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~
Manual for the software package SP3D
Sponsored by the following CEA Technologies Inc. Dam Safety
Interest Group members:
British Columbia Hydro and Power Authority
ELFORSK
Great Lakes Power Limited
Manitoba Hydro
New Brunswick Power
New York Power Authority
Ontario Power Generation
Hydro-Qubec
U.S. Bureau of Reclamation
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UBC-Geophysical Inversion Facility
Department of Earth and Ocean Sciences
University of British Columbia
Vancouver, BC, V6T 1Z4
GIF
CONTENTS
Introduction................................................................................................................ 1
Background Coupled Flow Theory ........................................................................... 1
Numerical Modelling Procedure ............................................................................... 3
General Procedure for Forward Modelling Self-Potential Fields using SP3D ......... 3
Define the problem ................................................................................................. 4
Discretize the earth ................................................................................................. 4
Construct the hydraulic model ................................................................................ 4
Run Visual MODFLOWTM ..................................................................................... 5
Construct and verify the electrical model ............................................................... 6
Run SP3D................................................................................................................ 8
View results ............................................................................................................ 8
Running SP3D from the Command Line................................................................... 8
SP3D Input File Format ............................................................................................. 9
SP3D Output Files .................................................................................................... 12
Viewing SP3D Results............................................................................................... 13
References.................................................................................................................. 14
Appendix I: SP3D example ...................................................................................... 15
Appendix II: Tips for embankment dam studies........................................................ 20
This manual is produced as part of the CEATI Dam Safety Interest Group Project
Investigation of Geophysical Methods for Assessing Seepage and Internal Erosion in
Embankment Dams, Project number T992700-0205, Initiative Development of Self-Potential
and Electrical Resistivity Methods for Investigation of Embankment Dam Conditions
Sub-task SP Modelling and Interpretation, Sub-task #SP3.
~
UBC-Geophysical Inversion Facility,
Department of Earth and Ocean Sciences,
University of British Columbia,
6339 Stores Road, Vancouver, BC, V6T 1Z4.
SP3D MANUAL
July 5, 2005
Introduction
SP3D is a flexible forward modelling program for calculating the self-potential distribution resulting from
seepage flow through a 3D volume of earth (such as an earthfill dam) that is discretized using a mesh of
rectangular cells. It is run in the MS Windows environment, using a graphical user interface (GUI) or
alternately from the command line. The UBC-GIF utility MeshTools3D is used to examine resulting
scalar or vector quantities throughout the model volume. A second UBC-GIF utility, SP-data-viewer,
enables the comparison of contour maps and line plots of data calculated by SP3D (predicted data) and
field measurements (observed data).
This document provides details regarding the use of SP3D. A brief outline of background theory is
presented, followed by an outline showing the essential procedure involved in using this program.
Finally, a short section outlines some suggestions for viewing calculated results, and a case example is
included as an appendix. The bulk of this manual provides details on file structures and parameters for
controlling the calculations. Other related documentation includes:
Theoretical papers published in the scientific literature (see References at the end of the document);
A manual in HTML format for the UBC-GIF 3D viewer and model builder called MeshTools3D (see
the UBC-GIF website at http://www.eos.ubc.ca/research/ubcgif/software/documentation.htm for the
latest version of this utility and its documentation);
A short instructions sheet for the UBC-GIF data viewer called SP-data-viewer.
SP3D requires several input files that describe mesh discretization and hydraulic conditions within the 3D
volume. The required format of these files matches that of output files generated from the software Visual
MODFLOW. General notes on the use of Visual MODFLOW for seepage analyses are outlined in
this document, with a focus on how to generate the files required for use with SP3D. However, the user is
directed to the documentation provided with Visual MODFLOW for a more thorough treatment of its
application to seepage or groundwater flow studies.
i = Lij j
(1)
pg. 1
Where thermal and chemical concentration gradients are considered negligible, two coupled flow
equations emerge in application to the study of streaming potential:
q = K h k e
J = J conv + J cond = L h
(2)
(3)
Equation 2 describes volumetric fluid flux, q [m/s] using Darcys law and an electro-osmotic fluid flow
term, where K [m/s] is hydraulic conductivity, h [m] is hydraulic head, ke [m/s per V/m] is the coefficient
of electro-osmotic permeability, and [V] is electrical potential. In the absence of external current
sources, the hydraulic flow equation may be decoupled and seepage analysed directly using Darcys law
in materials where K > 10-9 m/s (Mitchell, 1991), and particularly in application to embankment dams
where large hydraulic gradients exist.
