chapter 8 – rift2d preprocessor and post processors

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CHAPTER 8 – RIFT2D PREPROCESSOR AND POST PROCESSORS David Butler & Mark Person New Mexico Tech, Hydrology Program August 15, 2010 Introduction Before you launch the preprocessor application, you’ll need to create an image of your basin and then decide on the basin parameter information you want to use in your RIFT2D application. Some of the supported image files include BMP, JPEG, PNG, GIF, TIFF formats. You will need to create a digitized file of this image which will contain the positions of formation boundaries to define different periods of tectonic subsidence. Instructions on how to do this using Matlab based digitizing software is described at the end of this chapter. The image of your basin must display the boundaries of your stratagraphic units. This image should represent the basin at its maximum thickness of the basin prior to erosion. An example image is shown in Figure 8.1. The resulting digitized data deck for this example problem is shown in Table 8.1. If erosion hasn’t removed significant amounts of material, then this would simply be an image of the present day cross section. However, if you wish to represent erosion, then you’ll need to create a GIF image which represents the basin geometry prior to erosion. You’ll also need to know the material properties you wish to assign to various hydrostratigraphic units (e.g. thermal conductivity, permeability, porosity at land surface, compressibility, etc.) and boundary conditions parameters (e.g. basal heat flow, surface temperature, water table heads, etc.) information. Below we describe the steps required to generate a RIFT2D data set using the preprocessor. Note that these data sets can be run within the preprocessor using RIFT2D or saved as ASCII files for later use in RIFT2D.

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Page 1: CHAPTER 8 – RIFT2D PREPROCESSOR AND POST PROCESSORS

CHAPTER 8 – RIFT2D PREPROCESSOR AND POST PROCESSORS

David Butler & Mark Person New Mexico Tech, Hydrology Program August 15, 2010

Introduction

Before you launch the preprocessor application, you’ll need to create an image of

your basin and then decide on the basin parameter information you want to use in your

RIFT2D application. Some of the supported image files include BMP, JPEG, PNG, GIF,

TIFF formats. You will need to create a digitized file of this image which will contain the

positions of formation boundaries to define different periods of tectonic subsidence.

Instructions on how to do this using Matlab based digitizing software is described at the

end of this chapter. The image of your basin must display the boundaries of your

stratagraphic units. This image should represent the basin at its maximum thickness of the

basin prior to erosion. An example image is shown in Figure 8.1. The resulting digitized

data deck for this example problem is shown in Table 8.1. If erosion hasn’t removed

significant amounts of material, then this would simply be an image of the present day

cross section. However, if you wish to represent erosion, then you’ll need to create a GIF

image which represents the basin geometry prior to erosion. You’ll also need to know the

material properties you wish to assign to various hydrostratigraphic units (e.g. thermal

conductivity, permeability, porosity at land surface, compressibility, etc.) and boundary

conditions parameters (e.g. basal heat flow, surface temperature, water table heads, etc.)

information. Below we describe the steps required to generate a RIFT2D data set using

the preprocessor. Note that these data sets can be run within the preprocessor using

RIFT2D or saved as ASCII files for later use in RIFT2D.

Page 2: CHAPTER 8 – RIFT2D PREPROCESSOR AND POST PROCESSORS

Figure 8.1 Schematic diagram showing cross sectional representation of a rift basin with two periods of tectonic subsidence. The formation boundaries (sands and shales) are defined by the squares. The tectonic time period boundary is defined by the thick solid line. The open circles define digitized nodal columns where the elevation of the tectonic time period is determined.

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Table 8.1 Ascii data file containing information from Figure 8.1. NodalColumnsNodalRowsErosionalFlagErosionalAge(Myr)NumberofFaults73000TectonicTimePeriodInformationPhi_0Beta(1/m)DepositionalAge(Myr)0.52.0e‐4200.52.0e‐430XY0 00 20000 40005000 1465000 20175000 377512300 38312300 209612300 356120000 60820000 216320000 334632420 100332420 224232420 313247490 149947490 235547490 303160000 189360000 247960000 3008TopSurfaceXYZminitflagicflag0 38003600115000 360034001112300 340032001120000 320030001132420 313229321147490 303128311160000 3008280811NPolylines2NPointsMat91XY0 40004912 378612586 352720069 334632423 313247706 298660000 297560000 18700 0NPointsMat132XY0 37753480 35046888 32908704 30998100 27275714 23664569 20176735 16239951 156613582 142010369 6544639 3940 327

