import from the main menu. The following window will appear:

 For the Data Type, select Surface from the drop-down list.
In the Source File field click the [] button and navigate to your "My Documents" folder, then
Visual MODFLOW Flex\Projects\suppfiles\Surfer\airport-ground-surface.grd" and select [Open]
Click [Next>>]
Click [Next>>] (accept the defaults)
Click [Next>>] (accept the defaults)
Click [Finish]. You should now see a new "airport-ground-surface" data object appear in the
data tree, in the top left corner of the window.
Now, repeat the above steps to import the other Surfer .GRD files into the project:
airport-layer2-top.grd
airport-layer3-bottom.grd
airport-layer3-top.grd
When you are finished, you should see 4 Surface data objects in the data tree in the top left
corner.

 Now you are ready to define the grid layers using these surfaces. Under Define Vertical Grid,
select "Use Surface" check box for each grid layer. This is shown below

Next you will provide a surface for each layer;

Click on airport-ground-surface from the data object tree (it should become selected), then click
beside "Use Surface" under the Define Vertical Grid table (in
on the topmost blue arrow
the row that starts "Layer 1 - Top". If you have done this correctly, the table should appear as
shown below.

 Now repeat these steps for the remaining layers:

Select airport-layer2-top Surface data object to the tree, and insert this (using the
Surface for Layer 2 - Top

) as the

Select airport-layer3-top Surface data object to the tree, and insert this (using the
Surface for Layer 3 - Top

) as the

Select airport-layer3-bottom Surface data object to the tree, and insert this (using the
the Surface for Layer 3 - Bottom
When you are finished, the table should appear as shown below.

) as

 You are finished defining the layer elevations.

Click on the [Create Grid] button (near the top right of the window) to create the grid. You will
see the model tree will get generated on the left side of the window, and the NumericalGrid
should appear as the last item.

Refining the Grid

This section describes the steps necessary to refine the model grid in areas of interest, such as
around the water supply wells, refueling area, and area of discontinuous aquitard. The reason for
refining the grid is to get more detailed simulation results in areas of interest, or in zones where you
anticipate steep hydraulic gradients. For example, if drawdown is occurring around the well, the water
table will have a smoother surface if you use a finer grid spacing. Also, layer properties can be
assigned more correctly on a finer grid.
Right click on the NumericalGrid1 from the tree, and select Edit Numerical Grid...
Refine the Grid. The following window will appear.

 The grid refinement works by defining a starting row number, and ending row number, then a
"Refine by" factor; to help you define the limits of where the refinement should be applied, you
can add data objects to this display, such as well locations, arial maps, shapefiles, etc. When
you are using this feature with your own models, you just need to import these files before
launching the Grid Refinement step.
You will first start by refining the Rows. Enter 5 for the "Start", and enter "35" for the end.
For Refine by ,enter 2. Your screen should appear as follows:

 Click on the [Apply] button.

Next, you will refine the columns.
At the top left of the window, select the [Edit Columns] radio button.
You will first start by refining the Rows. Enter 5 for the "Start", and enter "35" for the end.
For Refine by ,enter 2
Click on the [Apply] button.
You should now see coarse grid sizes around the edge of the model domain, and a more finer
sized grid spacing in the middle of model (around the areas interest). This is shown below.

 Click on the [OK] button.

(Next Step) to proceed. This will generate the model run folder in the Model tree,
Click
which includes input and output directories, and default flow and transport properties.
Now is a good time to save the project. Click File/Save Project from the main menu.
In the next section, you will view the numerical grid that you just created.

View Grid
The View/Edit Grid step provides several views for displaying and the grid in 2D and 3D, along with
tools for refining and coarsening the grid.
There are numerous tools available to control and manipulate the grid views:

 Under Views, select the various views you want to see in the Flex viewer; VMOD Flex allows
you to simultaneously show a layer, row, column and 3D Views. Place a check box beside the
desired view and it will appear on the screen.
Adjust a specific layer, row, or column using the up/down arrows. Alternatively, click on the
button then click on any specific row, column, or layer in any of the 2D views, and the selected
row, column, or layer will be set automatically.
The standard navigation tools allow you to zoom, pan, and in the case of 3D view, rotate
Click

(Next Step) to proceed.

