VMOD 42 Manual

8/12/2019 VMOD 42 Manual

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i Waterloo Hydrogeologic Inc.

Visual MODFLOW v.4.2

Users Manual

For Professional Applications in Three-Dimensional

Groundwater Flow and Contaminant Transport Modeling

Images created using Visual MODFLOW Premium


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ii

Visual MODFLOW is a trademark, owned by Waterloo Hydrogeologic Inc. Microsoft is a registered trademark,

and Windows is a trademark of the Microsoft Corporation. Borland is a trademark of Borland International, Inc.

EXml is a trademark of CUESoft. Adobe, the Adobe logo and Acrobat are registered trademarks of Adobe

Systems, Inc. MODFLOW and MODPATH are trademarks of the United States Geological Survey. MODFLOW-SURFACT is a trademark of HydroGeoLogic, Inc. MT3DMS is a trademark of The University of Alabama.

MT3D96 and MT3D99 are trademarks of S.S. Papadopulos and Associates Inc. RT3D is a trademark of the Pacific

Northwest National Laboratory and the United States Department of Energy. PEST is a trademark of Watermark

Numerical Computing.

Visual MODFLOW Users Manual

Copyright 2006 Waterloo Hydrogeologic Inc.

All Rights Reserved. No part of this document may be photocopied, reproduced, or translated by any means with-

out the prior written consent of Waterloo Hydrogeologic Inc.

Visual MODFLOW 2006 Waterloo Hydrogeologic, Inc. All Rights Reserved.


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iv Waterloo Hydrogeologic Inc.


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v

Preface

Waterloo Hydrogeologic has been developing groundwater software since 1989 and our software isrecognized, accepted and used by more than 10,000 groundwater professionals in over 90 different

countries around the world. This type of recognition is invaluable in establishing the credibility of your

software to clients and regulatory agencies.

When you purchase any Waterloo Hydrogeologic software product, you not only get the best software in

the industry, you also gain the reputation of the company behind the product, and professional technical

support for the software from our team of qualified support specialists.

For product pricing information, please contact your local distributor. Use the address below to see a list

of distributors:

http://www.waterloohydrogeologic.com/software/software_international_dist.htm

Or, contact:

Waterloo Hydrogeologic, Inc.

A Schlumberger Company

460 Phillip Street - Suite 101

Waterloo, Ontario, Canada

N2L 5J2

Phone: (519)-746-1798

Fax: (519)-885-5262

E-mail: [email protected]

Web: www.waterloohydrogeologic.com

How to Contact WHI

If, after reading this manual and using Visual MODFLOW, you would like to contact Waterloo

Hydrogeologic Inc. with comments, suggestions, or if you need technical assistance on how Visual

MODFLOW works, you can reach us at:

Waterloo Hydrogeologic Inc.460 Phillip Street - Suite 101

Waterloo, Ontario, CANADA

N2L 5J2

Phone: (519) 746 1798

Fax: (519) 885 5262

E-mail: [email protected]

Web: www.waterloohydrogeologic.com


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vi Waterloo Hydrogeologic Inc.

Our technical support hours are 9:00 a.m. to 5:00 p.m. EST. Monday to Friday. To help us handle your

problem as quickly as possible, please carefully read the following section.

Obtaining Technical SupportWaterloo Hydrogeologic, Inc. provides technical support to registered users of Visual MODFLOW to

assist them in dealing with technical problems or difficulties encountered while using the software.

While we try to make the software as easy-to-use as possible, and we take great care in designing the

documentation to be comprehensive and easy-to-read, we also recognize that this software is highly

specialized and technically complex by its very nature. As a result, there may be situations you

encounter where the software does not behave as you would expect and you cannot find an

appropriate explanation in the documentation. This type of situation may require you to seek

assistance from a technical support specialist.

Technical support is intended as a support service for helping our clients effectively use their software

and successfully complete their projects. A valid technical support issue deals with problems you are

encountering with the functionality of the software. For advice on numerical modeling (e.g. how to

select the model domain, how to design the model grid, which boundary conditions are most

appropriate, model solution convergence problems, etc.) please inquire about our Extended Modeling

Support Service.

Waterloo Hydrogeologic also offers numerous open-enrolment groundwater modeling training courses

and specialized in-house training seminars. Please visit the Waterloo Hydrogeologic web site for more

information.

Generally, we reply to all valid technical support questions within one business day. However, please

allow up to two business days for a response if a review of your model data is required.

When requesting technical support assistance please be prepared to provide the following information:

Name of registered user

Product serial number

Product version number

Company name and office location

Telephone and fax numbers

E-mail address

Detailed description of the problem you are encountering

The version number can be found using the Help/About Visual MODFLOWon the top menu bar.

If your question is of a "How do I...?" type, the above information is generally sufficient. However, if

you are reporting a bug (especially one that causes a system crash) or are having technical problems

with the program please provide the following additional information: Current hardware setup (local or network installed)

Operating system you are using (Win2000/WinXP)

Amount of RAM that you have on your system

Amount of free hard disk space remaining on your machine


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vii

Detailed description of when and how the problem occurs

If we are unable to reproduce your problem, or are otherwise unable to solve it, we may ask you to send

us a copy of your project files.

Suggested Reference Books

A list of books that may be useful for hydrogeology theory and applications are listed below. The full

bibliographic references are included in the Bibliographysection.

Applied Groundwater Modeling: Simulation of Flow and Advective Transport, Anderson, M.P.

and Woessner, W. W., 1992.

Physical and Chemical Hydrogeology: 2ndEdition, Domenico, P.A. and Schwartz, F. W., 1997.