The current density J [A/m2] described in Equation 3 consists of Jconv, which represents the convection or
streaming current, and Jcond, which describes the flow of conduction current. Based on the convection
current approach developed by Sill (1983), the streaming current, Jconv is described using L [A/m2], the
streaming current cross-coupling conductivity. This cross-coupling term is a function of both a streaming
potential coupling coefficient C, which is defined through laboratory-based permeameter measurements,
and the bulk electrical conductivity of the medium, by the relation L = C . The term Jcond is described
using Ohms law where is electrical conductivity [S/m].
Because electrical charge is conserved, the divergence of total current density J in the domain must equal
the time rate of change of volumetric charge, e. That is J +
e
= 0 . The total current density is
t
equal to the sum of the convection and conduction current densities. Therefore, an equation used to solve
for electrical potentials can be written by taking the divergence of Equation 3, where e is the volumetric
charge density [C/m3] and I is the current flow per unit volume [A/m3].
( L h) ( ) =
e
I
t
(4)
Under steady-state flow conditions and in the absence of external current sources within the domain, the
right hand side of Equation 4 becomes zero. Regardless of the nature of the hydraulic flow regime,
steady-state behaviour may be assumed in the analysis of electrical flow, based on the magnitude of
hydraulic and electrical relaxation times (Wurmstich, 1995). The relations governing any analysis of the
self-potential response to seepage are given in Equations 5 and 6. Both transient and steady-state forms of
the hydraulic flow equation are given in Equation 5, where Q [m3/s.m3] is volumetric flow, and SS [m-1] is
specific storage.
h
+ Q; ( K h) = Q
t
( ) = ( L h)
( K h ) = S s
(5)
(6)
pg. 2
pg. 3
The remainder of this section outlines a 6-step procedure for modelling the self-potential response to
seepage flow using the program SP3D. In the appendix this procedure is illustrated by working through
each step for one example.
{Note: in the following text and in the GUI programs, we interchangeably describe the electrical
properties of the earth using electrical conductivity (S/m) and electrical resistivity (Ohm-m)}
1. Define the problem.
Delineate the area under study. The user must decide the physical extents of the model and what level of
analysis to perform, i.e. whether to perform a localized study of hydraulic flow or to include the influence
of regional flow in the analysis. The suitability of a steady-state versus transient seepage analysis, and a
saturated versus variably flow approach must also be assessed on a case-by-case basis. For the electrical
flow analysis in SP3D, a steady-state approach is always assumed, as discussed in the previous section
detailing coupled flow theory. SP3D is capable of analysing output resulting from both saturated and
unsaturated flow analyses.
2. Discretize the earth.
Discretization of the model domain is performed entirely in the Visual MODFLOW environment.
a. Define the dimensions of the model domain.
i. The user is prompted for domain dimensions and cell size upon creating a new project in Visual
MODFLOWTM, and a rectilinear grid is generated.
b. Design the mesh.
All functions pertaining to grid design are located within the Input Grid menu in Visual
MODFLOWTM.
i. Inactive cells within the rectilinear mesh may be used to delineate irregular topography, such as
the sloped surface of an embankment. Cells may be defined as inactive using the menu function
Inactive Cells, which restricts them from any calculations performed within Visual
MODFLOWTM. The discrete approximation of a stepped surface should not affect the final
solution given an appropriate choice of cell size.
ii. Mesh discretization is controlled through the Edit menu function. The level of discretization is a
compromise between calculation speed, memory capacity and accuracy. Calculations are faster
when fewer cells are used, yet higher accuracy requires a greater number of cells. For a given
problem, the cell size should be large enough to represent the average physical properties used to
characterize the material under study, but small enough to allow variations within a single soil or
geologic unit to be represented effectively. Consequently, the use of non-uniform mesh spacing is
preferred where large gradients are anticipated. A comparison of solutions resulting from a series
of coarser grids will help to determine the maximum cell size appropriate for a given zone.
