MODFLOW, with the GIS-based GUI FREEWAT and Calibration and Uncertainty Quantification Using UCODE

May 20-21, 2017


Click here to register using our secure CASHNET site.



To identify field data critical to decision making...

To calculate and understand reliability of model predictions...

To simplify modeling efforts by focusing on what is important...

To save time in pre- and prost-processing data with a new GIS-based GUI...

To use open-source freeware to serve all your data management and modeling needs...

To identify field data critical to decision making...

This course introduces groundwater professionals to FREEWAT (distributed in its beta version), MODFLOW, and the inverse modeling tools in UCODE.

Groundwater systems are largely hidden and some popular methods of groundwater model development obscure important results, consequently reducing prediction accuracy, stakeholder understanding, and wise decision making. We seek a better way to bring the information provided by data and insight of models together to serve what are becoming increasingly difficult resource management decisions.

Our methods are informed by Robust Decision Making. We encourage the use of computationally frugal methods that support rapid analysis using commonly available computer resources. We also teach the most popular computationally demanding methods and encourage users with sufficient computational power to make comparisons.



This course provides basic knowledge about MODFLOW, QGIS, building and running model applications using FREEWAT, data integration, and understanding of simulation dynamics using UCODE. By the end of the course, you will know how to:

  • Develop MODFLOW models using QGIS and FREEWAT
  • Check problem set-up
  • Analyze model fit to data
  • Identify parameters that can and cannot be estimated given the available data
  • Estimate parameter values; and much more, including:
    • a) identify existing and potential new observations important to predictions and forecasts
    • b) quantify uncertainty using a range of methods from those that are very fast (10s of models runs) and provide approximate values to computationally intensive methods such as MCMC (10,000s of model runs) that are less approximate
    • c) engage skeptical stakeholders using alternative models
    • d) account for alternative models in uncertainty evaluations
Strengths and weaknesses are discussed for all procedures and statistics.



Day 1

  • Student introductions with 1 slide each about a problem they are working on (1 hour)

  • Basics of QGIS (2 hours)

  • Using FREEWAT and QGIS to build and run a simple MODFLOW model (3 hours)

  • Estimating model parameters using UCODE, with a brief field example (2 hours)

  • Evening: Work on your student presentation to be given at the end of the second day

Day 2

  • More on estimating parameters. What’s important? Sensitivity analysis (3 hours)

  • Prediction, uncertainty, and risk using methods that are computationally fast to demanding, with discussion of pros and cons (4 hours)

  • Student presentations with 1 slide each: define parameters, observations, and predictions, and how to use methods from the course (1 hour)


The course features hands-on exercises using QGIS, FREEWAT, MODFLOW-2005, and UCODE_2014.


QGIS ( is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, Windows and Android and supports numerous vector, raster, and database formats and functionalities.


FREEWAT (FREE and open source software tools for WATer resource management) is an EU HORIZON 2020 project aimed at promoting the application of EU water-related Directives by means of an open source, public domain, GIS-integrated solution for planning and management of surface water and groundwater resources, along with dedicated participatory approach (

FREEWAT is a large QGIS ( plugin, which couples the power of GIS geo-processing and post-processing tools in spatial data analysis with that of process-based simulation models. As such, FREEWAT is conceived as a canvas, where several simulation codes, based on the hydrological cycle, hydrochemical or socio-economic processes, are virtually integrated and input and output data is managed through a SpatiaLite Data Base Management System.

The FREEWAT platform is designed for water authorities and public/private companies to build a highly informative and dynamically growing representation of hydrologic systems. Policy makers will benefit from its ability to produce scientifically and technically sound decision and policy making through a participatory approach by involving stakeholders (e.g., in the formation of River Basin Management Plans required by the Water Framework Directive in Europe, in TMDL plans required by the US EPA, and in the new Sustainable Groundwater Management act in California) not only in the final stage of modeling, but also during the scenario definition phase.