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The steps that need to be taken to implement the preprocessor are discussed below. STEP 1. START UP THE PREPROCESSOR Within MATLAB, navigate the directory where you have installed the preprocessor. The

folder should be named “Rift2D_Preprocessor_Package”. Then at the MATLAB

command line prompt, type

NMT_RIFT2D_Preprocessor_10 A GUI (graphical user interface) window containing a series of options and a graphics

window should appear (Figure 8.2). The GUI contains a series of buttons that allow the

user to modify preset parameters for material properties, boundary conditions, and input

Figure 8.2. Window which appears upon launching the preprocessor for RIFT2D. output options. The functions of these buttons are described in Table 8.2. A digitized file

containing information about your cross section is opened by clicking on the “Load Data

File” push button.

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Table 8.2 Description of Push Button Functions used in Rift2d Preprocessor GUI. Push Button Name Function Load Data File Imports ascii file containing digitized information

regarding the cross section to be modeled. Material Properties Allows user to adjust the permeability, porosity,

thermal and solute transport properties assigned to stratigraphic units.

Flow and Transport Flags Sets variables IFLOW, IHEAT, IBRINE to 1 or 0 by clicking on radio buttons

Boundary Conditions Allows user to turn off/on groundwater flow, heat, solute transport.

Column Wise B.C. Data Allows the user to specify column wise head, heat flux, temperature, and concentration data per tectonic time period.

Well and Element Output Data Allows the user to specify well and element data. IO – Time Step Control Allows the user to change the IPRINT value and the

number of timesteps. It also reports the DT that will be used for the number of timesteps.

Grid Parameters Allows the user to change the PHIGRD1, the PHIGRD2, and the Grid Tuning Factor.

Add Columns and Select Delz Allows user to increase the number of columns and change the vertical discretization. The default vertical discretization is initially set at 100m.

Save Session Allows the user to save the current session to be loaded at a later date.

Load Session Allows user to import a prior preprocessor session file Export Allows the user to export the data to a input file for the

rift2d fortran code. Run Rift2D Allows the user to run the rift2d fortran code from the

preprocessor. It exports to a pre-defined file and then runs rift2d with this file.

Open Post Processor Allows the user to open the post processor to view the results of the most recent run of rift2d. It opens the default rift2d output “rift_tec.dat”.

STEP 2. Importing Digitized Data of Basin Cross-Section Click the “Load Data File” button. A dialog window will appear. Select

“rift2d_preproc_example.txt” from the list of files in the desired directory and click open.

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It will now be displayed in the axes. A image containing your model section will appear

with 43 columns (Figure 8.3). Even though the input data set contained only 7 columns

Figure 8.3 Image of example data file in Rift2d preprocessor.

(Table 8.1), the rift2d preprocessor automatically determines the minimum number of

columns needed to construct a viable data deck for the Fortran computer code. A viable

data deck is one in which the number of nodes in an adjacent column during basin

evolution changes by no more node between adjacent columns. Also note that the vertical

discretization does not change between columns but the elements compact with depth.

Also note that while rift2d solves all transport equations using triangular finite elements,

only quadralaterals are displayed in the preprocessor window. A single value of Δz is

chosen for the entire mesh. The default value is 100m. As elements are buried by

subsidence, the Δz will decrease by mechanical compaction based on depth and the

parameters phigrd1, and phigrd2 according to Athy’s law.

φ = phigrd1⋅ exp −phigrd2 ⋅ depth[ ] (1)

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where φ is grid porosity, phigrid1 and phigrd2 are parameters from Athy’s law. Note that

porosity can also depend on pore pressure. Rift2d also computes porosity based on

effective stress and this porosity is used for the calculations of thermal conductivity,

permeability, etc. Porosity decreases with depth as a function of Athy’s law is shown

schematically in Figure 8.4.

