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Tutorials

for Leapfrog Hydro version 2.6


Copyright 2016 ARANZ Geo Limited
All rights reserved. Unauthorized use, reproduction, or disclosure is prohibited.
Patents pending. No patent liability is assumed with respect to the use of the information contained herein. While
every precaution has been taken in the preparation of this manual, ARANZ Geo assumes no responsibility for errors or
omissions. Neither is any liability assumed for damages resulting from use of the information contained herein.

ARANZ Geo Limited documentation often refers to hardware or software products by their trade names. In most, if
not all, cases these designations are claimed as trademarks or registered trademarks of their respective companies.
The trade names are used here for identification purposes only.

ARANZ Geo Limited


P O Box 3894
Christchurch 8140
New Zealand
Contents
Tutorials for Leapfrog Hydro 2.6 1
Tutorial 1: Introduction to Leapfrog Hydro 2
The Leapfrog Hydro Main Window 3
Displaying GISData 8
How Objects are Organised in the Project Tree 11
Exploring Additional Scenes 14
Tutorial 2: Building a Geological Model for a Depositional System 16
Setting Up the Project 16
Importing a Map 16
Setting the Clipping Boundary 18
Creating the Topography 19
Importing the Borehole Data 21
Analysing the Data 26
Creating a Geological Model 29
Using a Stratigraphic Sequence to Model Depositional Layers 36
Tutorial 3: Building a Geological Model from Contact Points 41
Importing the Contact Points 41
Setting the Geological Model Extents 43
Defining the Lithologies 43
Tutorial 4: Building a Simple Interpolant 47
Creating a New Interpolant 47
Changing the Isosurfaces 48
Changing the Trend 50
Tutorial 5: Building a ModFlow Model 54
Creating a ModFlow Grid 54
Changing Hydrological Properties 56
Tutorial 6: Importing, Creating and Working with FEFLOW Grids 57
Importing and Working with a Full 3D Grid 57
Creating a New FEFLOW Grid from an Existing 3D Grid 60
Importing a 2D FEFLOW Grid 63
Extruding a 2D Grid to Create a 3D Grid 64
Creating and Working with a 2D Grid 65

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Tutorials for Leapfrog Hydro 2.6
These tutorials introduce basic concepts in Leapfrog Hydro, such as setting up a project,
importing and working with data and building simple geological models. Download the tutorial
data at http://help.leapfrog3d.com/Tutorials/Hydro/2.6/en-
GB/LeapfrogHydroTutorialData.zip.
The data for the first tutorial is a Leapfrog Hydro project that includes a series of saved scenes
that are used to introduce different aspects of using Leapfrog Hydro. For subsequent tutorials,
you will import data and use it to build geological models.
The tutorials are:
l Tutorial 1: Introduction to Leapfrog Hydro
l Tutorial 2: Building a Geological Model for a Depositional System
l Tutorial 3: Building a Geological Model from Contact Points
l Tutorial 4: Building a Simple Interpolant
l Tutorial 5: Building a ModFlow Model
l Tutorial 6: Importing, Creating and Working with FEFLOW Grids
Throughout the tutorials, reference is made to topics in the Leapfrog Hydro help, which can be
found at http://help.leapfrog3d.com/Hydro/2.6/en-GB/Default.htm.
When using Leapfrog Hydro, you can find more information on the tools available by clicking
on the Help button that appears in many windows:

Pressing the F1 key also displays help for the current window.

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Tutorial 1: Introduction to Leapfrog Hydro
In this tutorial, we will work through an existing Leapfrog Hydro project. This project includes a
series of saved scenes that demonstrate different aspects of using Leapfrog Hydro.
1. Unzip the folder that contains the tutorial data and copy it to your hard drive.
The project file for this tutorial can be found in the Introduction folder and is called Leapfrog
Hydro Tutorial.
2. Launch Leapfrog Hydro.
The main window will appear with the Projects tab displayed.
The Recent projects list is a useful way of accessing the projects you are regularly working in.
Below the Recent projects list, the Search folder is displayed. This is useful if you have one
folder in which you will keep most of your Leapfrog Hydro projects. Click on the folder button (
) to change the Search folder. When there are Leapfrog Hydro projects in the Search folder,
thumbnails for them will be displayed.
3. In the Projects tab, click Open Project File:

4. Navigate to the folder where you saved the tutorial project files and click on the Leapfrog
Hydro Tutorial.aproj file.
The project will be opened and Leapfrog Hydro will display the Scene View tab.

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The Leapfrog Hydro Main Window | 3

The Leapfrog Hydro Main Window


The Leapfrog Hydro main window is divided into three parts:

The Project Tree contains all the data in the project and tools for working with that data. When you
want to change how this data is used in the project, work with the objects in the project tree.

The Scene View tab displays a 3D representation of selected objects from the project tree.
Changing how you view objects in the scene window does not change those objects in the project
tree.

Tools for changing the appearance of data in the scene window are available in the Shape List and
the Shape Properties Panel. Changing the appearance of these objects does not change those
objects in the project tree.

The series of folders in the project tree are used to organise objects such as maps, images and
data sets into categories. These folders also provide tools that let you import information into
the project and generate models. Right-click on each folder to view the actions you can
perform using that folder.
You can add objects to the scene window by dragging them from the project tree. You can
temporarily hide them in the scene or remove them altogether using the controls in the shape
list.
The current viewing angle and scale are displayed in the lower righthand corner of the scene
window. You can interact with the scene using the mouse or the keyboard:

Action Mouse Keyboard

Changing the Click and drag to rotate the Press the arrow keys to rotate the scene

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Action Mouse Keyboard

viewing angle scene For smaller steps, hold down the Shift key
while pressing the arrow keys

Use the scroll wheel Press the Page Up or Page Down keys
Zooming in and
out of the scene Hold the right mouse For smaller steps, hold down the Shift key
button while moving the while pressing the Page Up or Page Down
mouse keys

Click and hold both mouse


Panning the Hold down the Alt key while pressing the
buttons, then drag
scene arrow keys
Hold the scroll wheel and
drag

Centre an Click the scroll wheel


object in the Click both mouse buttons
scene together

Practise rotating the scene using mouse, arrows and modifier keys. The viewing angle and scale
in the lower righthand corner of the scene window change as you rotate the scene.

Toward the bottom of the project tree, the folder Saved Scenes and Movies contains a series of
scenes we will look at in order to understand how Leapfrog Hydro projects work.

