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Prévia do material em texto

CURSO BÁSICO DE MODELAGEM COM
VISUAL MODFLOW FLEX
Cursos Profissionais WST
Apostila Prática
Maio de 2021
© Waterloo Hydrogeologic Page 1 
 
 
Visual MODFLOW Flex Exercise – Intro 1 
An Introduction to Groundwater Flow and Contaminant Transport 
 
Problem Description 
The site is in an industrial park that has a leaky underground storage tank (UST) holding unleaded 
gasoline (illustrated in the figure below). The site is 200 meters by 150 meters by 30 meters deep, 
with the groundwater flow direction from left to right (west to east). 
 
Exercise Objectives 
• To create a groundwater flow model using Visual MODFLOW Flex and visually examine the 
results of your model using contours of hydraulic head, particle pathlines, and velocity 
vectors 
• Use Visual MODFLOW Flex to build a contaminant transport simulation and view the results 
using contours, color shading, and a concentration breakthrough curve from an observation 
well that you will add to the model. 
• Assign a remediation pumping well to assess the option of a pump and treat remedial 
measure. 
• Examine model results using state-of-the-art 3D graphics technology. Utilizing Visual 
MODFLOW Flex, you will create 3D volumetric shapes that represent contaminant plumes 
changing over time. 
 
 
H
e
a
d
 =
 2
6
.5
 m
 H
e
a
d
 =
 2
9
.5
 m
 
X = 200m, Y = 150m ➔ 
 X = 0m, Y = 0m 
© Waterloo Hydrogeologic Page 2 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Terms and Notations 
For the purposes of this tutorial, the following terms and notations will be used. (This assumes you 
are using a right-handed mouse.) 
type - type in the given word or value 
↔ - press the <Tab> key 
 - press the <Enter> key 
 - click the left mouse button where indicated 
 - double-click the left mouse button where indicated 
Starting Visual MODFLOW Flex 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex 
 Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
 
 
© Waterloo Hydrogeologic Page 3 
Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 1: CREATING A GROUNDWATER FLOW MODEL 
Section 1: Project Settings 
To create a new project: 
 File / New Project… from the top menu bar 
A Create Project dialog box will be displayed prompting you to enter the project name of the new 
Visual MODFLOW Flex project. 
 
 Type: Intro1 as the project name 
 Browse button under Data Repository 
 Select a directory on the hard drive (or use the default location) 
Note: By default, new Visual MODFLOW Flex projects will 
be saved to the following location - 
[C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects] 
The default units are appropriate and do not need to be changed. 
 OK button in the lower right corner of this window 
The following window will then appear: 
© Waterloo Hydrogeologic Page 4 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The Select Modeling Scenario allows you to choose whether to proceed with the Conceptual or 
Numerical modeling workflow. The conceptual modeling workflow allows you to import all data 
objects into Visual MODFLOW Flex and to build a conceptual site model (CSM). The CSM can then be 
used as a starting point for several different numerical models. In other words, numerical model (i.e. 
with different grid types, engines, etc.) can be quickly and easily created based on the same 
conceptual modeling. This makes it easy for the user to manage several different numerical models 
with slight variations. 
Conceptual modeling is not covered in this exercise, so we will proceed with the numerical modeling 
workflow: 
 Numerical Modeling 
Proceeding with the numerical modeling workflow will bring you to the first step in the that 
workflow, which is to define your model objectives. This step allows you to specify whether you will 
be running a fully saturated or variably saturated model, whether contaminant transport will be 
included, which flow/transport engines will be utilized, etc. You will see the following window open: 
© Waterloo Hydrogeologic Page 5 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
We will retain most of the default settings in this step, but we will change the start date: 
 Wednesday, January 1, 2014 (select from dropdown menu) 
We will keep the default flow parameter values. 
 [Next Step] proceed to the next step in the workflow 
The Define Numerical Model workflow step will appear, allowing you to select whether to import 
an existing grid or create a new one. We will create a new grid in this exercise: 
 Create Grid 
This will bring you to the ‘Create Grid’ step in the numerical modeling workflow. At this step you will 
specify the boundary/extents of your model and the structure of your model’s grid. Your screen 
should look like the image below: 
 
© Waterloo Hydrogeologic Page 6 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Section 2: Define Model Grid 
Now you will specify the number of rows, columns, and layers to be used in the model. Under the 
‘Grid Definitions’ frame, enter the following model rows, columns, layers and depth information in 
the appropriate boxes: 
 Rows = 30 
 Columns = 40 
 Xmin = 0 
 Xmax = 200 
 Cell width = calculated this value can be adjusted as per project requirements 
 Ymin = 0 
 Ymax = 150 
 Cell height = calculated this value can be adjusted as per project requirements 
For this exercise, you will ignore the option “Calculate extents from a polygon object”. Next, specify 
the parameters for the vertical grid discretization: 
 Type: 10 For the Number of Layers 
Specify the layer Elevations (typing the values directly into the grid): 
© Waterloo Hydrogeologic Page 7 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Layer1 - Top: 30 (replace 100) 
Layer2 - Top: 27 
Layer3 - Top: 24 
Layer4 - Top: 21 
Layer5 - Top: 18 
Layer6 - Top: 15 
Layer7 - Top: 12 
Layer8 - Top: 9 
Layer9 - Top: 6 
Layer10 - Top: 3 
Layer10 - Bott: 0 
The screen should now look like the image below: 
 
 Create Grid Click the ‘Create Grid’ button at the top-right 
© Waterloo Hydrogeologic Page 8 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 [Next Step] proceed to the next step in the workflow 
Visual MODFLOW Flex will then construct a 40 columns x 30 rows x 10 layers finite difference grid 
with uniform grid spacing in both the X and Y directions, and will automatically create the model run 
Input tree structure. By default, you will be taken to the View Grid step as shown in the following 
image: 
 
The ‘View/Edit Grid’ portion of the workflow allows the user to make any necessary changes to the 
grid structure. This is particularly useful if you are following the conceptual modeling workflow and 
would like to test slight variations in the grid structure. Since we’ve just created this grid and do not 
require any changes we will proceed to the next step in the workflow, ‘Define Properties’. 
Section 3: Define Properties 
 [Next Step] proceed to the next step in the workflow 
Under the ‘Toolbox’ in the main working window, ensure that conductivity has been selected from 
the first dropdown menu. 
© Waterloo Hydrogeologic Page 9 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 Conductivity from the list menu under the Toolbox 
 Edit option under the Toolbox 
The default property values will be displayed in the Conductivity dialogue box. 
 
For this simple model, we will assume all grid cells have the same hydraulic conductivity (values are 
defined in m/s) 
 Type: 2e-05 for Kx under Layer 1, Row 1, Column 1 
 (or F2) to assign this value to the entire column 
 Type: 2e-05 for Ky under Layer 1, Row 1, Column 1 
 (or F2) to assign this value to the entire column 
 Type: 2e-06 for Kz under Layer 1, Row 1, Column 1 
 (or F2) to assign this value to the entire column 
 OK to exit the dialogue window 
Now we will change the storageparameters of the model. 
 Storage from the list menu under the Toolbox 
 Edit option under the Toolbox 
Change the storage parameters as follows; 
 Type: 0.15 for Sy Specific Yield (dimensionless) 
 (or F2) to assign this value to the entire column 
 Type: 0.001 for Ss Specific Storage (1/m) 
 (or F2) to assign this value to the entire column 
 Type: 0.15 for Ep Effective Porosity (dimensionless) 
 (or F2) to assign this value to the entire column 
 Type: 0.20 for Tp Total porosity (dimensionless) 
© Waterloo Hydrogeologic Page 10 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 (or F2) to assign this value to the entire column 
The edit property dialogue box should look like the figure below: 
 
 OK to accept these storage values 
Now is a good time to save the project. 
 File/Save Project from the main menu 
Section 4: Add Basemap 
You will select a shapefile to be used as a background base map for your model. 
 File / Import Data… from the main menu 
A ‘Data Import’ window will open, 
 Select ‘Dxf’ in the ‘Data Type’ list menu 
 […] button next to ‘Source File’, to browse to 
 the data import file 
 Browse to the location where you downloaded the 
 ‘Supporting Files’ folder 
 ‘basemap.dxf’ in your project directory 
 Open to open the data file 
 Next >> to accept default settings 
 Next >> to accept default settings 
 Finish to import the map object 
The new data object will appear as the last item in the data tree. We can view the basemap in a new 
2D Viewer window: 
 Right-click on ‘Basemap’ in the ‘Data Tree’ 
 2D Viewer from the menu 
© Waterloo Hydrogeologic Page 11 
Visual MODFLOW Flex Exercise: Intro1 
 