Defining Flow Properties

This section will guide you through the steps necessary to design a model with layers of highly
contrasting hydraulic conductivities.
Click on the [Database] button and Type the following values in the window:
Kx (m/s): 2E-4
Ky (m/s): 2E-4
Kz (m/s): 2E-4
[OK] to accept these values.
Note that in this case the Kx, Ky, and Kz values are the same, indicating the assigned property values
are assumed horizontally and vertically isotropic. However, anisotropic property values can be
assigned to a model by modifying the Conductivity Database

In this three layer model, layer 1 represents the upper aquifer, and layer 3 represents the lower
aquifer. Layer 2 represents the aquitard separating the upper and lower aquifers. For this example,
we will use the previously assigned hydraulic conductivity values (Zone# 1) for
model layers 1 and 3 (representing the aquifers) and assign different Conductivity values (i.e. a new
Zone) for model layer 2 (representing the aquitard). Note that layer 1 is the top model layer.
Next you need to change to Layer 2. (using the up arrow under the Layer text box shown below)

You are now viewing the second model layer, representing the aquitard. The next step in this tutorial
is to assign a lower hydraulic conductivity value to the aquitard (layer 2). We can graphically assign
the property values to the model grid cells.
[Assign / Entire Layer] from the toolbox.
The following dialog will appear

Click on the [New] button at the top; this will create a new zone.
Enter the following values:
Kx (m/s): 1E-10
Ky (m/s): 1E-10

 Kz (m/s): 1E-11
The dialog should appear as shown below.

[OK] to accept these values. Once finished, the cells for Layer2 should change red, which
indicates these cells belong to Zone2; you can use the Legend under the toolbox as a guide,
and also mouse over cells in the grid view, and note the values in the status bar.

 Next you must assign the appropriate conductivity values to the discontinuous region. Although
the region where the aquitard pinches out is very thin, the conductivity values of these grid cells
should be set equal to the Conductivity values of either the upper or lower aquifers.In this
particular example, the zone of discontinuous aquitard is indicated on a shapefile.. We will
import this shapefile into the project:
File/Import...
For the Data Type, select Polygon from the drop-down list.
In the Source File field click the [] button and navigate to your "My Documents" folder, then
Visual MODFLOW Flex\Projects\\suppfiles\discontinuous-aquitard.shp, and click [Open]
Click [Next>>]
Click [Next>>] (accept the defaults)
Click [Next>>] (accept the defaults)
Click [Finish]. You should now see a new data object, "discontinuous-aquitard" appear in the
data tree, in the top left corner of the window.
Click on the box beside this data object in the tree
the Layer View of the grid.

The data object should now appear in

Zoom into this area (using the mouse wheel, or the Zoom in button on the toolbar).

 Click [Assign / Polygon] from the toolbox.

Trace a polygon overtop of this discontinuous-aquitard shape; when you have closed the
polygon, click the right-mouse button.
Select [Define Attributes] from the menu that appears
The "New Property Zone" dialog will appear.
We want to assign these cells to an existing Zone, Zone1 that represents the aquifer above. So
in this case, it is not necessary to create a new parameter zone. You will see that Zone1 is
selected by default. (in the top left of the window)
Click [OK] to assign this group of cells to Zone1. This display should appear as shown below.

Now view the model in cross-section to see the three hydrogeological units. First, zoom out to
the fill extent using one of the following options:

Zoom out button from the toolbar

Zoom full extents button from the toolbar

Scroll wheel on the mouse (scroll downwards)

View Column Check box. You will see another view appear beside the layer view, showing a

cross-section through the model domain (by default, through Column1). To improve this view,
you should change the Exaggeration
Enter 40 in the Exaggeration field, which is located in the toolbar directly above the Column
view window.
Enter 37 for the Column number, as this will provide a cross-section through the region with the
discontinuous aquitard. Take a moment to view the cross-section of the properties. You can
also change the cross-section view (change the Column number up, down, or enter a new
value), and use the zoom and pan tools on the Column view to improve the display. Note that
you can repeat the same steps above for Rows, instead of Columns, in order to see crosssections along the X-axis.
When you are finished, turn the Column View off, by removing the check-box beside "Column"
under Views.
Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed.

Define Boundary Conditions

The next step is to define the flow boundaries for the model. In this example you will define constant
heads along the north, in layer 1 and 3, and the Waterloo River along the southern edge in layer 1,
and a constant head along the south in layer 3.