Saved scenes provide a stable point of reference in a project and can explain important
aspects of the project. Saving a scene does not save copies of the objects in the scene, it
simply saves settings relating to how the objects are displayed. Deleting objects from the
project will not preserve those objects in any saved scenes.

The project was last saved with the first scene, 1. Maps and topography, displayed. If you have
changed the scene, you will need to redisplay the opening scene.

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1. Right-click on the 1. Maps and topography scene in the Saved Scenes and Movies folder
and select Display:

The scene will be updated to show a Topography object and two images:

All objects in the shape list have a button ( ) that will remove the object from the scene. Most
objects also have a visibility button ( ) that can temporarily hide that object in the scene. It is
often easier to make an object temporarily invisible than to remove it from the list. Some objects
have an edit button ( ) that you can click to begin editing the object.
The shape list also contains options for changing the appearances of the object in the scene.
For the images, you can only change the opacity by adjusting the slider. For the topography, the
GIS data dropdown list provides additional display options.
2. Click on the GIS data dropdown and select None:

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The scene will be updated so that the Topography object is displayed using the Flat colour
option. In the case of surfaces, different colours will be assigned to each side. The Topography
has an Above colour (yellow) and a Below colour (grey):

The colour used to display an object can be changed by clicking the colour chip. In the window
that appears, you can set a new colour or select from predefined colours:

Many objects can also be displayed using other available data. For example, the Topography
includes elevation data.
3. Click on Flat colour to view other display options:

Changing how you view objects in the scene window does not change those objects in the
project tree.

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4. Click on the ( ) button for each of the images in the shape list:

Removing objects from the scene by clicking the ( ) button does not remove them from the
project.

Only the topography remains in the scene.


The Z-Scale button in the lower righthand corner of the main window lets you set a value
greater than 1.0 for the z-axis relative to the x- and y-axes. This is useful when the area under
study is very planar and extends over a wide area. In such cases, scaling the Z-axis can
accentuate the distribution of data along the z-axis.

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5. Click the Z-Scale button and experiment with different z-scale settings to see the effects:

6. Return the Z-Scale setting to 2.0.

Displaying GISData
The GIS data dropdown list includes a number of GISdata objects and images that have been
imported into the project. There are three ways to view imported GIS data and images:
l Display the objects independently of the topography. To view data in this way, either drag
and drop the object into the scene or right-click on the object and select View Object.
l Display objects draped on the topography.
l Display objects as part of a custom topography view.
To display GIS data with the topography:
1. From the shape list, select the GIS data dropdown list and select GISobjects, then the lake_
bdy line.

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Displaying GISData | 9

The topography will be displayed with the GISline draped on it using the Flat colour option:

The lake_bdy object can also be displayed using the columns available in the data table, which
can be selected from the view list:

The GISdata list also contains options for creating and displaying custom topography views:

2. Click on the GIS data dropdown list and select Views, then the Topography + GISdata
option.

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The Topography will be displayed with map images and a number of GISdata objects draped
on it:

3. Click on the GIS data dropdown list and select Views, then the Edit views option.
4. In the window that appears, experiment with adding and removing layers and changing how
they are displayed:

The scene will be updated as you make changes in the Edit GIS Views window.
5. When you have finished, click Revert All to discard your changes, then click Close.

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How Objects are Organised in the Project Tree | 11

How Objects are Organised in the Project Tree


The way folders and objects are organised in the project tree lets you reveal or hide information
about an object to focus on objects you are currently working with. This is also useful when you
are exploring a project and want to determine how something was put together. Leapfrog
Hydro projects can be complex and the number of objects in the project tree can seem
overwhelming. The arrows next to objects in the project tree let you reveal or hide an objects
details to focus on objects you are currently working with. Lets look at three objects in this
project to see how this works, the Topography object, a geological model and a static model.
In Leapfrog Hydro, the topography is used to define the elevation of the grounds surface. The
topography can be defined using a single digital terrain model (DTM), but often data from
several sources is combined to ensure the data is consistent.

The topography is used as the upper boundary for geological models and to position
GISdata. As a result, changing the topography will cause geological models to be
recomputed and GIS data to be repositioned. This can be time-consuming, which is why it is
best to define the topography before GIS data is added to the project and before any models
are created.

To determine how the topography was created, we need to find the topography in the project
tree.
1. Right-click on the Topography object in the shape list and select Go to Project Tree:

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The Topography object ( ) in the Topographies folder is selected:

Objects displayed in bold in the project tree are those objects visible in the scene.
2. To see how the Topography was created, click on the arrow to expand it.
The Topography was created from an imported DTM:

The object is hyperlinked because it is stored elsewhere in the project tree.


3. Click on the hyperlink to view the source object:

The imported DTM is stored in the Meshes folder.


Now lets look at the components of a geological model.
4. Click on the Clear scene button ( ).
The Geological Models folder contains a model called GM.
5. Drag the GM model into the scene.
6. In the project tree, click the arrow for the model to expand it.

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7. Click the arrows for the models Boundary, Lithologies, Surface Chronology and Output
Volumes objects.

The four objects underneath the geological model GM represent the four basic parts of a
geological model:
l The Boundary object defines the outer limits of the geological model. It is made up of a basic
GM Extents object, the Topography and a North_boundary object.
l The Lithologies object defines the lithologies in the model. Because the model was made
from borehole data, this object is hyperlinked to the imported borehole data.
l The Surface Chronology object defines the structure of the models contact surfaces. The
contact surfaces are used to divide the model Boundary into the Output Volumes.
l The Output Volumes folder contains the generated units (outputs) that make up the
geological model. The model has been displayed in the scene and so the volumes are shown
in the project tree in bold.
8. Expand the objects under the Boundary object to see the data used to make the extents:

The Topography object is included as the models upper boundary. The North_boundary
object was created using a GIS data object in the GIS Data, Maps and Photos folder. Clicking
on the hyperlinks will locate the object from which the extent was created.
Also in the Geological Models folder is another object, called Static GM.

