GMS Tutorials Geostatistics – 3D

v. 10.7

GMS 10.7 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 isosurfaces.

Prerequisite Tutorials Required Components Time

 Geostatistics – 2D  Geostatistics  30–45 minutes
 GMS Basic

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1 Introduction ......................................................................................................................... 2
1.1 Getting Started ............................................................................................................. 2
2 Importing a Scatter Point Set ............................................................................................. 3
3 Displaying Data Colors ....................................................................................................... 4
4 Z Magnification ................................................................................................................... 4
5 Creating a Bounding Grid .................................................................................................. 5
6 Simple IDW Interpolation .................................................................................................. 6
7 Displaying Isosurfaces ........................................................................................................ 6
7.1 Interior Edge Removal ................................................................................................. 7
7.2 Specified Range............................................................................................................ 8
7.3 Using the Vertical Anisotropy Option .......................................................................... 8
8 Interpolation ........................................................................................................................ 9
8.1 IDW Interpolation with Gradient Planes ...................................................................... 9
8.2 IDW Interpolation with Quadratic Functions ............................................................. 10
8.3 Other Interpolation Schemes ...................................................................................... 11
9 Viewing the Plume with a Cross Section ......................................................................... 11
9.1 Using the Truncation Option ...................................................................................... 13
10 Setting up a Moving Cross Section Animation ............................................................... 14
10.1 Display Options .......................................................................................................... 14
10.2 Setting Up and Playing the Animation ....................................................................... 14
11 Setting up a Moving Isosurface Animation ..................................................................... 14
12 Conclusion.......................................................................................................................... 15

1 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.
This tutorial describes and demonstrates the tools for manipulating 3D scatter point sets
and the interpolation schemes supported in GMS. This includes importing a scatter point
set, creating a bounding grid, creating isosurfaces by interpolating scatter points to a 3D
grid using different interpolation methods, creating cross sections, making a moving
cross section animation, and making a moving isosurface animation.

1.1 Getting Started

Do the following to get started:

1. If necessary, launch GMS.

2. If GMS is already running, select File | New to ensure that the program settings
are restored to their default state.

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2 Importing a Scatter Point Set

It is first necessary to import a 3D scatter point set. These are similar to 2D scatter point
sets except that each point has a z coordinate (elevation) in addition to xy coordinates. As
with the 2D scatter point set, one or more scalar datasets can be associated with each
scatter point set. These can represent values such as contaminant concentration, porosity,
hydraulic conductivity, and so on.
The 3D scatter point set that will be imported and used with this tutorial has previously
been exported to a text file using a spreadsheet application. The file was imported into
GMS using the Import Wizard, and then saved as a GMS project file. Refer to the
“Geostatistics – 2D” tutorial for details on using the Import Wizard.
To import the project, do as follows:

1. Click Open to bring up the Open dialog.

2. Select “All Files (*.*)” from the Files of type drop-down.
3. Browse to the geos3d directory and select “tank.gpr”.

4. Click Open to import the project and close the Open dialog.

5. Switch to Oblique View .

A set of points should appear on the screen (Figure 1).

Figure 1 Oblique view of set of contaminant concentration points

Notice that the points are arranged in vertical columns (Figure 1). This hypothetical set
of points represents 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.

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3 Displaying Data Colors

Next, it is necessary to change the display options so that the color of each point is
representative of the concentration at that point.

1. Click Display Options to bring up the Display Options dialog.

2. Select “3D Scatter Data” item in the list on the left.
3. On the 3D Scatter Point Set tab, turn on Contours.

4. Click the Options… button to the right of Contours to bring up the Dataset
Contour Options – 3D Scatter Points – c dialog.
5. At the bottom left of the dialog, turn on Legend.

6. Click OK to exit the Dataset Contour Options – 3D Scatter Points – c dialog.

7. Click OK to exit the Display Options dialog.

Notice that most of the values are zero (Figure 2). 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) that form a pancake-shaped plume and float on the
water table.

Figure 2 Contaminant concentrations shown with contour coloring

4 Z Magnification

It is necessary to magnify the z coordinate so that the vertical variation in the data is
more apparent.