Figure 8.4 Schematic diagram illustrating how grid porosity changes with depth and how elements consolidate in response to changes in porosity. The grid porosity parameters are updated by selecting the “Grid Parameter” Button

(Figure 8.2). When this is selected the GUI shown in Figure 8.5 appears.

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Once the file is read in, the basin will appear in the preprocessor window. For example,

the data file presented in Table 8.1 will appear as shown in Figure 8.5.

Figure 8.5. The grid parameters window. Note that there is a grid tuning factor in this GUI. We recommend setting this to between

100-105%. This was added because the Δz generated by the preprocessor are slightly

different from the grid produced in rift2d fortran code. This is due to the number of times

the code updates the grid. In the preprocessor, a backstripping algorithm is used which

doesn’t produce identical results to the forward model used in rift2d.

STEP 3. CHOOSING MATERIAL PROPERTIES FOR HYDROSTRATIGRAPHIC UNITS. Now select the “Material Properties” push button in the upper left hand corner of the

GUI. The following window will appear (Figure 8.6). You can modify the values of the

hydrogeology, thermal, and solute transport parameters for each hydrostratigraphic unit

for this cross section (in this case 2 material types). The material properties are described

in detail in Chapters 5 of the Rift2d documentation and will not be repeated here. You

can change which hydrostratigraphic unit is active with the drop down menu in the top

left hand corner of this GUI window.

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Figure 8.6 Material Properties Window. See Chapter 5 of Rift2d documentation for an explanation of these parameters. STEP 4. REFINING VERTICAL AND HORIZONTAL DISCRETIZATION Much of the grid refinement is done automatically by the preprocessor. The preprocessor

ensures that the mesh is sufficiently discretized so that rift2d won’t crash when you run it

(at least this is what we hope will happen). However, if you wish to increase the number

of nodal rows or nodal columns, you can do so. Click the “Add Columns and Select

Delz” button. This will launch a new GUI, which will allow you to add columns and

change the delz value for each tectonic time period (Figure 8.7). When a column is

selected, its color is darker than the others so you can tell which column you are splitting.

To add a column you must split a current column into two or more columns. From the

drop down menu select the column you wish to split, then select how many columns you

want to split it into, then click “Split Column”. You can only select one column or one

tectonic time period to adjust Delz at one time. To change the number of rows and the

row thickness of a given tectonic time period, edit the table of delz values. Once you

have decided on a delz value for each tectonic time period click “Apply Delz”. This will

then recalculate the rows and re-plot them. An example where Delz was changed to 80 m

for the second tectonic time period is shown in Figure 8.8.

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Figure 8.7 Add Columns and Select Delz GUI STEP 5. Selecting Transport Processes Select the push button “Flow and Transport Flags” directly to the right of the “Material

Properties” button. A series of radio buttons will appear (Figure 8.9, Table 8.3). All or

none of the flags can be turned on. If none of the flags are turned on, rift2d will generate

the grid upon execution. We recommend turning all the transport parameters off at first

allow the grid to evolve. If the mesh looks acceptable, turn flow on (IFLOW). If the flow

field looks acceptable, then turn on additional transport flags.

Table 8.3 Description of Radio Button Functions used in Flow & Transport Flags GUI. Radio Button Name Function IFLOW Turns on Groundwater Flow IHEAT Turns on Heat Transport IBRINE Turns on Brine/Solute Transport ICOUP Couples computed temperatures and salinity to fluid density and viscosity and

permits variable density flow ISTREAM Solves stream function equation. Not valid if active sediment deposition or

erosion is active IO18 Solve for kinetic models of fliuid-rock isotope exchange and transport (see

Bowman et al., 1994) IHEL Solves for 4-Helium Transport (see Bethke et al., 199x) ICOND Only permits conductive heat transport IOIL Kinetic models of oil generation and Hubbert Oil Heads IICE Allows ice sheets to modify hydraulic head boundary conditions. Ice sheets are

represented as polynomial functions (Person et al. 2003).

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The Add Column and Select Delz window. Figure 8.8 Updating vertical discretization between tectonic time periods. Tectonic time period 1 has a delz of 100m. Tectonic time period 2 has a delz of 80 me.

field looks viable. Then additional transport processes can be turned on. Note that rift2d

will soon be able to represent groundwater age, isotope transport, 4-Helium transport, and

ice-sheet aquifer interactions. Radio buttons exist for these but these options are not

active in the code.