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9. Expand the Static GM model in the project tree:

The Static GM model is made up of the same objects as the GM model, but most of these
objects cannot be edited. You can change the colours used to display the output volumes by
clicking on the Legend object.
10. Right-click on the Static GM model and select Properties.
In the window that appears, we can see the date the static model was created and information
about its volumes:

The Properties window is a useful way of finding out more information about objects in the
project. The information available in the Properties window depends on the type of object and
is available for most types of objects.
The Static GM model is a static copy of the GM model. Models in Leapfrog Hydro will be
updated when changes are made to the data objects used to create them. A static copy,
however, is a snapshot of a model that does not change, even when changes are made to the
data on which the original model was dependent. A static copy is a useful way of storing
historical models and comparing models.

Exploring Additional Scenes


There are other saved scenes in the project that demonstrate different aspects of using
Leapfrog Hydro, including:
l Displaying borehole data
l Defining a models boundary
l Using the slicer to slice objects in the scene
l Using the moving plane to measure trends
l Using the ruler to measure distances
l Creating and evaluating cross sections
Explore these saved scenes to see how different objects are managed in Leapfrog Hydro. You
can display each saved scene by dragging it into the scene window. You can find out more

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about each scene by viewing the comments. To do this, right-click on the saved scene in the
project tree. Any comments on the scene will be displayed along with the right-click menu:

In the next tutorial, we will import borehole data and use it to build a geological model.

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Tutorial 2: Building a Geological Model for a
Depositional System
In this tutorial, we will use borehole data to build two geological models of a series of deposits.
l For the first model, we will build deposit contact surfaces one-by-one.
l For the second model, we will build the deposit contact surfaces using a stratigraphic
sequence.
This tutorial also includes an introduction to setting up project files, importing topographical
and borehole data and setting up a topography.

Setting Up the Project


Data for this tutorial can be found in the Depositional Model folder.
To start:
1. Launch Leapfrog Hydro.
The main window will appear with the Projects tab displayed:

2. In the Projects tab, click New Project.


The Create Project window will appear:

3. Enter the name Deposit GM tutorial for the new project and click Browse to select a folder
where the project will be saved.
4. Click OK to create the project.
The project will be created and Leapfrog Hydro will display the Scene View tab for that project.

Importing a Map
When first created, a project has only a basic set of X-Y-Z coordinates, and the coordinate
system used by the project is determined by the data imported to the project. It is not necessary
to specify what coordinate system is used; however, it is necessary to ensure that data you

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Importing a Map | 17

import into the project uses the same coordinate system. Often, the best way to set the
coordinates for the project as a whole is to import a map or aerial photo. Adding georeference
data to a map will set the location of the map in three-dimensional space and set the
coordinates for the project. For this project, we will import a georeferenced map.
1. Right-click on the GIS Data, Maps and Photos folder and select the Import Map option:

The map for this part of the tutorial can be found in the Depositional Model folder.
2. In the window that appears, navigate to the Depositional Model folder, select the file called
Area map.tif, then click Open.
The Import Map tab then displays the image:

In this window, you can enter georeferencing information for an image, if it is not included in
the image. In this case, the image includes georeference data and nothing needs to be
changed.
3. Click Import to import the map.
The imported map will be saved in the project tree in the GIS Data, Maps and Photos folder.

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4. Display the map by clicking on it and dragging it into the scene:

The map appears in both the shape list and the shape properties panel. There are three shape
list controls for the image:
l Click the visibility button ( ) to show or hide the photo.
l Click the ( ) to remove the image from the scene. This does not remove the image from the
project, as displaying objects and removing them from the scene do not change the data.
l Adjust the photos opacity using the slider.
These controls appear for most objects when they are in the shape list. The visibility button ( )
and the opacity slider are useful when analysing relationships between objects in the scene.

Setting the Clipping Boundary


The clipping boundary is the part of the project space in which processing is carried out. When a
project is created, Leapfrog Hydro automatically sets the clipping boundary. As data is added to
the project, the clipping boundary expands to fit that data. For models with large data sets,
setting the clipping boundary to a fixed size will reduce the amount of time Leapfrog Hydro
required for performing calculations.
For this project, we will set the clipping boundary to the area indicated by the imported map.
1. Press the D key to view the map from above.
2. Right-click on the Topographies folder and select Set Clipping Boundary.

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Creating the Topography | 19

The Set Clipping Boundary window will be displayed, together with controls in the scene that
will help you to set the clipping boundary:

3. Use the handles in the scene to adjust the clipping boundary so it is slightly smaller than the
map.
4. Click OK.
Data subsequently imported into the project will be clipped to the clipping boundary.

Creating the Topography


In Leapfrog Hydro, the topography is used to define the elevation of the grounds surface. The
topography can be defined using a single digital terrain model (DTM), but often data from
several sources is combined to ensure the data is consistent.

The topography is used as the upper boundary for geological models and to position
GISdata. As a result, changing the topography will cause geological models to be
reprocessed and GIS data to be repositioned. This can be time-consuming, which is why it is
best to define the topography before GIS data is added to the project and before any models
are created.

For this tutorial, a single DTM file will be used to define a topography. It is called Tekapo
DTM.asc.
To define the topography from the DTM:
1. Right-click on the Topographies folder and select New Topography > Import Elevation
Grid.
2. Navigate to the folder that contains the Tekapo DTM.asc file and open the file.

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The Import Elevation Grid window will be displayed:

3. Click Import.
The New Topography window will appear:

4. Click OK to accept the default name and create the topography.


5. Click on the Clear scene button ( ) to clear any objects from the scene window.
6. Drag the newly-created topography into the scene.
The topography is displayed in three dimensions:

The topography appears in both the shape list and the shape properties panel and has more
display options than the imported image.

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Importing the Borehole Data | 21

7. Click on the GIS data dropdown list, then on Maps and Photos, then select the imported
map:

The photo will now appear draped over the topography:

Importing the Borehole Data


In Leapfrog Hydro, borehole data is managed using the Borehole Data folder in the project
tree.
Leapfrog Hydro expects borehole data that is stored in a collar table, a survey table and interval
tables. Each project can have only one collar file and one survey file, but multiple interval tables
can be imported. A screens table can also be imported, if available.
For this tutorial, there are four data files, which can be found in the Depositional Model >
Boreholes folder:
l Collar.csv contains the collar definitions.
l Lithology.csv contains the interval definitions that describes the lithology. Information in this
file will be used to build a simple geological model.
l Contaminant.csv contains an interval table that describes contaminant levels for each
borehole.
l Screen.csv contains the locations of the screen(s) for each borehole.
To start importing borehole data:
1. Right-click on the Borehole Data folder and select Import Boreholes.

