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

Features of RT3D

Summary — What is RT3D?

RT3D is a software package for simulating three-dimensional, multi-species, reactive transport of chemical compounds (solutes) in groundwater.  RT3D provides an easy-to-use and flexible framework applicable to natural attenuation, accelerated bioremediation, or other reactive transport modeling scenarios.  Predefined modules are available for common bioremediation scenarios, but you have the flexibility to add any reaction kinetics desired/suitable to represent multiple chemical species in aqueous and sorbed phases.  Several graphical user interfaces to RT3D are available to organize the process of defining the required RT3D input information and to provide visualization capabilities for the RT3D output.  At the same time, the availability of the Fortran 90 source code provides flexibility for advanced users, regardless of the target computing platform.

RT3D Reaction Modules

Pre-Programmed Modules

As a convenience to the user, RT3D comes with a set of pre-programmed reaction modules (listed below).  The first 7 modules are available starting in RT3D version 1.0, while the latter 8 are available as DLL files for use as user-defined reaction modules (discussed below).  Details of the reaction mechanisms and enumeration of the adjustable parameters for these pre-programmed modules are provided in the RT3D Users Manual (PNNL-11720) and the document on RT3D Reaction Modules for Natural and Enhanced Attenuation of Chloroethanes, Chloroethenes, Chloromethanes, and Daughter Products (PNNL-15938).

  1. Tracer Transport
  2. Two Species Instantaneous Reaction (BIOPLUME-II type reactions; e.g., Hydrocarbon & Oxygen)
  3. Six Species, First-Order, Rate-Limited, BTEX Degradation using Sequential Electron Acceptors (e.g., O2, NO3-, Fe2+, SO42-, CO2)
  4. Rate-Limited Sorption
  5. Double Monod Model
  6. Sequential First-Order Decay (up to 4 species, e.g., PCE/TCE/DCE/VC)
  7. Aerobic/Anaerobic Chlorinated Ethene Dechlorination
  8. Mixed Chloroethene/Chloroethane/Chloromethane Dechlorination
  9. Chloromethane Dechlorination
  10. Dechlorination of 1,1,2,2-Tetrachloroethane and Chloroethenes
  11. Dechlorination of 1,1,1,2-Tetrachloroethane and Chloroethenes
  12. Chloroethene Dechlorination
  13. Redox-Linked Dechlorination of Chloroethenes
  14. Substrate-Linked Reductive Dechlorination of Chloroethenes
  15. Cometabolic Aerobic Dechlorination of Chloroethenes

User-Defined / Custom Reaction Modules

A key feature of RT3D is the high degree of flexibility the user has in adding other reaction kinetics via the user-defined module.  For instance, coupled reactions for substrate use and subsequent dechlorination could be described for improved accelerated in situ bioremediation modeling (see example figures below).  Standard first-order representation of dechlorination for evaluation of natural attenuation could be improved to include non-sequential dechlorination pathways, inhibition terms (competitive or otherwise), and electron acceptor dependencies for the reactions.  The user can implement their own user-defined reaction module, or the PNNL RT3D Team can be contracted to provide that service for those who are not comfortable with the process of developing custom reaction modules.

Comparison of laboratory data and RT3D simulation results for sealed microcosm (batch) tests with sediment, groundwater, lactate (500 mg/L), and PCE.

Plot of substrate utilization - data versus reaction model.

A.  Measurements indicated complete removal of lactate in the first 12 days of incubation.  Propionate and acetate were produced and slowly degraded thereafter.

Plot of contaminant dechlorination - data versus reaction model.

B.  Measurements showed PCE dechlorination with TCE and DCE intermediates.  RT3D simulation modeled dechlorination as a reaction coupled to lactate and propionate fermentation.

RT3D is Widely Applicable

With a variety of pre-programmed reaction packages and the flexibility to insert user-specific kinetics, RT3D can simulate a multitude of scenarios.

As part of a natural attenuation evaluation, RT3D can be used to predict fate and transport of groundwater plumes.  A sensitivity analysis can be performed to evaluate the range of potential outcomes.  Such predictions may be used to define a long-term monitoring program that will feed back into future reactive transport simulations and model refinement.  The PPI Brooklawn site is an example where RT3D simulations were performed using kinetics derived from laboratory microcosm experiments with site sediments; the predictions indicated that natural attenuation would be an appropriate strategy for the PPI Brooklawn site and the resulting monitoring plan is now being implemented.

Active remediation can also be simulated, whether it be air sparging, chemical oxidation or accelerated bioremediation.  The key is understanding the reaction kinetics of the remediation process and applying that knowledge in a user-defined reaction module.  Reactive transport simulations could potentially be applied to scenarios involving contaminants such as heavy metals, explosives, petroleum hydrocarbons, and/or chlorinated solvents.  The Point Mugu IRP Site 24 is an example where RT3D was used to design an effective accelerated in situ bioremediation system.

Graphical User Interfaces for RT3D

RT3D may be run in a stand-alone configuration by creating input files in a text editor and running RT3D from a command prompt.  However, the following popular groundwater modeling packages provide graphical user interfaces for setting up a simulation model and post-processing data.  The interface software often provides default values for key parameters (e.g., reaction rates), but the user will want to adjust those values based on information reported in the literature or results of site-specific tests (e.g., laboratory microcosms or field tests).  A few example figures of post-processed data with some of these interface sofware are presented; more examples and details are available at the vendor websites.

  1. The U.S. Department of Defense Groundwater Modeling System (GMS) commercially distributed by Aquaveo (formerly EMS-i)
    (Certain government users can contact the U.S. Army Corps of Engineer's Coastal & Hydraulics Laboratory about GMS)
  2. Visual Modflow from Schlumberger Water Services (formerly Waterloo Hydrogeologic, Inc.)
  3. Groundwater Vistas by Environmental Simulations, Inc
  4. Processing Modflow Pro by Excel Info Tech, Inc.

System Requirements


  • The full download package requires about < 10 MB of hard drive space when decompressed.
  • A version of MODFLOW with the LKMT package (or a comparable flow model that can output a MODFLOW-style head and flow file) is required.  A modified version of MODFLOW-96 is included in the RT3D distribution.
  • The more RAM, the better; memory requirements will depend on the size of the model (or vice versa)

For User Compilation of Source Code

  • A Fortran 90 compiler.  Testing has been done with Visual Fortran (Intel and Compaq/Digital versions) and a Fortran compiler on a DEC Alpha system.  The DLL option for the user-defined reaction module has been tested with Visual Fortran and Microsoft Fortran Powerstation v. 4.0.

For Pre-Compiled Binaries for Windows/Intel x86

  • IBM Compatible PC, 486/66 or better
  • Microsoft Windows 95 or newer

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