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Figure 8.8 Flow and Transport Flags Window. STEP 6. ASSIGNING BOUNDARY CONDITIONS Click on the “Boundary Conditions” button is used to assign hydrologic, thermal, and

solute boundary conditions. The GUI shown in Figure 8.9 will appear. The

implementation of the boundary conditions are described in detail in Chapter 5 of the

Rift2d documentation and the variable definitions are only briefly repeated here for the

the groundwater flow boundary conditions. The head conditions are similar for the heat

flow and solute transport boundary conditions in Table 8.5.

Figure 8.9 Boundary Conditions Window.

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Table 8.4 Description of Radio Button Functions used in Boundary Conditions GUI. Property Name Function ihchk ihchk = 1; head assigned based top node elevation

ihchk=2; head = hdbase+hdinc*(time-tha) ihchk=3; head = msl+sin( ((time-tha)*2.*3.14)/thb))*hdinc

hdbase Base head (if you want to assign a different value for the head boundary than the elevation)

hdinc Slope parameter to increase specified head condition ihchk Couples computed temperatures and salinity to fluid density and

viscosity and permits variable density flow tha Constant to correct between absolute and local time for a given

tectonic time period (so that time starts at zero).

thb Scaling factor to determing the period of sea level cycle (only used when ihchk=3)

Msl Mean sea level (m) It is also possible to specify spatially varying concentrations, heads, temperatures and

heat flow along the top and bottom boundaries by clicking on the button “Column Wise

B.C. Data’. The following GUI will appear (Figure 8.10). This spreadsheet like GUI

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Figure 8.10 The Column Wise B.C. Data window.

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allows you to specify a linear variation across the entire grid but selection values for the

first and last columns. You can also subsequently modify individual column values.

STEP 8. Select Number of Time Steps and Graphical Output

The user can specify the number of time steps and how many time steps between when

graphical output is saved (IPRINT) by cliking on the “IO Time Step” Button. The GUI

shown in Figure 8.11 will appear. The time step size is determined by the preprocessor

and can’t be change directly. However, if a smaller time step size is desired, increase the

number of time steps.

Figure 8.11 The Time Step Control window.

STEP 8. DEFINE WELL AND ELEMENT OBSERVATIONS If you want to monitor time dependent output at points or profiles within the basin, select

“Well and Element Output” button. The GUI shown in Figure 8.12 will appear. You can

select up to six points. These will be written to the files point1_tec.dat: elem1_tec.dat,

elem2_tec.dat, elem3_tec.dat elem4_tec.dat, elem5_tec.dat, elem6_tec.dat). The vertical

profiles are written to the files well1_tec.dat, well2_tec.dat, well2_tec.dat, well3_tec.dat,

well4_tec.dat, well5_tec.dat, well6_tec.dat, well7_tec.dat, well8_tec.dat, well9_tec.dat.

The element numbers must be determined by the column and row location within the

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mesh. Elements increase from left to right and bottom to top. Element 1 is in the lower

left hand corner of the domain. If multiple fault blocks are included, element numbers

increase within the first fault block before moving to fault block 2 and so on.

Figure 8.12 Element and Well Output Window.

STEP 9. RUNNING RIFT2D Once you have created a data set, Rift2d can be run within the preprossor or as a stand

alone application that can be run later. Within the preprocessor, simply select the “run

rift2d” . You can also type rif2d from the dos command prompt window on a PC or

./rift2d on a linux or mac window. For long overnight runs, the later is recommended.

STEP 10. VIEWING RESULTS 10.1 Viewing Rift2d Output using Matlab Based Postprocessor The post processor allows you to view the output file from rift2d in MATLAB. The

postprocessor is called “NMT_RIFT2D_PostProcessor_10”. You can launch

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NMT_RIFT2D_PostProcessor_10 in the command line prompt of Matlab or from the

preprocessor. The “NMT_RIFT2D_Preprocessor_10” program includes a button that

allows you to launch the post processor. In this mode the file that is read is the default

“rift_tec.dat”. By loading through the post processor you can select the a unique file

name.