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The Import Borehole Data window will be displayed:

2. For the Collar, click on the Browse button to locate the tutorial file collar.csv.
3. Click on the file, then click Open.

When a collar file is added to the Import Borehole Data window, Leapfrog Hydro will look
for interval tables with names such as lithology or geology in the same location and will
add them to the Interval Tables list. If an interval table file is not automatically added to the
list, click Add and browse for the required file.

In this case, adding the Collar.csv file has resulted in only the Lithology.csv file being added to
the Interval Table list:

4. Add the second interval table to the list by clicking on the Add button and navigating to the
Contaminant.csv file.
5. Click on the file, then click Open to return to the Import Borehole Data window, where the
contaminants file has now been added to the Interval Tables list:

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Importing the Borehole Data | 23

6. Click on Import to start the process of importing data.


First, the collar file is processed. Leapfrog Hydro displays the data in the file and summarises
how each column will be imported:

Leapfrog Hydro expects four columns for the collar data and attempts to match imported
data to these expected formats. For the collar file, Leapfrog Hydro expects a borehole
identifier (Hole ID) and the location of the top of the borehole, in X, Y and Z coordinates. The
Hole ID is used to associate data in different tables with a single borehole. Inconsistencies in
the way boreholes are identified is a common source of errors.

7. Leapfrog Hydro has correctly mapped the data in the collar file to the expected format. Click
Next to proceed to the next file.
The interval table is displayed. The lithology column has been correctly mapped as lithology
data:

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8. Click Next to proceed to the next file.


The contaminant table is displayed. Leapfrog Hydro has not marked the Contaminant or Mean
columns for import, so we need to select those manually.
9. In the File Data part of the window, click on the dropdown list for the Contaminant column
and select Numeric:

10. Click on the dropdown list for the Mean column and select Numeric.
The Column Summary is updated to indicate that the Contaminant and Mean columns will be
imported as numeric data:

11. Click Next to proceed to the next file.


The Screen table is displayed, and the Value column has not been selected for import.
12. Click on Import All Columns.
The Column Summary now shows that the Value column will be imported as Numeric data.

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Importing the Borehole Data | 25

13. Click on Finish to import the data.


The data tables will be added to the project tree as part of a new Boreholes object:

Leapfrog Hydro automatically identifies and flags common borehole data errors when
borehole data tables are imported. There are three ways Leapfrog Hydro marks tables that
contain conflicts or errors:
l Tables containing errors are marked with a red X ( ). These errors must be fixed before the
affected boreholes can be used for processing.
l Numeric data columns with non-numeric values are marked with a red X ( ), which means
that the rules that are used to handle non-numeric and negative values need to be reviewed.
If a borehole has intervals that contain non-numeric and negative values, the borehole
cannot be used for further processing until the rules are verified.
l Tables containing warnings are marked with a yellow exclamation mark ( ). Affected
boreholes can be used for further processing, but the information in the warning can
indicate that the data requires further attention. For example, if a warning indicates there is
data missing for a borehole defined in the collar table, it may be that a borehole has been
duplicated or that not all required data files have been loaded. Warnings are listed along
with table errors in the Database Errors window.
Until errors are corrected, the rows that contain those errors are excluded for all processing that
uses the table, including viewing in the scene. For example, if the ID for a collar position
contains an invalid coordinate, that collar will not be displayed in the scene as its location is not
known. Likewise, any processing will ignore data associated with this borehole.
It is worth correcting errors as soon as possible, as correcting them later can result in significant
recomputation time.
The Contaminant and screen tables are still marked as having errors because they have numeric
data columns with missing intervals and/or non-positive values. We need to decide how those
values will be handled.
14. Expand the Contaminant table.
The numeric data columns are each marked with a red X ( ).
15. Double-click on the Contaminant column.

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The Errors tab will open with the invalid handling errors highlighted:

Default rules for handling missing intervals and non-positive values have been applied to those
found in the Contaminant column. You can change these rules, if required. For now, we will
accept the defaults.
16. Tick the These rules have been reviewed box and click the Save button ( ).
The Contaminant table no longer has a red X, but is now marked with a warning ( ), which we
will not correct.
17. Click on the Mean column to review its rules.
18. Expand the Screen table and review the rules for the Value column.
19. Close the table.

Analysing the Data


Once Leapfrog Hydro has imported the data, we can view it and analyse it to make decisions on
how to build the geological model.
1. Click on the Clear scene button ( ) to clear any objects from the scene window.

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Analysing the Data | 27

2. Display the data by dragging the Boreholes object in to the scene:

3. Zoom in to get a better view of the data.


The data tables are displayed and an entry for each appears in the shape list:

Changing how the boreholes are displayed can help in analysing the data and making
modelling decisions.

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Boreholes can be displayed as lines or as cylinders, which is controlled using the Make lines
solid button ( ) button.
4. Click the Make lines solid button ( ) for the Lithology table to display the boreholes as
cylinders:

The width of the cylinders can be changed in the shape properties panel:

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Creating a Geological Model | 29

5. Click the Show legend button ( ) for the table:

6. In the shape list, click the ( ) buttons for the collar, Screen and Contaminant tables to
remove them from the scene.
We can see that the lithology layers, from oldest to youngest, are:
l Basement Granite Aquifer Miocene Alluvium
l Aquifer Miocene Alluvium Lower Gravel
l Lower Gravel Glacial Till
l Glacial Till Gravel
l Gravel Alluvium
l Alluvium Coarse Sand
The Coarse Sand lithology is interbedded with the Alluvium lithology, which requires that we
build an additional contact surface from the contacts below the Alluvium layer.

Creating a Geological Model


For the first geological model we will create, we will build the deposit contact surfaces one-by-
one.
To create the first geological model:
1. Right-click on the Geological Models folder and select New Geological Model.
2. In the window that appears, change the following settings:
l Set the Surface resolution to 100.
l From the Enclose Object dropdown, select the lithology table.

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All settings can be changed after the model is created, except for the Base lithology
column. For the Surface resolution, Leapfrog Hydro sets a value based on the data
available, but you can set a higher (coarser) value when you first create the model in order to
reduce processing time. Lower resolution values provide more detail, but surfaces will take
longer to process.

