Geostatistics 3D

v. 10.
GMS 10.0 Tutorial

Geostatistics – 3D
Learn the various 3D interpolation methods available in GMS
Objectives
Explore the various 3D interpolation algorithms available in GMS including IDW and kriging. Visualize
the results of interpolation though cross sections and iso-surfaces.
Prerequisite Tutorials Required Components Time

• Geostatistics 2D • Geostatistics • 30-60 minutes
• Grid
Page 1 of 12 © Aquaveo 2014

1 Contents
1 Contents ............................................................................................................................... 2
2 Introduction ......................................................................................................................... 2
2.1 Outline .......................................................................................................................... 2
3 Getting Started .................................................................................................................... 3
4 Importing a Scatter Point Set ............................................................................................. 3
5 Displaying Data Colors ....................................................................................................... 4
6 Z Magnification ................................................................................................................... 4
7 Creating a Bounding Grid .................................................................................................. 4
8 Simple IDW Interpolation .................................................................................................. 5
9 Displaying Iso-surfaces ....................................................................................................... 6
10 Interior Edge Removal........................................................................................................ 6
11 Specified Range ................................................................................................................... 7
12 Using the Vertical Anisotropy Option ............................................................................... 7
13 IDW Interpolation With Gradient Planes ......................................................................... 8
14 IDW Interpolation With Quadratic Functions ................................................................. 8
15 Other Interpolation Schemes ............................................................................................. 9
16 Viewing the Plume With a Cross Section .......................................................................... 9
17 Using the Truncation Option ........................................................................................... 10
18 Setting up a Moving Cross Section Animation ............................................................... 10
18.1 Display Options .......................................................................................................... 11
18.2 Setting up the Animation ............................................................................................ 11
18.3 Playing Back the Animation ....................................................................................... 11
19 Setting up a Moving Iso-Surface Animation ................................................................... 12
20 Conclusion.......................................................................................................................... 12
2 Introduction
Three-dimensional geostatistics (interpolation) can be performed in GMS using the 3D
Scatter Point module. The module is used to interpolate from sets of 3D scatter points to
3D meshes and 3D grids. Several interpolation schemes are supported, including
kriging. Interpolation is useful for defining initial conditions for 3D ground water
models or for 3D site characterization.
The tools for manipulating 3D scatter point sets and the interpolation schemes supported
in GMS are described in this tutorial.
2.1 Outline
This is what you will do:
1. Import a scatter point set.
2. Create a bounding grid.

GMS Tutorials Geostatistics - 3D
3. Create iso-surfaces by interpolating scatter points to a 3D grid using different

interpolation methods.
4. Create cross sections.
5. Make a moving cross section animation.
6. Make a moving iso-surface animation.
3 Getting Started
Let’s get started.
1. If necessary, launch GMS. If GMS is already running, select the File | New
command to ensure that the program settings are restored to their default state.
4 Importing a Scatter Point Set

To begin the tutorial, we will import a 3D scatter point set. A 3D scatter point set is
similar to a 2D scatter point set except that each point has a z coordinate in addition to
xy coordinates. As with the 2D scatter point set, one or more scalar data sets can be
associated with each scatter point set representing values such as contaminant
concentration, porosity, hydraulic conductivity, etc. The 3D scatter point set we will
import and use with this tutorial has previously been entered into a text file using a
spreadsheet. The file was then imported to GMS using the Import Wizard (refer to the
Geostatistics - 2D tutorial for details on using the Import Wizard). The project was then
saved.
To read the project:
1. Select the Open button .
2. Open the directory entitled Tutorials\geos3d.
3. Open the file named tank.gpr.
4. Select the Oblique View button .
A set of points should appear on the screen. Notice that the points are arranged in
vertical columns. This hypothetical set of points is meant to represent a set of
measurements of contaminant concentration in the vicinity of a leaky underground
storage tank. Each column of points corresponds to a borehole or the path of a
penetrometer along which concentrations were measured at uniform intervals. The goal
of the tutorial is to use the tools for 3D geostatistics in GMS to interpolate from the
scatter points to a grid and generate a graphical representation of the plume.