 
The basemap will become visible in a new view window which appears as a new tab. To change the 
background colour of the 2D viewer: 
 Right-click anywhere within the window 
 Background colour from the pop-up menu 
 Select: Grey 
 OK 
Your display should look like the figure below: 
 
Close the viewer window by selecting the ‘X’ in the tab labelled ‘2DViewer -1’. 
Section 5: Input of Boundary Conditions 
The following section of the exercise describes some of the steps required to assign the various 
model boundary conditions. 
Ensure that you return to the ‘NumericGrid1-Run’ tab and close the 2D viewer tab to continue. 
Assigning Constant Head 
 [Next Step] proceed to the next step in the workflow 
© Waterloo Hydrogeologic Page 12 
Visual MODFLOW Flex Exercise: Intro1 
 
 
To view the model grid in relation to the basemap, check mark the basemap data object from the 
tree. 
  Basemap activate the basemap by clicking from the ‘Data Tree’ 
 Right-click anywhere within the window 
 Background colour from the pop-up menu 
 Select: Grey 
 OK 
To assign a constant head boundary ensure that this boundary condition type is selected from the 
‘Toolbox’: 
 Constant Head under the toolbox 
You will use a constant head boundary to represent the heads along the east and west sides of the 
model. From the toolbox menu: 
 Assign under the toolbox 
 Polyline from the menu that appears 
You will assign a vertical line coinciding with the equipotential of 29.5 m on the left side of the 
domain. 
 Move the mouse-pointer to the upper-left corner of the grid 
 Left-click the center of the cell 
 Move the mouse-pointer to the lower-left corner of the grid (you should 
see a red line being drawn) 
 Right-click the center of the cell. A small menu will appear after 
completion of drawing the line: 
 Click Finish from the menu that appears. 
The Define Boundary Conditions dialog will appear. 
 Next >> we will keep the default name 
Enter the following values: 
 Starting head = 29.5 
 (or F2) to assign this value to the entire column 
 Ending head = 29.5 
 (or F2) to assign this value to the entire column 
Since the model is steady-state (boundary condition values do not change over time), no time values 
are required. The Define Boundary Condition window should look like the figure below: 
© Waterloo Hydrogeologic Page 13 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 Finish to confirm and create this constant head 
 boundary condition 
A set of red points will now fill the selected cells, indicating that a constant head boundary value has 
been applied. 
Now assign a constant head boundary to the right (east) side of the model in a similar fashion. 
 Assign under the toolbox 
 Polyline from the menu that appears 
 Move the mouse-pointer to the upper-right corner of the grid 
 Left-click the center of the cell 
 Move the mouse-pointer to the lower-right corner of the grid (you should 
see a red line being drawn) 
 Right-click the center of the cell. A small menu will appear after 
completion of drawing the line: 
 Click Finish from the menu that appears. 
The Define Boundary Conditions dialog will appear. 
 Next >> 
Enter the following values: 
 Starting head = 26.5 
 (or F2) to assign this value to the entire column 
 Ending head = 26.5 
 (or F2) to assign this value to the entire column 
 Finish to confirm and create this constant head 
 boundary condition 
© Waterloo Hydrogeologic Page 14 
Visual MODFLOW Flex Exercise: Intro1 
 
 
The constant head cells on the right edge were automatically moved down to the second model layer 
(Layer 2). Visual MODFLOW Flex’s "smart" interface recognizes that the assigned head (26.5 m) is 
below the bottom of the first model layer (elevation = 27.0 m), which is not permitted by MODFLOW. 
Visual MODFLOW Flex takes care of this automatically. 
 Type: 2 under Layer to display 
You will see the line of constant head cells on the right side of the model domain. 
Now you will examine the model in cross-section to verify the location of these boundary condition 
cells: 
  Row from the list of available views 
By default, Row 1 will be shown in the cross-section view. You can see that the constant head has 
been assigned to the cells in the second layer (red cell on the right side). To view the model in more 
detail, you can apply a vertical exaggeration factor. The following screen will appear: 
© Waterloo Hydrogeologic Page 15 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
 
Assigning Recharge 
The annual recharge to the water table at the site is approximately 150 mm/year. Recharge must be 
assigned in the Layer view, specifically to Layer1. 
 □ Row from the list of available views (remove the checkbox) 
 Type: 1 under the Layer to display 
Follow the steps below specify the annual recharge in layer 1. Change the Boundary condition type 
to Recharge under the Toolbox 
 Recharge from the list of available boundary conditions 
 Assign button, under the Toolbox 
 Entire Layer from the menu that appears 
The Define Boundary Condition window will appear. 
 Next >> 
 Recharge (mm/yr) = 250 
 (or F2) to assign this value to the entire column 
 Ponding (m) = 0 
© Waterloo Hydrogeologic Page 16 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 (or F2) to assign this value to the entire column 
 Static select this from the menu for ‘Schedule’ 
The Define Boundary Condition window should look like the figure below: 
 
 Finish to confirm and create this recharge 
 boundary condition 
Upon completion, you should see a set of white points in all the cells in layer 1, indicating that the 
cells belong to RechargeZone1; feel free to click on the Database button, to see the list of Recharge 
zones and corresponding values. 
Now is a good time to save the project. 
 File/Save Project from the main menu 
Section 6: Adding Particles 
 [Next Step] proceed to the next step in the workflow 
The next step in the workflow is to select a type of run (single or PEST run), but there are a few 
optional tasks to complete beforeselecting the run type, such as assigning tracking particles, 
ZoneBudget zones or observation wells. You will be presented with a choice screen with several 
options. 
 Define Particles 
First, turn on the basemap in the viewer window 
© Waterloo Hydrogeologic Page 17 
Visual MODFLOW Flex Exercise: Intro1 
 
 
  Basemap from the data tree 
You will place particles in a vertical line down-gradient of the contaminant source in order to examine 
their pathlines later. Particle pathline analysis is a useful tool in rapidly assessing the risk potential 
to down-gradient receptors from a groundwater contamination plume. 
There are several ways of assigning particles. The user can manually select points where particles 
will be placed, place a circle of particles around a single point, or use an imported data object to 
specify the origin of the particles. We will use the imported data object option in this exercise. 
First you must import the particles from XYZ points defined in an excel file. 
 File a dropdown menu will appear 
 Import Data… from the menu 
 Point from the data type dropdown menu 
 […] to browse to the correct file 
A dialogue box opens that allows you to browse for the appropriate file. In the project directory 
choose the following file: 
 Particles.xlsx 
 Open 
 Next >> from the Data Import window 
 Next >> accept the defaults in the Data Import Window 
 Next >> accept the defaults in the Data Import Window 
 Next >> accept the defaults in the Data Import Window 
 Finish 
You should see a new ‘particles’ data object appear in the data tree, in the top left corner of the 
window. 
From the main window, under the “Toolbox” 
 Assign 
 Using Data Object from the pop-up menu 
The following window will appear: 
© Waterloo Hydrogeologic Page 18 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
At this step, you choose the desired points data object and convert these into particles. 
 Particles select the points data object from the data tree 
 under ‘Select Point Object’ 
  Forward select forward as the particle type 
The window should appear as follows: 
 