3. Click OK to create the geological model.


The new geological model will be created in the Geological Models folder:

l The Boundary object defines the limits of the geological model. When the model is first
created, this is the rectangular model extents. If a topography has been defined, it is
automatically used for as the upper boundary.
l The Lithologies object describes all the lithological units to be modelled in the geological
model and the colours that are used to display them on the screen. It is generated
automatically from all the lithologies identified in borehole data selected when the model is
created. If no column was selected, you will need to define the lithologies manually before
you start modelling the lithology layers.
l The Surface Chronology object describes the contact surfaces in the model, organised in
chronological order, from youngest to oldest. These surfaces and their chronology
determine how the volume inside the model extents is divided into lithological units. When
the model is first created, the Surface Chronology is empty, but it will eventually hold all
contact surfaces and inputs to them.
l The Output Volumes folder contains all the volumes generated in building the geological
model in chronological order, from youngest to oldest. When the model is first created, the
Surface Chronology is empty and so there is only a single output volume that fills the
models extents, called Unknown.

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4. Double-click on the Lithologies object.


The Geological Model window opens with the Lithologies tab displayed. The lithologies for the
new geological model include those from the borehole data and the lithology Unknown:

5. Click Cancel to dismiss the Geological Model window.


6. Clear the scene.
7. Display the geological model by dragging it into the scene or by right-clicking on it and
selecting View Output Volumes.

At this point, the model is a single volume of lithology Unknown. In order to divide this
Unknown volume into volumes that represent known lithologies, we need to define the
models internal structure. This involves:
l Generating contact surfaces that correspond to the boundaries between lithological units
l Refining the contact surfaces
l Arranging them in chronological order
l Using the surfaces and the chronological order to divide the geological model into units.
There are different types of contact surfaces that interact with other surfaces and volumes in
different ways:
l Deposit contact surfaces do not cut older volumes. A volume defined by a deposit contact
surface will, therefore, appear conformably on top of older volumes.

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l Erosion contact surfaces cut other contact surfaces on the older side of the erosion contact
surface.
l Intrusion contact surfaces remove existing lithologies and replace them with the intrusive
lithology on the younger side of the contact surface. Often, the older side of an intrusion
contact surface is labelled Unknown as typically intrusions displace multiple older
lithologies.
It is not always necessary to model geological formations according to their corresponding
contact surface type. For example, it might make sense to model basement granite as a deposit
rather than as an intrusion when it forms the lowest layer in a geological model: if there are no
older layers for an intrusion-type contact surface to remove and it is apparent from the
borehole data that the lithology simply fills the lowermost parts of the model, then it makes
sense to model it as a deposit.
For the geological model in this tutorial, we can model each lithology as a deposit.
As discussed in Analysing the Data, the lithology layers, from oldest to youngest, are:
l Basement Granite Aquifer Miocene Alluvium
l Aquifer Miocene Alluvium Lower Gravel
l Lower Gravel Glacial Till
l Glacial Till Gravel
l Gravel Alluvium
l Alluvium Coarse Sand
We will build a contact surface from Basement Granite contacts first.
8. Click on the Clear scene button ( ) to clear any objects from the scene window.
9. Right-click on the Surface Chronology object and select New Deposit > From Base
Lithology.

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The New Contact Points window will be displayed:

10. Select Basement Granite from the Select primary lithology:

A name for the new contact surface is automatically assigned from the lithologies used to
create the surface.
11. Click OK.

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12. When Leapfrog Hydro has finished generating the contact surface, double-click on the
Surface Chronology object.
The Geological Model window will be opened with the Chronology tab displayed:

13. Tick the box to add the new contact surface to the chronology.
14. Click OK.
This results in Leapfrog Hydro generating the first volumes, which are added to the Output
Volumes folder.
At this point, the geological model is not yet visible in the scene.
15. Add the geological model to the scene to see the new volumes:

16. Repeat steps 9 to 14 to generate the following contact surfaces, working from oldest to
youngest:
l Aquifer Miocene Alluvium Lower Gravel
l Lower Gravel Glacial Till
l Glacial Till Gravel
l Gravel Alluvium
l Alluvium Coarse Sand

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Creating a Geological Model | 35

After creating each contact surface, add it to the Surface Chronology, then drag the model
into the scene to check the order of the processed volumes. Leapfrog Hydro will usually orient a
surface correctly, but if this is not the case, you can correct the orientation by right-clicking on
the surface and selecting Swap Young Side.
The model should appear similar to this:

This does not include the Coarse Sand lithology, which is interbedded with the Alluvium
lithology. We need to build an additional contact surface from the contacts below the Alluvium
layer. To do this:
17. Right-click on the Surface Chronology object and select New Deposit > From Base
Lithology.
18. In the New Contact Points window, select Alluvium from the Select primary lithology
list.
19. Click the Use contacts below button.
20. Drag Gravel into the Ignored lithologies list:

21. Click OK.

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22. Double-click on the Surface Chronology.


23. Enable the new layer and click OK.
Once all volumes have been generated and displayed and you have added them to the Surface
Chronology, the model should appear similar to the one below:

Using a Stratigraphic Sequence to Model


Depositional Layers
In Creating a Geological Model, we modelled each layer in the geological model individually,
then assembled the layers using the surface chronology. When you have a series of continuous
layers of fairly uniform thickness, you can model these layers as a single stratigraphic sequence.
For this part of the tutorial, we will use a stratigraphy to define the layers in the geological model
created in the previous parts. We will then use the tools available in Leapfrog Hydro to
determine which layers to include in the stratigraphy and which layers to model separately.
To start, we will look at the imported borehole data to see what layers to include in the
stratigraphic sequence.
1. Click on the Clear scene button to clear any objects from the scene window.
2. Add the lithology borehole data table to the window to view the lithologies.
3. Click the Show legend button ( ) for the table.

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Using a Stratigraphic Sequence to Model Depositional Layers | 37

The Alluvium and Coarse Sand lithologies are interbedded layers, and Aquifer Miocene Alluvium
is not present in all boreholes:

The Lower Gravel, Glacial Till and Gravel lithologies appear to be continuous and we could
build a stratigraphic sequence containing only these layers. However, we will use all existing
lithologies in order to illustrate the tools available in Leapfrog Hydro for building a stratigraphy.
4. Clear the scene.
5. Right-click on the geological model created in Creating a Geological Model and select
Copy.
6. In the window that appears, enter a name for the copy:

7. Click OK.

Making a copy of a geological model is a useful way of experimenting with refinements to a


model without having to undo changes.