FREEWAT (v.0.3) is integrated into the QGIS GIS desktop ( FREEWAT supports groundwater flow and solute transport numerical models (from the MODFLOW USGS family) and modules for:

  • Interpretation and visualization of hydrogeological data using QGIS.
  • Time series analysis with the Observations Analysis Tools (OAT).
  • Managed aquifer recharge (MAR) using the integrated groundwater-surface water flow and transport with different approaches (a simplified water balance approach and an advanced approach based on the new MT3D-USGS software)
  • Water management and planning in agricultural to urban settings, based on MODFLOW-OWHM and its FARM Process.
  • Calibration, uncertainty and sensitivity analysis based on UCODE_2014.
  • Tools for analysis of groundwater quality issues (e.g. ionic balance calculations, chemical time-series analysis, hydrogeochemical diagrams, piezometric maps, maps of hydrogeological units, etc.)
  • Solute transport in the unsaturated zone.

FREEWAT is in its beta version and will be officially released as open source platform by the end of 2017. Over the last year, FREEWAT has been used for more than 20 short courses all over Europe and for semester courses on groundwater modelling in Europe and US.


MODFLOW has been the most widely used groundwater model worldwide since the 1980s, and continues to maintain that popularity. The versions of MODFLOW used in this class are MODFLOW-2005 and MODFLOW-OWHM.


UCODE_2014 is a universal inversion code. UCODE_2014 can be used with any process model (physical, chemical, biological); the only requirement is that they have numerical (ASCII or text only) input and output files and that the numbers in these files have sufficient significant digits. Process models can be programs such as MODFLOW, or models developed using MatLab, and can include pre-processors and post-processors.

An estimated parameter can be any quantity that appears in the input files of the application model(s), or used to calculate such quantities.

An observation can be any quantity for which a simulated equivalent value can be produced for comparison with the observation. UCODE_2014 can produce simulated equivalent values using data that appear in the application model output files and a set of additive and multiplicative functions defined by the user.

Prior, or direct, information on estimated parameters can be included in the regression.

Observations and prior information often need to be weighted to account for different units. UCODE supports full weight matrices.

The nonlinear regression problem is solved by minimizing a weighted least-squares objective function with respect to the parameter values using a modified Gauss-Newton method. Sensitivities needed for the method are calculated by forward or central differences. Sensitivities calculated by process models, such as MODFLOW-2000, also can be read and used by UCODE_2014.

UCODE_2014 includes re-parameterization using singular value decomposition (SVD) and uncertainty evaluation using Markov-Chain Monte Carlo (MCMC).

UCODE_2014 is intended for use on any computer operating system: it consists of algorithms programmed Fortran90/95, the fastest language for numerical calculations. It is constructed using the Joint Universal Parameter Identification and Estimation of Reliability (JUPITER) Application Programming Interface (API).



This course is designed for modelers seeking better ways to use data and their models. Knowledge of ground-water modeling and basic statistics is useful but not necessary. Anyone interested in modeling will learn important skills in this course.



Attendees will receive:

  • Electronic version of all class presentations;
  • “Effective groundwater model calibration, with analysis of data, sensitivities, predictions, and uncertainty”, by Mary C. Hill and Claire R. Tiedeman. John Wiley and Sons, 2007, 455p.
  • QGIS software and manual
  • MODFLOW_2005, MODFLOW-OWHM, and UCODE_2014 software and manual and associated USGS and IGWMC reports.
  • FREEWAT software and tutorials
  • Data files for example problems that enable attendees to use the exercises to refresh their inverse modeling skills at home!



Dr. Iacopo Borsi is an applied mathematician with more than 15 years of experience on modeling industrial and environmental processes. Presently he is Senior Environmental Modeler at TEA SISTEMI SpA, an Italian private company delivering research and consultancy services in energy and environment sector. He is in charge of developing ICT, GIS-integrated, environmental modelling tools (water resources estimation, wastewater treatment, air pollution, etc.) connected to real-time sensing technologies and relational databases. He is responsible of development activities in FREEWAT project, and project manager of several R&D projects (national and international). He is author of 1 monograph and more than 25 papers in international journals. Since 2012, he has been Co-Editor in Chief of Acque Sotterranee – Italian Journal of groundwater.