Constant Heads
The first Constant Head boundary condition to assign will be for the upper unconfined aquifer along
the northern boundary of the model domain. To do this you will use the [Assign >Polyline] tool.
First, you need to go back to Layer 1
[Assign / Polyline] from the toolbox. Move the mouse pointer to the north-west corner of the grid
(top-left grid cell) and left-click on this location to anchor the starting point of the line. Now move
the mouse pointer to the north-east corner of the grid (top-right grid cell) and Right-Click on this
location to indicate the end point of the line. You should then see a small menu appear "Define
Attributes".
Click on [Define Attributes]. The "Define Boundary Condition" dialog will appear.
Click [Next >>] to accept the default name. The following dialog will appear:

 Enter Starting Head (m) of 19

Enter Ending Head (m) of 19
Conc001 (leave the default value of -1; this indicates that contaminant mass will be assigned to
these cells)
Click [Finish] to complete the boundary condition. The hand-drawn polyline will now turn to a set
of red points, indicating that a Constant Head boundary condition has been assigned to these
cells.
Next you will assign a Constant Head boundary condition along the northern boundary for the
lower confined aquifer.
Locate the "Layer" selection (located to the top-left of the grid display), and change this to Layer
3


[Assign / Polyline] from the toolbox. Move the mouse pointer to the north-west corner of the grid
(top-left grid cell) and left-click on this location to anchor the starting point of the line. Now move
the mouse pointer to the north-east corner of the grid (top-right grid cell) and Right-Click on this
location to indicate the end point of the line. You should then see a small menu appear "Define
Attributes".
Click on [Define Attributes]. The "Define Boundary Condition" dialog will appear.
Click [Next >>] to accept the default name.
In the Define Boundary Condition dialog, enter the following values:
Enter Starting Head (m) of 18
Enter Ending Head (m) of 18
Click [Finish] to complete the boundary condition. The hand-drawn polyline will now turn to a set
of red points, indicating that a Constant Head boundary condition has been assigned to these
cells
Next, assign the Constant Head boundary condition to the lower confined aquifer along the
southern boundary of the model domain.
[Assign / Polyline] from the toolbox. Move the mouse pointer to the south-west corner of the
grid (bottom-left grid cell) and click on this location to anchor the starting point of the line. Now
move the mouse pointer to the south-east corner of the grid (bottom-right grid cell) and RightClick on this location to indicate the end point of the line. You should then see a small menu
appear "Define Attributes".
Click on [Define Attributes]. The "Define Boundary Condition" dialog will appear.
Click [Next >>] to accept the default name.
In the Define Boundary Condition dialog, enter the following values:
Enter Starting Head (m) of 16.5
Enter Ending Head (m) of 16.5
Click [Finish] to complete the boundary condition. The hand-drawn polyline will now turn to a set
of red points, indicating that a Constant Head boundary condition has been assigned to these
cells

River
The following instructions describe how to assign a River boundary condition in the top layer of the

model, along the southern edge of the model.

First, you need to go back to Layer 1 (using the steps explained previously)
Next you need to import a polyline that defines the location of the River.
File/Import from the main menu. The following window will appear:

For the Data Type, select Polyline from the drop-down list.
In the Source File field click the [] button and navigate to your "My Documents" folder, then
Visual MODFLOW Flex\Projects\suppfiles\river.shp" and select [Open]
Click [Next>>]
Click [Next>>] (accept the defaults)
Click [Next>>] (accept the defaults)
Click [Finish]. You should now see a new "river" data object appear in the data tree, in the top
left corner of the window.
Place a check box beside this data object, and it should appear in the layer view at the Define
Boundary Conditions step.
Select River from the list of boundary conditions in the toolbox as shown below.

 [Assign / Polyline] from the toolbox.

Beginning on the south-west side of the grid and using the river polyline as a guide, digitize a line that
traces over the river by clicking along its path with the left mouse button. When you have reached the
south-east boundary, Right-Click the mouse button at the end
point of the line.You should then see a small menu appear "Define Attributes."
Click [Next >>] to accept the default name.
The Define Boundary Condition dialog will appear as shown below.

Traditionally, the River boundary condition has required a value for the Conductance of the

riverbed. However, the Conductance value for each grid cell depends on the length and width of
the river as it passes through each grid cell. Therefore, in a model such as this, with different
sizes of grid cells, the Conductance value will change depending on the size of the grid cell. In
order to accommodate this type of scenario, Visual MODFLOW allows you to enter the actual
physical dimensions of the river at the Start point and End point of the line, and then calculates
the appropriate Conductance value for each grid cell according to the standard formula., enter
the following values:
Under "Select how the attributes are defined", select the [Define Values at vertices (Linear
Interpolation)] option. After doing so, the settings in the top right should appear as shown
below.

