Introduction To Numerical Modeling

May 30 - June 2, 2013

Learn to use numerical models to simulate environmental systems...

Better understand numerical model results that are presented to you...

Learn how to build and calibrate a MODFLOW-2005 model...

Learn about new MODFLOW-2005 capabilities

Click here to register.



This course introduces ground-water professionals to numerical modeling. The basic modeling concepts covered include using MODFLOW-2005 for

  • conceptual model development,
  • definition of boundary and initial conditions,
  • parameter specification,
  • spatial discretization,
  • time stepping, and
  • solution control
Basic modules of MODFLOW are explained and concepts are reinforced with hands-on exercises.

New modules of MODFLOW are described.

Calibration is presented via the public domain universal inversion codes, UCODE and PEST. Basic concepts covered include

  • Analyze data to be used for model development. Consider data accuracy and ability of the model to produce comparable values. Determine what to use as observations (targets) and prior information on parameters.
  • Based on knowledge of the system, decide how to define parameters.
  • Using the initially constructed model, identify parameters important to observations, parameters important to predictions, and observations important to predictions. We will question whether these simulated relations are consistent with real-world conditions.
  • Determine parameter values that provide a best fit to observations.
  • Calculate predictions.
  • Obtain measures of prediction uncertainty.

At every step we will ask “Does this make sense”? Models are artificial constructs that sometimes are useful in understanding real world systems. Diligent analysis is critical to useful models.

Course sessions are from 8:00 AM to 5:00 PM.

Participants should bring their own laptop computer with the Windows XP or later operating system.



The course begins with discussion of the phases of a modeling project, followed by presentation of concepts related to:

  • conceptual model development,
  • definition of boundary and initial conditions,
  • parameter specification,
  • finite-differencing,
  • gridding,
  • time stepping, and
  • solution control.
Soon thereafter, hands-on sessions begin with a simple problem using text-based interfaces. Gradually, subsequent exercises use more MODFLOW packages, develop a more complex model, and evaluate transient situations.

The exercises continue with a discussion of, introduction to, and use of graphical user interfaces. The course emphasizes use of text files. If you have the ability to look in, and understand the content of these files or control these commands, you will be a valuable modeler. Inevitably, in your project work, something does not work correctly in a GUI and you need to track down and resolve the problem. Or, you want to do something unique with your project that the GUI developer hadn't planned on. If you do not understand the file structure and commands, you cannot move forward, and your project is in jeopardy. This is why the course emphasizes the use of text files, but uses GUIs to facilitate visualization.

The course continues with a brief review of calibration concepts, followed by an introduction to inversion theory and description of the input, output and special topics associated with using UCODE_2005 and PEST. This is followed by hands-on exercises demonstrating model calibration including:

  • checking problem set-up;
  • estimating parameters; and
  • evaluating statistics to:

      a) identify inadequate data and parameters that probably cannot be estimated
      b) evaluate estimated parameter values,
      c) evaluate the accuracy of the model's representation of the active processes, and
      d) quantify the uncertainty associated with predictions made using the estimated parameters

  • use of output files from UCODE_2005 and PEST to:

      a) test the validity of your model,
      b) guide further work, and
      c) present the certainty of your results.

Once the model is calibrated, we proceed to use it to make predictions. The course first explains how to run MODFLOW-2005 using UCODE and PEST to obtain predictions and how to use the associated code LINER_UNCERTAINTY to evaluate the certainty of the predictions given the calibrated model. More general global methods for evaluating uncertainty will be discussed.

Brief lectures between exercises discuss results of the previous exercise, potential pitfalls, and set the stage for the subsequent exercise.

Every project is unique. Modeling requires fundamental understanding of modeling concepts applied to each specific situation. Approaches to resolving such model-specific problems are discussed. Attendees who are already working on a modeling project are encouraged to bring questions.

As a final part of the MODFLOW part of the course, new capabilities will be briefly presented.

There is a lot going on with MODFLOW! This session provides an overview of the following new capabilities

  • Newton (NWT) version with the Upstream Weighting (UPW) and Unsaturated Zone Flow (UZF) package that together allow perched layers to form within the unsaturated zone and affect the distribution and timing of recharge to the saturated zone
  • Surface-Water Routing (SWR) process that supports simulation of estuaries and swamps.
  • Unstructured Grid (USG) version that supports unstructured grids in part of all of a modeled domain.
  • Local grid Refinement (LGR) version capabilities now allow SFR-represented streamflow and MODPATH-LGR particle to travel between regional and local structured grids
  • MODPATH-OBS that supports the use of quantities such as water age, time of travel, location of flow paths, and fractional contributions for different sources as observations and predictions
  • Farm (FMP) version that integrates more recent developments such as NWT/UPW, PCGN, SWR1, SWI1, LGR, etc

We will also discuss ongoing efforts (many include MT3DMS!) and seek comments from attendees.



This course is designed for hydrogeologists, environmental engineers and resource managers familiar with ground-water flow concepts, but who have limited or no experience with ground-water flow modeling.



Attendees will receive course notes; the MODFLOW-2005, UCODE, and PEST software as well as pdfs of their basic manuals.