Applied Hydrogeology: 4th Edition, Fetter, C.W., Prentice Hall, New Jersey, 2001.

Applied Contaminant Transport Modeling; Theory and Practice: 1stEdition 1995 and 2nd

Edition 2002, Zheng, C. and Bennett, G. D. John Wiley & Sons, New York. ASTM Standard on Analysis of Hydrologic Parameters and Ground Water Modeling: ASTM,

1996. Practical Applications of Groundwater Models: National Ground Water Association, published

Biannually.

WHI Training and Consulting

Waterloo Hydrogeologic, Inc. offers both individually tailored and open-enrollment training courses in

groundwater flow and contaminant transport modeling. For more information contact WHI Training

Division ([email protected]).

Waterloo Hydrogeologic also has a professional consulting division specializing in groundwater flow

and contaminant transport modeling and geo-environmental database management and analysis. For

more information contact the WHI Consulting Division.

Other Products by WHI

At WHI we are continually improving our existing products and developing new and innovative

software products to meet the advancing technology requirements of groundwater and environmental

professionals around the world. The following is a brief description of some other software products

developed and distributed by Waterloo Hydrogeologic, Inc.

AquaChem

AquaChem is a fully-integrated software package developed specifically for graphical and numerical

analysis of geochemical data sets. It features a powerful database of common geochemical parameters

and automated calculations, a comprehensive selection of 13 different geochemical data plottingtechniques, and a built-in interface to PHREEQC geochemical modeling.

AquiferTest


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viii Waterloo Hydrogeologic Inc.

The most complete and easy-to-use software package for graphical analysis and reporting of pumping

test and slug test analysis data. It comes with a comprehensive selection of built-in solution methods for

estimating transmissivity, hydraulic conductivity and storage properties for confined, unconfined, leaky

and fractured rock aquifers.

Visual Groundwater

Visual Groundwater is the one 3-D visualization software package that any groundwater and

environmental professional can use to deliver high-quality, three-dimensional presentations of

subsurface characterization data and groundwater modeling results.

Visual HELP

Visual HELP is the most advanced hydrological modeling environment available for designing landfills,

predicting leachate mounding and evaluating potential leachate seepage to the groundwater table. Visual

HELP combines the latest version of the HELP model (Hydrologic Evaluation of Landfill Performance

model v.3.07) with an easy-to use interface and powerful graphical features for designing the model and

evaluating the modeling results.HydroGeo Analyst

HydroGeo Analyst represents the next generation in groundwater and borehole data management and

visualization technology. HG Analyst integrates a complete range of easy-to-use analysis and reporting

tools, with a powerful yet extremely flexible database technology - all wrapped into an innovative

graphical user interface. With HydroGeo Analyst, you can expect the highest level of performance and a

completely scalable solution to meet your project demands.

WHI UnSat Suite Plus

WHIs UnSat Suite is a fully-integrated software package that combines the most popular and widely-

used models for simulating one-dimensional groundwater flow and contaminant transport in the

unsaturated zone (includes SESOIL, VS2DT, VLEACH, PESTAN and the HELP model). These modelshave all been compiled and optimized to run as native Windows applications and are seamlessly

integrated within the WHI UnSat Suite graphical modeling environment.

We want your feedback

At Waterloo Hydrogeologic Inc., we are dedicated to providing a product that is tailored to our

customers needs. Therefore, we are very interested in your thoughts on Visual MODFLOW and

welcome your suggestions and comments. We cannot promise to include all your suggestions in the

next release, but you have our assurance that all suggestions will be carefully considered. Please

indicate a priority or an importance ranking for each of your suggestions.


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Table of Contents ix

Table of Contents

1. Introduction to Visual MODFLOW ........................................... 1

Whats New in Visual MODFLOW ............................................................................. 1New Features in Visual MODFLOW 4.2......................................................................................... 2

New Features in Visual MODFLOW 4.1......................................................................................... 3



New Features in Visual MODFLOW 3.0....................................................................................... 11

Visual MODFLOW Installation .................................................................................... 14

Hardware Requirements ............................................................................................. 14Installing Visual MODFLOW........................................................................................................ 14

Starting Visual MODFLOW .......................................................................................................... 15Un-installing Visual MODFLOW.................................................................................................. 15

Visual MODFLOW Features...................................................................................... 15

About the Interface......................................................................................................... 16Getting Around In Visual MODFLOW ......................................................................................... 17

Screen Layout ................................................................................................................................. 18

Visual MODFLOW Project Files .................................................................................. 21

Visual MODFLOW On-Line Help................................................................................ 22

Software Maintenance and Technical Support............................................................ 24

2. Getting Started ............................................................................ 25

Opening older Visual MODFLOW models .................................................................. 25

Importing MODFLOW Data Sets................................................................................. 25

Using the MF96to2K.exe conversion tool.................................................................. 26

Importing a MODFLOW 2000 data set...................................................................... 29Determining Property Values for Confining Bed Layers ........................................... 33Calculating Kz Values Using VCONT....................................................................... 34Importing Same Cell Boundary Conditions................................................................ 36Importing Initial Heads from a MODFLOW model................................................... 36

Limitations of MODFLOW data import..................................................................... 37

Creating a New Model.................................................................................................... 37Selecting the Model Region ........................................................................................................... 48

Entering the Model Data................................................................................................ 50


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3. Global Operations....................................................................... 53

Saving the Model............................................................................................................. 53

Changing your Model Preferences................................................................................ 53

Three-Dimensional Visualization.................................................................................. 55

Importing Site Maps....................................................................................................... 55

Georeferencing a Graphics File .................................................................................. 55Adding Georeference Points ........................................................................................................... 57

Deleting Georeference Points ......................................................................................................... 57