In the parameters grid at the bottom, enter the following values (for the start point). (This is
indicated as Point0, under the Points box.)
Stage (m)
Bottom (m)
Leakance

16.0
15.5
(do not enter any
values)
Riverbed Thickness (m) 0.1
River Width (m)
25
Riverbed Conductivity
10
(m/day)

Leakance from the river will be calculated based on the parameters you define. For
more details on the calculation, refer to Boundary Conditions Theory
Now you will define the values for the End Point of the line.
Click on "Point15" under the Points box, as shown below. (note, the Point name may be
different, it will depend on how many vertices you drew on the line. Simply click on the second
item in the list)

Now define the values at this end point, in the parameters grid, based on the values below"
Stage (m)
Bottom (m)
Leakance

15.5
15.0
(do not enter any
values)
Riverbed Thickness (m) 0.1
River Width (m)
25
Riverbed Conductivity
10
(m/day)

Click [Finish] to complete the boundary condition. The hand-drawn polyline will now turn to a set
of blue points, indicating that a River boundary condition has been assigned to these cells

Recharge
In most situations, aquifers are recharged by infiltrating surface water. In order to assign recharge in
Visual MODFLOW, you must be viewing the top layer of the model. Check the Navigator Cube in the
lower left-hand side of the screen to see which layer you are currently in. The first boundary condition
to assign is the recharge flux to the aquifer
[Recharge] from the list of boundary conditions in the toolbox.
[Assign / Entire Layer] from the toolbox. The Define Recharge Boundary Condition dialog will
appear.
Click [Next >>] to accept the default name.
In the Define Boundary Condition dialog, enter 100 for "Rate", as shown below.
Leave the default value of -1 for Conc001; this indicates that no contaminant mass will be
assigned to the recharge flux.

Click [Finish]. All cells in the top layer will be assigned a recharge rate of 100.
Now you will assign a higher recharge value at the Refuelling Area where jet fuel has been spilled on
a daily basis. First you need to import a polygon shapefile that delineates this area.
File/Import...
For the Data Type, select Polygon from the drop-down list.
In the Source File field click the [] button and navigate to your "My Documents" folder, then
Visual MODFLOW Flex\Projects\\suppfiles\refuelling-area.shp, and click [Open]
Click [Next>>]

 Click [Next>>] (accept the defaults)

Click [Next>>] (accept the defaults)
Click [Finish]. You should now see a new data object, "refuelling-area" appear in the data tree,
in the top left corner of the window.
Click on the box beside this data object in the tree
. The data object should now appear in
the Layer View of the grid (it is located in the top middle of the site)
Zoom into this area (using the mouse wheel, or the Zoom in button on the toolbar).
Click [Assign / Polygon] from the toolbox.
Digitize a polygon that traces over the refuelling area. When finished, Right-Click the mouse
button to close the polygon. You should then see a small menu appear "Define Attributes."
[Define Attributes]
The Define Recharge Boundary Condition dialog will appear.
Click [Next >>] to accept the default name.
In the Define Boundary Condition dialog, enter 250 for "Rate" (in units of mm/yr). Notice that
Conc001 has a default of -1 indicating that there is no defined mass flux assigned to this
boundary condition. You will modify this later on in the Transport section of the tutorial.

Click [Finish]. You should now see a new zone of cells colored red, indicating the new
RechargeZone2, with this new value
Click [Database] to see the recharge zones you created, and their corresponding values.

 Click [OK] to close the window

Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed.

Define Pumping Wells

To generate a pumping well boundary condition, you must have a wells data object loaded in the
VMOD Flex project. You will begin by importing a wells data object into this project.
File/Import from the main menu
Select "Well" as the data object type.
[] to choose the Source File
Browse to "My Documents" folder, then Visual MODFLOW Flex\Projects\suppfiles\
Pumping_Wells.xls file.
Open
[Next>>]. The next window will show a preview of the data to be imported.

 [Next>>]. VMOD Flex provides you with various options to import well data. In this window, you
must select to import the well heads, screens, and pumping schedules:
[Well heads with the following data]
[Pumping Schedule] check box

[Next>>]
[Next>>] to accept the default Coordinate System
The following Data Mapping window will then appear:

In this screen, you need to map the fields from the spreadsheet to required fields in the Wells Import
utility. If you prepare your Excel file with the exact filenames that are required by VMOD Flex, then no
mapping is required and this can save you time. For this exercise, the source Excel file has the map
names pre-defined. Take a moment to review the required fields for the Wells import:
Well heads: Well ID, XY Coordinates, Elevation, and Bottom
Screens: Screen Id, Screen top Z, Screen bottom Z
Pump Schedule: Pumping start date, Pumping end date, Pumping rate
When working with your own pumping well data for your models, you can use this
Excel file as a template; by having all the fields automatically mapped this reduces the
effort required during the import process, and minimizes the source of errors.