1. Click Display Options to bring up the Display Options dialog.

2. Below the list on the left, enter “2.0” for Z magnification.

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3. Click OK to close the Display Options dialog.

4. Frame the project.

5 Creating a Bounding Grid

To generate a graphical representation of the contaminant plume, first create a grid that
bounds the scatter point set. It will then be possible to interpolate the data from the
scatter points to the grid nodes. The grid will be used to generate isosurfaces.
Do the following to create the grid:
1. In the Project Explorer, expand all of the entries.

2. Right-click on “ tank.sp3” and select Bounding 3D Grid… to bring up the

Create Finite Difference Grid dialog.
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. Default values have also been entered for the number of cells in each direction.
3. In the Orientation / type section, select “Mesh Centered” from the Type drop-
down.
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.

4. Click OK to close the Create Finite Difference Grid dialog.

5. Frame the project.

A 3D bounding grid encompassing the scatter point set should appear (Figure 3).

Figure 3 The 3D bounding grid

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6 Simple IDW Interpolation

An interpolation scheme needs to be selected next. First use the inverse distance
weighted interpolation scheme (IDW).

1. Select “ tank.sp3” in the Project Explorer to make it active.

2. Select Interpolation | Interpolation Options… to bring up the 3D Interpolation

Options dialog.
3. In the Interpolation method section, select Inverse distance weighted.

4. Click Options… to bring up the 3D IDW Interpolation Options dialog.

5. In the Nodal function section, select Constant (Shepard’s method).
6. In the Computation of interpolation weights section, select Use subset of points.

7. Click the Subset… button to bring up the Subset Definition dialog.

8. Select Use nearest ___ pts and enter “64” for the number of points.

9. Click OK to exit the Subset Definition dialog.

10. Click OK to exit the 3D IDW Interpolation Options dialog.

11. Click OK to exit the 3D Interpolation Options dialog.

12. Select Interpolation | Interpolation → 3D Grid to bring up the Interpolate →

Object dialog.

13. Click OK to accept the defaults and close the Interpolate → Object dialog.

7 Displaying Isosurfaces

Now that interpolation has been completed on the nodes of the 3D grid, there are several
ways to visualize the contaminant plume. One of the most effective ways is to use
isosurfaces. Isosurfaces are the three-dimensional equivalent of contour lines
representing a surface of a constant value (contaminant concentration, in this case).
To define and display isosurfaces, do the following:

1. Click Display Options to bring up the Display Options dialog.

2. Select “ 3D Grid Data” from the list on the left.

3. On the 3D Grid tab in the top section, turn off Cell edges and turn on Grid shell.
4. In the Active dataset section, turn on Isosurfaces.

5. Click the Options… button to the right of Isosurfaces to bring up the Isosurface
Options dialog.

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6. On the first row of the table, enter “3000.0” in the Upper Value column.
7. On the second row, check the box in the Fill between column.
8. In the section on the right, turn on Isosurface faces.

9. Click OK to exit the Isosurface Options dialog.

10. Click OK to exit the Display Options dialog.

11. Frame the project.

The isosurface should now be visible (Figure 4).

Figure 4 Visible isosurface

7.1 Interior Edge Removal

A series of edges are draped over the isosurface plot. These edges represent the
intersection of the isosurface with the grid cells. The edges are displayed to help
visualize the spatial variation or relief in the isosurface. 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 isosurface is flat. It is advisable to 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 to make it active.

2. Select Grid | Isosurface Options… to bring up the Isosurface Options dialog.

3. In the section on the right, turn on Interior edge removal option.
This removes the edges between adjacent planar facets that are coplanar.

4. Click OK to close the Isosurface Options dialog.

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7.2 Specified Range

Notice that the shell of the isosurface is all one color, but the interior of the isosurface
(where the isosurface intersects the grid boundary) varies in color according to the
contaminant concentration. To show more distinct color variation, do the following:

1. Select Grid | Isosurface Options… to bring up the Isosurface Options dialog.

2. In the section on the right, turn on Contour specified range, enter “3000” for
Minimum value, and “9000” for Maximum value.