Loading a New Map File ................................................................................................................ 57

Modifying Site Map Images ....................................................................................... 57Dual Co-ordinate Systems .......................................................................................... 58

Changing Measurement Units and Model Start Time ................................................ 59

Overlay Control Options................................................................................................ 60Overlay Groups............................................................................................................................... 60

Overlay Display Settings ................................................................................................................ 61

Printing the Model Display Area................................................................................... 67

Page Setup................................................................................................................... 69Page Layout .................................................................................................................................... 69

Plot Description .............................................................................................................................. 71

Project Name................................................................................................................................... 71

Company Name .............................................................................................................................. 72

Print............................................................................................................................. 73

Print Preview............................................................................................................... 73Save as graphics file ................................................................................................... 74Copy to Clipboard....................................................................................................... 74Show Legend .............................................................................................................. 74

Edit Legend..................................................................................................................................... 74

Show Color Legend .................................................................................................... 75Annotate...................................................................................................................... 75Image Editor Help....................................................................................................... 76

Image Title.................................................................................................................. 76Printing Methods......................................................................................................... 76

Selecting Numeric Engines............................................................................................. 77

Groundwater Flow Numeric Engines ......................................................................... 77Mass Transport Numeric Engine ................................................................................ 78

Defining Flow Engines and Transport Variants ............................................................................. 79

Export Options................................................................................................................ 84


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Exporting Graphics Image Files ................................................................................. 84Exporting Data Files ................................................................................................... 86

Exporting GIS Files .................................................................................................... 89

4. Model Input Data........................................................................ 91

General Input .................................................................................................................. 92

The File Menu ................................................................................................................. 93

Grid Design...................................................................................................................... 94

Assigning Inactive/Active Regions ............................................................................ 95Gridlines (Rows and Columns) .................................................................................. 96Grid Layers ................................................................................................................ 98

Model Extents .......................................................................................................... 100Grid Smoothing ........................................................................................................ 101

Fixing Gridlines............................................................................................................................ 104

Importing Surfaces.................................................................................................... 105As is .............................................................................................................................................. 107

Import data.................................................................................................................................... 107

Specified Elevation....................................................................................................................... 114

Specified Thickness...................................................................................................................... 115

Constant Slope.............................................................................................................................. 116

Previewing the Layer Elevations to be Imported...................................................... 118Assign Elevations .................................................................................................... 127

A note about Zero Thickness Cells: ............................................................................................. 128

Single............................................................................................................................................ 131

Line............................................................................................................................................... 131

Polygon......................................................................................................................................... 132Window ........................................................................................................................................ 132

Database ....................................................................................................................................... 133

Contouring ............................................................................................................... 134

Wells............................................................................................................................... 135

Pumping Wells.......................................................................................................... 135Well Name and Co-ordinates ....................................................................................................... 138

Well Screen Intervals ................................................................................................................... 139

Pumping Well Schedule ............................................................................................................... 141

Importing Pumping Well Data ..................................................................................................... 144

Graphing Pumping Well Schedules.............................................................................................. 147

Head and Concentration Observation Wells............................................................. 148Observation Points........................................................................................................................ 150

Observations................................................................................................................................. 151

Importing Observation Well Locations ........................................................................................ 154

Observation Groups...................................................................................................................... 160


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Properties....................................................................................................................... 162Constant Value Property Zones .................................................................................................... 163

Distributed Value Property Zones ................................................................................................ 163

Tools for Assigning and Editing Properties.............................................................. 165Importing Distributed Property Data ............................................................................................ 166

Assigning Property Zones............................................................................................................. 182

Copying Property Zones ............................................................................................................... 183

Editing the Property Database ...................................................................................................... 184

Contouring Property Data ............................................................................................................ 186

Conductivity.............................................................................................................. 186Storage ...................................................................................................................... 190Initial Heads.............................................................................................................. 192Vadose Zone ............................................................................................................. 192

Sample Index of Soil Hydraulic Properties* ................................................................................ 193

Vadose Zone Properties Settings .................................................................................................. 195

Bulk Density ............................................................................................................. 197

Species Parameters ................................................................................................... 199Edit Constant Parameters.......................................................................................... 201Initial Concentration ................................................................................................. 202

Importing Initial Concentrations................................................................................................... 203

Assigning Inactive Transport Zones ............................................................................................. 204

Dispersion ................................................................................................................. 205

Boundary Conditions.................................................................................................... 206

Tools for Assigning and Editing Boundary Conditions............................................ 208Flow Boundary Conditions....................................................................................... 209

Importing Transient Boundary Condition Data ............................................................................ 218

Constant Head (CHD) Boundary Conditions ............................................................................... 225River (RIV) Boundary Conditions................................................................................................ 227

Stream (STR) Boundary Conditions............................................................................................. 231

General-Head (GHB) Boundary Conditions................................................................................. 237

Drain (DRN) Boundary Conditions .............................................................................................. 241

Wall (HFB) Boundary Conditions ................................................................................................ 244

Recharge (RCH) Boundary Conditions ........................................................................................ 246

Evapotranspiration (EVT) Boundary Conditions ......................................................................... 251

Mass Transport Boundary Conditions...................................................................... 256Constant Concentration Boundary Conditions ............................................................................. 256

Recharge Concentration Boundary Conditions ............................................................................ 258

Evapotranspiration Concentration Boundary Conditions ............................................................. 260

Point Source Boundary Conditions............................................................................................... 262

Import MIKE 11 River Network................................................................................................... 263

Particles (MODPATH)................................................................................................. 264Particle Release Time ................................................................................................................... 266

Particle Discharge Options ........................................................................................................... 267