To launch the post processor from the preprocessor simply click the “Open Post

Processor” button from the preprocessor. It will then read the default file “rift_tec.dat”

and launch. If your running the postprocessor from the MATLAB command window,

load a file into the post processor by first clicking on the “File” menu then select “Load

File” (see Figure 8.12). This will open a window that will allow you to select a file to

load. Once you have selected the file you wish to open click “Open”. It will then begin

reading in the file. This can take quite some time depending on the size of the file. There

are message boxes that pop up to inform you of the progress. You will need to know the

number of time steps and the value of IPRINT to open a file from the command line

prompt of Matlab. Once the box that says, “Done” appears click “OK” and your file will

be displayed in the post processor.

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Figure 8.12. Loading a file into the post processor.

By changing the zone that you are viewing under “Select Zone to View” you will

progress the model through time. If you wish to select a specific zone use the drop down

menu. If you wish to progress the model forward or backwards in time by one time step

use the “Down Zone” and “Up Zone” buttons, respectively. By changing the variable

under “Select Variable to View” you will be able to view that specific variable at the

current zone. Under the “Display Options” menu and then the “Velocity Display

Options” sub-menu you can select which velocities you wish to view, if any. The

displayed velocities will correspond to the current zone (Figure 8.13). The minimum and

maximum velocities for the whole model are displayed in the bottom right hand corner of

the post processor. You can also choose to turn the mesh on or off in “Mesh Display

Options” sub-menu (See Figure 8.14).

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Figure 8.13. The post processor with the zone set to 40, the variable set to head, the scale adjusted to go from 3000 to 4000, the H2O velocities on, and the mesh off.

The scale on the right is set to the minimum and maximum values that the current

variable reaches throughout the whole run of the model. By altering the values in the

“Set Scale” boxes you can force the scale bar to a different range; however, it is

important to note that if you exclude valid values they will be assigned to the closest

possible value. For example, if the scale bar ranges from 0 to 100 and this range of

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values is displayed in your current zone and you change the scale to 40 to 80 then

everything with a value of 40 and below will be assigned a value of 40 and everything

with a value of 80 and up will be assigned a value of 80.

Figure 8.14. The post processor when it first launches. Zone 1 and temperature are selected.

By opening the “Animate” menu and then selecting “Animate Zones” you can

watch as the grid evolves over time. The animation will run based off of your current

variable selection and your current velocity and mesh display selections. The animation

tends to be a little slow and choppy the first time around, because MATLAB is plotting

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each zone one at a time. So once the animation has finished, you can click “Replay” in

the “Animate” menu to view the animation again. This time the animation will run much

more smoothly and will be easier to follow. If you wish to save a copy of this animation

you can click “Export Movie” this will save an AVI file, with the filename that you

specify, to the directory that you specify. If you do not edit the filename, the default

“postproc_movie.avi” will be used.

You can also save an image of a particular zone and variable selection. You can

do this by clicking “Save Image” in the “File” menu. It will save an image with the

specified filename and with the selected extension. If you do not change the filename or

extension it will export a PNG with the name “postproc_image”.

You can also zoom in, zoom out, pan, and reset the view. To do this, use the

icons on the toolbar below the menu bar. Starting from the left the icons are zoom in,

zoom out, pan, and reset.

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10.2 Viewing Rift2d Output using TECPLOT

RIFT2D output can also be viewed using the commercial software package

TECPLOT by Amtec Engineering. As of the publishing of this manual, the package sells

for $1200 dollars for private companies and $1000 for Universities. This graphics

package is especially suited for display and animation of finite element model output. In

addition, TECPLOT can generate graphical output in many formats including postscript,

TIFF, GIF, and EMF. The package is menu driven and fairly easy to use.