3. Construct the hydraulic model.
The hydraulic model is defined within Visual MODFLOW. The model property zones defined within
MODFLOWTM are subsequently used in SP3D to delineate the distribution of electrical properties.
pg. 4
Solutions generated using this approach give predicted hydraulic head values in cells at or below
the phreatic surface. MODFLOW-SURFACT is an advanced module that may be used to perform
variably saturated flow analyses from the Visual MODFLOWTM platform, and is a useful tool in
solving difficult unconfined flow problems. Users of the MODFLOW-SURFACT numeric engine
must specify additional parameters that define properties of the unsaturated zone above the
phreatic surface, which are not discussed here. Solutions generated using MODFLOWSURFACT give the predicted hydraulic head distribution throughout the domain. When running
SP3D using the output from a MODFLOW-SURFACT analysis, the user may choose whether or
not to include the head distribution above the phreatic surface in the calculation of streaming
current sources.
ii. Parameters influencing the forward modelling solution, including analysis type, solver
parameters, initial head values, and recharge options, are controlled within the Run menu. The
hydraulic flow analysis is initiated by selecting Run Translate/Run.
iii. Visual MODFLOWTM files required by SP3D include *.vmg (grid) and *.vmp (parameter) files,
which are automatically output when running Visual MODFLOWTM. An output *.asc file that
defines the hydraulic head in each grid cell must be created by the user. This file should be
generated from the Output menu in Visual MODFLOWTM, when hydraulic head contours are
displayed in the Output window. The user must select File Export XYZ ASCII using the
preferred coordinate system, and must specify the *.asc file extension. {Note: the model may
have to be viewed in layer mode in order to export valid head data.}
5. Construct and verify the electrical model.
The electrical model is defined within SP3D, and six input files are required. Three files are generated
from the Visual MODFLOWTM analysis (*.vmg, *.vmp, *.asc), and three files are specific to SP3D
(sp3d.inp, zone file, receiver locations file). Complete descriptions of these files are included in the
SP3D Input File Format section.
SP3D may be run as a Windows-based program (SP3Dgui.exe) or directly from the command line
(sp3d.exe). Usage of the Windows-hosted program SP3Dgui is outlined here. Instructions on running
sp3d.exe are included in the section entitled Running SP3D from the Command Line.
a. Specify input files.
i. Note that file names and paths should not contain spaces.
ii. Each input filename can be specified with a path that is absolute or relative to the working
directory so it does not matter where they reside on your computer.
MODFLOW file names: Specify MODFLOW file names (*.vmg, *.vmp, *.asc) and the numeric
engine used in the seepage analysis. If MODFLOW was used to perform the hydraulic analysis,
hydraulic head values are only calculated below the phreatic surface, and SP3D considers all
hydraulic head values above the phreatic surface to be zero. If MODFLOW-SURFACT was used to
perform the hydraulic analysis, hydraulic head values are calculated for the unsaturated zone above
the phreatic surface. The user may choose to include or discard these head values for the purposes of
the electrical flow analysis in SP3D. If SURFACT (sat) is selected, a saturated-flow approach is
used to calculate the streaming current source distribution in the model. If SURFACT (unsat) is
pg. 6
chosen, all predicted head values are accepted and included in the SP3D forward model.
