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U.S. Department of Energy
Reactive Transport in 3-Dimensions


Getting Help

There are a number of resources for getting help in using/applying RT3D.  Start with the first item and continue down the list as needed...

  1. RT3D Documentation – The manuals are there to tell you about the code and how to use it.
  2. MT3DMS Manual – RT3D is an offshoot of MT3DMS, thus much of the information in the MT3DMS manual applies to RT3D (the biggest exception being the reaction package).
  3. RT3D FAQ – The FAQ covers many common questions and points to relevant resources.
  4. Training Short Courses – Provides hands-on training in how to use groundwater modelling software.
  5. Contact the RT3D Developers – This option would be for issues not covered by the above resources.  Keep in mind this FAQ.
  6. Hire PNNL (Battelle PNWD) or Dr. Clement as a consultant – If you have a challenging problem, need customization of RT3D, or otherwise need further assistance, it may be most cost effective to hire us (see what we do below).  We have a wide range of expertise, are focused on solving your problem, and provide quality work.

Training Opportunities

Training opportunities are periodically available for hands on short courses in using RT3D.  Many of these training opportunities are offered by the Graphical User Interface developers.  Additional opportunities are available from national organizations such as the National Ground Water Association.  The RT3D Development Team participates in some of these training opportunities as well as other venues, on occasion.

Working with the PNNL RT3D Team

The PNNL RT3D Team is a component of the Field Hydrology and Chemistry (FH&C) Group in the Energy and Environment Directorate of the Pacific Northwest National Laboratory and is a portion of the RT3D Development Team (see Who We Are below).  For more information on working with PNNL see the web pages on Doing Business with PNNL.

What We Do

The RT3D Team at PNNL has been developing and applying in situ remediation technologies and reactive transport software since the early 1990s.  We have demonstrated strong capabilities in accelerated in situ bioremediation (ISB) design and evaluation of monitored natural attenuation (MNA) in numerous projects for federal government agencies and private clients.  While the PNNL RT3D Team has focused on applications of RT3D, especially for treatment of groundwater contaminated with chlorinated solvents (e.g., TCE, carbon tetrachloride), we and our FH&C colleagues have broad experience in development and application of many kinds of remediation technologies for both vadose zone and groundwater. 

  • Customized Reaction Modules for RT3D – PNNL can efficiently develop customized reaction expressions within the RT3D reaction module framework to describe reactions at the level of detail needed for specific sites.  For instance, coupled reactions for substrate use and subsequent dechlorination can be used to describe reductive dechlorination induced by lactate amendment or methanotrophic cometabolic dechlorination.  Standard first-order representation of dechlorination for evaluation of natural attenuation can be improved to include non-sequential dechlorination pathways, inhibition terms, and electron acceptor dependencies for the reactions.  Customized reaction modules provide a technical basis for reactive transport simulations that supports better designs for accelerated ISB and better defensibility with regulatory authorities for evaluations of MNA.  PNNL has a variety of technical resources and can develop custom reaction modules for RT3D for applications other than chlorinated solvent bioremediation.  For instance, descriptions of biological or chemical (e.g., oxidation) reactions for other organic contaminants or inorganic contaminants can be included in custom reaction modules.
  • Customizations of RT3D – In some cases, modifying the RT3D code may help in conducting simulations for your site.  For example, in one recent project, PNNL modified RT3D to accommodate cyclic flow conditions induced by seasonal variations in river stage at one of the boundaries for the simulation.  Instead of entering boundary conditions for 120 time points to describe this variation over the 30-year simulation, only 4 time points were input.  Additional features can also be added to RT3D.  An example is the ability to calculate injection well concentrations during recirculation between an extraction and injection well pair.
  • Laboratory Microcosms – PNNL has extensive experience evaluating a variety of microbial metabolisms for reductive and cometabolic dechlorination through use of laboratory microcosms studies.  PNNL structures these studies within a context of reactive transport analysis to specifically obtain the information important to design an accelerated ISB system or evaluate natural attenuation.
  • Accelerated ISB Design – PNNL has significant experience in designing accelerated in situ bioremediation systems.  PNNL personnel have performed all system design aspects, including well network design, nutrient amendment strategy, equipment specification, system installation, and system operation.
  • Natural Attenuation Evaluation – PNNL provides technical support for evaluation of natural attenuation and development of long-term monitoring plans associated with implementation of MNA.  For sites requiring significant fate and transport analysis, PNNL can provide technical support for RT3D-based modelling.  PNNL also has significant resources for addressing site-specific technical issues such as including the evaluation of DNAPL source areas (e.g., multi-phase transport assessment and estimates of source flux) with the evaluation of MNA for the dispersed plume.  MNA evaluations require a thorough description of relevant attenuation mechanisms and development of lines of evidence for how these attenuation mechanisms are occurring at the site.  PNNL can provide the technical information needed for these descriptions and serve as a respected technical expert when communicating these lines of evidence to regulatory authorities.
  • Remediation Alternative Evaluation – PNNL can efficiently evaluate the viability of accelerated ISB or natural attenuation options through application of RT3D-based reactive transport assessment.  PNNL has performed this type of remediation alternative evaluation for sites at Hanford, Point Mugu, and INEEL.  PNNL has ready access to experts on non-bioremediation technologies as well if the client is interested in a broader assessment of potential remediation alternatives.