The MODFLOW part of the course will be taught by Drs. Suzanne Paschke and Mary C. Hill. The model calibration part of the class will be taught by Drs. Mary C. Hill, Matthew Tonkin, and Suzanne Paschke. We are grateful to Dr. Eileen Poeter for sharing materials upon which this course is constructed. Biographies are listed in alphabetical order.

MARY C. HILL, is a senior research scientist with the U.S. Geological Survey in Boulder, Colorado. She has authored over 120 reports and articles. She focuses on using models and data to understand natural environmental systems through sensitivity, calibration, and uncertainty methods. She co-authored UCODE, MODFLOW-2000, UCODE_2005, OPR-PPR, and MMA. She has experience modeling saltwater intrusion, groundwater supply, stream interaction, regional groundwater flow and transport, and integrated hydrologic systems. She has taught semester and short courses for 30 years. Dr. Hill holds a PhD in Civil Engineering from Princeton University.

SUZANNE PASCHKE, is a section chief in the Colorado Water Science Center of the U.S. Geological Survey. She has completed studies of the Denver Basin and other aquifer systems. Dr. Paschke holds a PhD from the Colorado School of Mines.

MATTHEW TONKIN, is a partner at S.S. Papadopulos & Associates, Inc., and. He has focused on the management of environmental data gathering efforts, data synthesis, and the application of models to support decision-making. He provides modeling support and oversight at several large fuel-spill sites, is a member of the Interstate Technology and Regulatory Council (ITRC) MTBE Team, and instructs at the "MTBE and TBA Comprehensive Site Assessment and Successful Groundwater Remediation" workshops organized by ITRC. Matt has completed contracts to the USGS, USEPA, and California Department of Water Resources in the areas of contaminant transport, model calibration and predictive uncertainty analysis. He co-teaches calibration and uncertainty analysis courses with John Doherty (author of PEST and coauthor of the JUPITER API) and hosts a model calibration technical support forum. Dr. Tonkin holds a PhD from the University of Queensland.



The fee for the short course is $1195 by 4PM Mountain Daylight Time, May 15, 2013 ($1395 after May 15).  You will be invoiced for the tuition balance. The fee covers instruction, course notes, refreshments, and continuing education units. Lodging and meals are not covered. Payment in full must be received prior to the beginning of the course. The registration fee may be paid by check, VISA, MasterCard, AMEX, Discover or purchase order (US Only). A maximum of 20 applicants will be able to attend the course due to space limitations.

If cancellation is made before May 15, 2013, tuition will be refunded except for the $100 deposit. Cancellations made after that date will forfeit a $150 processing fee in addition to the $100 deposit. In case of cancellation, the right to course material is forfeited. Substitutions are permitted at any time prior to the start of the course. Please be advised that if the program is cancelled due to insufficient enrollment, Colorado School of Mines will return all course fees, but will not be liable for any other expenses incurred by the prospective attendees.

To register click here.



The Colorado School of Mines is located in Golden, which is 20 minutes west of Denver, 1 hour west of the Denver International Airport and can be reached by taxi, airport shuttle or rental car. It is strongly recommended that for events held on the CSM campus, attendees select accommodations within .5 miles of the campus if a rental car or personal transportation will not be available, as taxi service and public transportation from other areas may involve significant delays and costs. Lodging is available in Golden, within walking distance of the campus.

Denver Shuttle Service from Denver Airport

To get to SuperShuttle when you land, take the train from the Concourse to the Terminal. Pick up your luggage and proceed to the SuperShuttle counter located on Level 5/Baggage Claim, adjacent to the water feature in the center of the terminal. Counter staff will issue tickets and give directions to the van loading areas. For information, call 1-800-BLUEVAN. Their ticket counters are closed between 12am and 6am. If you arrive between these hours, please use the courtesy phone located at the ticket counter to notify dispatch of your arrival. Please contact a shuttle provider directly for more information on fees and destinations served. Shuttles pick-up and drop-off from Jeppesen Terminal Level 5, Island 3, outside doors 505-507 (east side) and 510-512 (west side).

Super Shuttle International Denver

Phone: (800) 525-3177

Web site:

Rental Cars

All Rental car companies at DIA are located on airport property but are away from the main terminal. Each rental company provides a courtesy shuttle to and from Jeppesen Terminal from their locations. All courtesy shuttles pick-up and drop-off from Jeppesen Terminal Level 5, Island 4, outside doors 505-513 (east side) and 504-512 (west side). If you are arriving in Denver, please follow the overhead signage for the appropriate pick-up location, or check-in at your company's counter in the center of the Terminal.
For more information, please visit at


Taxis are readily available and service within the eight counties that make up the Denver metro area. Some companies may also provide service to other destinations within the state of Colorado. Check with your cab company of choice (or directly with your driver at the airport) for more information on fares and destinations served. Fares to Golden area are based on the taxi’s meter and it costs about $70-85 plus the $3.75 airport access fee. Taxis pick-up and drop-off from Jeppesen Terminal Level 5, Island 1, outside doors 507-511 (east side) and 506-510 (west side).




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