Mt3dmain is a graphical user interface for MT3D, a modular three-dimensional transport program developed by Papadopulos and Associates for the U.S. Environmental Protection Agency (EPA). MT3D is a program designed to model contaminant transport based on a pre-solved ground-water flow model (MODFLOW is often used to solve the ground water flow equations (Chapter 15). MT3D uses the solution aquifer heads to base the transport results). In its basic form, MT3D can be difficult, or awkward to use. The mt3dmain program module is designed to simplify data entry, model editing, and analysis of results.

This chapter goes into the details of using mt3dmain as an interface for MT3D. It however does not explain the theory or use of MT3D, that is better left to the MT3D user's manual (Zheng, 1990).

WARNING: To use mt3dmain and MT3D effectively, you must have the MT3D user's manual, and it should be readily available whenever you are building data sets with mt3dmain. In the current release, mt3dmain does not error check data file formats; this can lead to incorrect numbers for any variable, and it can cause "segmentation faults" which will terminate mt3dmain. To find the problem, the data files may have to be examined line by line to determine where the problem is. This can only be done if the MT3D user's manual is available!

The mt3dmain application is composed of two sections; the main menu-bar, and the status and log text area. The menu-bar is used to select all mt3dmain commands, and the log/status area is used by the program to report important messages or results. In addition to the main window and supporting pop-up dialog windows, a graphical editor is available for creating and modifying two-dimensional arrays. Mt3dmain also use's other UNCERT (grid, contour, surface, and block) modules for visualizing model output.

NOTE: There is a public domain (Zheng, 1990, EPA) version of MT3D and a proprietary version (Zheng, 1990, Papadopulos). Both version are supported by this interface.

Figure 16.1

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Open Project:

View Project:

Save Project:

Save Preferences:

WARNING: if "mt3dmain.prf" already exists, you will be warned that it is about to be over-written. If you do not want the old version destroyed you must move it to a new file (e.g. the UNIX command mv mt3dmain.prf mt3dmain.old.prf would be sufficient). When you press OK the old version will be over-written! This cannot be done currently from within the application. To rename the you will have to execute the UNIX mv command from a UNIX prompt in another window.

If "mt3dmain.prf" does not exist in the current directory, it is created. This is an ASCII file and can be edited by the user. See Appendix C for details.

Quit:

Quit Without Saving:

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Each package has a pull-down sub-menu with five menu options: Open Package, View Package:Save, Save as, and Modify. The Open option generates a dialog similar to that shown in Figure 5.2. The dialogs works the same as that dialog too, except that the default file name extensions are different. For each package the default file name extensions are:

BASIC: *.bas
ADVECTION: *.adv
DISPERSION: *.dsp
SINK & SOURCE MIXING: *.ssm
CHEMICAL REACTION: *.rct

These file extensions are strictly conventions, and do not have to be followed. It, however, is recommended that you follow some consistent naming convention. The View menu option will display the last saved or loaded version of the data file.

NOTE: Changes made to a package within the mt3dmain application (using Modify below) will not be reflected in the data file until the changes have been saved (see Save below).

The Save menu option will save any modifications, overwriting the last opened or saved package file. If no package file has been loaded or saved previously, a pop-up dialog will appear similar to Figure 5.2, but showing the appropriate default file extension. To save the package file, select an existing file, or enter a new file name, then press the "Save" button on the dialog. Save as is similar to Save, except that you are queried for a file name. Modify will generate a new pop-up dialog which will allow the user to enter all the appropriate data for that particular package. These package dialogs are discussed below.

NOTE: The packages and dialogs discussed below explain how and where to enter data and package parameter values. The meaning of different variables is not discussed, and is left to the MT3D user's manual (Zheng, 1990).

WARNING: As dialogs are generated, default values will be assumed. These values though may have no meaning with regard to a particular model and it is the modeler's responsibility to insure all entries are correct.

NOTE: The LOCAT (Chapter 15, Utility Section) identifiers allowed by MT3D of 100, 101, 102, and 103 will be read from existing files correctly, but the data will be saved using conventional MODFLOW formatted formatting. When specifying unit numbers for the different MT3D packages, the following unit numbers must be used.

	BTN	= 1
	ADV	= 11
	DSP	= 12
	SSM	= 13
	RCT	= 14
	FLOW	= 15  (Ground water flow file)

Flow File:

Figure 16.2

Basic:

Figure 16.3

1).