Our research directorate at PNNL, the Energy and Environment Directorate, hosts an extremely broad range of expertise in all environmental aspects (geology, hydrology, ecology, risk assessment, environmental biomarkers, marine science, radiological science, and more).  The RT3D Team can draw upon this wealth of expertise as needed to provide a quality solution that addresses the problem at hand.  See the discussion and website links below to find out more about the capabilities and research performed by personnel in the Energy and Environment Directorate at PNNL.

Who We Are

The RT3D Development Team operates within the collaborative context of a world-class national laboratory and a comprehensive land, space, and sea grant research university.

RT3D Development Team

RT3D development is a collaborative effort, with two principal leaders as well as a number of supporting contributors.

Dr. Prabhakar Clement

The lead author is Dr. Prabhakar Clement, who is currently a full professor and the Arthur H. Feagin Chair of Civil Engineering at Auburn University.  Dr. Clement's work on RT3D began at PNNL, continued while a senior lecturer at the University of Wester Australia, and is now ongoing at Auburn University.


Mr. Chris Johnson

Mr. Johnson is a senior development engineer at PNNL in the Field Hydrology and Chemistry Group within the Environment and Energy Directorate at PNNL.  Mr. Johnson develops aspects of RT3D, notably reaction modules and customizations for specific applications applicable to active remediation and natural attenuation.  In addition to code development, Mr. Johnson performs code testing, writes code documentation, oversees distribution of the RT3D code, and is the primary contact for questions on application of the RT3D code.


RT3D Team at PNNL

The RT3D Team at PNNL is led by Mr. Johnson and Mr. Michael Truex, both of the PNNL Field Hydrology and Chemistry Group.  The RT3D Team provides high quality problem solving capabilities for government and industrial customers in the realm of hazardous waste site evaluation, remediation technology development, and remediation system design.

Battelle—Pacific Northwest Division (Battelle PNWD)

Battelle Memorial Institute's Pacific Northwest Division (Battelle PNWD) operates the Pacific Northwest National Laboratory for the U.S. Department of Energy.  That is, Battelle PNWD is the contractor that runs PNNL and the personnel at PNNL are employees of Battelle PNWD.  Battelle PNWD has a unique situation among the national laboratories that allows Battelle PNWD to work (as Battelle) for industrial clients under certain conditions, although this lattitude is set to expire in 2012. 
(Aside:  There is no such thing as Battelle Pacific Northwest Laboratory(ies) – this term is (on occasion) erroneously used by those who misunderstand the relationship between Battelle—Pacific Northwest Division and the Pacific Northwest National Laboratory.)

Pacific Northwest National Laboratory (PNNL)

The Pacific Northwest National Laboratory in Richland, Washington is a U.S. Department of Energy Office of Science national laboratory where interdisciplinary teams advance science and technology and deliver solutions to America's most intractable problems in energy, national security, and the environment.  PNNL employs 4,250 staff, has a $918 million annual budget, and has been managed by Ohio-based Battelle since the lab's inception in 1965.

PNNL is at the forefront of innovative environmental technology.  In addition to bioremediation, scientists and engineers at PNNL perform research and development (both fundamental and applied) on a wide variety of technologies and environmental problems.  Visit the following web pages for more information on environmental research and development at PNNL.  From Division to Laboratory, the perspectives go from more specific to a broader overview.

Field Hydrology and Chemistry Group
Environmental Sustainability Division
Energy and Environment Directorate
Pacific Northwest National Laboratory

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