Several output files can be generated by RIFT2D by specifying PTEC = 1 on line

13 of the input data decks. RIFT2D will generate the following TECPLOT formatted

output files:

Unit #11 rift_tec.dat Contour fields, Velocity Vectors Unit #50 sfc_tec.dat Surface heat and fluid flux scattergram plots Unit #65 prf_tec.dat Field variables/depth scattergram plots Unit #66 elem1_tec.dat Flux/Temperature/Head

time scattergram plots for element (NREL) 1 Unit #67 elem2_tec.dat Flux/Temperature/Head

time scattergram plots for element (NREL) 2 Unit #68 elem3_tec.dat Flux/Temperature/Head

time scattergram plots for element (NREL) 3 Unit #69 elem4_tec.dat Flux/Temperature/Head

time scattergram plots for element (NREL) 4 Unit #70 elem5_tec.dat Flux/Temperature/Head

time scattergram plots for element (NREL) 5 Unit #71 elem6_tec.dat Flux/Temperature/Head

time scattergram plots for element (NREL) 6 Details of using TECPLOT to display RIFT2D model results can be found in the

TECPLOT Users guide. Below we provide a brief primer on how to display model

results. Once TECPLOT is installed and launched on your machine or Unix workstation,

go to the file menu and select the load option. Before displaying your data, TECPLOT

will convert RIFT2D data to binary format (Note that this can be done in advance of

implementing TECPLOT by typing “PREPLOT filename”).

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Displaying contour maps and Velocity Vectors

The following steps will allow you to view RIFT2D mesh and select field variables:

1. Select the file “rift_tec.dat” (or whatever name you have selected for Unit #11). Each

time step output will be read into TECPLOT as a separate “zone”. Recall that the total

number of zones is NTIME/IPRINT. Initially only the finite element mesh will be

graphically displayed (each zone in a different color).

2. To display the mesh and stratigraphy together, click on the “Contour” box in the

upper left hand corner of the TECPLOT window. The contour variable selection

window will appear. Select the “STRAT” variable (MTAG).

3. Select “Plot Attributes” at the bottom left part the the TECPLOT window (just above

the “snap to grid button”). Click on “Zone Num” button and select “select all”. All

zones should be highlighted now.

4. Click on the “Cont Plottype” button. Select the “Corner” option. This contour style is

ideal for stratigraphy while for other field variables such as HEAD or TEMP, we

recommend selecting “Flood” or “Both Flood and Line”. Next, select the “Mesh”

option at the top left part of the “Contour Attributes” window. Click on “Mesh Color”

button and choose a color for your mesh (we recommend black).

5. To view an individual zone, select that “Zone Show” in the Plot Attributes menu and

activate that zone (select “activate”). All other zones should be deselected (highlight

these and select “deactivate”). Then click on “Redraw” button on the left side of the

TECPLOT window. To animate all of the zones select “Tools>Animate>Zones”.

animation window will appear. Click on “Animate”.

6. To view heads and velocity vectors, go the the “Field” menu and select

“Field>Contour Variable”. Choose “HEAD”. Next Click on the “Vector” button on

the left edge of the TECPLOT window. A “Select Variables” window will appear.

Enter “VX” for “U” and VZ for “V” (the x and z components of the velocity vector).

Click on “Redraw”.

7. Select “Plot Attributes” and choose “Vector”. Select “Zone Num” and choose “Select

All”. Now select “Vect Color” and choose a color (we recommend black). If the

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velocity vectors are too small. Go to the “Field” menu and select “Field>Vector

Length”. To increase the size of the vector shaft, make the number larger in the

“Relative (grid units/cm) Field”. To make all vectors the same size, select the

“Uniform” option.

You can save a file graphics options you have selected by choosing “File>Save Layout”.

Displaying Scattergrams of Temperature and Groundwater Flux Verses Time

It some instances, the RIFT2D user may wish to display temporal output at a given

location (PELM=1). RIFT2D allows the user to generate up to six output files (elem1-

6_tec.dat; units 66-71). In addition, the user may wish to view surface conductive heat

flow and/or recharge/discharge across the top boundary (unit 55, scf_tec.dat). Finally,

profiles of head may be viewed along a well(s) using TECPLOT (unit 65; prf_tec.dat).

These scattergram plots can be displayed in TECPLOT by reading one or more of these

files. The instructions for viewing elemental output are as follows:

1. Select the file “elem1_tec.dat” (or whatever name you have selected for Unit #66).

Each time step will be read into TECPLOT. The total number of records is NTIME.