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Zone Budget................................................................................................................... 267Flow Observations........................................................................................................................ 269

Tools ............................................................................................................................... 271

Cell Inspector............................................................................................................ 272Annotate.................................................................................................................... 273Units Converter......................................................................................................... 274

Copy Image to Clipboard.......................................................................................... 274Enviro-Base Pro........................................................................................................ 275

5. Run Section - Model Run Settings........................................... 277

File .................................................................................................................................. 278

MODFLOW Run Settings............................................................................................ 278

Time Steps ................................................................................................................ 279Initial Heads.............................................................................................................. 284

Calculating VCONT Values......................................................................................................... 285

Importing Initial Heads................................................................................................................. 285

Solver Settings .......................................................................................................... 286Preconditioned Conjugate-Gradient Package (PCG2) ................................................................ 287

Strongly Implicit Procedure Package (SIP) ................................................................................. 289

Slice-Successive Overrelaxation Package (SOR) ....................................................................... 291

WHS Solver for Visual MODFLOW (WHS) ............................................................................. 292

Algebraic Multigrid Methods for Systems (SAMG) and Algebraic Multigrid Solver (AMG) ... 294

Preconditioned Conjugate-Gradient Package (PCG4) ................................................................. 298

Geometric Multigrid Solver (GMG) ............................................................................................ 301

Recharge Settings ..................................................................................................... 303

Surface Water Leakage Settings ............................................................................... 305Layer Type Settings .................................................................................................. 306Re-wetting Settings................................................................................................... 309Anisotropy Settings................................................................................................... 312Output Control Settings ............................................................................................ 312

List File Options ...................................................................................................... 314

MODPATH Run Settings............................................................................................. 316

Discharge Options..................................................................................................... 316Reference Time Settings........................................................................................... 317

MT3D/RT3D/PHT3D Run Settings ............................................................................ 318Solution Method ....................................................................................................... 319

Solution Method Settings ............................................................................................................. 321

A Technical discussion of the MT3D Solution Methods............................................................. 322

Particle Options ............................................................................................................................ 326

Implicit Generalized Conjugate Gradient (GCG) Solver Settings ............................................... 329


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Particle-Based Methods ................................................................................................................ 331

Finite Difference Methods ............................................................................................................ 332

TVD Method................................................................................................................................. 333

A Technical Note on the Generalized Conjugate Gradient Solver ............................................... 334

Output/Time Steps Settings ...................................................................................... 335Calculating Transport Timestep Sizes ......................................................................................... 336

Initial Concentrations Settings.................................................................................. 337Importing Initial Concentrations................................................................................................... 338

Concentration Import file Conversion and Viewing Utility..................................... 340PHT3D Run Settings ................................................................................................ 341

General.......................................................................................................................................... 342

Aqueous Components ................................................................................................................... 343

Minerals ........................................................................................................................................ 344

Equilibrium Gas Phases ................................................................................................................ 346

Exchange Species.......................................................................................................................... 347

SEAWAT Run Settings ................................................................................................ 347Simulation Scenario.................................................................................................. 348

VDF Settings................................................................................................................................. 348

Flow Settings ................................................................................................................................ 350

Transport Settings ......................................................................................................................... 351

SEAWAT Flow......................................................................................................... 351SEAWAT Transport ................................................................................................. 352

Optimization Settings ................................................................................................... 352

6. Running your Model - VMEngines ......................................... 353

Advanced MODFLOW Run Settings....................................................................... 355Advanced Zone Budget Run Settings....................................................................... 357Advanced MT3D Run Settings................................................................................. 358

VM Engine..................................................................................................................... 359

Running the Model(s) ............................................................................................... 361MODFLOW Display Options................................................................................... 363MODPATH Display Options.................................................................................... 365

Zone Budget Options................................................................................................ 366MT3D Display Options ............................................................................................ 367

7. Parameter Optimization: PEST and Predictive Analysis ..... 369Getting Started.............................................................................................................. 370

Selecting Model Parameters ........................................................................................ 371

Selecting Parameters................................................................................................. 371Clearing Selected Parameters ................................................................................... 372


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Resetting Parameter Selections................................................................................. 372Saving Parameter Selections..................................................................................... 372

Defining Parameter Settings ..................................................................................... 372

Description of Parameter Settings ................................................................................................ 373Parameter Groups ......................................................................................................................... 376

Prior Information ......................................................................................................... 378

Adding Prior Information ......................................................................................... 379Deleting Prior Information........................................................................................ 380Editing Prior Information.......................................................................................... 381Resetting Prior Information ...................................................................................... 381Saving Prior Information .......................................................................................... 381

Assigning the Objective Function................................................................................ 381

Selecting the Observation Data Type(s) ................................................................... 382

Selecting the Observation Groups ............................................................................ 383Filtering the Observation Groups List .......................................................................................... 383

Editing User-Defined Observation Groups .................................................................................. 383

PEST Controls............................................................................................................... 384

PEST Control Parameters ......................................................................................... 385PESTMODE................................................................................................................................. 385

Marquardt Lambda Settings......................................................................................................... 385

Parameter Change Constraints ..................................................................................................... 387

Method Separation Value - PHIREDSWH .................................................................................. 389

Precision - PRECIS ...................................................................................................................... 390

Termination Criteria ..................................................................................................................... 390

Output Control - ICOV, ICOR, IEIG........................................................................................... 391

Enable Restart - RSTFLE............................................................................................................. 391

Predictive Analysis Settings ......................................................................................... 392

Prediction Data ......................................................................................................... 393Analysis Mode - NPREDMAXMIN............................................................................................ 394

Data Type ..................................................................................................................................... 394