Switch to the Screens Tab to see the mapped fields

 [Next>>]
The Data Import preview will appear:

[Next>>]
The Pumping_Wells will now appear as a new data object in the Data tree. .
Next, you need to add these wells to the Numerical Model
At the Define Boundary Conditions step in the workflow, under Toolbox, choose "Wells" from

the list of Available Boundary Conditions.

Click on the [Assign] button. A "Pumping Wells Boundary Condition" dialog will appear.
Select (highlight) the "Pumping_Wells" data object from the Data tree (you may need to move
the Pumping Wells Boundary Condition dialog to the right in order to see this).

button located in the middle of the Define Well Boundary Condition, under Select Wells
Data Object". Once completed, you display should appear as shown below.

[Next>>]
[Next>>] (in the preview screen)
[Next>>] to accept the default, which is to include all the wells
[Finish]. The pumping wells have now be added to the numerical model.
In order to see these wells, you need to turn off the Recharge coverage and change to layer 3.
Click on the box beside "Recharge" in the model explorer, to remove the check box
Change to Layer 3 (as explained earlier). You should see the two points representing the wells,
located in the lower right corner of the model domain, as shown in the following figure.

 Now is a good time to save the project. Click File/Save Project from the main menu.
Click
(Next Step) to proceed.
Select "Define Observation Wells"

Define Head Observations

Field observations of groundwater heads and fluxes are essential in order to calibrate the results
obtained by MODFLOW. In this exercise, you will add several head observations wells, and analyze
these against the corresponding calculated values after the model run is complete. First we need to
import the observation wells:
File / Import Data from the main menu bar
Ensure Well is selected as the Data Type
[] to choose the Source File.
Browse to "My Documents" folder, then Visual MODFLOW
Flex\Projects\suppfiles\Head_Observations.xls file.
Open
Next>>

A preview window will appear displaying the source data.

Next>>. VMOD Flex provides you with various options to import well data.
Choose the radio button "Well heads with the following data"
Then select "Observations points"
Then select "Observed heads"
Ensure you have the options selected as shown below.

Next>>
Next>> to accept the default Coordinate System
In this screen, you need to map the fields from the spreadsheet to required fields in the Wells Import
utility.

To save time, you can prepare your Excel file with the exact filenames that are required by VMOD
Flex, and then no mapping is required. For this exercise, the source Excel file has the map names
pre-defined. Take a moment to review the required fields for the Wells import:
Well heads: Well ID, XY Coordinates, Elevation, and Bottom
Observation points: Logger Id, Logger Z, Head observation date, Observed head
[Next>>]
The Data Import preview will appear:
[Finish]
The Heads_Observations will now appear as a new data object in the Data tree. Take a moment and
visualize this in the 3D Viewer.
Next you need to add these raw observation wells as observation points for the numerical model.
Be sure that the "Head_Observations" data object is selected in the Data tree
Click on the
step.

button located under the toolbox in the "Define Observation Wells" workflow

The observation wells will be added to the display and the numerical model tree. You should
see several green points in the model domain that represent the locations where head
measurements were taken. (in this example, all the head observations are in layer 1).

 Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed.

Select Run Type and Engines

From the "Select Run Type" window, choose "Single Run"
From the Compose Engines step, you will see MODFLOW-2005 is selected along with
MT3DMS;
For the first run, we will run the flow solution only, without transport.
De-select the checkbox beside MT3DMS
Click

(Next Step) to proceed.

MODFLOW-2005 Translation Settings

At the Translate step you have the option to adjust the various parameters and flags for the
MODFLOW packages and run time settings. Available options include: Settings (General), Time

Steps (only appropriate for transient simulations), Solvers, Recharge and Evapotranspiration
package, Lake package settings, Layer types, Rewetting options, Initial Heads, Anisotropy, and
Output control
MODFLOW-2005 / Settings
Enter 7300 for steady-state simulation length (in the grid in the main window).

Click
Click

to create the MODFLOW-2005 packages.

(Next Step) to proceed.

Run MODFLOW-2005

Click the
button to run MODFLOW-2005.
The model run should complete in a few seconds. Once finished, you should see " Normal
termination of simulation" in the engine progress window. In addition, you will see Heads and
Drawdown items will be added to the model tree, under "Output"
Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed.

View Maps (Heads and Drawdown)

The following "View Results" window will then appear; you have the option to View Maps or
View Charts. We will start by viewing maps of heads

 Click [View Maps] button to proceed. You will then see color shading of the calculated heads, in
layer view.