5 Displaying Data Colors

Next, we will change the display options so that the color of each point is representative
of the concentration at the point.
1. Select the Display Options button .
2. In the 3D Scatter Data Section turn on the Contours option.
3. Select the Options button.
4. Turn on the Legend option.
5. Select the OK button twice to exit both dialogs.
Notice that most of the values are zero. The nonzero values are all at about the same
depth in the holes. This pattern is fairly common when dealing with light non-aqueous
phase liquids (LNAPLs) which form a pancake shaped plume and float on the water
table.
6 Z Magnification
Next, we will magnify the z coordinate so that the vertical variation in the data is more
apparent.
2. Enter a value of 2.0 for the Z magnification.
3. Select the OK button.
4. Select the Frame button .
7 Creating a Bounding Grid

To generate a graphical representation of the contaminant plume, we must first create a
grid that bounds the scatter point set. We will then interpolate the data from the scatter
points to the grid nodes. The grid will then be used to generate iso-surfaces.
To create the grid:
1. In the Project Explorer, right-click on the tank.sp3 scatter point set and
select the Bounding 3D Grid menu command.
2. Notice that the x, y, and z dimensions of the grid are already defined. The
default values shown in the dialog cause the grid to extend beyond the scatter

points by 10% on each side. Also, default values have also been entered for the
number of cells in each direction. We will leave the default values.
3. Check to ensure that the default grid type is Mesh Centered.
Two types of grids are supported in GMS: cell-centered and mesh-centered. While cell-
centered is appropriate for groundwater models (MODFLOW), the mesh-centered
approach is more appropriate when the grid will be used solely for interpolation.
5. Select the Frame button .
A grid should appear on the screen that just encompasses the scatter point set.
8 Simple IDW Interpolation

The next step is to select an interpolation scheme. First, we will use the inverse distance
weighted interpolation scheme (IDW).
1. Select the Interpolation | Interpolation Options menu command.
2. Select the Inverse distance weighted option.
3. Select the Options button to the right of the Inverse distance weighted option.
4. In the Nodal function section at the top of the dialog, select the Constant
(Shepard’s method) option.
5. In the section entitled Computation of interpolation weights, select the Use

subset of points option.
6. Select the Subset… button in the Computation of interpolation weights section.
7. Select the Use nearest ___ points option and enter 64 for the number of points.
8. Select the OK button to exit the Subset Definition dialog.
9. Select the OK button to exit the IDW Interpolation Options dialog.
10. Select the OK button to exit the Interpolation | Interpolate Options dialog.
To interpolate to the grid:
11. Select the Interpolation  3D Grid menu command.

9 Displaying Iso-surfaces
Now that we have interpolated to the nodes of the 3D grid there are several ways to
visualize the contaminant plume. One of the most effective ways is to use iso-surfaces.
Iso-surfaces are the three-dimensional equivalent of contour lines. An iso-surface
represents a surface of a constant value (contaminant concentration in this case). To
define and display iso-surfaces:
2. Select the 3D Grid Data option .
3. Turn off the Cell edges option, and turn on the Grid shell, and Iso-surfaces
options.
4. Select the Options button to the right of the Iso-Surfaces option.
5. On the first row, enter 3000.0 for the Upper Value.
6. On the second row, turn on the Fill between option.
7. Turn on the Iso-surface faces option.
8. Select the OK button to exit the Iso-Surface Options dialog.
9. Select the OK button to exit the Display Options dialog.
You should now see the iso-surface.
10 Interior Edge Removal

A series of edges are draped over the iso-surface plot. These edges represent the
intersection of the iso-surface with the grid cells. The edges are displayed to help the
user visualize the spatial variation or relief in the iso-surface. However, it is sometimes
useful to inhibit the display of the edges in some areas. For example, in the regions
where the plume intersects the grid the iso-surface is flat. We will turn off the display of
the edges in this area since they provide little benefit.
1. Select the 3D Grid Data folder in the Project Explorer.
2. Select the Grid | Iso-Surface Option menu command.
3. Select the Interior edge removal option. This removes the edges between
adjacent planar facets that are coplanar.

11 Specified Range
You may have noticed that the shell of the iso-surface is all one color, but the interior of
the iso-surface (where the iso-surface intersects the boundary of the grid) varies in color
according to the contaminant concentration. We can change the display options so that
the color variation in this region is more distinct.
1. Select the Grid | Iso-surface Options menu command.
2. Select the Contour specified range option.
3. Enter 3000 for the Minimum value.
4. Enter 9000 for the Maximum value.
12 Using the Vertical Anisotropy Option