3. Click OK to close the Isosurface Options dialog.

The isosurface should appear similar to Figure 5.

Figure 5 Isosurface with contouring

7.3 Using the Vertical Anisotropy Option

The scatter points being used were obtained along vertical traces. This means 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 vertical anisotropy.
The z coordinate of each of the scatter points is multiplied by one over the vertical
anisotropy parameter prior to interpolation. Thus, if the vertical anisotropy parameter is
less than 1.0, scatter points along the same vertical axis appear farther apart, and scatter
points in the same horizontal plane appear closer together.
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

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vertical correlation (e.g., horizontal layering of soils, spreading of the plume on the top
of the water table).
To change the vertical anisotropy, do the following:

1. Select the “ 3D Scatter Data” folder in the Project Explorer to make it active.

2. Select Interpolation | Interpolation Options… to bring up the 3D Interpolation

Options dialog.
3. In the Anisotropy section, enter “0.4” for the Vertical anisotropy.

4. Click OK to close the 3D Interpolation Options dialog.

5. Select Interpolation | Interpolate → 3D Grid to bring up the Interpolate →

Object dialog.
6. Enter “c_idw_const2” as the Interpolated dataset name.

7. Click OK to close the Interpolate → Object dialog.

More correlation now exists in the horizontal direction (Figure 6).

Figure 6 Isosurface contours using vertical anisotropy

8 Interpolation

8.1 IDW Interpolation with Gradient Planes

As discussed in the “Geostatistics—2D” tutorial, IDW interpolation can often be

improved by defining higher order nodal functions at the scatter points. The same is true
in three dimensions. The next step will be to use IDW interpolation with gradient plane
nodal functions.

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1. Select Interpolation | Interpolation Options… to bring up the 3D Interpolation

Options dialog.

2. In the Interpolation method section, click the Options… button to the right of
the Inverse distance weighted option to bring up the 3D IDW Interpolation
Options dialog.
3. In the Nodal function section, select the Gradient plane option.

4. Click OK to exit the 3D IDW Interpolation Options dialog.

5. Click OK to exit the 3D Interpolation Options dialog.

6. Select Interpolation | Interpolate → 3D Grid to bring up the Interpolate →

Object dialog.

7. Click OK to accept the defaults and close the Interpolate → Object dialog.
The Graphics Window will appear similar to Figure 7.

Figure 7 IDW with gradient planes

8.2 IDW Interpolation with Quadratic Functions

Next, try IDW interpolation with quadratic nodal functions.

1. Select Interpolation | Interpolation Options… to bring up the 3D Interpolation

Options dialog.

2. In the Interpolation method section, click the Options… button to the right of
Inverse distance weighted to bring up the 3D IDW Interpolation Options dialog.
3. In the Nodal function section, select Quadratic.
4. In the Computation of nodal function coefficients section, select Use all points.

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5. Click OK to exit the 3D IDW Interpolation Options dialog.

6. Click OK to exit the 3D Interpolation Options dialog.

7. Select Interpolation | Interpolate → 3D Grid to bring up the Interpolate →

Object dialog.

8. Click OK to accept the defaults and close the Interpolate → Object dialog.
The Graphics Window will appear similar to Figure 8. Notice how the contour of the
isosurface layers has changed slightly from that in the previous section.

Figure 8 IDW using quadratic functions

8.3 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. Feel
free to experiment with these techniques at a later time.

9 Viewing the Plume with a Cross Section

While isosurfaces are effective for displaying contaminant plumes, it is often useful to
use color-shaded cross sections to illustrate the variation in the contaminant
concentration.
To do this, first cut a horizontal cross section through the center of the plume:

1. In the Project Explorer, select the “ 3D Grid Data” folder.

2. Switch to Side View .

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3. Using the Create Cross Section tool, cut a horizontal cross section through
the grid and the middle of the isosurface by clicking to the left of the grid,
moving the cursor to the right of the grid, and double-clicking.