 By default, VMOD Flex will display 10 contour lines, with an arbitrary interval. However, if you
do not like the default contour interval or line color, you can customize the contour map
settings. To access the contouring options for Heads, right-click on "Heads" from the model
tree, and select "Settings". The following dialog will appear

From the Settings tree on the left, select "Style" followed by "Contour Lines". This will expand
the settings window and give you access to the Contour Line settings.
Under "Interval options", select "Contour Interval", then enter 0.5 for the contour interval. This
is shown below:

Preview Display Settings before Committing

All of the Settings windows have an [Apply] button in the lower right
corner. This means you can Apply the adjusted changes and see the
impact in the current 2D or 3D, before you close the window. This
makes it easier to obtain the desired display without having to open and
close this window several consecutive times.

You can display heads along a row, and along a column, and in 3D, using the same tools as
you used earlier.

 When you are finished, click [OK].

Take a moment to view the Heads in other layers (by changing layers as described earlier)
You can also view the heads along specified row or column, and in 3D view.

View Charts (Heads)

Click on View Charts from the workflow tree, and the chart window will appear:
In the side toolbar, turn on the check box beside "All Times" and "All Obs".
Click [Apply] and the chart should appear as shown below.

 Take a moment to view the correlation between calculated and observed heads
Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed

In the next section of the tutorial, you will define the inputs for the transport run (properties and
boundary conditions), then run MT3MDS along with MODFLOW-2005, and view and interpret the
results.

Define Transport Model

The following section outlines the steps necessary to complete a simplified transport model.
Similar to a groundwater flow model, a contaminant transport model requires properties (including
initial concentrations), boundary conditions (sinks/sources), and observations in order to calibrate the
transport model run against observed field conditions. These steps are described in the following
sections.

Define Transport Properties

Sorption
In this example, the only reaction that will be simulated is linear equilibrium adsorption of a single
dissolved species (the Jet fuel compound JP-4). However, depending on the complexity of the
problem you are dealing with, your model may have several different zones with different sorptive and
reactive properties (distribution coefficients, decay coefficients and yield coefficients) for each
dissolved species in the model. In Visual MODFLOW Flex, the properties and processes for the
transport model are assigned using the same types of graphical tools as you used for assigning the
flow model properties.
For this tutorial you will not need to modify the Distribution Coefficient value you defined during the
transport model setup, but you may examine the sorption parameter values as follows.
From the workflow tree, click on [Define Properties] to go return back to this step.
Under the toolbox, choose [Species Parameters]
Click on [Database]. The Parameters Database window will appear as shown below.
The default distribution coefficient (Kd = 1.0e-7 L/mg) was specified during the setup of the transport
numeric engine. If this is not so (e.g. if you did not enter this value when creating the project), enter
this now.
The Kd values for each zone can be modified to accommodate heterogeneous soil properties and
reactions throughout the model domain. However, for this example you will keep it simple and use a
uniform Distribution Coefficient for each layer of the model.
[OK] to close the Database window.

Dispersion Coefficients
The next step is to define the dispersion properties for the model.
Visual MODFLOW automatically assigns a set of default values for each of the dispersivity variables.
The following table summarizes these values.
Longitudinal Dispersivity
Horizontal to Longitudinal Ratio
Vertical to Longitudinal Ratio
Molecular Diffusion Coefficient

10
0.1
0.01
0.0

It is possible to assign alternate values for the longitudinal dispersivity by using the [Assign>] option
buttons from the left toolbar.
However, for this example, you will use a uniform dispersion value for the entire model domain.
In order to modify the horizontal or vertical dispersivity ratios and/or the molecular diffusion values
you need to load the Layer Options.
Right-click on "Longitudinal Dispersion" from the model tree, under Input/Properties/Transport
Select "Dispersion Parameters". The following window will appear.

These parameters can be modified on a "per-layer" basis. For this example you will not need to
modify the defaults
Click [Cancel] to close this window
Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed

Define Transport Boundaries (Sinks/Sources)

In this section you will define the location and concentration of the contaminant source. The source of
contamination will be designated at the refueling area as a Recharge Concentration that serves as a
source of contamination to infiltrating precipitation.