Zone file: The user may create a new file by selecting Edit. The electrical properties for each model
zone defined in Visual MODFLOWTM must be entered. These include saturated and unsaturated
resistivity, and streaming current cross-coupling coefficient. {Note: the streaming current crosscoupling conductivity (L) should be entered as a positive quantity.} In embankment dam studies, the
resistivity of the reservoir water and the elevation of upstream and downstream water levels must be
specified. The water levels should coincide with Constant head boundaries specified in Visual
MODFLOWTM and should be consistent with the height/elevation system used to define the z-axis,
as defined in the *.asc file. Hydraulic conductivity is read in from the .vmp file and displayed for
reference. The user can add an optional comment to help identify the zone.
The padding resistivity must be specified by the user. This value is used to help define the electrical
properties of the padded grid (see item b below). In embankment dam studies, the padding resistivity
is often used to represent foundation material/bedrock.
The position of the phreatic surface is used to assign saturated and unsaturated resistivity values
within a given zone. When SURFACT (sat) or SURFACT (unsat) is selected as the numeric
engine, the phreatic surface is defined using the condition: head = elevation (z). If a distinct zone is
used to delineate surface water, the user should identify this zone number as it is also used to help
identify unsaturated cells in the model.
When all parameters are entered, use the Save button to create the zone file.
Receiver locations file: The user must specify a 3 column file containing the reference electrode
position (to which all electrical potential data predicted by the forward model are referenced) that
also includes at least one coordinate defining an actual or simulated measurement electrode position.
These data points are used to create the data_phi.txt output file; see input line E below.
b. Specify padding conditions.
In order to solve for the distribution of streaming potentials throughout the model, SP3D imposes an
electrical no-flow boundary at the edges of the mesh. In order to prevent boundary effects from
influencing the solution within the limits of the model, the extents of this original mesh must be
expanded with the use of padding cells.
i. The user must specify the electrical resistivity structure of the padding cells, using one of four
options. The dimensions of the padded grid must also be specified (see descriptions for
sp3d.inp Lines G and H in the SP3D Input File Format section).
c. Specify the solver parameters.
Solver parameters determine how the large system of equations is solved. They include
preconditioner type and convergence criteria (see descriptions for sp3d.inp lines K and L in the
SP3D Input File Format section). The default solver parameters should be sufficient for most
applications. See Haber et al (2000).
d. Save input parameters.
Once the user has entered parameters for the required forward calculations, this run-specification
must be saved by selecting File Save. The details of this set of SP3D calculations will be saved
in a file called sp3d.inp in the working directory. All output files created by SP3D will be stored
pg. 7
pg. 8
For each zone as defined in Visual MODFLOWTM, the following 3 values are entered per line (separated
by spaces):
Saturated electrical resistivity [Ohm.m]
Unsaturated electrical resistivity [Ohm.m]
Streaming current coupling coefficient [A/m2] (Note: positive value must be entered)
After the zone information, the following values are included on separate lines:
Resistivity of water [Ohm.m]
Padding resistivity [Ohm.m] (used to simulate foundation or host material)
Upstream reservoir level [metres]
Downstream surface water level [metres]
Upstream base level [metres] (default = 0)
Downstream base level [metres] (default = 0)
Zone value that corresponds to water (OPTIONAL if no individual zone is defined in Visual
MODFLOWTM to delineate surface water, the user may leave the line blank or enter zero).
N.B.: The water levels should be consistent with the height/elevation coordinate system used to
define the z-axis, as defined in the SP3D input *.asc file.
Input File Line E:
receiver locations file: (e.g. recv.txt)
A three column file listing the coordinates of all measurement points (actual or simulated) for which
electrical potential (SP) data is required. The first line in the file specifies the coordinates of the reference
electrode. All subsequent lines should contain measurement electrode coordinates according to the format
shown below. Note that SP3D calculates potentials (phi) at the centers of all active cells in the 3D model.
However, measurement points in the recv.txt file can be anywhere in the model. Measurements at
specified points will be interpolated from potentials in the nearest cells.
Xbase Ybase Zbase
X1 Y1 Z1
:
Xn Yn Zn
If the Z value is less than -9999, the electrode is placed on the ground surface (uppermost active cell). All
coordinates should follow the convention given by the *.asc file.