Location........................................................................................................................................ 394

Obs. Point ..................................................................................................................................... 394

Obs. Time ..................................................................................................................................... 394

Objective Function Criteria ...................................................................................... 394Inside Limit - PD0........................................................................................................................ 394

Outside Limit - PD1 ..................................................................................................................... 395

Threshold - PD2 ........................................................................................................................... 395Iteration Change Criteria .......................................................................................... 395

Relative Change - RELPREDLAM.............................................................................................. 395

Absolute Change - ABSPREDLAM ............................................................................................ 396

Derivation Calculation Switch.................................................................................. 396Relative Change - RELPREDSWH.............................................................................................. 396


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Absolute Change - ABSPREDSWH............................................................................................. 396

Line Search ............................................................................................................... 396Maximum Model Runs - NSEARCH........................................................................................... 397

Initial Search Factor - INITSCHFAC ........................................................................................... 397

Multiplication Factor - MULSCHFAC......................................................................................... 397

Termination Criteria ................................................................................................. 397Optimization Attempts - NPREDNORED.................................................................................... 397

Number of Best Predictions - NPREDSTP................................................................................... 397

Relative Distance - RELPREDSTP .............................................................................................. 398

Absolute Distance - ABSPREDSTP............................................................................................. 398

Running the Parameter Estimation Simulation......................................................... 398

Loading PEST Input Files......................................................................................... 400Validating PEST Input Files..................................................................................... 400

Starting the PEST Simulation................................................................................... 401Interacting with the PEST Simulation ...................................................................... 401Displaying Reports and Graphs................................................................................ 401Updating your Model................................................................................................ 415

8. Well Optimization..................................................................... 417

Introduction............................................................................................................... 417Assumptions and Limitations of Well Optimization................................................ 418

Well Optimization Settings .......................................................................................... 419

Management.............................................................................................................. 420Decision Variables ........................................................................................................................ 420

Decision Variable Groups............................................................................................................. 423

Constraints ................................................................................................................ 425Global Constraints ........................................................................................................................ 426

Pumping Balance Constraints ....................................................................................................... 427

State Variable Constraints............................................................................................................. 429

Objectives ................................................................................................................. 431Controls..................................................................................................................... 432

Optimization Solver Options ........................................................................................................ 433

Solution Options ........................................................................................................................... 437

Output Control Options................................................................................................................. 438

Running Well Optimization......................................................................................... 438

Interpreting and Utilizing Well Optimization Results.............................................. 439

9. Output Section - Displaying Model Results............................ 443

File Options ................................................................................................................... 445


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Table of Contents xvii

Maps............................................................................................................................... 446

Calibration Residual Maps........................................................................................ 446Calibration Residual Display Options .......................................................................................... 447

Contour Maps ........................................................................................................... 450Contour Map Display Options...................................................................................................... 452

Color Map Display Options.......................................................................................................... 454

Removing Contour Maps ............................................................................................................. 455

Selecting Output Times................................................................................................................ 455

Selecting Chemical Species.......................................................................................................... 456

Selecting Observation Points........................................................................................................ 456

Exporting Contour Data ............................................................................................................... 457

Pathline Maps ........................................................................................................... 457Pathline Display Options.............................................................................................................. 458

Removing the Pathlines Map........................................................................................................ 459

Exporting Pathlines ...................................................................................................................... 459

Velocity Vectors Maps ............................................................................................. 460

Velocity Vectors Display Options................................................................................................ 460Selecting Output Times................................................................................................................ 461

Removing the Velocity Vectors Map........................................................................................... 462

Exporting Flow Velocity Data...................................................................................................... 462

Zone Budget Maps.................................................................................................... 463Zone Budget Listing..................................................................................................................... 463

Mass Balance Report.................................................................................................................... 464

Graphs............................................................................................................................ 466

Calibration Graphs.................................................................................................... 466Calculated vs. Observed Scatter Graphs ...................................................................................... 472

Calibration Residuals Histogram.................................................................................................. 477

Time-Series Graphs .................................................................................................. 478Head or Concentration vs. Time Graphs ...................................................................................... 482

Drawdown vs. Time Graphs......................................................................................................... 483

Saturation vs. Time Graphs.......................................................................................................... 485

Calibration Statistics vs. Time Graphs ......................................................................................... 486

Mass Balance Graphs................................................................................................ 487Flow Mass Balance Graphs .......................................................................................................... 487

Transport Mass Balance Graphs................................................................................................... 489

Zone Budget Graphs ................................................................................................. 491Flow Zone Budget Graphs............................................................................................................ 491

Transport Zone Budget Graphs .................................................................................................... 493

Tools ............................................................................................................................... 494

Cell Inspector............................................................................................................ 495Annotate.................................................................................................................... 495Units Converter......................................................................................................... 495Copy Image to Clipboard.......................................................................................... 495Enviro-Base Pro........................................................................................................ 495


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10. IChart - Graphing and Mapping Component...................... 497

Toolbar Icons................................................................................................................. 498

Graph Properties .......................................................................................................... 499Save and Load Settings................................................................................................................. 499

Axis Settings............................................................................................................. 500Titles Settings ........................................................................................................... 501Series Settings........................................................................................................... 501Legends Settings....................................................................................................... 503Operations Settings................................................................................................... 504General Settings........................................................................................................ 505

Info Settings.............................................................................................................. 507

Map Properties.............................................................................................................. 508

Contour Settings ....................................................................................................... 509Color Map Settings ................................................................................................... 510

Annotation Tools........................................................................................................... 510

Printing Options............................................................................................................ 511

Page Setup................................................................................................................. 512Plot Description ........................................................................................................ 513Project Name............................................................................................................. 514Company Name ........................................................................................................ 515