8. Expand the copy of the geological model in the project tree.


9. Right-click on the Surface Chronology object and select New Stratigraphy.

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The New Stratigraphic Sequence window will appear:

10. Select Alluvium for the Lithology Above.


11. Select Basement Granite for the Lithology Below.
12. Click on the Add Lithologies button.
13. Click the Lithology tick box to select all available lithologies:

14. Click OK in the Select Lithologies and New Stratigraphic Sequence windows.

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15. When Leapfrog Hydro has finished generating the stratigraphy, expand it in the project tree:

The stratigraphic sequence object contains its own series of contact surfaces, plus a set of
points that shows where pinch-out errors occur. We can use this information to refine the
sequence.
16. Right-click on the stratigraphic sequence object and select List Errors.
The Stratigraphic Errors window will appear, providing details of each error that will help us
decide what changes to make to the stratigraphic sequence:

The Coarse Sand and Aquifer Miocene Alluvium lithologies are not continuous, so we will
remove them from the sequence. We will also make Lower Gravel the lithology at the bottom of
the stratigraphic sequence.
17. Click OK to close the Stratigraphic Errors window.
18. Double-click on the stratigraphic sequence to open it.
19. Remove Coarse Sand, Lower Gravel and Aquifer Miocene Alluvium from the Stratigraphic
Lithologies list.
20. Change the Lithology Below to Lower Gravel.
21. Click OK.
When processing is complete, the stratigraphic sequence should be free of errors. Now we will
add it to the geological model and rearrange the layers so the stratigraphic sequence replaces
individual contact surfaces.

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22. Double-click on the Surface Chronology object.


23. Tick the box for the stratigraphic sequence to enable it.
24. Move the stratigraphic sequence so it is lower (older) than the Alluvium - Coarse Sand
contacts.
25. Untick the boxes for the contact surfaces modelled using the stratigraphic sequence:

26. Click OK.


27. When processing is complete, add the geological model to the scene:

Compare this model with the stratigraphic sequence to the original model.

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Tutorial 3: Building a Geological Model from
Contact Points
For this tutorial, we will build a geological model directly from contact points rather than from
contact points extracted from boreholes.
In general, it is better to build a geological model directly from boreholes as borehole data
contains more information about the position of surfaces than is present in the contact points
themselves. A simple example of modelling the surface between red and blue is shown below:

Because Leapfrog Hydro compares the surface to the lithological segments and alters the
surface to pass smoothly under lithological segments, the surface defined from the boreholes
will not pass through any segments of the contacting lithologies. In addition, Leapfrog Hydro
uses the borehole data to label both sides of the contact surface with the correct lithologies.
Extracting contact points from the borehole logs, however, destroys information about where
the contact surface should not pass, which can result in erroneous results, as indicated by the
dashed line in the image above. You will also need to manually specify lithologies on each side
of the contact surface.
For this tutorial, we are going to import a set of contact points and use them to build a
geological model. The lithological sequence for this model is:
l Alluvium (youngest)
l Gravel
l Aquifer Miocene Alluvium
l Basement granite (oldest)
This sequence is defined by three sets of contact points:
l Top of the basement granite
l Top of the aquifer miocene alluvium
l Top of the gravel (bottom of the alluvium)

Importing the Contact Points


Data for this tutorial can be found in the Geological Model from Contacts folder.
1. Launch Leapfrog Hydro.
2. In the Projects tab, click New Project.

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The Create Project window will appear:

3. In the Create Project window, enter the name Contact GM tutorial and click Browse to
select a folder where the project will be saved.
4. Click OK to create the project.
5. Right-click on the Points folder and select Import Points:

6. Navigate to the Geological Model from Contacts folder and select the file Top of Aquifer
Miocene Alluvium.csv.
7. Click Open.
8. In the Import Points window, there is no need to change any settings, so click Finish:

The points file will appear in the project tree under the Points folder.
9. Repeat steps 5 to 8 for the remaining two files.

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Setting the Geological Model Extents


We will use the points data to set the extents for a new geological model.
1. Add the Points objects to the scene.
2. Press the Dkey to view the scene from above.
3. Right-click on the Geological Models folder and select New Geological Model.
4. Select <Everything> from the Enclose Object list:

This will set the size of the model boundary to be slightly larger than the contact points
imported into the project.

Because this project contains no borehole data, the Base Lithology Column is automatically
set to <None>. If, however, you create a geological model from points in a project that
contains borehole data, be sure to set the Base Lithology Column to <None> as it cannot be
changed once the model has been created.

5. Click OK.

Defining the Lithologies


Next, we need to manually add the names of the lithologies and the colours that will be used to
display them.
1. Right-click on the Lithologies object for the new geological model and select Open.
2. In the Lithologies tab, click Add.
3. Enter the name Alluvium.

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4. Repeat steps 2 and 3 for the lithologies Basement Granite, Gravel and Aquifer Miocene
Alluvium:

5. Click OK.
6. Next, right-click on the Surface Chronology object and select New Deposit > From Points.
We will build the oldest lithology first, Basement Granite.
7. In the New Depositional Contact window, select the Top_of_Basement_granite points.
8. Set First Lithology to Basement Granite and Second Lithology to Aquifer Miocene Alluvium.
9. Set First Lithology to is Older:

10. Click OK.


The new contact surface will appear under the Surface Chronology object.
11. Right-click on the Surface Chronology object and select New Deposit > From Points.
12. Select the Top_of_Aquifer_Miocene_Alluvium points.
13. Set First Lithology to Aquifer Miocene Alluvium and Second Lithology to Gravel.

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Defining the Lithologies | 45

14. Set First Lithology to is Older:

15. Click OK.


16. Right-click on the Surface Chronology object and select New Deposit > From Points.
The Top_of_Gravel points should be automatically selected it is the only set of points not yet
used.
17. Set First Lithology to Gravel and Second Lithology to Alluvium.
18. Set First Lithology to is Older:

19. Click OK.


20. Double-click on the Surface Chronology object.
21. Tick the Contact surface box to add all surfaces to the chronology.
22. Organise the layers so that the youngest is at the top of the list:

23. Click OK.

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24. Clear the scene.


25. Add the geological model to the scene. It should appear similar to this:

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Tutorial 4: Building a Simple Interpolant
An interpolant is used to describe how a real, numerical quantity such as nitrate concentration
varies in three-dimensional space.
Leapfrog Hydro contains a powerful 3D interpolation engine that can be used to interpolate
any numeric data (e.g. piezometric head measurements). Interpolants are built from either:
l Columns of borehole data imported as numeric values
l Location arrays loaded with associated numeric values
In this tutorial, you will create a simple interpolant using points data. We will use the project
from Tutorial 2: Building a Geological Model for a Depositional System.