 OK to accept the default settings and create the particles 
The particles should now appear as points, in the layer view. These are located along column 11 in 
the grid, as shown below: 
© Waterloo Hydrogeologic Page 19 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Now is a good time to save the project. 
 File/Save Project from the main menu 
Section 7: Running MODFLOW and MODPATH 
You are now ready to perform the groundwater flow and particle pathline simulation by running 
MODFLOW 2005 and MODPATH. From the top of the main workflow window, 
 [Next Step] proceed to the next step in the workflow 
You will be presented with an option to Select Run Type 
 Single Run 
You will be prompted to select which engines to run. By default, MODFLOW-2005 should already be 
selected; you also need to include MODPATH in the model run: 
  MODPATH from the list of available engines 
© Waterloo Hydrogeologic Page 20 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 [Next Step] proceed to the next step in the workflow 
The translation settings will appear; this allows you to adjust solvers and their parameters (number 
of iterations, head-change criterion, damping factors), package settings, output control, etc.. In the 
future, you might wish to increase the maximum number of iterations if the model does not 
converge. For now, we will simply use the default settings. 
The model run is setup as a steady-state simulation. You can see this defined as follows: 
 Settings under MODFLOW-2005, in the settings tree 
 Type: 3650 for steady-state simulation time 
The MODFLOW-2005 settings tree should look like the figure below: 
 
Note: The ‘Steady-State Simulation Time’ is not used if you 
have selected Transient Flow. However, a number must 
still be entered. Although the simulation will always be run 
to the same equilibrium solution in Steady State, the total 
amount of water passing through boundary conditions 
depends on the amount of time simulated. For example, 
Zone Budget analysis of a Steady State solution would be 
affected by the simulation time, whereas regional head 
values would not. 
You are now ready to create the input files (packages) for MODFLOW and MODPATH. 
 button located on the workflow toolbar 
Visual MODFLOW Flex will now create the files necessary to run the USGS MODFLOW and MODPATH 
programs. You will see a progress of the Translation, which should take approximately 5-10 seconds. 
Once complete you will see ‘Translation Finished’ at the bottom of the translation log details window. 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
© Waterloo Hydrogeologic Page 21 
Visual MODFLOW Flex Exercise: Intro1 
 
 
The numeric engines will start running and display progress in the main window. MODFLOW-2005 
will run first followed by MODPATH. Each engine will have an information window that displays 
simulation results and progress. Clicking on the tab of the respective window will enable you to view 
detailed results of each run. 
 
The model run should take approx. 10-30 seconds. Once completed, you should see a few new 
objects appear in the model explorer tree, under “Outputs / Flow” 
• Heads 
• Drawdown 
• Fluxes 
• Water Table 
• Forward Pathlines 
Section 8: Output Visualization 
 [Next Step] proceed to the next step in the workflow 
You will be presented with an option to View Results, and select the desired results type 
© Waterloo Hydrogeologic Page 22 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 View Maps 
 
The head equipotential lines for your simulation will be displayed initially by default. 
Take a moment to review the range of calculated head values over layer 1; note that as you mouse 
over the Layer view of the grid, the values in the status bar at the bottom of the window, will display 
the X,Y position of the mouse cursor, along with the layer, row, and column for the cell and the 
calculated head value for that cell. 
Notice the olive-colored cells on the right of the model, which indicate cells that are “dry”. Dry cells 
occur when the calculated hydraulic head is below the bottom of that particular cell (thus 
representing the unsaturated zone). To better visualize and understand what is meant by dry cells, 
we will view the model in cross-section. 
  Row from the list of views 
 Type: 15 under the Row, to display row 15 
 □ Layer to remove from the list of views 
© Waterloo Hydrogeologic Page 23 
Visual MODFLOW Flex Exercise: Intro1 
 
 
Also, we will turn on the calculated water table location for the model. Locate the Model Explorer, 
and the items under “Outputs/Flow” in the lower right corner of the window: 
  Water Table from the model explorer tree, under Outputs/Flow 
The water table will appear as a solid blue line. 
Now decrease the Vertical Exaggeration of the Row view to improve the display: 
 Type: 5 under Exaggeration (located above the 2D View) 
We can now see the equipotential lines from 29.5 m on the left to 26.5 m on the right. Examination 
of column 38 shows that the water table near the down-gradient boundary, is located entirely below 
the bottom of Layer 1, thus causing MODFLOW to treat these cells in Layer 1 as dry. You can see that 
in the adjacent cell, Layer 1, Column 37, the calculated head is 27.1, which is just above the cell 
bottom of 27.0 m (you can see these values in the status bar by placing the mouse cursor in the cell 
to the left of the dry cell, in layer 1.) 
 
Section 9: Viewing Particle Pathlines 
To see the results of the particle tracking pathline simulation, you must set the Pathlines visible in 
the model tree: 
© Waterloo Hydrogeologic Page 24 
Visual MODFLOW Flex Exercise:Intro1 
 
 
  Forward Pathlines from the model explorer tree, under Outputs/Flow 
This will display the pathlines of the forward tracking particles that you specified. You may scroll 
through the various rows of the model domain, by using the up/down arrows under rows. In addition, 
you may turn on the 3D view, to see the color maps of heads and pathlines. 
 
This completes Part 1 of the Intro exercise. 
In Part 2 of this exercise, you will set up and run a contaminant transport simulation using MT3DMS. 
Now is a good time to save the project. 
 File/Save Project from the main menu 
 
© Waterloo Hydrogeologic Page 25 
Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 2: RUNNING A TRANSPORT SIMULATION USING MT3DMS 
In this section, you will simulate the transport and fate of a dissolved-phase groundwater 
contaminant plume. The evolution of the contaminant plume will be simulated for a ten-year period. 
Section 10: Setting Up a Transport Model 
 Define Modeling Objectives from the workflow tree 
In the right side of the window, you can define the settings for the Transport Model run. 
  Transport Active add a check box beside this setting 
Next you will define the sorption and reaction options. Using the settings in this window, you can: 
1. Select the desired sorption and reaction options 
2. Add and remove chemical species 
3. Set the initial concentration of those species 
4. Set transport and reactive parameters used in the transport calculations. In this example 
MT3DMS v.5.3 will be used as the transport engine. 
By default, you will be viewing the ‘Species Parameters’ tab. Under default initial concentration 
(SCONC), you will see this is set as 0 mg/L. This means that the initial concentration in every cell is 
zero. If you wanted to alter this value it could be done at this time. Otherwise you can define spatially 
distributed initial concentrations at the Define Properties step. For this simulation, you will use the 
default value of 0 mg/L. 
Section 11: Creating a Refined Grid 
Before assigning the concentration source, it is important to create a more refined grid in our area 
of interest, where predictions will be made of plume concentration. This will allow us to improve the 
accuracy of the simulated plume and therefore better predict the ultimate fate of the groundwater 
contaminant. 
Fortunately, Visual MODFLOW Flex allows us to create multiple numerical representations for the 
site, and derive the inputs for each numerical model from the conceptual objects that were 
generated while drawing the property zones and boundary conditions in Part 1 of this exercise. 
From the model explorer tree, locate the ‘Simulation Domain’ folder. Under this, find the item Model 
Domain. 
 Right-click on NumericGrid1 from the workflow tree 
 Edit Numerical Grid… from the menu that appears 
 
 
© Waterloo Hydrogeologic Page 26 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 
A Grid Refinement window will appear. Enter the following values, under the ‘Grid Edit Details’ tab: 
 Type: RefineGrid for the New Grid Name 
 Type: 10 for From 
 Type: 20 for To 
 Type: 2 row(s) with 
 Apply grid edit to apply this row refinement 
Once finished, the display should appear as below. 
 