HEADNG(32)

Heading (#1)

2).

HEADNG(continued)

Heading (#2)

3).

NLAY

Layers

NROW

Rows

NCOL

Columns

NPER

Stress Periods

4).

TUNIT

Name of Time Units (e.g. DAY or HOUR)

LUNIT

Name of Length Units (e.g. FT or CM)

MUNIT

Name of Mass Units (e.g. LBS of KG)

5).

TRNOP(10)

Transport Options logical flags: Ten entries are required on this line. Each entry is either a T or an F. One entry is required for each of the following package (XXX is a package that may be added at a later date, but is not currently used. Each of these options should receive a F).

ADV = advection module
DSP = dispersion module
SSM = sink & source module
RCT = chemical reaction module
XXX = Uninstalled
XXX = Uninstalled
XXX = Uninstalled
XXX = Uninstalled
XXX = Uninstalled
XXX = Uninstalled

6).

LAYCON

Layer Types button: To enter the layer type for each layer the dialog shown in Figure 16.4 is used. Note, only the top layer can be unconfined (Type 1). If there are more than ten layers, use the Next and Previous buttons to define all layers.

Figure 16.4

7).

DELR

Cell Width (along rows (x)) button: This calls the 1D utility array editor (See Chapter 15, U1DREL).

8).

DELC

Cell Height (along columns (y)) button: This calls the 1D utility array editor (See Chapter 15, U1DREL).

9).

HTOP

Top Elevation button: This defines the top elevation of the first (top) layer. To define the layer, press the Define Array Control Data button. This calls the utility 2D real array editor (See Chapter 15, U2DREL).

Figure 16.5

10).

DZ

Layer Thickness button: This calls the utility 2D real array editor (See Chapter 15, U2DREL).

11).

PRSITY

Layer Effective Porosity button: This calls the utility 2D real array editor (See Chapter 15, U2DREL).

12).

ICBUND

Layer Boundary Conditions button: This calls the utility 2D integer array editor (See Chapter 15, U2DINT).

<0 = Constant Concentration Cell
0 = Inactive Concentration Cell
>0 = Variable (active) Concentration Cell

13).

SCONC

Layer Starting Concentration button: This calls the utility 2D real array editor (See Chapter 15, U2DREL).

14).

CINACT

Dummy Inactive Cell Concentration Value

15).

IFMTCN

Print Concentration button: This flag indicates whether the calculated concentration should be printed. It also serves as a print format code. This value is entered using the pop-up dialog shown in Figure 16.6. The concentrations can be printed with different formats, using a Wrap or a Strip Format. They also can be Not Printed at all.

Figure 16.6

IFMTNP

Print Number of Particles button: This flag indicates whether the number of particles in each cell should be printed. It also serves as a print format code. This value is entered using a pop-up dialog similar to that shown in Figure 16.6.

IFMTRF

Print Retardation Factor button: This flag indicates whether the model calculated retardation factor should be printed. See Figure 16.6.

IFMTDP

Print Dispersion Coefficient button: This flag indicates whether the model calculated distance weighted dispersion coefficient should be printed. See Figure 16.6.

SAVUCN

Save Concentration toggle: This flag indicates whether the concentrations should be saved in the default unformatted file (MT3D.UCN).

16).

NPRS

Output Frequency: This flag indicates whether the output frequency is specified in terms of elapsed time, or transport step number.

<0 = simulation results will be printed or saved whenever the number of transport evens is an even multiple of NPRS.

0 = simulation results will only be printer and saved at the end of the simulation.

>0 = simulation results will be printed or saved according to the record #17 (TIMPRS).

If NPRS (record #16) is greater than 0, the next card needs to be defined for each output time.

17).

TIMPRS

Output Times button: This option creates the pop-up dialog shown in Figure 16.7. This dialog allows the user to specify which simulation results are printed to the standard output file or are saved to the file MT3D.UCN.

Figure 16.7

18).

NOBS

Number of Observation Points: This is the number of observation points at which the concentration will be printed or saved (file MT3D.OBS) at every transport step.

If NOBS (record #18) is greater the 0, the next card needs to be defined for each observation point. The values are entered using the pop-up dialog shown in Figure 16.8.