Transport Boundary Conditions: VMOD Flex vs. VMOD

Classic
If you are used to working with Visual MODFLOW Classic, you will
notice a difference in how transport boundary conditions are handled in
Visual MODFLOW Flex. In VMOD Classic, transport boundary
conditions were defined separately from the flow boundary conditions
using the types Constant Concentration, Recharge Concentration,
Evapotranspiration Concentration, and Point Source. In Visual
MODFLOW Flex, the sink/source parameters for transport models
(which are time and species concentrations) are defined as part of flow
boundary conditions, which is a more natural representation. This means
you do not define separate cell geometries for transport boundaries, you
simply define species concentrations while defining the flow boundary
conditions, where required. Constant Concentration is an exception to
this rule, since it does not need to coincide with a prescribed flux, you
will still see a "Constant Concentration" boundary condition type,
allowing you to define the geometry (cells) and parameters (time and
species concentrations) for this Boundary Condition type.
When Transport is active in your model run, and you define a new
boundary condition, you will see parameters for Species Concentration
as part of the Boundary Condition attributes (eg. Conc001, Conc002,
etc..). These will have a default value of -1, indicating that no mass sink/
source is defined for this group of boundary condition cells. As soon as
you change this value to 0 or greater, then these cells will be treated as
sinks/sources

Assign Species Concentrations for the Recharge Boundary

When you defined the flow model, you created a separate recharge zone that covers the refuelling
area. Now you will add a defined species concentration to this recharge flux.
Check to ensure that you are viewing Layer 1.
Select "Recharge" from the list of boundary conditions under the toolbox.
You will recall there were two recharge zones created for the flow model: background recharge
of 100 mm/yr covering the entire model top, and a small area over the refueling area with a
higher recharge rate of 250 mm/yr. The mass of contaminants will be assigned only to this
smaller recharge zone.
You must make the Recharge zones visible. In the model tree, locate the "Recharge" node,
under "Inputs / Boundary Conditions", as shown below.
Click on the box beside Recharge in the tree

 The recharge cells should now appear in the Layer View of the grid
[Database] button and the following window will appear.

When the recharge zones were previously created, the values for the chemical species (Conc001)

were left as undefined, indicated by -1. You will modify this for the smaller recharge area.
Locate Zone3 (the second row in the table)
Enter 5000 for Conc001 (thereby replacing the -1 value).
[OK] to close the Database window
Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed

Select "Define Observation Wells"

Define Concentration Observations

The final step before running the transport simulation is to add the three observation wells to the
model to monitor the jet fuel concentrations at selected locations down-gradient of the Refueling
Area. The first observation well (OW1) was installed immediately down-gradient
of the Refuelling Area shortly after the refuelling operation started. The other two observation wells
(OW2 and OW3) were installed two years later when elevated JP-4 concentrations were observed at
the first well (OW1).
You will import the concentration observations from an Excel file.
File / Import Data from the main menu bar
Ensure Well is selected as the Data Type
[] to choose the Source File.
Browse to "My Documents" folder, then Visual MODFLOW
Flex\Projects\suppfiles\Concentration_Observations.xls file.
Open
Next>>

A preview window will appear displaying the source data.

Next>>
VMOD Flex provides you with various options to import well data.
Choose the radio button "Well heads with the following data" radio button
Then select "Observations points"
Then select "Observed concentrations"

Next>>
Next>>to accept the default Coordinate System.

 In this screen, you need to map the fields from the spreadsheet to required fields in the Wells
Import utility. To save time, you can prepare your Excel file with the exact filenames that are
required by VMOD Flex, and then no mapping is required. For this exercise, the source Excel
file has the map names pre-defined. Take a moment to review the required fields for the Wells
import:
Well heads: Well ID, XY Coordinates, Elevation, and Bottom
Logger Id, Logger Z, Head observation date, Observed head

Next>>]
The Data Import preview will appear:

 [Finish]
The Concentration_Observations will now appear as a new data object in the Data tree.
Next you need to add these raw observation wells as observation points for the numerical model.
Be sure that the "Concentration_Observations" data object is selected in the tree

button located under the toolbox in the "Define Observation Wells" workflow step.

The observation wells will be added to the display and the numerical model tree, under Inputs/
Observations/
Locate Concentration Observations, and click on the box beside this data object in the tree
.
You should see several orange points in the model domain that represent the locations where
head measurements were taken.

 Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed.

Select [Single Run], and click

(Next Step) to proceed

At the "Compose Engines" step, be sure to include MT3DMS in the engine run; place a check
box
Click

beside this engine in the list.

(Next Step) to proceed.

MT3DMS Translation Settings

This section will guide you through the selection of the advection method, solver settings, and output
times that you will use to obtain the solution and results for the contaminant transport model.

Solution Method
Expand the "MT3DMS" item under the Translation settings, and select [Solution Method]. A
Solution Method settings will appear, as shown in the following figure.