 
 
© Waterloo Hydrogeologic Page 27 
Visual MODFLOW Flex Exercise: Intro1 
 
 
The rows between the 2 selected gridlines will automatically double. Now, we must perform the 
same task to the columns in the model. 
  Edit Columns from the top left of the window 
Enter the following values, under the ‘Settings’: 
 Type: 10 for From 
 Type: 20 for To 
 Type: 2 row(s) with 
 Apply grid edit to apply this row refinement 
The number of columns between these 2 gridlines should automatically double. Once completed, 
your grid should look like the following figure: 
 
 OK to apply the grid edits and close the window 
Please note that a whole new file structure has been generated within the Model Explorer, as shown 
in the image below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The new refined grid will be automatically populated with the property zones and boundary 
conditions as defined in the original model run. You will also notice that a new tab is generated 
within the Visual MODFLOW interface, named ‘RefineGrid-Run1’. This new tab contains the 
workflow associated with the new refined grid. This tab will open automatically and you should be 
redirected to the Define Model Objectives step associated with the new workflow. 
We won’t make any changes to the grid structure, so let’s proceed to the Define Boundary Conditions 
step: 
 Define Boundary Conditions from the Worflow menu 
Now is a good time to save the project. 
 File / Save Project from the main menu 
Section 12: Adding the Contaminant Source Concentration 
You are now ready to represent the contaminant source by assigning a constant concentration to 
the cell where the storage tank is located (in Layer 3). Change the Boundary condition type to 
Constant Concentration under the Toolbox 
 Constant Concentration under the Toolbox 
 Type: 3 under Layer to view layer 3 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
This is the model layer associated with the location of the leaking storage tank. We will need to view 
the basemap in order to assign the contaminant source to the correct location. 
  Basemap under the Data Tree 
You should now zoom into the storage tank area using the tools at the top of the 2D viewer window. 
 to zoom to a box 
Digitize a box around the storage tank so that this becomes more visible. 
 Left-click in the region of row 17, column 8 
 While holding the button: 
 Pan the mouse to row 24, column 15 
 Release the button. 
The viewer window should look like the following: 
 
 Assign button under the Toolbox 
 Polygon from the menu that appears 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Assign the constant concentration boundary condition by digitizing a polygon on top of the circular 
storage tank, using the left mouse button to assign vertices where necessary. Double-click to close 
the polygon and then right-click in the polygon. A small menu will appear after completion of drawing 
the polygon: 
 Finish from the menu that appears 
The Define Boundary Condition dialog will appear: 
 
 Next >> 
 Type: 250 for Conc001, replacing the -1 value 
 (or F2) assigns this value to the entire column 
You will assume that the solubility limit will be maintained for the duration of the simulation. 
 
 Finish 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You should see a few new points appear on top of the circle in the layer view, which indicates that 
those grid cells have a Constant Concentration boundary condition assigned to them. 
Section 13: Adding a Concentration Observation Well 
 [Next Step] proceed to the next step in the workflow 
The Select the Next Step window will appear 
 Define Observation Wells 
In order to see how the plume concentration changes over time down-gradient from the source of 
contamination, you will add a monitoring well. Later, you will use this monitoring well to assess 
plume concentration at this point by displaying a concentration versus time breakthrough graph. 
The well location must be imported from an excel file. 
 File / Import Data… from the main menu 
A Data Import dialog box will appear. 
 Well from the data type drowdown list 
 […] to browse to the correct file 
A dialogue box opens that allows you to browse for the appropriate file. In the project directory 
(C:\VMODFlex\Intro1\), choose the following file: 
 Conc_obs_well.xls 
 Open 
 Next >> from the data import window 
 Next >> in the preview window 
The followingwindow will appear: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
In this window, you define what well data to import. Under the “Select the type of data you want to 
import” 
  Well heads with the following data from the top left of the window 
  Observation points 
  Observed concentrations 
Once done correctly, you should have the following options defined 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 Next >> from the data import window 
 Next >> in the preview window 
 Observation points tab at the top of the data import window 
 Conc Obs. Map to field for Concentration 
 Time Map to field for Concentration observation data 
 
 Next >> in the preview window 
 Finish 
A new data object, conc_obs_well will appear in the model tree 
 conc_obs_well from the Data Tree 
 button under the Toolbox in the main window 
A concentration observation well will appear as a point down-gradient of the source area. However, 
it will be displayed in Layer 3 corresponding to the vertical observation point (e.g. screen elevation). 
 Type: 3 under Layer to change view to layer 3 
  Concentration Observations in the Model Explorer 
Since well OW-1 is an observation well, you have entered a zero concentration. If this well were used 
as a calibration point to calibrate (qualify) the results of a contaminant transport simulation, you 
would enter the actual contaminant concentrations measured at the site, over several periods of 
time. 
Now is a good time to save the project. 
 File / Save Project from the main menu 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Section 14: Assigning Dispersion Properties 
 Define Properties option in the Workflow tree 
 Change the Parameter group to Dispersion under the Toolbox 
 Longitudinal Dispersion from the menu under Toolbox 
 Edit… 
Change the default Dispersion to 2.0. 
 Type: 2.0 in the Dispersion column 
 (or F2) assigns this value to the entire column 
 
 OK 
The ratio of the horizontal and vertical dispersivity to the longitudinal dispersivity has default values 
assigned for this model; default value for Horiz/Long. Dispersivity is 0.1; default value for Vert./Long 
Dispersivity is 0.01. These values are assigned for all layers in the model and do not need to be 
adjusted for this exercise. 
Section 15: Running MT3DMS 
You are now ready to run MT3DMS. Navigate to the Single Run step in the workflow, 
 Single Run option in the Workflow tree 
  Run Transport Engine to include this engine in the model run 
 Select MT3DMS from the transport engine dropdown menu 
 [Next Step] proceed to the next step in the workflow 
 Settings under the MODFLOW-2005, in the Settings Tree 
 Type: 3650 for Steady-state simulation time 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Next setup the MT3DMS option 
 General under MT3DMS, in the Translation settings tree 
The first line contains the Porosity options. By default, the “Effective” porosity option is selected. 
 Total for the Porosity option 
MT3DMS allows you to select the solution method for the advection component of the transport 
equation. Depending on the situation, each solution method presents advantages and 
disadvantages. For this exercise, you will select the Upstream Finite Difference, which based on trial-
and-error has proven to reduce the amount of numerical dispersion in this exercise. 
 Solution Method under MT3DMS, in the Translation settings tree 
 You will see the Solution Method settings on the right side of the window. 
 Yes for the Use Implicit GCG Solver 
Although the flow field is steady-state, you will run a transient transport simulation to see the 
evolution of the plume with time. This requires that you specify the duration of the simulation. 
 Output Control under MT3DMS, in the Translation settings tree 
The MT3DMS Output Settings will appear. Here you can define the total time of the transport 
simulation. 
 Type: 3650 under Simulation time length 
 Type: 10000 under Max Number of Transport Steps 
Next you will define the different times where you want the simulation results to be saved. 
 button to add an additional row to the grid 
 button 7 additional times to add a total of 8 rows 
Enter the following values in the grid, starting at the first (top) row (values expressed here are in 
days): 
 1 
 30 
 60 
 180 
 365 
 730 
 1825 
 3650 
Your screen should look like the image below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
You are now ready to create the input files (packages) for MODFLOW and MT3DMS. 
 button located on the workflow toolbar 
Visual MODFLOW Flex will now create the files necessary to run MT3DMS and MODFLOW-2005. You 
will see a progress of the Translation which should take approximately 5-10 seconds. Once complete, 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
The numeric engines will start running, and display progress in the main window. MODFLOW-2005 
will run first, followed by MT3DMS. This simulation should take a minute or less to complete, 
depending on computer speed. MT3D automatically determines the step size for contaminant 
transport by attempting to minimize numerical dispersion and oscillations as the functions relate to 
flow velocities and grid size of the model. 
In this simulation, the optimal time step determined is less than 30 days. Depending on the 
simulation, the optimal time step may be quite small and result in extremely long run times. 
Extended run times are common when pumping wells develop high flow velocities in the area around 
the well screen. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The engines progress window will once again appear. MODFLOW will run as before, followed by 
MT3DMS. As MT3D runs, the transport step, step size, and total elapsed time are displayed. 
The current period and transport step being analyzed is displayed in the progress window. 
Once the simulation is complete, you should see a line entry “Program completed.” in the progress 
window. In addition, you will see a new item “Concentration (Conc001)” appears on the model tree, 
under Outputs / Transport. 
Section 16: Viewing Concentration Simulation Results 
 [Next Step] proceed to the next step in the workflow 
You will be presented with an option to View Results, and select the desired results type 
 View Maps 
The concentration distribution can be visually analyzed in Visual MODFLOW in a variety of ways. One 
option is to contour and customize the concentration distribution. Contouring simulation results 
allows you to produce a range of contour plots for your site-specific results. 
By default, Heads will be displayed in the View Maps step. You will remove Heads from the view, and 
display Concentrations. 
 □ Heads remove the check box beside Heads in the Model Explorer 
  Concentrations (Conc001) add a check box to Conc001 in the Model Explorer 
Examine your simulation results in cross-section. 
 Type: 3 under Layer to display layer 3 
  Row from the list of views 
 Type: 20 under Row, to display row 20 
 to remove gridlines 
You will now see a Layer (plan) view of the plume and a cross sectional view, or slice, through the 
contaminant plume for the first time step (1 day). Adjust the vertical exaggeration as required 
(ensure you have the Row view selected to enable changes to the vertical exaggeration). Your 
interface should look like the image below: 
Note: if your results display a uniform concentration of 0 
mg/L across the entire model domain it is likely that your 
concentration input values were overwritten. If you notice 
abnormallylow concentrations please revisit your boundary 
condition inputs to ensure that concentrations have been 
applied correctly. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Notice the Observation Well 1 (OW-1) you specified earlier does not appear in the cross- sectional 
view. You can show/hide these objects from the model tree, by adding/removing the check box 
beside the desired data object. The same is true for any raw data you wish to display, such as 
shapefiles, air photos, etc. 
Next, step through the model output time steps to examine the evolution of the contaminant plume. 
Above the Layer and Row views, you will see a toolbar; in the middle, is a combo box, which display 
all the output times you previously defined. 
 to display the Next Time Step 
 