Input File Line F:
NONE
Reserved for future use.
Input File Line G:
padding type (1 - 4)
Used to specify the electrical resistivity values of the padding cells.
Type 1 - Extend all model boundary properties to edges of padded grid.
Type 2 - Assign padding resistivity (used to simulate foundation or host material) to all padding cells
below the model, and air to all padding cells above. Existing X and Y boundaries are extended
pg. 10
only used if ILU preconditioner is chosen. Sets the threshold for dropping small terms in
the factorization.
tolerance for convergence.
maximum number of iterations to perform.
zone model
Div * -sigma*Grad*phi model
Div * -L*Grad*h model
Div*J = Div*(-sigma*G*phi - L*G*h)
-sigma*G*phi - L*G*h field
These files define the 3D mesh used by SP3D. They have the following format:
nx ny nz
x0 y0 z0
dx_1 dx_2 ... dx_nx
dy_1 dy_2 ... dy_ny
dz_1 dz_2 ... dz_nz
Parameters are defined as follows:
nx, ny, nz - number of cells in the X, Y, and Z directions.
x0, y0, z0 - coordinates of the top south west corner of the mesh:
dx, dy, dz - cell widths.
An example of mesh files is given in the Appendix I showing the embankment example.
sigma.txt :
Conductivity model {based on mesh.txt}.
sigma_padd.txt : Padded conductivity model {based on mesh_padd.txt}.
These files contain the electrical conductivity for all cells in the model. The first number is the
value of the top south-western cell. The values are ordered such that Z (depth) changes the fastest,
followed by X (easting), followed by Y (northing).
Although electrical resistivity values are input to define each zone of the model, the electrical
conductivity structure of the model is listed in the output file. These values may be toggled to be
displayed as resistivity within MeshTools3D. Air cells are assigned an electrical conductivity value
pg. 12
of 1e-8 S/m. For improved visual representation of topography in MeshTools3D, these cells may
be ignored.
head.txt :
Kx.txt :
Inactive cells are assigned hydraulic conductivity values in Visual MODFLOW, even though they
are not included in the calculation of hydraulic flow. Consequently, SP3D assigns a dummy
hydraulic conductivity of 1e-30 m/s to all inactive cells to improve the visual representation of this
parameter in MeshTools3D.
L.txt :
Air cells are assigned a null cross-coupling coefficient value of 1e-12 A/m2. When MODFLOW or
SURFACT (sat) are selected for numeric engine, all cells above the phreatic surface are assigned a
cross-coupling coefficient value of 1e-12 A/m2. For improved visual representation of surface
topography and/or topography of the phreatic surface in MeshTools3D, these cells may be ignored.
I_src.txt :
In a steady-state electrical flow analysis, the streaming current source terms are equal in
magnitude and opposite in sign to the conduction current source terms.
phi.txt :
q.fld :
Jconv.fld :
Jcond.fld :
When vector fields are displayed in MeshTools3D, the colour bar displays the log10 (amplitude).
The three columns of the *.fld files list the x, y and z components of the vector field.
data_phi.txt :
sp3d.log :
Alternatively, the forward modelled measurements (predicted data) can be viewed by clicking the data
button on the tool bar (or using the View menu). This will pop up the UBC-GIF utility called sp-dataviewer with a contour map of the predicted measurements that were specified by the receiver locations
file (see Input File Line E). This viewer can also display a second data set, for example one that contains
measurements from a field survey. Line profiles can be selected on either of these contour maps by
clicking with the mouse, and line graphs of the selected profile from both contour maps will be displayed
together for comparison. The UBC-GIF utility also has a short instruction page with details about using
this tool.
References
De Groot, S.R. (1951), Thermodynamics of Irreversible Processes , in Selected Topics in Modern
Physics, Vol.3, J.de Boer, H.Brinkman and H.B.G.Casimir, ed. North Holland Publishing Company,
Amsterdam.
