Reactive Transport with Sophisticated Reaction Networks: Hands-On Experience with the PFLOTRAN Reaction Sandbox

November 6 - 9, 2023

Registration Deadline 9.14.2023

Location: Pacific Northwest National Laboratory, Richland, WA
Registration Website


Glenn Hammond
Pacific Northwest National Laboratories
Xingyuan Chen
Pacific Northwest National Laboratories

CUAHSI is excited to work with Pacific Northwest National Labs to bring this new workshop to the water science community!

Gain training in using reactive transport modeling to resolve environmental problems. There are a limited number of spots available for this short course. We recommend registering as soon as possible.


Reactive transport modeling is increasingly important for solving real-world environmental issues related to water quality, and ecological habitats, and evaluating the performance of environmental restoration and remediation efforts. This short course will train participants in conceptualizing, implementing, and troubleshooting reaction networks in reactive transport models through hands-on experience.

During this short course, participants will:

  • Learn reactive transport modeling fundamentals
  • Be introduced to simulation tools, focusing on PFLOTRAN (
  • Gain experience with flow and reactive transport problems
  • Learn to design and encode new reaction networks in the PFLOTRAN Reaction Sandbox

Course Eligibility and Requirements

The course is aimed at graduate students, post-docs, professionals, and scientists at all career stages, who are interested in using reactive transport modeling in their research.


  • Participants must receive security clearance by PNNL after registration to attend this short course. Please feel free to contact us with any questions.
  • Participants are subject to an approval process to gain physical access to PNNL
  • Due to facility regulations, participants must be at least 18 years of age to participate in this short course.
  • Participants must bring their own laptop with at least 8 GB of memory

Course Requirements:

  • Experience with water chemistry
  • Experience with the Linux operating system and command-line environment
  • Familiarity with text-based input files
  • Entry-level scripting experience (i.e. Python or R)
  • Entry-level programming experience (e.g. C/C++/Fortran)

Short Course Location and Cost

The short course will be held on-site at PNNL. Attendance is contingent on security clearance by PNNL. Registered participants will be contacted to begin the screening process.

  • Registration Cost:
    • $350 Student - CUAHSI Member Organization Affiliated
    • $400 Student - Not CUAHSI Member Organization Affiliated
    • $450 Professional - CUAHSI Member Organization Affiliated
    • $500 Professional - Not CUAHSI Member Organization Affiliated

In the event that security clearance is not granted, CUAHSI will reimburse your registration fee.

A room block has been arranged at a local hotel at a discounted rate. Participants are responsible for the cost of their own lodging. Transportation to and from the classroom from the hotel will be provided. A light breakfast and lunch are included in the registration cost.

A limited number of travel grants are available for graduate students to help defray the cost of travel to the short course.

Information on PFLOTRAN

PFLOTRAN is an open source reactive multiphase flow and multicomponent transport code. PFLOTRAN’s reactive transport process model supports biogeochemical reactions including aqueous speciation, sorption (isotherm-based, ion exchange, surface complexation), mineral precipitation-dissolution and general Nth-order reactions. Although PFLOTRAN provides support for microbially-mediated reactions with inhibition (i.e. multiplicative Monod), many researchers prefer PFLOTRAN’s Reaction Sandbox where the scientist may implement custom rate expressions and reaction networks for a specific application. This topic (i.e., the Reaction Sandbox) will be covered in the short course. Note that PFLOTRAN will be provided to attendees in a virtual Linux environment that will run on a laptop. For more information on PFLOTRAN, please see .


This agenda is approximate and subject to change.

Day 1 – Reactive Transport Modeling Fundamentals

  • Morning
    • Introduction to PNNL – Badging, safety training, etc.
    • Setup – Configuration of virtual short course environment
    • Reactive transport modeling fundamentals
  • Afternoon
    • Introduction to PFLOTRAN
    • Overview presentation
    • Conceptual model setup
    • Discussion of PFLOTRAN input deck specification
    • Example problems (e.g.)
      • 1D variable saturated flow
      • 1D solute transport
      • 1D Calcite (mineral precipitation-dissolution)Copper leaching
      • Error messaging

Day 2 – PFLOTRAN Reaction Sandbox

  • Morning
    • Introduction to the PFLOTRAN Reaction Sandbox

    • Example problems
      • Reaction Sandbox Simple
      • Reaction Sandbox Calcite
      • Reaction Sandbox Biodegradation
  • Afternoon
    • Developing new reaction sandboxes
      • Conceptualization
      • Implementation – software development
      • Object-oriented design
      • Modern Fortran
      • Debugging
      • Application to an example reaction

Day 3 – Developing New Reaction Sandboxes

  • Morning
    • Open stage: Attendee flash talks on reaction conceptual models to be implemented in a reaction sandbox.
    • Conceptualizing and encoding a new reaction sandbox
  • Afternoon
    • Python scripting for visualization

Day 4 – Developing New Reaction Sandboxes (cont.)

  • Morning
    • Continue encoding a new reaction sandbox
  • Afternoon
    • Wrap Up