The Layer and Row views should update to reflect the values of concentrations calculated for 30 
days. 
 to display the Last Time Step 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
Note: if the toolbar for selecting output times does not 
appear simply deselect/reselect the Concentration output 
object under the Model Explorer. Refreshing the view in this 
way typically resolves any display issues relating to the 
time-step buttons. 
The Layer and Row views should update to reflect the values calculated for 3650 days (alternatively, 
you can select a specified time from the combo box adjacent to the time advancer buttons, to 
proceed directly to the desired time). 
 
Note that like the display of heads values, you can move the mouse around the Layer or Row view, 
and see the calculated values for each cell in the status bar at the bottom of the window. 
Section 17: Displaying a Concentration versus Time Graph 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
Using OW-1, Visual MODFLOW can produce and display a contaminant concentration versus time 
breakthrough graph. This feature is useful for examining the predicted contaminant concentration 
at any point you specify in the model. To display the graph, follow these steps: 
 View Charts from the Workflow tree 
 Transport from the Parameter menu 
 Time Series from the Chart Type menu 
  All Obs. check box under Chart Type 
 Apply at the bottom of the window 
 
This will display a concentration-versus-time graph. Double clicking on any point or any portion of 
the plotted curve will display a pop-up, which will give you the exact data pertinent to that point 
(clicking again will remove it). 
From this graph, the maximum BTEX concentration after approximately 1460 days of transport is 
about 76 mg/L. 
Now is a good time to save the project. 
 File / Save Project from the main menu 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 3: DEFINING A REMEDIATION CAPTURE WELL 
The remedial option to be evaluated in this exercise is a single-well pump-and-treat system to 
capture the groundwater plume, preventing further contaminant migration and removing the 
groundwater for treatment. Apart from the contaminant plume that you have calculated in Part 2 of 
this exercise you will utilize backward tracking particles to determine the area of influence, or 
capture zone, for this pumping well operating at a specified rate. You will also determine the optimal 
pumping rate for the single well that maximizes the operational effectiveness of the system by 
capturing and removing the entire groundwater contamination plume. 
Design Objectives 
The design process of a pump-and-treat remediation system focuses on the maximization of both 
the operational effectiveness and the efficiency of the remediation system, while simultaneously 
meeting clean-up targets. 
Visual MODFLOW Flex models can be very powerful tools. Remediation engineers commonly use 
these models during the initial feasibility study stage of remedial alternative selection, and later in 
the design process of groundwater remediation systems. The model enables you to develop an initial 
system design to meet operational goals and clean-up targets. The model also enables you to explore 
cause-and-effect scenarios to assess overall remediation system sensitivity to local geologic and 
hydrologic extremes. 
In this exercise, you will use particles and the calculated contamination plume distribution to 
evaluate the effectiveness of the pump-and-treat remediation system. You will design the system to 
hydrodynamically capture and remove all of the contaminant particles in the groundwater with the 
interceptor well, while trying to minimize the amount of clean water removed for treatment. 
Section 18: Assigning the Pumping Well 
 Define Boundary Conditions from the workflow tree 
 Wells from the list menu under Toolbox 
Before you proceed, make sure you are viewing model Layer 1. You can quickly determine your 
present location in the model by viewing the values for Layer, Column and Row under the Views 
section. 
The well must be imported from an excel file. 
 File / Import Data… a Data Import window will open 
 Well from the data type drodown list 
 […] to browse to the correct file 
A dialogue box opens that allows you to browse for the appropriate file. In the project directory 
(C:\VMODFlex\Intro1\), choose the following file: 
 Pumping_wells.xls 
 Open 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 Next >> from the Data Import window 
 Next >> in the preview window 
The following window will appear: 
 
In this window you define what well data to import. Under the “Select the type of data you want to 
import” 
  Well heads with the following data 
  Screens 
  Pumping Schedule 
 Next >> from the Data Import window 
 Next >> 
 Next >> fields are mapped automatically 
 Finish 
A new data object, Pumping_wells will appear in the Model Explorer tree. 
 Pumping_wells select from the Data Tree 
 Assign from the Toolbox in the main window 
 Using Data Object from the dropdown menu for Assign 
A new window ‘Create Well Boundary Condition’ will open. 
 in the upper left corner, under Select 
 Raw Wells Data Object 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 OK 
The well will now appear in the grid view, located at X=94, Y=86 in layers 3 and 4 – the layers where 
the well is screened. If the well is not visible, please ensure you have zoomed out to view the full 
extents of the model. 
 from the toolbar above the Layer view window 
 Type: 3 under Layer to display layer 3 
Your display should appear as shown below: 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
A circle will appear indicating the location of the interceptor well. The well is screened over the 
interceptor trench, with a top at 23.6, and a bottom at 18.25 m. 
The screened interval for PW-1 has been restricted to Layer 3 and Layer 4, which are the numerical 
model layers most likely to be exposed to contamination. This approach will help minimize problems 
associated with drying of cells at the pumping well. Specifically, as MODFLOW 2005 attempts to find 
a solution, it will iteratively assign heads at all cells, including the cells representing the pumping 
well. If the head falls below the bottom of a cell that represents part of a screen for the pumping 
well screened over more than 1 layer, the cell is automatically turned off and the pumping rate is 
decreased proportionately. 
The well is pumping at a rate of -60 m3/day for a duration of 3650 days (10 years) 
Note on convention: The pumping rate must be a negative 
value to establish an extraction well. A positive pumping 
rate would indicate an injection well. 
Now is a good time to save the project. 
 File / Save Project from the main menu 
Section 19: Assigning Particles 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
The forward particles that you assigned previously will be re-assigned to the refined grid and to Layer 
2, 3 and 4 to determine if the water flowing through the contaminated area will be captured by the 
pumping well. Another aspect of well design is to minimize the amount of uncontaminated water 
that is being collected. This can be assessed by assigning backward-tracking particles in a circle 
around the well. These particles will help to delineate the capture zone of that well and we will be 
defining them in the screened Layers 3 and 4. If the capture zone is significantly larger than the 
contaminated zone, the design should be modified e.g. lower pumping rate, more wells, etc. 
First, we need to redefine the particles, in the workflow select: 
 Define Particles from the main Workflow menu 
 Assign from the Toolbox 
 Using Data Object… from the pop-up menu 
At this step, you choose the particles points data object, and convert these into particles. 
 particles points data object, from the Data Tree 
 from the Create New Particles window 
  Forward as the Particle Type 
  Layers 2, 3 and 4 to assign particles to additional layers 
The window should appear as follows: 
 
 OK to accept the default settings, and create the particles 
The particles should now appear as points, in the layer view. These are located along column 13 in 
the grid. 
We will now add a circle of backward tracking particles around the well in layers 3 and 4. Change 
the layer to layer 3 
 Type: 3 under Layer to display layer 3 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You should now be viewing Layer 3. Ensure the pumping well is visible in the model domain. 
 Well1 from the Model Explorer, under Inputs 
 
 Assign from the Toolbox in the main window 
 Circle from the pop-up menu 
 Left-click on the point representing the pumping well 
The following window will appear: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 Radius: 1.8 to change the radius of deployment 
  Layer 4 to deploy particles in layers 3 and 4 
The window should appear as follows: 
 
 OK to create the particles 
A circle of particles should appear around the well location, colored in maroon red. If you wish, you 
can zoom into this region to check the particle location. Once you are done, be sure to zoom back 
out to full extents (click the Zoom Full Extents button from the toolbar). 
 