Haber, E., Ascher, U., Aruliah, D., and D.W. Oldenburg (2000), Fast Simulation of 3D Electromagnetic
Problems using Potentials, J. Comput.Phys., 163, p.p.150171.
Mitchell, J. K. (1991), Conduction Phenomena: From Theory to Geotechnical Practice, Geotechnique,
43(3), p.p. 299-340.
Sheffer, M.R. (2002), Response of the Self-Potential Method to Changing Seepage Conditions in
Embankment Dams. M.A.Sc. thesis, University of British Columbia.
Sill, W.R. and T.J. Killpack (1982), SPXCPL: Two-Dimensional Modeling Program of Self-Potential
Effects from Cross-Coupled Fluid and Heat Flow -Users Guide and Documentation for Version 1.0,
Earth Sciences Laboratory, University of Utah Research Institute, Salt Lake City. Report for U.S.
Department of Energy, Division of Geothermal Energy.
Sill, W.R. (1983), Self-Potential Modeling from Primary Flows, Geophysics, 48(1), p.p.76-86.
Wilt, M.J. and D.K. Butler (1990), Numerical Modeling of SP Anomalies: Documentation of Program
SPPC and Applications , in Geotechnical Applications of the Self Potential (SP) Method , Report 4,
Department of the Army, US Army Corps of Engineers, Technical Report REMR-GT-6.
Wurmstich, B. (1995), 3-D Self-Consistent Modeling of Streaming Potential Responses: Theory and
Feasibility of Applications in Earth Sciences. Ph.D. thesis, Texas A&M University.
pg. 14
2.
3.
4.
5.
6.
Run SP3D
7.
View Results
Steps 1 through 4 are carried out within the Visual MODFLOWTM environment. For this example, the zones
employed for this model are shown in the image below, taken from the Visual MODFLOWTM program.
pg. 15
!
!
!
!
!
!
!
!
!
!
units
Kx.txt
mesh.txt
m/s
L.txt
mesh.txt
A/m^2
head.txt
mesh.txt
hydraulic head
I_src.txt
mesh_padd.txt
A/m^3
sigma.txt
mesh.txt
Electrical conductivity
S/m
sigma_pad.txt mesh_padd.txt
Jconv.fld
mesh.txt
q.fld
mesh.txt
Fluid flux
m/s
pg. 16
L.txt
head.txt
sigma.txt
For comparison the padded version of the conductivity model (sigma_padd.txt) is shown below (as a mesh
rather than with solid blocks):
The following files are available for viewing in MeshTools3D after SP3D has calculated all potentials.
File name
units
phi.txt
mesh_padd.txt
Volts
Jcond.fld mesh.txt
phi.txt
Jcond.fld
q.fld
Two other text files are produced when SP3D performs calculations, data_phi.txt and sp3d.log. Details follow:
data_phi.txt: contains measured potentials according to locations
specified in the recv.txt file - see SP3D manual, Input Files line E. It is a
four column file with locations (X, Y, Z) and potential referenced to the
location in the first line of recv.txt. The image to the right shows the data
plotted using the UBC-GIF SP-data-viewer, with one curving profile
plotted as a line graph.
The next image shows this viewer comparing calculated data to field measurements (simulated, and based on
data_phi.txt) in the left-hand contour plot. In this mode both profiles are plotted on the graph.
pg. 18
Finally, there is a file called data_phi2.txt provided with the example. This was created to simulate a field data set. It
was not produced by SP3D. You can change this file with a text editor or spreadsheet to more closely resemble a
likely field survey data set. Dont forget to replace TAB characters with spaces if you make files for UBC-GIF
codes using a spreadsheet.
pg. 19
Drain cells are the most effective way to model a seepage face using MODFLOW.
In cases of complicated geometry where steep gradients exist, delineation of the reservoir as an
independent zone exhibiting a high hydraulic conductivity value may help to ensure convergence
of the model.
the user should be careful with the selection of Model coordinates versus World coordinates in
Visual MODFLOWTM when creating the *.asc file. The user should always output the coordinate
system they wish to work with in SP3D.
pg. 20