Figure 16.8

19).

KOBS

Observation Layer

IOBS

Observation Row

JOBS

Observation Column

20).

CHKMAS

Save Mass Balance toggle: This flag indicates whether the mass balance information should be saved in the default unformatted file (MT3D.MAS).

Figure 16.9

21).

PERLEN
NSTP
TSMULT

Define Stress Periods button: An entry is needed for each stress period. If more then 10 stress periods are required, using the Previous and Next buttons will allow you to proceed through them. Length is equivalent to PERLEN, No. Steps to NSTP, and Multiplier to TSMULT.

If TSMULT for the stress period is less then or equal to 0.0, enter record #22. This is done by pressing the appropriate Transport Time Steps button. The pop-up dialog is Figure 16.10 is used to enter the time step length values.

Figure 16.10

22).

TSLNGH

Time Step Length

22).

DT0

Transport Step Size: The is the user specified transport step size. If the value is to large, MT3D may change the value. If 0.0 or a negative number is entered, MT3D will calculate a step size (it may not be optimal though).

MXSTRN

Maximum Number of Transport Steps: If the number of transport steps within one time step exceeds MXSTRN, the simulation is terminated.

Figure 16.11

1).

MIXELM

Advection Solution Scheme menu option: There are four options:

1 = Method of Characteristics (MOC)
2 = Modified Method of Characteristics (MMOC)
3 = Hybrid MOC./MMOC (HMOC)
0 = Upstream Finite-Difference

PERCEL

Courant Number

MXPART

Maximum Number of Moving Particles

Figure 16.12

If MIXELM equals 1, 2, or 3 (MOC, MMOC, or HMOC) enter the following record.

2).

ITRACK

Particle Tracking Algorithm menu option: There are three options:

1 = First-Order Euler
2 = Fourth-Order Runge-Kutta
3 = Runge-Kutta and Euler

WD

Weighting Factor: This value is between 0.0 and 1.0; 0.5 is normally a good choice.

If MIXELM equals 1 or 3 (MOC or HMOC) enter the following record.

3).

DCEPS

Negligible Concentration Gradient

NPLANE

zParticle Placement Pattern: Refer to the MT3D users manual for the different pattern ID's.

NPL

Number of Initial Particles per Cell to be placed at cells where DCCELL <= DCEPS.

NPH

Number of Initial Particles per Cell to be placed at cells where DCCELL > DCEPS.

NPMIN

Minimum Number of Moving Particles Allowed per Cell

NPMAX

Maximum Number of Moving Particles Allowed per Cell

SRMULT

Particle Multiplier

If MIXELM equals 2 or 3 (MMOC or HMOC) enter the following record.

4).

INTERP

Concentration Interpolation Method: Set this equal to 1. Linear (1) is the only option currently available.

NLSINK

Sink Placement Pattern: Refer to the MT3D users manual for the different pattern ID's.

NPSINK

Number of Particles to Approximate Sink Cells in MMOC scheme.

If MIXELM equals 3 (HMOC) enter the following record.

5).

DCHMOC

Critical Relative Concentration Gradient.

Figure 16.13

The Longitudinal Dispersivity button allows the user to define card #1 for each item. The individual layers are defined in the utility dialog (See Chapter 15, Figure 15.31).

1).

AL

Longitudinal Dispersivity button: To define the layer, press the Define Array Control Data button. This calls the utility 2D real array editor (See Chapter 15, U2DREL).

2).

TRPT

Horizontal Transverse Dispersivity Ratio button: To define the layer, press the Define Array Control Data button. This calls the utility 1D real array editor (See Chapter 15, U1DREL).

3).

TRPV

Vertical Transverse Dispersivity Ratio button: To define the layer, press the Define Array Control Data button. This calls the utility 1D real array editor (See Chapter 15, U1DREL).

4).

DMCOEF

Effective Molecular Diffusion Coefficient button: To define the layer, press the Define Array Control Data button. This calls the utility 1D real array editor (See Chapter 15, U1DREL).

Figure 16.14

1).

FWEL

Well

FDRN

Drain

FRCH

Recharge

FEVT

Evapotranspiration

FRIV

River

FGHB

General-Head-Dependent Boundary

If any of these options were used in the flow model, its representative flag must be set to T, otherwise, it should be set to F.

2).