Now is a good time to save the project. 
© Waterloo Hydrogeologic Page 48 
Visual MODFLOW Flex Exercise: Intro1 
 
 
 File / Save Project from the main menu 
Section 20: Running the Pump-and-Treat Remediation Simulation 
To run a simulation with the new data set, 
 Single Run from the main Workflow menu 
You will be presented with an option to Compose Engines. This dialogue will list the numeric models 
that can be used to simulate groundwater flow, particle tracking, water budgets, contaminant 
transport, and parameter estimation. For this simulation you should select MODFLOW- 2005 and 
MODPATH to be run (as indicated by a  in the box), uncheck MT3DMS. It is generally a good idea 
to run a quick MODFLOW & MODPATH simulation prior to running MT3DMS since this will allow you 
to see if the pumping rate provides suitable capture zone coverage of the plume; in addition, 
MT3DMS simulations can often require much longer run times (typically several hours) as the model 
size, complexity and time length increase. 
 □ Run Transport Engine to deselect MT3DMS 
  MODPATH ensure MODPATH is selected 
 [Next Step] proceed to the next step in the workflow 
The Translate step will appear; there are no changes need for this step, so you are now ready to 
create the input files (packages) for MODFLOW and MODPATH. 
 button located on the workflow toolbar 
Visual MODFLOW Flex will now create the files necessary to run the USGS MODFLOW and MODPATH 
programs. You will see a progress of the Translation, which should take approximately 5-10 seconds. 
Once complete, 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
MODFLOW-2005 will run first, followed by MODPATH. Each engine will have an information window 
that displays simulation results and progress. Clicking on the tab of the respective window will enable 
you to view detailed results of each run. You will notice two tabs for MODPATH, one representing 
the forward tracking particles and one representing backwards tracking particles. 
The run should take 10-20 seconds. Once the simulation is complete, you should see a summary of 
the results from the MODPATH run in the MODPATH tab. 
Section 21: Displaying the Pump and Treat Simulation Results 
 [Next Step] proceed to the next step in the workflow 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You will be presented with an option to View Results, and select the desired results type 
 View Maps button from the main window 
To determine if the interceptor well was effective in capturing the plume, you will need to display 
the pathlines. 
 □ Row to view only in plan/layer view 
  Backward Pathlines from the Model Explorer, under Outputs 
  Well 1 from the Model Explorer, under Wells 
A plot of the head equipotentials and particle pathlines will be displayed as shown in the figure 
below. You will see that a pumping rate of 60 m3/d is sufficient to capture the plume fully (as 
indicated by the fact that no pathlines are going beyond the extraction well). 
 
If you wish, you can also experiment with more than one extraction well. Using multiple wells in an 
interception system is generally advisable because it allows the system to continue functioning if one 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
of the pumps breaks down or when the wells require maintenance. In the next section, you will re-
run the simulation but this time including MT3DMS in the calculations. 
Section 22: Running the Pump-and-Treat Remediation Simulation with MT3DMS 
Now let us run MT3DMS to check if the plume is fully captured also for the contaminant transport. 
To run a simulation with the new data set: 
 Single Run option in the Workflow tree 
You will be presented with an option to Compose Engines and the dialogue box will list the numeric 
models. For this simulation you should select MODFLOW 2005, MODPATH and MT3DMS to be run. 
  Run Transport Engine to select MT3DMS 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
Once complete the translation is completed, 
 [Next Step] proceed to the next step in the workflow 
 button located on the workflow toolbar 
The MT3DMS simulation will be completed once you see a message at the bottom of the run log 
which says ‘***** The run was successful. *****’. 
To visually analyze the modeling results: 
 [Next Step] proceed to the next step in the workflow 
 View Maps button from the main window 
To see if the interceptor well was effective in capturing the contamination plume, you will need to 
display the concentration distribution. 
 □ Heads remove the check box in the Model Explorer Tree 
  Concentration (CONC001) add a check box in the Model Explorer tree 
Examine your simulation results in cross-section. 
  Row from the list of views 
 Type: 17 under Row to display row 17 
A plot of concentration isolines with colors will be displayed. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
Now, step thru the model output time steps to examine the evolution of the contaminant plume. 
You can also add the pumping well to this view by selecting this in the Model Explorer 
Above the Layer and Rowviews, you will see a toolbar which controls the output times. 
 to display the Next Time Step 
The Layer and Row views should update to reflect the values of concentrations calculated for 30 
days. To see the concentration distribution after 10 years or 3650 days: 
 to display the Last Time Step 
Your screen display should look like the figure below. 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The pumping well seems to be capturing the contaminant plume, indicating that the pumping rate is 
sufficient. However, if you wish to optimise the pumping rate, the model provides a useful tool for 
designing the number of wells, well location and total pumping rate. 
The lesson that we can learn from this simulation is that a full simulation of MODFLOW, MODPATH 
and MT3DMS are necessary to understand the impact of remediation well capture of a contaminated 
plume. 
A color map of the results can also be shown in the 3D viewer. 
  3D from the list of views 
 □ Layer from the list of views 
 □ Row from the list of views 
This view will show three slices through the model (along the selected layer, row, and column). 
Ensure the initial particle locations are active and navigate to layer 3. 
  Forward Pathlines add a checkbox in the Model Explorer Tree 
  Backward Pathlines add a checkbox in the Model Explorer Tree 
  Particles add a checkbox in the Model Explorer Tree 
 Type: 3 under Layer to view layer 3 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
Now is a good time to save the project. 
 File / Save Project from the main menu 
 
© Waterloo Hydrogeologic Page 54 
Visual MODFLOW Flex Exercise: Intro1 
 
 
PART 4: 3D VISUALIZATION AND INTERPRETATION 
Viewing modeling results in three dimensions is often the best way to gain insight into the flow and 
transport characteristics of a site. For example, you may wish to create: 
• Arbitrary horizontal slices through a model domain; 
• Vertical cross-sections along or perpendicular to a flowline; 
• Vertical cross-sections through a set of receptors, such as drinking-water wells; 
• Three-dimensional isosurfaces that represent migrating contaminant plumes. 
These types of views allow the hydrogeologist to examine the results in a way that is most relevant 
to the purpose of the analysis. Furthermore, two and three-dimensional animation techniques can 
be useful for illustrating time-dependent processes such as contaminant transport or water table 
drawdown. This section of the exercise will familiarize you with some techniques for assessing your 
transport modeling results in three dimensions using the 3D Explorer. 
Section 23: View 3D Contaminant Plume as an Isosurface 
Next, you will create a 3D volumetric representation of the contaminant plume within the model 
domain by creating an isosurface for a selected concentration value. A value of 10 mg/l will be used 
as it represents the maximum allowed concentration for the local water quality guidelines. The 
isosurface will encapsulate (and draw) any grid cells that have a concentration value greater than or 
equal to 10 mg/l. 
 Window / New 3D Window from the main menu 
A 3D visualization window will open in a new tab. Activate elements of your model by using the check 
boxes in the Model Explorer and Data Tree. 
  Concentration(Conc001) from the Model Explorer, under Outputs 
The 3D grid of the MT3DMS results will appear, with all cells drawn. 
 Right-click on Concentration(Conc001) from the Model Explorer, under 
 Outputs 
 Settings from the menu that appears 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
The Settings dialog will appear. Next you will turn off the Cells view and turn on the desired color 
map and Isolines. 
 + Style from the settings tree on the left 
 Cells from the settings tree on the left 
 □ Show Cells uncheck box from the top of the settings window 
 Isosurfaces from the settings tree on the left 
  Show Isosurfaces check box from top of the settings window 
 Add click this button 
This will produce the Isosurface properties dialogue window, which allows you to specify the 
concentration value and visual attributes for the isosurface. 
 Type: 10 in the Attribute Value field 
  Visible check box to activate the isosurface 
  Show Border check box to activate border 
Once completed, your dialogue window should appear as seen below: 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 OK to close the window 
 Apply tp update the 3D View with new settings 
Your screen should now display an isosurface for BTEX equal to 10 mg/L. (you may need to move the 
settings window to the side to see the main VMOD Flex window in the background) 
 + Time from the settings tree on the left 
 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
You can see that the default output time that is selected is the end of the simulation (3650 days). To 
show the time label on the 3d view, 
  Show Time Label check box to include time label 
 Select time = 3650 days to display output results at final time step 
 Apply to update the 3D View with new settings 
 OK to close the window 
Your display should now appear similar to the figure on the following page, as the contaminant 
plume (isosurface) now displays at 10 mg/L after 3650 days. 
 