The scatter points we are using were obtained along vertical traces. In such cases, the
distances between scatter points along the vertical traces are significantly smaller than
the distances between scatter points along the horizontal plane. This disparity in scaling
causes clustering and can be a source of poor results in some interpolation methods.
The effects of clustering along vertical traces can be minimized using the Vertical
Anisotropy option in the Interpolation Options dialog. The z coordinate of each of the
scatter points is multiplied by the vertical anisotropy parameter prior to interpolation.
Thus, if the vertical anisotropy parameter is greater than 1.0, scatter points along the
same vertical axis appear farther apart than they really are and scatter points in the same
horizontal plane appear closer than they really are. As a result, points in the same
horizontal plane are given a higher relative weight than points along the z axis. This can
result in improved accuracy, especially in cases where the horizontal correlation between
scatter points is expected to be greater than the vertical correlation (which is typically the
case due to horizontal layering of soils or due to spreading of the plume on the top of the
water table).
To change the vertical anisotropy:
1. In the Project Explorer select the 3D Scatter Data folder .
3. Change the Vertical anisotropy value to 0.4.
5. Select the Interpolation | Interpolate  3D Grid menu command.
6. Enter c_idw_const2 for the new data set name.

As can be seen, there is now much more correlation in the horizontal direction.
13 IDW Interpolation With Gradient Planes

As discussed in the 2D Geostatistics tutorial, IDW interpolation can often be improved
by defining higher order nodal functions at the scatter points. The same is true in three
dimensions. Next, we will try IDW interpolation with gradient plane nodal functions.
3. In the Nodal function section at the top of the dialog, select the Gradient plane
option.
5. Select the OK button to exit the Interpolation Options dialog.
14 IDW Interpolation With Quadratic Functions

Next, we will try IDW interpolation with quadratic nodal functions.
3. In the Nodal function section at the top of the dialog, select the Quadratic
option.
4. In the section entitled Computation of nodal function coefficients, select the Use
all points option.
6. Select the OK button to exit the Interpolation Options dialog.

15 Other Interpolation Schemes

Two other 3D interpolation schemes, natural neighbor interpolation and kriging, are
supported in GMS. However, these schemes will not be reviewed in this tutorial. You
are encouraged to experiment with these techniques at your convenience.
16 Viewing the Plume With a Cross Section

While iso-surfaces are effective for displaying contaminant plumes, it is often useful to
use color-shaded cross sections to illustrate the variation in the contaminant
concentration. Next, we will cut a horizontal cross section through the center of the
plume.
1. In the Project Explorer select the 3D Grid Data folder .
2. Select the Side View button .
3. Select the Create Cross Section tool .
4. Cut a horizontal cross section through the grid by clicking to the left of the grid,
moving the cursor to the right of the grid, and double clicking. Cut the cross
section through the middle of the iso-surface.
5. Select the Oblique View button .
Before we examine the cross section, we will turn off the display of the iso-surfaces.
7. Turn off the Iso-surfaces option.
Next, we will set up the display options for the cross-section.
9. Select the Display Options menu command and select Cross Sections.
10. Turn on the Interior edge removal option.
11. Turn on the Contours option.
Finally, we will reset the Contour options.

13. Select the Display Options menu command and select Cross Sections.
14. Select the Options button to the right of the Contours option.
15. For the Contour method, select the Color Fill option.
16. Select the OK button for both dialogs.
17 Using the Truncation Option

Notice the range of contaminant concentration values shown in the color legend at the
upper left corner of the Graphics Window. A large percentage of the values are negative.
This occurs due to the fact that a higher order nodal function was used. Both the
quadratic and the gradient plane nodal functions infer trends in the data and try to
preserve those trends. In some regions of the grid, the values at the scatter points are
decreasing as you move away from the center of the plume. This decreasing trend is
preserved by the interpolation scheme and the interpolated values approach zero and
eventually become negative in some areas. However, a negative concentration does not
make sense. This problem can be avoided by turning on the Truncate values option in
the Interpolation Options dialog. This option can be used to force all negative values to
have a value of zero.
1. In the Project Explorer select the 3D Scatter Data folder .
3. Turn on the Truncate values option.
4. Select the Truncate to min/max of data set option.
6. Select the Interpolation  3D Grid menu command.
7. Enter c_idw_quad_trunc for the name of the new data set.
Notice that the minimum value listed in the color legend is zero.
18 Setting up a Moving Cross Section Animation

It is possible to create several cross sections at different locations in the grid to illustrate
the spatial variation of the plume. This process can be automated using the Animation
utility in GMS. An animation can be generated showing a color shaded cross section
moving through the grid.