Exporting Data.............................................................................................................. 516

Saving to a Graphics File.......................................................................................... 517

11. Visual MODFLOW 3D-Explorer.......................................... 519

Getting Started.............................................................................................................. 520Opening VMOD 3D-Explorer ...................................................................................................... 520

Closing VMOD 3D-Explorer........................................................................................................ 520

VMOD 3D-Explorer Data Files.................................................................................................... 521

VMOD 3D-Explorer On-Line Help.............................................................................................. 521

Software Performance Considerations.......................................................................................... 522

OpenGL Settings........................................................................................................................... 522

About the Interface ................................................................................................... 523Positioning the Panels ................................................................................................................... 524

Exaggeration ................................................................................................................................. 5253D Navigation Tools..................................................................................................................... 525

Model Elements and Display Settings......................................................................... 529Default Settings............................................................................................................................. 530

VMOD Project Display Settings................................................................................................... 533


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Axis Properties ............................................................................................................................. 533

Sitemaps Display Settings ............................................................................................................ 534

Input Model Elements............................................................................................... 534Domain Display Settings.............................................................................................................. 535

Grid Display Settings ................................................................................................................... 535Wells Display Settings ................................................................................................................. 536

Properties Display Settings........................................................................................................... 537

Boundaries Display Settings......................................................................................................... 539

Output Model Elements ............................................................................................ 540Heads Display Settings................................................................................................................. 540

Drawdowns Display Settings ....................................................................................................... 543

Concentrations Display Settings................................................................................................... 544

Pathlines ....................................................................................................................................... 545

Isosurfaces ................................................................................................................ 546Creating Isosurfaces ..................................................................................................................... 546

Isosurface Display Properties ....................................................................................................... 548

Color Maps ............................................................................................................... 548Creating a Color Map................................................................................................................... 548

Color Map Display Settings ......................................................................................................... 549

Contour Maps ........................................................................................................... 550Creating Contour Maps ................................................................................................................ 550

Contour Map Display Settings ..................................................................................................... 551

Color Fields............................................................................................................... 553Color Field Display Settings ........................................................................................................ 554

The Color Palette ...................................................................................................... 554

The Color Legend ..................................................................................................... 556

Creating Slices and Cross-Sections ............................................................................. 556

Creating a Vertical Slice ........................................................................................... 557Creating a Horizontal Slice....................................................................................... 558

Creating a Vertical Cross-Section............................................................................. 559Deleting a Slice......................................................................................................... 560Moving a Slice .......................................................................................................... 560

Creating Cut-aways ...................................................................................................... 561

Creating an Animation.............................................................................................. 562

Scene Configurations.................................................................................................... 564

Saving to a Graphics File ............................................................................................. 565

Printing the 3D Image .................................................................................................. 566

Page Setup................................................................................................................. 568Page Layout.................................................................................................................................. 568

Plot Description............................................................................................................................ 569

Project Name ................................................................................................................................ 570


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Company Name ............................................................................................................................ 571

Print........................................................................................................................... 572Print Preview............................................................................................................. 572Save as graphics file ................................................................................................. 573Copy to Clipboard..................................................................................................... 573

Show Legend ............................................................................................................ 573Edit Legend................................................................................................................................... 573

Show Color Legend .................................................................................................. 574Annotate.................................................................................................................... 574

Image Editor Help..................................................................................................... 575Image Title................................................................................................................ 575Select......................................................................................................................... 575Zoom......................................................................................................................... 575Printing Methods....................................................................................................... 575

12. Appendix A: Visual MODFLOW Data Files ....................... 581

Model Data Files ........................................................................................................... 582

Visual MODFLOW Data Files................................................................................. 582General Files ................................................................................................................................. 582

MODFLOW.................................................................................................................................. 582

MODPATH................................................................................................................................... 582

MT3D/RT3D................................................................................................................................. 582

Zone Budget.................................................................................................................................. 583

Numerical Model Input Files.................................................................................... 583MODFLOW.................................................................................................................................. 583

MODPATH................................................................................................................................... 584

MT3Dxx/RT3D............................................................................................................................. 584Zone Budget.................................................................................................................................. 584

Output Files............................................................................................................... 584MODFLOW.................................................................................................................................. 584

MODPATH................................................................................................................................... 585

MT3Dxx/RT3D............................................................................................................................. 585

PEST ............................................................................................................................................. 585

Zone Budget.................................................................................................................................. 586

Visual MODFLOW Input Data Formats ................................................................... 587

VMA - Particle File Format...................................................................................... 587VMB - Flow Boundary Conditions File Format....................................................... 588

VMG - Grid File Format........................................................................................... 590VMO - Heads Observation File Format ................................................................... 592VMP - Flow Property File Format............................................................................ 593VMW - Pumping Well File Format.......................................................................... 595VMZ - Zone Budget File Format.............................................................................. 595


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1Introduction to Visual MODFLOWVisual MODFLOW is the most complete, and user-friendly, modeling environment for

practical applications in three-dimensional groundwater flow and contaminant transport

simulation. This fully-integrated package combines powerful analytical tools with a

logical menu structure. Easy-to-use graphical tools allow you to:

quickly dimension the model domain and select units

conveniently assign model properties and boundary conditions

run model simulations for flow and contaminant transport

calibrate the model using manual or automated techniques

optimize pumping and remediation well rates and locations, and

visualize the results using 2D or 3D graphics.

The model input parameters and results can be visualized in 2D (cross-section and plan

view) or 3D at any time during the development of the model or the displaying of the

results. For complete three-dimensional groundwater flow and contaminant transport

modeling, Visual MODFLOW is the best software package available.