MXSS

Maximum Number of All Point Sink and Sources simulated in flow model.

NOTE: This option is not user definable in the mt3dmain interface. This value is calculated based on the settings in CARD #1.

The Stress Period Parameter button allows the user to define cards 3 - 8 for each stress period with the pop-up dialog shown in Figure 16.15.

Figure 16.15

If FRCH = T specify whether recharge flux must be described for the stress period.

3).

INCRCH

Define Recharge: If this option is true (>=0), a flux array containing the concentration of recharge flux will be required for the specified stress period.

If FRCH = T and INCRCH >= 0, an array entry is required, for the recharge flux described on card 4.

4).

CRCH

Recharge Flux (o) button: This is the concentration of recharge flux. If recharge flux is negative, the recharge acts as a sink (discharge), otherwise the recharge acts as a source. This calls the utility 2D real array editor (See Chapter 15, U2DREL).

If FEVT = T specify whether evapotranspiration flux must be described for the stress period.

5).

INCEVT

Define Evapotranspiration: If this option is true (>=0), a flux array containing the concentration of evapotranspiration flux will be required for the specified stress period.

If FEVT = T and INCEVT >= 0, an array entry is required, for the evapotranspiration flux described on card 6.

6).

CEVT

Evapotranspiration Flux (o) button: This is the concentration of evapotranspiration flux. This calls the utility 2D real array editor (See Chapter 15, U2DREL).

7).

NSS

Point Sources Number: This is the number of points sources whose concentration must be specified.

If NSS > 0, the location, concentration, and type must be specified for each point source, using the pop-up dialog in Figure 16.16.

Figure 16.16

8).

KSS

Layer

ISS

Row

JSS

Column

CSS

Concentration

ITYPE

Type: Identify whether the concentration source is from a Constant-Head (CH), Well, Drain, River, or General-Head Boundary (GHB) cell. Only one option can be selected per point source ID. If more then one type is applicable, the point source must be entered multiple times.

Figure 16.17

1).

ISOTHM

Simulation Sorption Type: There are four sorption option:

1 = Linear Isotherm
2 = Freundich Isotherm
3 = Langmuir Isotherm
0 = None (No sorption isotherm used)

IREACT

Simulate First-Order radioactive decay or biodegradation Rate Reaction

If ISOTHM > 0, cards 2 - 4 must be defined.

2).

RHOB

Bulk Density of porous medium button: This calls the utility 1D real array editor (See Chapter 15, U1DREL).

3).

SP1

First Sorption Constant button: This calls the utility 1D real array editor (See Chapter 15, U1DREL).

4).

SP2

Second Sorption Constant button: This calls the utility 1D real array editor (See Chapter 15, U1DREL).

If IREACT > 0 (True), cards 5 & 6 must be defined.

5).

RC1

First-order rate constant for the Dissolved Phase button: This calls the utility 1D real array editor (See Chapter 15, U1DREL).

6).

RC2

First-order rate constant for the Sorbed Phase button: This calls the utility 1D real array editor (See Chapter 15, U1DREL).

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Now:

NOTE: MT3D is executed with a system call; as a result mt3dmain cannot independently determine when MT3D is done or if there has been a problem. The standard MT3D messages, however will still be printed to the xterm window that launched mt3dmain. When MT3D is complete, "STOP" will be printed in the xterm window.

Save Script:

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NOTE: These options are not available until MT3D has been run.

WARNING: Because there is currently no error checking on whether MT3D completed successfully, mt3dmain may try to map head values that do not exist. Before you try to make a grid or block file, examine the file to insure it has completed successfully.

MT3D Output File:

as Contoured Surface:

as Block:

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The first step is to run MODFLOW to create a flow field for MT3D. To do this, execute modmain, and load the project file js.prj (Use the Project:Open Project menu-bar option). Opening the project will load several files into the application. These files are display in the log/status window and are also listed below:

js.bas : BASIC INPUT PACKAGE
js.bcf : BLOCK CENTERED FLOW INPUT PACKAGE
js.oc : OUTPUT CONTROL INPUT PACKAGE
js.pcg : PRECONDITIONED CONJUGATE-GRADIENT 2 INPUT PACKAGE
js.well : WELL INPUT PACKAGE

When modmain reads in js.bas, it recognized that the BCF, OC, PCG, and WELL packages are also required. These are defined by the Packages Used and Solver Used toggles and toggle menu (IUNIT variables, Figure 15.2). To execute MODFLOW with these modules, select the Run:Now menu-bar option. A pop-up dialog will appear (similar to Figure 5.2) asking for the name of a script file. Select js.csh. Modmain will determine what files are needed, build the script file, and tell the UNIX operating system to execute the script. In the log/status window a message will be printed:

Executing MODFLOW
SYSTEM CALL: $PWD/js.csh &
NOTE: WAIT for "STOP" to appear in the xterm text window before continuing.