In the Solution Method dialogue, Advection term frame, you will be using the Upstream Finite
Difference solution method with the Implicit GCG Solver. The Upstream Finite Difference method
provides a stable solution to the contaminant transport model in a relatively short period of time. The
GCG solver uses an implicit approach to solving the finite difference equations, and is usually much
faster than the explicit solution
method.
Click the button in the Advection term frame, and select Upstream Finite Difference (UFD)
To select the GCG Solver, select [Yes], beside "Use Implicit GCG Solver". The Implicit GCG
Solver Settings window will appear in the lower half of the Solution Method settings.
Though the Upstream Finite Difference method and the Implicit GCG Solver are
computationally efficient, the tutorial simulation tracks contaminant transport over a 20 year
period. In order to speed up the modeling process, you will use a nonlinear time step. Type the
following information in the fields at the bottom of the window.
Multiplier: 1.1
Maximum transport step size: 200, as shown below

Output Settings
Next, you will define the output times at which you would like to see the contaminant transport
modeling results.
Expand the "MT3DMS" item under the Translation settings, and select [Output Control]. The
Translation settings will update as shown below.

 Enter 7300 for the simulation time length (measured in days)

Enter 5000 for Max number of transport steps
The remaining defaults can be left as is.

Output Times
Select [Output Times], under the MT3DMS / Output Control tree, and the following display will
appear

For this tutorial you will define specified times at which you would like to see the transport

simulation results.
[Add Row] button; repeat this 6 more times.
Enter the following output times in the grid. If you wish, you can copy directly from this list
below, and paste into the table using the Paste button.
1
730
1460
2190
2920
3650
5475
7300
Now is a good time to save the project. Click File/Save Project from the main menu.
You are now ready to translate the inputs into the MT3DMS packages.

to create the MODFLOW-2005 and MT3DMS packages. (this should take

Click
approximately 10-20 seconds)
Click

(Next Step) to proceed.

Run MODFLOW-2005 and MT3DMS

Click the
button to run MODFLOW-2005 and MT3DMS.
The MODFLOW model run should complete in a few seconds; the MT3DMS run should also
complete in 5-10 seconds.
Once finished, you should see " Normal termination of simulation" in the engine progress
window. In addition, you will see Heads and Drawdown items will be added to the model tree,
under "Output". You should also see "Concentrations" added under the model output tree,
under Output/Transport.
Now is a good time to save the project. Click File/Save Project from the main menu.
Click

(Next Step) to proceed.

[View Maps] option when presented with the desired output format.

View Maps (Concentrations)

By default, the Heads will be shown in the Maps view. In order to see the Concentrations, you
need to turn off Heads from the model tree, and set "Concentrations" to be visible
Locate the Output node on the model tree.
Remove the Checkbox beside Heads
Add a checkbox beside "Concentrations"

 The concentration contours will be plotted for the first transport output time (in this case the first
transport output time is 1 day).
In order to see the concentration results at the other output times, you need to advance the
output time. Click on the "Next Time Step" button located on the toolbar above the Layer view,
as shown below. Alternately, you can expand the list of output times, and navigate directly to
the desired output time.

This display will then update with a plot of plot of concentration contours for selected output
time

 Advanced to the last output time, 7300 days, and the concentrations in the first layer of the
model should look similar to the following figure:

You can determine the risk that the contaminant front poses to the discontinuous aquitard by
doing the following:
Locate the data object "discontinuous-aquitard" from the tree, and turn it on. It should appear in
the layer view. Take a moment to navigate through the other layers, to see the calculated
concentrations.
Move your mouse cursor to specific areas of the interest (such as in the discontinuous aquitard
region), and note in the status bar the calculated concentrations for the selected cell.
After 7300 days (20 years) of simulation time it is clear that the plume has migrated to the
holes in the aquitard.
To see how the plume looks in cross-section, turn on the [Column] view, and enter column 25
Advance the times to see the plume migrating the upper layers down to the lower layers.

View Charts (Concentrations)

In this section you will learn how to compare the observed concentration data to the concentration
values calculated by the model.

 Click
(Next Step) to proceed, or select [View Charts] item from the workflow tree.
From the "Parameter" combo box to the left of the main chart window, choose "Transport"
You will then be presented with the graph for Concentration vs. Time, enabling you to view the
breakthrough curves at each of your concentration observation wells.
All from the Groups box on the left side of the window
[Apply]
You should now be viewing the breakthrough curves for each of the three concentration
observation wells defined earlier in the model (see following figure).

This time-series graph shows the calculated result using a line-and-point data series while the
observation data is displayed only as data point symbols.
Now is a good time to save the project. Click File/Save Project from the main menu.
*****This concludes the tutorial exercise.*****