You may need to adjust the 3D Viewer zoom and rotation in order to get a better perspective of the 
3D groundwater model. 
 Left-click near the bottom of the 3D Viewer window. While 
 holding down the button drag the mouse toward 
 the top of the screen, then release the button 
 Zoom out using the button on the 3D viewer toolbar, or by 
 scrolling down on your mouse cursor wheel 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
If you wish, you can view the isosurface for other time steps by using the same procedure as outlined 
above. 
Section 24: Viewing Input Data 
The Visual MODFLOW Flex 3D Viewer also allows you to display the model input data in this 3D 
perspective. Select different model objects from the Data tree and the Model Explorer tree to view 
these in 3D. Add checkmarks to the objects you wish to view. You may adjust the exaggeration of 
the viewer at the bottom of the viewer window. 
The settings of the model objects can also be modified individually to user specification. Please spend 
time to familiarize yourself with these options. Your viewer window may appear similar to the one 
below when you are finished. (in this example, the following data objects are set to visible: 
• basemap and Pumping_wells (from the data panel) 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
• Constant Head 1 and Constant Head 2 (from Model Explorer in the model Inputs) 
• Forward Pathlines and Backward Pathlines (from Model Explorer in the model Outputs) 
 
Section 25: Defining Colormap with Isolines 
The Visual MODFLOW Flex 3D Viewer allows you to plot colormaps and contour maps of selected 
model properties on any horizontal, vertical, or cross-sectional surface through the model domain. 
Let’s add a colormap of the calculated head values in the model domain. 
  Heads from the Model Explorer tree, under Outputs 
The 3D grid of the Heads results will appear, with all cells drawn. 
 Right-click on Heads from the Model Explorer tree 
 Settings from the menu that appears 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 
 
 + Style from the settings tree on the left 
 Cells from the settings tree on the left 
 □ Show Cells uncheck box from the top of the settings window 
 Colormap from the settings tree on the left 
  Show Colormapcheck box from top of the settings window 
 Type: 10 as the row number 
 Apply to apply changes and add the colormap 
We will make a few additional changes before closing the settings window. 
 + Isolines from the settings tree on the left 
  Show Isolines check box from the top of the settings window 
 Slice Type to expand this combo box 
 Layer from the list of slice types 
 Type: 3 for the Layer Number 
Next you will adjust the contour interval from the settings at the bottom half of the window 
  Contour Interval select radio button 
 Type: 0.25 for the Contour Interval 
The settings should now appear as shown below. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
 Apply to apply changes and add the contour intervals 
 OK 
The 3D Display should now appear as shown below. 
Note: your display may appear differently, depending on the 
rotation or zoom level you have set). Use the rotate and pan 
options to adjust the view as desired. 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
3D view is zoomed in view with Exaggeration = 5 
You may also export this view to an image file. 
 Right-click in the 3D Viewer window 
 Save As Image from the pop-up menu 
 […] beside the File Name field 
Browse to the project location (default is C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects\Intro1) 
 Type: 3D Image as the File Name 
 Save 
 OK to save the image 
The image will be saved as a bitmap for further use in reports, documentation, etc. 
 
 
***** This concludes the Intro exercise ***** 
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Visual MODFLOW Flex Exercise: Intro1 
 
 
 
References 
Borden, R.C., et al., 1997. Anaerobic Biodegradation of BTEX in Aquifer Material, Environmental 
Research Brief, US Environmental Protection Agency, EPA/600/S-97/003 (copy included in course 
notes) 
Clement, T.P., C.D., Johnson, Y. Sun, G.M. Klecka, C. Bartlett, Natural attenuation of chlorinated 
solvent compounds: Model development and field-scale application, vol.42, p.113-140, Journal 
of Contaminant Hydrology, 2000. 
Clement, T.P., Y. Sun, B.S. Hooker, and J.N. Petersen, 1998. Modeling multi-species reactive 
transport in groundwater aquifers, Groundwater Monitoring & Remediation Journal, vol 18(2), 
spring issue, p. 79-92. 
Johnson, C.D., R.S. Skeen, D.P. Leigh, T.P. Clement, and Y. Sun, 1998. Modeling natural attenuation 
of chlorinated ethenes at a Navy site using the RT3D code, Proceedings of WESTEC 98 conference, 
sponsored by Water Environmental Federation, Orlando, Florida, October 3-7th. 
Guoping & Clement, Prabhakar & Zheng, Chunmiao & Wiedemeier, Todd. (1999). Natural 
Attenuation of BTEX Compounds: Model Development and Field‐Scale Application. Ground 
water. 37. 707-17. 10.1111/j.1745-6584.1999.tb01163.x. 
McDonald, M.G., and A. W. Harbaugh, 1988. A modular three-dimensional finite- difference flow 
model, Techniques in Water Resources Investigations of the U.S. Geological Survey, Book 6., 586 
pp. 
Sun, Y. and T.P. Clement, 1998. A decomposition method for solving coupled multi- species 
reactive transport problems. Transport in Porous Media Journal, 1404, p. 1-20. 
Wiedemeier, T.H., et al., 1995. Technical protocol for implementing intrinsic remediation with 
long-term monitoring for natural attenuation of fuel contamination dissolved in groundwater, 
Volume 1 & 2, Air Force Center for Environmental Excellence, Technology Transfer Division, 
Brooks AFB, San Antonio, Texas. 
Zheng, C., 1990. A modular three-dimensional transport model for simulation of advection, 
dispersion and chemical reactions of contaminants in groundwater systems, 
U.S.E.P.A. Report. 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
Visual MODFLOW Flex Exercise – 3D Capture 
3D Pathline and Capture Zone Analysis 
Exercise Objectives 
• Develop a Visual MODFLOW Flex model using a georeferenced Bitmap (BMP) as a basemap 
• Evaluate effects of vertical anisotropy and recharge on 3D containment volumes and 
capture zones for wells in multi-aquifer systems 
• Perform particle tracking, and evaluate two-dimensional versus three-dimensional capture 
zones 
• Determine effect of all no-flux boundary conditions on steady-state simulations 
Problem Description 
In capture zone and containment volume analysis for groundwater clean-up, the presentation by 
Larson et al. (1987) is one of the first attempts to illustrate the significant differences between 
three-dimensional and two-dimensional model results of capture zones and containment volumes. 
Until that time, and even today, most aquifers were analyzed with two-dimensional models, the 
majority isotropic in nature. 
These authors point out how: 
• Horizontal area of the containment volume at the water table (for a pumping well) is 
determined by the rate of recharge [Area = Pumping rate/Recharge]; and, 
• Shape of the containment volume below the water table is determined by the degree of 
partial penetration, the horizontal to vertical hydraulic conductivity ratio, the rate and 
direction of groundwater flow and any present heterogeneities. 
These generalities are valid provided recharge is the major source of water (surface water sources 
are negligible). For example, homogeneous, anisotropic aquifers show that deeper penetration of 
the pumping well and/or a higher vertical hydraulic conductivity will increase the depth of 
containment and decrease the width. The opposite is true for shallow penetrating wells and low 
vertical hydraulic conductivities. 
Several examples illustrating these concepts are presented including a three-dimensional, 
contaminant capture zone problem for an anisotropic [Kh/Kv], multi-aquifer system with recharge. 
In this example, which models the capture of a contaminant plume, despite a well-placed fully 
penetrating well at the head of the plume, the resulting three-dimensional containment volume 
showed most of the plume was not captured. Although not widely cited in the literature, their 
work is very instructive for the implications it has for contaminant plume capture designs and 
wellhead protection analyses in heterogeneous, anisotropic, three-dimensional aquifers in which 
recharge plays a significant role. 
The dotted line in the upper figure of Figure 1 (below) shows the shape of the contaminated 
containment volume for the middle of the sand layer, predicted by a two-dimensional model that 
did not account for vertical flow. The lower figure in Figure 1 shows a vertical profile of the true 
containment zone, using a three-dimensional model that did account for vertical flow. If this clean-
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
up design had been based on a two-dimensional model, it would fail since most of the "expected" 
containment volume would not be captured. Indeed, in the case of a two-dimensional design, a 
plot of concentration vs. time would show a decrease until zero was reached, at which point one 
might erroneously conclude there is no more contamination and the operation was a success. 
 