When you purchase Visual MODFLOW, or any Waterloo Hydrogeologic Inc. software

product, you not only get the best software in the industry, you also gain the reputation

of the company behind the product, and professional technical support for the software

from our team of qualified groundwater modeling professionals. Waterloo

Hydrogeologic Inc. has been developing groundwater software since 1989, and our

software is recognized, accepted, and used by more than 10,000 groundwater

professionals in over 90 different countries around the world. This type of recognition

is invaluable in establishing the credibility of your modeling software to clients and

regulatory agencies. Visual MODFLOW is continually being upgraded with new

features to fulfill our clients needs and requests.

1.0.1 Whats New in Visual MODFLOWThe main interface for Visual MODFLOW has much of the same user-friendly look and

feel as previous versions of Visual MODFLOW, but whats under the hood has been

dramatically improved to give you more powerful tools for entering, modifying,

analyzing, and presenting your groundwater modeling data. Some of the more


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significant upgrade features in the latest versions of Visual MODFLOW are described

below.

New Features in Visual MODFLOW 4.2

MIKE 11 Integration

DHI's MIKE 11 software package is a versatile and modular engineering tool for

modeling conditions in rivers, lakes/reservoirs, irrigation canals and other inland water

systems. The basic river network/channel modeling component of MIKE 11 is now

integrated into Visual MODFLOW with the use of OpenMI technology, providing the

tools for integrated surface water - groundwater flow.

PHT3D Integration

PHT3D is a multi-component transport model for three-dimensional reactive transportin saturated porous media. It couples the two existing and widely used computer

programs, the solute transport model MT3DMS (v5.1, Zheng and Wang, 1998) and the

USGS geochemical code PHREEQC-2 (v2.9, Parkhurst and Appelo, 1999). The

coupled model forms a powerful and comprehensive three-dimensional reactive multi-

component transport model (Prommer et al., 2003), which can handle a broad range of

equilibrium and kinetically controlled biogeochemical processes.

The present version of Visual MODFLOW includes the following two reaction module

templates that allow the user to develop their own reaction modules and to customize

them to site-specific aquifer conditions:

The original PHREEQC-2 database

An extended PHREEQC-2 databaseFor demonstration purposes Visual MODFLOW includes several sample reaction

modules that enable the user to simulate selected, well-known benchmark problems for

reactive transport such as:

Single species transport with Monod kinetics (Parlange et al., 1984)

Propagation of mineral dissolution and precipitation fronts (Walter et al., 1994)

Mineral buffering during acid mine drainage (Engesgaard and Kipp, 1992)

Cation exchange during flushing of a Na-K-NO3 solution with Ca-Cl (Appelo,

1994)

Cation exchange and precipitation/dissolution during injection of anionic

Tenside (Sardin et al., 1986)

Cation exchange (water-rock interactions) during artificial recharge (Valocchiet al., 1981)

and, furthermore, additional reaction module templates that can be adapted by the user

to address specific reactive transport problems, for example:


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VCONT Calculation Options Implemented

Users now have the option (depending on the Layer Property package selected for their

model), to choose between VCONT values calculated from the Ground Surface (top of

layer 1), or from the Initial Heads.

MT3DMS Version Update

The MT3DMS Engine (version 4.5) has been incorporated into Visual MODFLOW.

LATEST MODFLOW-2000 Release

The latest version of the USGS MODFLOW 2000 Engine (version 1.15.00, August 6,

2004) has been incorporated into Visual MODFLOW.

SAMG Solver Update

The latest version of the Algebraic Multigrid Methods for Systems (SAMG) solver,

optimized for MODFLOW, has been implemented. The SAMG solver (developed by

the SCAI-Frauhofer Institute) has been demonstrated to be 3 to 11 times faster than the

traditional PCG solver for medium sized models, and even faster for large models

containing one million or more grid cells.

GMG Solver Implementation

The new Geometric Multigrid Solver (GMG) solver from USGS has been integrated

with the MODFLOW-2000 and SEAWAT-2000 Engines. In contrast to the AMG solver,

the preconditioning in GMG is based on the geometric multigrid solver method. The

GMG solver has been demonstrated to greatly reduce model run times relative to othersolvers using a comparable amount of memory.

New Features in Visual MODFLOW 4.0

Exporting Gridded Model Data

Visual MODFLOW v.4.0 allows you to export virtually any model property values, and

simulation results, to a variety of ASCII and binary data formats including:

ASCII XYZV (.TXT) -consists of four or more columns containing X, Y, and

Z co-ordinates for each cell, and one or more selected model parameters. Cellco-ordinates can be in either world co-ordinates, model co-ordinates, or IJK

cell indexes. Data can be exported with multiple layers in a single file, or as

separate files for each selected layer.

ASCII Array (.TXT) - consists of an NR x NC array of values for each selected

parameter, for each selected model layer. The data can be exported with


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multiple layers in a single file, or as separate files for each selected layer.

SURFER Grid (ASCII or Binary) (.GRD) - consists of a single file for each

selected parameter, for each selected layer, with a user-defined grid density.

Some averaging of parameter values occurs where the model grid differs from

the Surfer grid, and inactive or dry cell values can be excluded.

Tecplot Data files (.DAT) - consists of four or more columns containing

column, row, Z co-ordinates for each cell, and one or more selected model

parameters. Cell co-ordinates can be in either world co-ordinates or model co-

ordinates. Data can be exported with multiple layers in a single file, or as

separate files for each selected layer.

Please refer to Export Options on page 84, and Exporting Data on page 516, for a

detailed explanation of the options available.