4. Switch to Oblique View .

To turn off the display of the isosurfaces and make the contours visible on the cross
section, do the following:

5. Click Display Options to bring up the Display Options dialog.

6. Select “3D Grid Data” from the list on the left.
7. On the 3D Grid tab in the Active dataset section, turn off Isosurfaces.
8. Select “Cross Sections” from the list on the left.
9. In the first section on the Cross Sections tab, turn on Interior edge removal.
10. In the 3D Grid section, turn on Contours.

11. Click the Options… button to the right of Contours to bring up the Dataset
Contour Options – 3D Grid – c_idw_quad dialog.
12. In the Contour method section, select “Color fill” from the drop-down.

13. Click OK to close the Dataset Contour Options dialog.

14. Click OK to close the Display Options dialog.

The isosurface will disappear, and the contours will be visible on the cross section.
(Figure 9)

Figure 9 Cross section with contours

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9.1 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 (Figure 9). 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 when moving
away from the center of the plume. This decreasing trend is preserved by the
interpolation scheme; moreover, 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
truncating the values in order to force all negative values to have a value of zero.

1. In the Project Explorer, select the “ 3D Scatter Data” folder.

2. Select Interpolation | Interpolation Options… to bring up the 3D Interpolation

Options dialog.
3. In the section on the lower right, turn on Truncate values.
4. Select Truncate to min/max of dataset.

5. Click OK to close the 3D Interpolation Options dialog.

Because the interpolation options were changed, the data needs to be reinterpolated:

6. Select Interpolation | Interpolation → 3D Grid to bring up the Interpolate →

Object dialog.
7. Enter “c_idw_quad_trunc” as the Interpolated dataset name.

8. Click OK to close the Interpolate → Object dialog.

Notice that the minimum value listed in the color legend is zero (Figure 10).

Figure 10 Truncated values

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10 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.

10.1 Display Options

Before setting up the animation, 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. Using the Select Cross Sections tool, select the cross section by clicking on
it, then press the Delete key.

3. Select Grid | Isosurface Options… to bring up the Isosurface Options dialog.

4. Turn on Contour specified range, then enter “1000.0” for Minimum value and
“15000.0” for Maximum value.

5. Click OK to close the Isosurface Options dialog.

10.2 Setting Up and Playing the Animation

To set up the animation:

1. Select Display | Animate… to bring up the Options page of the Animation

Wizard dialog.

2. In the Options section, turn on Cross sections / Isosurfaces and click Next to go
to the Cross Sections / Isosurfaces page of the Animation Wizard dialog.
3. Turn on the Animate cutting plane over specified XYZ range section.
4. Turn on Z.

5. Click Finish to close the Animation Wizard dialog.

Open a media player application outside of GMS and open the mp4 file. Feel free to
adjust the speed of the animation to allow more time to examine each cross section.
When finished, close the application and return to GMS.

11 Setting up a Moving Isosurface Animation

Another effective way to visualize the plume model is to generate an animation showing
a series of isosurfaces corresponding to different isovalues.

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To set up the animation, do as follows:

1. Select Display | Animate… to bring up the Options page of the Animation

Wizard dialog.

2. In the Options section, turn on Cross sections / Isosurfaces and click Next to go
to the Cross Sections / Isosurfaces page of the Animation Wizard dialog.
3. Turn off the Animate cutting plane over XYZ range section.
4. Turn on the Animate isosurface over specified data range section.
5. Enter “1000.0” for the Begin value.
6. Enter “15000.0” for the End value.
7. Turn on Cap above and Display values.

8. Click Finish to close the Animation Wizard dialog.

Open a media player application outside of GMS and open the mp4 file. Feel free to
adjust the speed of the animation to allow more time to examine each layer of the
isosurface. When finished, close the application and return to GMS.

12 Conclusion

This concludes the “Geostatistics – 3D” tutorial. The key concepts discussed and
demonstrated in this tutorial include the following:

 There are several 3D interpolation algorithms available in GMS.

 Mesh-centered grids are better than cell-centered grids if using interpolation and
not using MODFLOW.

 Isosurfaces 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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