Creating a New Interpolant


Data for this tutorial can be found in the Interpolation folder.
To start building the interpolant, first import the points data that will be used:
1. Open the tutorial project from Tutorial 2: Building a Geological Model for a Depositional
System.
2. Clear the scene.
3. Right-click on the Points folder and select Import Points.
4. Navigate to the Interpolation folder and select the Point data.csv file.
5. Click Open.
6. In the Import Points window that appears, click Import All Columns, then click Finish.
The imported points data will appear in the project tree under the Points folder.
7. Right-click on the Interpolants folder and select New Interpolant.
The New Interpolant window will appear.
8. From the Numeric values dropdown box select the value points object ( ):

9. Make sure Use only data within boundary is unticked and Volumes enclose is set to
Intervals.

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10. From the Enclose Object dropdown box, select the Point_data object ( ).
11. Click OK to create the new model.
Leapfrog Hydro will generate the new model, which will appear in the project tree under the
Interpolants folder:

12. Add the model to the scene by either dragging and dropping the model into the scene or by
right-clicking on the model and selecting View Output Volumes.

A default trend is used when generating the model. Later, we will change this trend.

Changing the Isosurfaces


To adjust the isosurfaces Leapfrog Hydro generated:
1. Double-click on the interpolant in the project tree.

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The Edit Interpolant window will appear.


2. Click on the Outputs tab:

3. Click on the Iso Value for the 38.0 surface and change it to 35:

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4. Click Add to add a new surface and give it an value of 55:

5. Click OK.
When the interpolant has recalculated, the original isosurfaces will be automatically added
back to the scene. The new isosurfaces, however, need to be added.
6. Add the interpolant to the scene:

Changing the Trend


When an interpolant is first created, Leapfrog Hydro uses a default trend. To change this:
1. Expand the interpolant in the project tree.

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2. Double-click on the interpolants Trend object.


3. Click View Plane to add the moving plane to the scene.
The moving plane will be added to the scene, but may be difficult to see as it will be obscured
by the interpolant volumes.
4. Click on an interpolant volume in the scene.
This will select the volume in the shape list.
5. Click the visibility button ( ) in the shape list to hide the volume in the scene.
Once you have hidden some volumes, the scene will appear similar to this:

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6. Click on the plane to view its controls:

7. Use the moving plane controls to adjust the plane in the scene.
8. Click Set From Plane to update the values in the Trend tab:

9. Click OK to generate the model.

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10. Make the hidden volumes visible once again:

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Tutorial 5: Building a ModFlow Model
Flow models are based on volumetric grids, which can be created in Leapfrog Hydro or created
in external software and visualised in Leapfrog Hydro.
Creating grids in Leapfrog Hydro has the advantage that the resolution can be easily changed,
and the properties of the grid can be made to honour boundaries defined within geological
models.
In this tutorial, we will create a basic ModFlow model and its associated volumetric grid based
on the first geological model created in Tutorial 2: Building a Geological Model for a
Depositional System.

Creating a ModFlow Grid


To start creating a new ModFlow grid:
1. Open the tutorial project from Tutorial 2: Building a Geological Model for a Depositional
System.
2. Clear the scene.
A new ModFlow grid will be based on a geological model, which is used for the initial grid
dimensions.
3. Drag the GM geological model into the scene.
4. Right-click on the Flow Models folder and select New ModFlow Model.
The New ModFlow Model window will be displayed, together with controls in the scene that
will help you to set the grid extents:

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The Gridding from field should be set to the GM geological model.


The size of the cells in the horizontal grid is determined by the Default Cell Size setting. You can
also set a custom horizontal grid by changing the Row Spacings and Column Spacings. For this
tutorial, though, set a uniform horizontal grid that includes all the layers of the geological
model. To do this:
5. Set the Default Cell Size to 100.
Note how the default cell size is updated in the scene.
6. Click on the Layers tab.
7. Click on the Select Layer Guides button. The Layer Guides window will appear:

8. Click on the Select All button.


9. Click OK to return to the New ModFlow Model window.
10. Click OK.
The new grid will be created and added to the Flow Models folder. To view it:
11. Clear the scene.

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Changing Hydrological Properties | 56

12. Drag the new ModFlow grid into the scene:

Changing Hydrological Properties


Once a ModFlow grid has been created, you can set conductivity, specific storage and specific
yield models for each lithology.
1. Right-click on the ModFlow grid in the project tree and select Edit Hydrological Properties.
2. In the Edit Hydrological Properties window, click in a cell to change a value:

You can use the Enter key to move down each column, editing the values as you go.
3. Click OK to save changes made.

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Tutorial 6: Importing, Creating and Working
with FEFLOW Grids
In Leapfrog Hydro, 2D and 3D FEFLOW grids can be created and visualized. You can also set a
grids material properties according to the lithological units in the geological model.
In this tutorial, we will create and import 2D and 3D FEFLOW grids. We will use the geological
model built in Tutorial 2: Building a Geological Model for a Depositional System to evaluate
imported grids and to create new grids.

Importing and Working with a Full 3D Grid


Data for this tutorial can be found in the Flow Modelling folder.
In this part of the tutorial, we will import a 3D FEFLOW grid, display it and evaluate it against a
geological model.
1. Open the project used for Tutorial 2: Building a Geological Model for a Depositional
System.
2. Click on the Clear scene button to clear any objects from the scene window.
3. Right-click on the Flow Models folder and select Import FEFLOW (ASCII Fem) Model.
4. Navigate to the folder that contains the TekFemTri.fem file and select the file.
5. Click Open.
The grid will be imported and will appear in the project tree under the Flow Models folder.
6. Add the grid to the scene:

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In the shape list, a number of options are available for displaying the different properties of the
grid:

You can restrict the view to a single layer using the controls in the shape properties panel. To do
this, tick the box for One layer and select the different layers in the grid by changing the value of
One layer:

For example, setting One layer to 2 displays only the grids second layer:

7. Untick the One layer option.

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Evaluating a 3D FEFLOW grid against a geological model assigns a particular lithology to a grid
cell. To do this:
8. Expand the FEFLOW model in the project tree.
9. Right-click on the grid and select Evaluations:

The window that appears shows all geological models available in the project.
10. Move the GM model to the Selected list and click OK:

11. In the shape list, select the geological model evaluation as the display option.

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The colours of the grid cells are updated to reflect the selected geological model:

You can also set the material types using information in the geological mode by right-clicking
on the FEFLOW model and selecting Edit Material Types:

In the Edit Material Types window, click on a value to edit it. You can use the Enter key to move
down each column, editing the values.
Fill in appropriate values for Kx, Ky, Kz, Drain and Specific Storage, then click OK.