Exporting and Capturing Images

The exporting capabilities of Visual MODFLOW have been greatly expanded,providing a full suite of common graphical image and GIS formats (including ESRI

.SHP, AutoCAD .DXF, .GIF, .JPG, .TIF, .PNG, and .BMP) with options for increasing

image resolution and controlling image quality of graphics image files. These high-

resolution images can either be exported to a separate graphics file for manipulation

with third-party editing software, or inserted directly into a report document.

Please refer to Export Options on page 84, and Exporting Data on page 516, for a

detailed explanation of the options available.

Pumping Well Optimization

Visual MODFLOW v.4.0 includes an interface supporting pumping well optimization

using the Modular Groundwater Optimizer (MGO) program. This program is primarily

used to determine the optimal well pumping and/or injection rates at one or more wells,

in order to achieve a specific objective while maintaining reasonable system responses.

Some of the more common scenarios include:

Minimizing the pumping/treatment cost of a pump-and-treat groundwater

remediation system while maintaining capture of a contaminant plume.

Minimizing the mass removal cost of a pump-and-treat groundwater

remediation system while maintaining capture of a contaminant plume.

Minimizing pumping costs of a dewatering system while maintaining head

levels below excavated areas.

Maximizing mass removal rates.

Maximizing the pumping rate at one or more water supply wells whilemaintaining a minimum drawdown level in the aquifer.

Maximizing the pumping rate at one or more water supply wells while

maintaining the concentration of an identified pollutant below a specified level.


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MGO has been developed by Dr. Chunmiao Zheng under a contract for the U.S.

Department of Defense. A public domain version is available with similar optimization

capabilities.

Please refer to Well Optimization on page 417 for a detailed explanation of the WellOptimization feature.

Printing Options

Previous versions of Visual MODFLOW offered few options for customizing the print

layout, and a limited amount of space for description of the image being printed. Visual

MODFLOW v.4.0 includes a more flexible page layout designer for adding image

descriptions, project descriptions, and a company logo.

Please refer to Printing the Model Display Area on page 67, and Printing Options

on page 511, for a detailed explanation of the options available.

Faster Solver (available as an add-on package)

Visual MODFLOW now includes the new SAMG solver developed by the SCAI-

Frauhofer Institute in Germany. This solver has been demonstrated to be from 3 to 11

times faster than the traditional PCG solver for medium sized models, and much faster

still for large models containing one million or more grid cells.

Please refer to Algebraic Multigrid Methods for Systems (SAMG) and Algebraic

Multigrid Solver (AMG) on page 294 for a detailed explanation of the SAMG solver

features.

2D Color Shading with transparency control

The drawing tools and algorithms used to render the color shaded contour maps of

distributed data have been upgraded to include rich RGB color schemes, and to allow

for color map transparency in order to see underlying model features. The color

schemes remain the same, however, the colors themselves are much more vibrant, and

the transition between colors is much smoother.

Importing MODFLOW data sets

Although previous versions of Visual MODFLOW were able to import MODFLOW-88

data sets, the import process often ignored important data such as Specific Storage and

Specific Yield values, and it was not able to accommodate quasi-3D models containing

implicitly represented aquitards. Visual MODFLOW v.4.0 has a significantly improvedimporting process that supports MODFLOW-2000, MODFLOW-96, and MODFLOW-

88 data sets. This new process utilizes a modified version of the USGS utility

(MF96to2K.EXE) to convert MODFLOW-96 and MODFLOW-88 data sets into

MODFLOW-2000 format, and then imports the MODFLOW-2000 data set into the

Visual MODFLOW graphical environment.


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Please refer to Importing MODFLOW Data Sets on page 25 for a detailed

explanation of the import capabilities of Visual MODFLOW 4.0.

Importing Property Zones and Recharge Zones from Polygon Shape FilesVisual MODFLOW v.3.0 introduced the capability to import and interpolate

Conductivity and Storage zone distributions from external data sources including XYZ

ASCII .TXT files, MS Access .MDB files, MS Excel .XLS files, Surfer .GRD files, and

ESRI Point and line .SHP files. Visual MODFLOW v.4.0 extends this capability to

additional model properties including Initial Heads, Initial Concentrations, and

Dispersivities. The ability to map property zones and recharge zones from ESRI

Polygon .SHP files is also included.

Please refer to Tools for Assigning and Editing Properties on page 165 for a detailed

explanation of the options available.

Assigning Grid Cell Elevations

Visual MODFLOW v.4.0 incorporates graphical selection and assignment of grid cell

elevations. You can easily digitize the desired cell area using a polygon or rectangle

selection, or simply paint a group of cells, and then assign a constant elevation to the

top or bottom of the layer surface. Built-in data validation checks prevent layer surfaces

from intersecting adjacent layers, and provides suggested remedies in situations where

this would occur.

Please refer to Grid Design on page 94 for a detailed explanation of the options

available.

Importing and Editing Layer Surface ElevationsVisual MODFLOW v.4.0 provides a dramatically improved set of tools for importing,

creating, and modifying layer surface elevations for the finite difference model grid.

From importing USGS .DEM files, to specifying a constant slope using Strike and Dip

information, no other graphical interface offers a more complete set of features for

designing the model grid layer surfaces, including:

Importing layer surface elevations from gridded data files including USGS

.DEM files, Surfer .GRD files, ESRI .GRD files, and MapInfo .GRD files.

Importing and interpolating sparse elevation data from XYZ ASCII .TXT files,

MS Access .MDB files, MS Excel .XLS files, and ESRI point and line .SHP

files, using either Natural Neighbor, Kriging, or Inverse Distance interpolation

methods. Adding Control Points to a sparse data set in order to direct the interpolation

Documents

VMOD 42 Manual