2. Initially, temperature (TEMP) verse time will be plotted as a scattergram. Other

variables that may be displayed include head (HEAD), the horizontal component of

velocity (QX), the vertical component of velocity (QZ), and the spatial coordinates

(X,Z). These are represented as different “maps”.

3. To display different variables, select “Plot Attributes” button. Then simply select

(highlight) a given map number and click on “map show”. Activate that scattergram

(e.g. map 7; time verses head). Be sure to deselect all other variables.

4. Select the menu option “View>Fit to Full size” to resize the scattergram.

5. To print output, select “File>Print”. To export in various formats, select

“File>Export”.

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The Preprocessor with the example file loaded. MATLAB BASED DIGITIZATION SOFTWARE

The preprocessor requires an ascii based file. There are many different digitizing

programs that can be used to create Ascii data file for the rift2d preprocessor (see

example, Table 8.1). A commercial code ArgusOne could be used for this. However, the

following public domain Matlab program available from the matlab file exchange. When

this document was written the program was available at

http://www.mathworks.com/matlabcentral/fileexchange/8139-digitize.

A copy of this program is available with the Rift2d_NMT distribution. It is in the

same folder with rift2d, rift2d_preprocessor_10, rift2d_postprocessor_10 (i.e.

Rift2D_Preprocessor_Package). Below we provide step by step instructions on how to

use this software to create the data that you will need for the preprocessor.

Step 1. Open Matlab

Then open Matlab and set the default directory to Rift2D_Preprocessor_Package.

Now type

Digitize

in the command prompt window. This will open the program, it may open in a window

larger than your screen, just resize it. The GUI shown in Figure 8.15 should appear.

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Figure 8.15 Digitizing GUI Image

Step 2. Load Image & Set Registration Points

The next step is to import your image with the requisite information regarding tectonic

time periods, erosion amounts, etc (see Figure 8.16). Click “Load” then “Image File” and

select the file you wish to digitize. Now you must set your known register points. This

allows the program to convert your selected points into real world coordinates. To do

this click “Transformation” then “Add Points”. Now simply click on the image at known

points. We recommend that you register at least four points. I always make them into a

square but in theory any shape will do. Once you have placed all of your points right-

click to exit the placing mode. Now you must input the true coordinates for each of these

points, to do this right-click on the point and select “Reference”. If you added an extra

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point by accident you can delete it by clicking “Delete” in the right-click menu. Once

you have referenced all of the points “Reference Data Complete” will be checked in

Figure 8.16 Basin cross section image read into digitizing software. Note that four registration points are included with this image: (0,0), (0,60,000) and (60,000, 4000) and (0,4000).

the “Transformation” menu.

Step 3. Digitizing Points.

Now that your image is registered, you can add in the points you want. To do this select

“Add Points” in the “Digitization” menu. It is important to note that the software will not

export your reference points so you must add these (again) while digitizing if they are

needed for your model. For this software to export the points in the format required by

the rift2d preprocessor, the order in which you digitize the points in is important. Start in

the bottom left hand corner of your model, and then add points up each column in the

model. So you will be working bottom to top, left to right. Once you have finished

digitizing the last column of your model right-click to exit the add points mode. You

may exit the add points mode and then continue adding points later, however, you must

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continue to add them in the same pattern or the output file will not be correct. If you add

in a point that you do not need, you can delete it at any time, when you delete it will not

affect the output. After you are satisfied with your points you must export them, to do

this click “Export” then click “Digitized Points to ASCII File”. This will allow you to

save a file with the X and Y coordinates of each point. These coordinates can then be

used in the preprocessor input file. For more information on what is needed in the input

file see “The Input Data File” section of the preprocessor user’s guide which is

“NMT_RIFT2D_Preprocessor_10_User_Guide.doc”.

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References

Bethke, C., Zhao, X, and Torgersen, T., 1999, Groundwater flow and 4He distribution in the Great Atresian Basin of Australia: Journal of Geophysical Research, v. 104, p. 12,999–13,011. Bowman, J.R., Willlett, S. D., and S. J. Cook, 1994, Oxygen isotopic transport and exchange during fluid flow: One-dimensional models and applications, American Journal of Science, v. 294, p. 1-55. Goode, D., Direct simulation of groundwater age. Water Resources Research, 1987. 32(2): p. 289-296.