Figure 1 - Simulated 3D Containment Volume for Multi-Aquifer System 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
These results were obtained using the USGS's Trescott and Larson (1976) three-dimensional flow 
model together with a simple pathline model. The use of the USGS's MODFLOW and MODPATH 
for the same problem results in very similar, but not equal, results. Let's use Visual MODFLOW Flex 
(and the USGS MODFLOW-2005 and MODPATH programs) to simulate this problem. 
References 
Larson, S.P., C.B. Andrews, M.D. Howland and D.T. Feinstein (1987). Three-Dimensional Modeling 
Analysis of Ground Water Pumping Schemes for Containment of Shallow Ground Water 
Contamination. Proceedings of the Conference on Solving Ground WaterProblems with Models, 
Volumes 1 & 2, Denver, CO. National Ground Water Association, Dublin, OH. pp. 517-530 
US EPA, 2002. Elements for Effective Management of Operating Pump and Treat Systems. EPA 
report 542-R-02-009, OSWER 9355.4-27FS. Can be downloaded at http://clu-
in.org/techpubs.htm 
US Army Corps of Eng., 2000. Operation and Maintenance of Extraction and Injection Wells at 
HTRW Sites. Engineers Pamphlet EP 1110-1-27. Can be downloaded at: 
http://www.usace.army.mil 
US EPA, 2008. A Systematic Approach for Evaluation of Capture Zones at Pump and Treat Systems. 
EPA Report 600/R-08/003, Office of Research and Development, National Risk Management 
Research Laboratory, Ada, OK. 
Terms and Notations 
For the purposes of this tutorial, the following terms and notations will be used. (This assumes you 
are using a right-handed mouse.) 
type - type in the given word or value 
↔ - press the <Tab> key 
 - press the <Enter> key 
 - click the left mouse button where indicated 
 - double-click the left mouse button where indicated 
Starting Visual MODFLOW Flex 
On your Windows desktop, you will see an icon for Visual MODFLOW Flex 
 Visual MODFLOW Flex to start the program. 
The following Visual MODFLOW Flex window will appear: 
http://www.usace.army.mil/
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
PART 1: CREATING A PROJECT AND GENERATING A GRID 
The first step to groundwater modeling with Visual MODFLOW Flex is to create your project and 
generate a grid. 
Section 1.1: Create Project 
To create a new project: 
 File / New Project… from the top menu bar 
A Create Project dialog box will be displayed prompting you to enter the project name of the new 
Visual MODFLOW Flex project. 
 
 Type: 3DCapture as the project name 
 Browse button under Data Repository 
 Select a directory on the hard drive (or use the default location) 
Note: By default, new Visual MODFLOW Flex projects will 
be saved to the following location - 
[C:\Users\<username>\Documents\Visual MODFLOW 
Flex\Projects] 
Ensure that the correct system of units has been specified. Select the following units: 
 Length: ft 
 Time: day 
 Conductivity: ft/d 
 Pumping Rate: GPM 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 Recharge: in/year 
 Specific Storage: 1/ft 
 Mass: kg (irrelevant – no transport simulation) 
 Concentration: mg/L (irrelevant – no transport simulation) 
All other values can remain at their default settings. 
 OK button in the lower right corner of this window. 
The following window will then appear: 
 
The Select Modeling Scenario allows you to choose whether to proceed with the Conceptual or 
Numerical modeling workflow. The conceptual modeling workflow allows you to import all data 
objects into Visual MODFLOW Flex and to build a conceptual site model (CSM). The CSM can then be 
used as a starting point for several different numerical models. In other words, numerical model (i.e. 
with different grid types, engines, etc.) can be quickly and easily created based on the same 
conceptual modeling. This makes it easy for the user to manage several different numerical models 
with slight variations. 
Conceptual modeling is not covered in this exercise, so we will proceed with the numerical modeling 
workflow: 
 Numerical Modeling 
Proceeding with the numerical modeling workflow will bring you to the first step in the that 
workflow, which is to define your model objectives. This step allows you to specify whether you will 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
be running a fully saturated or variably saturated model, whether contaminant transport will be 
included, which flow/transport engines will be utilized, etc. You will see the following window open, 
which displays the Define Modeling Objectives step in the numerical modeling workflow: 
 
The Define Modeling Objectives step allows you to specify what kind of model will be run (i.e. flow 
type, whether contaminant transport will be considered, etc.) and to specify some default project 
settings (i.e. default conductivity, storage values, etc.). 
For this exercise, the Start Date can be left at the default setting (i.e. today’s date). However, if time-
stamped data are to be imported from outside sources, then it is necessary to have the start date 
fall at or prior to the oldest data point. 
We will retain most of the default settings in this step, but we will provide new values for the Default 
Project Property Settings: 
 Type: 8.8 for Kx 
 Type: 8.8 for Ky 
 Type: 0.0628 for Kz 
 Type: 0.001 for Ss 
 Type: 0.27 for Sy 
We will leave the remaining default flow parameter values as they were: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 [Next Step] proceed to the next step in the workflow 
 Yes to dismiss the warning regarding model 
 start date 
Section 1.2: Define Model Grid 
The Define Grid window will appear, allowing you to select whether to import an existing grid or 
create a new one. We will create a new grid in this exercise: 
 Create Grid 
This will bring you to the Create Grid step in the numerical modeling workflow. At this step you will 
specify the boundary/extents of your model and the structure of your model’s grid. Your screen 
should look like the image below: 
 
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Now you will specify the number of rows, columns, and layers to be used in the model. Under the 
Grid Definitions frame, enter the following model rows, columns, layers and depth information in 
the appropriate boxes: 
 Rotation = 275 
 Rows = 21 
 Columns = 30 
 Xmin = 15000 
 Xmax = 21000 
 Cell height = calculated this value can be adjusted as per project requirements 
 Ymin = 45000 
 Ymax = 48000 
 Cell width = calculated this value can be adjusted as per project requirements 
For this exercise, you will ignore the option “Calculate extents from a polygon object”. Next, specify 
the parameters for the vertical grid discretization: 
 Type: 10 For the Number of Layers 
Specify the layer elevations (typing the values directly into the grid): 
Layer Name Elevation 
Layer1 - Top: 280 
Layer2 - Top: 220 
Layer3 - Top: 205 
Layer4 - Top: 190 
Layer5 - Top: 180 
Layer6 - Top: 165 
Layer7 - Top: 150 
Layer8 - Top: 142.5 
Layer9 - Top: 135 
Layer10 - Top: 80 
Layer10 - Bott: 20 
The screen should now look like the image below: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
 Create Grid Click the ‘Create Grid’ button at the top-right 
 [Next Step] proceed to the next step in the workflow 
Visual MODFLOW Flex will then construct a 30 columns x 21 rows x 10 layers finite difference grid 
with uniform grid spacing in both the X and Y directions, and will automatically create the model run 
Input tree structure. By default, you will be taken to the View/Edit Grid step as shown in the 
following image: 
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Visual MODFLOW Flex Exercise: 3D Capture 
 
 
 
The ‘View/Edit Grid’ portion of the workflow allows the user to make any necessary changes to the 
grid structure. This is particularly useful if you are following the conceptual modeling workflow and 
would like to test slight variations in the grid structure. Let’s load a site map to ensure that the model 
extents match-up with our desired model boundary. 
Section 1.3: Add Basemap 
You will select a bitmap file (.BMP) to be used as a background base map for your model. 
 File / Import Data… from the main menu 
 Select ‘Map’ in the ‘Data Type’ list menu 
 […] button next to ‘Source File’, to browse to 
 the data import file 
 Browse to the location where you downloaded

Outros materiais