The system call executes the script. Because a shell script is being executed, however, modmain has no way of knowing when MODFLOW is complete; this has to be determined by the user. In the xterm window were modmain was executed, when MODFLOW is done, the word "STOP" will be printed (For this data set, you will only have to wait a few seconds).

Once MODFLOW is complete, the next step is to run mt3dmain. To do this, execute mt3dmain, and load the project file jsmt.prj (Use the Project:Open Project menu- bar option). Opening the project will again load several files into the application. The files listed below are display in the log/status window:

jsmt.btn : BASIC INPUT PACKAGE
jsmt.adv : ADVECTION INPUT PACKAGE
jsmt.dsp : DISPERSION INPUT PACKAGE
jsmt.ssm : SINK & SOURCE MIXING INPUT PACKAGE

When mt3dmain reads in jsmt.btn, it recognized that the ADV, DSP, and SSM packages are also required. These are defined by the Packages Used and Solver Used toggles and toggle menu (TRNOP variables, Figure 16.2). To execute MT3D with these modules, select the Run:Now menu-bar option. A pop-up dialog will appear (similar to Figure 5.2) asking for the name of a script file. Select jsmt.csh. Mt3dmain will determine what files are needed, build the script file, and tell the UNIX operating system to execute the script. In the log/status window a message will be printed:

Executing MT3D
SYSTEM CALL: $PWD/jsmt.csh &
NOTE: WAIT for "STOP" to appear in the xterm text window before continuing.

To view the text file, select the View:MT3D output file menu-bar option. Press the View Output Filename button (Figure 15.32) and the standard output file generated by MT3D will be displayed (Figure 15.33). To make a contour map of the model head results, select the View:as Contoured Surface menu-bar option. The model was steady-state, so there is only one stress period; it was also, only a one layer X-Y plane model, so the default values shown in Figure 15.34 are correct. To create a data file containing the X, Y coordinates and head value for each cell, press the Grid Data button.

Once the file has been created, grid (Chapter 10) is called, and several parameters are passed to that application. The most important are the X, Y, head value file name, and the number of columns and rows to use to build the grid (By default, twice the MT3D rows and columns plus 1 are used; this reduces some of the problems with the inverse-distance gridding algorithm honoring the MT3D results). For this example, it is sufficient to select Method:Calculate from the grid menu-bar. When the grid is calculated, select View:Contour Map from the grid menu-bar, and save the file to junk.srf (See Chapter 10 for further detail on using grid). Once the file is saved, the grid file will be passed to contour (Chapter 11) and displayed. A map similar to Figure 16.18 will be displayed.

Figure 16.18

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Syntax: mt3dmain [project file name]

NOTE: Parameters in [] brackets are optional.

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Project File:

Associated Files
MT3D Package Files (Basic Package file first)
Ground Water Flow File

For each file, two or three pieces of information are needed: 1) the files unit ID, 2) the files name, and 3) the unit ID of the owning package (e.g. block.ctc might be owned by the Block Center Flow Package, unit 11). The third item is only needed for "associated" files. A sample file might look like:

41 top_elev.dat 1
1 sample.btn
11 sample.adv
15 modflow.flo

Script File:

	\cp top_elev.dat	fort.41
	mt3d << end-mt3d
	mt3d.out
	sample.btn
	sample.adv
	modflow.flo
	Y
	end-mt3d
	\rm 			fort.41

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Zheng, C., 1990, MT3D, A Modular Three-Dimensional Transport Model, S.S. United States Environmental Protection Agency and Papadopulos and Associates, Inc., Rockville, Maryland.

Zheng, C., 1991, MT3D, A Modular Three-Dimensional Transport Model, S.S. Papadopulos and Associates, Inc., Rockville, Maryland.

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