Dr. Laura Foglia is an adjunct assistant professor at University of California Davis, and a consultant senior engineer with Larry Walker Associates, a private environmental company in Davis, California. She holds a Master in Physics from University of Milan, Italy, and a PhD in Environmental Engineering from ETH Zurich, Switzerland. Her research focuses on understanding integrated groundwater/surface water systems at local and macro-scale. Her emphasis is on model calibration and uncertainty analysis applied to different watersheds and different water management problems, from ecohydrological problems to optimization of conjunctive use of surface water/groundwater She has been a research assistant at the Technical University of Darmstadt, Germany, where she taught groundwater and vadose zone modelling courses, and short courses for other universities. At University of California, Davis, she developed a new class on “Inverse Problems” for students in the Civil and Environmental Engineering and Land, Air and Water Resources Departments.

Dr. Dan Lu is a research scientist in the Computer Science and Mathematics Division at the Oak Ridge National Laboratory. She authored the MCMC chapter of UCODE-2014, and several articles on uncertainty quantification and experimental design methodology. Her expertise is in groundwater reactive transport modeling, parameter optimization, uncertainty quantification, experimental design and computational methods for efficient forward and inverse modeling. Dr. Lu holds a PhD in computational hydrology from Florida State University.

Dr. Mary C. Hill is a Professor in the Geology Department at the University of Kansas, and emeritus at the US Geological Survey following a 33-year career there. She authored the popular PCG2 solver for MODFLOW, and 140 reports and articles on solvers, nonlinear regression, confidence intervals, and calibration methodology. She co-authored UCODE, MODFLOW-2000, OPR-PPR, and MMA.  She has experience modeling saltwater intrusion, groundwater supply, stream interaction, and regional groundwater flow and transport beneath the proposed Yucca Mountain USA high-level nuclear waste site. She has taught semester and short courses since 1981. She has received many awards and honors. Most recently, she was elected as Fellow of AGU in 2016. Dr. Hill holds a PhD in Civil Engineering from Princeton University.

Dr. Eileen Poeter is Emeritus Professor of Geological Engineering at Colorado School of Mines (, Past Director of the International Ground Water Modeling Center, and currently Proprietor of Poeter Engineering. With 36 years of experience modeling groundwater systems, she has provided consultation to attorneys, industries, engineering companies, government agencies, research labs, and citizen groups on groundwater modeling projects including water rights, construction disputes, aquifer storage and recovery, slurry wall performance, drainage at proposed nuclear power plant facilities, regional groundwater management, impacts of proposed large-scale regional pumping, dam seepage, contaminant migration, impacts of dewatering, and stream-aquifer interaction. She is an author of computer codes that facilitate groundwater modeling including UCODE (a universal model calibration code), MMA (a multi-model analysis code), SimAdjust (a code to support calibration of models with dry cells), and JUPITER (an application programming interface to support model applications).



The course will be held on Colorado School of Mines campus (room and building TBA). For parking availability, please refer to the campus map below.

All Visitor parking areas will have a pay and display parking meter. When arriving on campus for the first time, look for a parking meter, find a space in that location, pay the meter and display the receipt on your dash. You will find brochures at each of our parking meters that can also help guide you around the campus.



The fee for the short course is $650 by 5:00PM Mountain Daylight Time, April 21, 2017 ($750 after April 21). Students receive a 30% discount on the short course fee ($455.50 before 4/21/17, $525.00 after). 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 by purchase order (US Only). Spaces will be filled at a first come, first serve basis, so be sure to sign up as early as possible.

If cancellation is made by April 21, 2017, the entire tuition will be refunded. Cancellations made after that date will forfeit a $150 processing fee. 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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