Creating a New FEFLOW Grid from an Existing 3D


Grid
In the FEFLOW model imported in Importing and Working with a Full 3D Grid, the grid cells
are evenly distributed in the z-direction. All cells are the same height, except the top layer of
cells, where the different cell heights reflect the height of the topography. In order for the cell
heights to reflect the lithological layers, we will create a new FEFLOW model based on the
imported TekFemTri model and set the layers in the model using the lithology layers of a
geological model.
1. Right-click on the Flow Models folder and select New FEFLOW Model.
The Extrude 3D FEFLOW Grid window will appear.

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2. Select the TekFemTri grid from the FEFLOW Grid list and the GM geological model created
in from the Geological Model list.

3. Click the Select Layer Guides button.


The Layer Guides window will appear showing all the layers in the selected geological model.
4. Click Select All to move all the layers to the Selected pane.
5. Click OK to return to the Extrude 3D FEFLOW Grid window.
6. Set the Minimum Thickness to 10 and enter the name GM Grid:

7. Click OK.
If the selected geological models boundaries are not large enough to enclose the FEFLOW
grid, this will result in an error. If this occurs, we need to adjust the geological models boundary
to ensure it encloses the FEFLOW grid. To do this:
8. Dismiss the error.
9. If the TekFemTri grid is not already in the scene, add it to the scene.
10. Press the D key on your keyboard to view the model from above.

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11. Expand the selected geological model in the project tree, right-click on the Boundary object
and select Open.
Controls for adjusting the boundary will appear in the scene:

12. Use the handles to adjust the boundary so that it is slightly larger than the grid:

13. Click OK to update the geological models boundary.


All processing tasks in the queue will run, including the creation of the FEFLOWgrid that earlier
resulted in an error.

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Importing a 2D FEFLOW Grid | 63

14. Clear the scene, then add the new FEFLOW simulation to the scene:

Cell height is now determined by the contact surfaces used to build the geological model.

Importing a 2D FEFLOW Grid


The steps for importing a 2D FEFLOW are nearly identical to those for a 3D grid. A 2D grid
cannot, however, be evaluated against a geological model, nor can the material properties be
set.
1. Open the project used for the earlier parts of this tutorial.
2. Clear the scene.
3. Right-click on the Flow Models folder and select Import FEFLOW (ASCII Fem) Model.
4. Navigate to the folder that contains the TekFemTriFine2D.fem file and select the file.
5. Click Open.
The grid will be imported and will appear in the project tree under the Flow Models folder.

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6. Add the grid to the scene:

Note that the 2D FEFLOW object and its grid have different icons than those for 3D grids.

Extruding a 2D Grid to Create a 3D Grid


A 2D grid can be used as the basis for a 3D grid. To create a 3D grid from the 2D grid imported in
Importing a 2D FEFLOW Grid:
1. Clear the scene.
2. Right-click on the Flow Models folder and select New FEFLOW Model.
The Extrude 3D FEFLOW Grid window will appear.
3. Select the TekFemTriFine2D grid from the FEFLOW Grid list and the GM geological model
created in from the Geological Model list.
4. Click the Select Layer Guides button.
5. In the Layer Guides window, click Select All to move all the layers to the Selected pane.
6. Click OK to return to the Extrude 3D FEFLOW Grid window.

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Creating and Working with a 2D Grid | 65

7. Set the Minimum Thickness to 10 and enter the name GM Grid Fine 2D:

8. Click OK.

If you get an error because the geological models boundaries are not large enough to
enlose the FEFLOW grid, add the TekFemTriFine2D grid to the scene and resize the
geological model boundary as described in Creating a New FEFLOW Grid from an Existing
3D Grid.

9. Clear the scene, then add the GM Grid Fine 2D object to the scene, selecting GM as the
display option:

You can assign material properties to this grid and export it to FEFLOW.

Creating and Working with a 2D Grid


You can also create a 2D grid in Leapfrog Hydro and use it to create a 3D grid.
In this part of the tutorial, we will create a 2D grid bounded by the geological model created in
Tutorial 2: Building a Geological Model for a Depositional System and use it as the basis for a
3D grid. To start:
1. Right-click on the Flow Models folder and select New 2D FEFLOW Model.

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The New 2D FEFLOW Grid window will appear.


2. Select the GM Extents object from the Enclose Object list.
3. Untick the Simplify boundary box.
4. Enter the name GM Rectangular Grid:

5. Click OK.
6. Clear the scene.
7. Add the GM Rectangular Grid to the scene.
8. Press the D key to view the grid from above:

This creates a basic rectangular FEFLOWgrid based on the geological model extents selected.
Next, we can start adding features to the grid.
9. Add the borehole collar points to the scene.
10. Expand the GM Rectangular Grid in the project tree

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Creating and Working with a 2D Grid | 67

11. Right-click on the grid object ( ) and select New Feature:

12. In the window that appears, select the collar points for the Feature Object:

13. Click OK.


14. Double-click on the grid in the project tree.
15. Tick the box for the collar feature.
16. Set the value of Refinement Steps to 5:

17. Click OK.

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68 | Leapfrog Hydro Tutorials

The vertices have snapped to the collar points:

You can continue adjusting the grid properties and adding features to refine the grid. The grid
can then be used as the basis for a 3D grid.
18. Right-click on the Flow Models folder and select New FEFLOW Model.
19. In the Extrude 3D FEFLOW Grid window, select the GM Rectangular Grid for the
FEFLOWGrid.
20. Click Select Layer Guides and add all the layers to the grid.
21. Set the Minimum Thickness to 10.
22. Name the grid GM Rectangular 3D Grid:

23. Click OK.

2016 ARANZ Geo Limited


Creating and Working with a 2D Grid | 69

24. Clear the scene.


25. Add the new grid to the scene:

2016 ARANZ Geo Limited

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