18.1 Display Options

Before setting up the animation, we will first delete the existing cross section, turn off
the color legend, and reset the contour range.
1. In the Project Explorer select the 3D Grid Data folder .
2. Select the Select Cross Sections tool .
3. Select the cross section by clicking on it.
4. Select the Edit | Delete menu command.
5. Select the Grid | Iso-surface Options menu command.
6. Select the Contour specified range option.
7. Enter 1000.0 for the Minimum value.
8. Enter 15000.0 for the Maximum value.
18.2 Setting up the Animation

To set up the animation:
1. Select the Display | Animate menu command.
2. Turn on the Cross sections / Iso-surfaces option and click Next.
3. Turn on the Animate cutting plane over specified XYZ range option.
4. Turn on the Z cutting plane.
5. Select the Finish button.
18.3 Playing Back the Animation

You should see some images appear on the screen. These are the frames of the
animation which are being generated. Once they are all generated, they are played back
at a high speed.
1. After viewing the animation, select the Stop button to stop the animation.
2. When you are finished, close the window and return to GMS.

19 Setting up a Moving Iso-Surface Animation

Another effective way to visualize the plume model is to generate an animation showing
a series of iso-surfaces corresponding to different iso-values.
To set up the animation:
1. Select the Display | Animate menu command.
2. Turn on the Cross sections / Iso-surfaces command and click Next.
3. Turn off the Animate cutting plane over XYZ range option.
4. Turn on the Animate iso-surface over specified data range option.
5. Enter 1000.0 for the Begin value.
6. Enter 15000.0 for the End value.
7. Select the Cap above option.
8. Select the Display values option.
9. Select the Finish button.
10. After viewing the animation, select the Stop button to stop the animation.
11. When you are finished, close the window and return to GMS.
20 Conclusion
This concludes the tutorial. Here are some of the key concepts in this tutorial:
• There are several 3D interpolation algorithms available in GMS.
• Mesh-centered grids are better than cell-centered grids if you are just doing
interpolation and not using MODFLOW.
• Iso-surfaces can be used to visualize the results of an interpolation.
• Vertical anisotropy can be used to help overcome the problem of grouping that is
common with data collected from boreholes.

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v. 10.

GMS 10.0 Tutorial

Prerequisite Tutorials Required Components Time

Page 1 of 12 © Aquaveo 2014

1. Import a scatter point set.

2. Create a bounding grid.

Page 2 of 12 © Aquaveo 2014

3. Create iso-surfaces by interpolating scatter points to a 3D grid using different

4. Create cross sections.

5. Make a moving cross section animation.

6. Make a moving iso-surface animation.

4 Importing a Scatter Point Set

To read the project:

1. Select the Open button .

2. Open the directory entitled Tutorials\geos3d.

3. Open the file named tank.gpr.

4. Select the Oblique View button .

Page 3 of 12 © Aquaveo 2014

5 Displaying Data Colors

1. Select the Display Options button .

2. In the 3D Scatter Data Section turn on the Contours option.

3. Select the Options button.

4. Turn on the Legend option.

5. Select the OK button twice to exit both dialogs.

1. Select the Display Options button .

2. Enter a value of 2.0 for the Z magnification.

3. Select the OK button.

4. Select the Frame button .

7 Creating a Bounding Grid

To create the grid:

Page 4 of 12 © Aquaveo 2014

3. Check to ensure that the default grid type is Mesh Centered.

4. Select the OK button.

5. Select the Frame button .

8 Simple IDW Interpolation

1. Select the Interpolation | Interpolation Options menu command.

2. Select the Inverse distance weighted option.

5. In the section entitled Computation of interpolation weights, select the Use

6. Select the Subset… button in the Computation of interpolation weights section.

8. Select the OK button to exit the Subset Definition dialog.

9. Select the OK button to exit the IDW Interpolation Options dialog.

To interpolate to the grid:

11. Select the Interpolation  3D Grid menu command.

12. Select the OK button.

Page 5 of 12 © Aquaveo 2014

1. Select the Display Options button .

2. Select the 3D Grid Data option .

4. Select the Options button to the right of the Iso-Surfaces option.

5. On the first row, enter 3000.0 for the Upper Value.

6. On the second row, turn on the Fill between option.

7. Turn on the Iso-surface faces option.

8. Select the OK button to exit the Iso-Surface Options dialog.

9. Select the OK button to exit the Display Options dialog.

You should now see the iso-surface.

10 Interior Edge Removal

1. Select the 3D Grid Data folder in the Project Explorer.

2. Select the Grid | Iso-Surface Option menu command.

4. Select the OK button.

Page 6 of 12 © Aquaveo 2014