This section lists documents that explain details of RT3D. This includes documents written by the RT3D development team, as well as documents on MT3DMS and MODFLOW. Publications are nominally listed in order of importance. Several white papers on RT3D updates or functionality are not listed here, but are available from the Code Documentation page.

RT3D

• Clement, T.P. 1997. RT3D - A Modular Computer Code for Simulating Reactive Multi-Species Transport in 3-Dimensional Groundwater Aquifers. PNNL-11720. Pacific Northwest National Laboratory, Richland, Washington PDF file
• Clement, T.P.Y. Sun B.S. Hooker J.N. Petersen. 1998. “Modeling Multispecies Reactive Transport in Ground Water.” Ground Water Monitoring & Remediation 18279-92 [Abstract] (Reprint available upon request.)
• Johnson, C.D.M.J. Truex T.P. Clement. 2006. Natural and Enhanced Attenuation of Chlorinated Solvents Using RT3D PNNL-15937. Pacific Northwest National Laboratory, Richland, Washington PDF file
• Johnson, C.D.M.J. Truex. 2006. RT3D Reaction Modules for Natural and Enhanced Attenuation of Chloroethanes, Chloroethenes, Chloromethanes, and Daughter Products. PNNL-15938 Pacific Northwest National Laboratory, Richland, Washington PDF file
• Johnson, C.D.M.J. Truex. 2006. rtFlux: RT3D Flux Plane Utility. PNWD-3720 Battelle – Pacific Northwest Division, Richland, Washington PDF file
• Johnson, C.D.J.R. Spencer. 2003. “Modifications to MODFLOW and RT3D for Modelling Cyclic Seasonal Variations in Groundwater Flow.” Proceedings of Modflow and More 2003: Understanding through Modelling (Volume II) 
• E. Poeter, C. Zheng, M. Hill, and J. Doherty. International Ground Water Modelling Center, Colorado School of Mines, Golden, Colorado pp. 764-768

MT3DMS

• Zheng, C.P.P. Wang. 1999. MT3DMS:  A Modular Three-Dimensional Multispecies Transport Model for Simulation of Advection, Dispersion, and Chemical Reactions of Contaminants in Groundwater Systems; Documentation and User's Guide. SERDP-99-1. United States Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, Mississippi PDF file
• Zheng, C. 2006. MT3DMS v5.2: Supplemental User's Guide. University of Alabama, Tuscaloosa, Alabama PDF file
• Zheng, C.M.C. Hill P.A. Hsieh. 2001. Modflow-2000, the U.S. Geological Survey Modular Ground-Water Model – User Guide to the LMT6 Package, the Linkage with MT3DMS for Multi-Species Mass Transport Modeling. Open File Report 01-82. U.S. Geological Survey, Reston, Virginia PDF file

​​​​​​​MODFLOW

• Harbaugh, A.W.E.R. Banta M.C. Hill M.G. McDonald. 2000. MODFLOW-2000, the U.S. Geological Survey Modular Ground-Water Model – User Guide to Modularization Concepts and the Ground-Water Flow Process. Open File Report 00-92. U.S. Geological Survey, Reston, Virginia PDF file available
• Harbaugh, A.W. 2005. MODFLOW-2005, The U.S. Geological Survey Modular Ground-Water Model – the Ground-Water Flow Process. Techniques and Methods 6-A16 U.S. Geological Survey, Reston, Virginia PDF file available

​​​​​​​Other

• Clement, T.P.N.L. Jones. 1998. RT3D Tutorials for GMS Users. PNNL-11805. Pacific Northwest National Laboratory, Richland, Washington PDF file

​​​​​​​Application of RT3D

These publications discuss application of RT3D to field and theoretical problems and may involve case studies, laboratory work, and/or development of RT3D reaction modules. Includes articles by the RT3D development team and third parties (sorted by author). This list is intended to be representative, but not exhaustive. Note that articles by third parties may (usually unwittingly) misrepresent the nature or capabilities of RT3D (e.g., see public availability and Battelle Laboratories [sic]); contact us if something appears confusing.

If you have used RT3D for reactive transport modeling and have published an article on the work, send an e-mail to Chris Johnson with details, so we can list it here.

• Atteia, O.M. Franceschi A. Dupuy. 2008. “Validation of Reactive Model Assumptions with Isotope Data:  Application to the Dover Case.” Environ. Sci. Technol. 4293289-3295
• Biteman, S.E.D.W. Hyndman M.S. Phanikumar G.S.Weissmann. 2004. “Integration of Sedimentologic and Hydrologic Properties for Improved Transport Simulations.” Aquifer Characterization J.S. Bridge and D.W. Hyndman eds SEPM Special Publication 80 Society for Sedimentary Geology (SEPM), Tulsa, Oklahoma pp. 3-13
• Bolisetti, T.S. Reitsma. 2003. “Numerical Simulation of Chemical Grouting in Heterogeneous Porous Media.” Grouting and Ground Treatment L.F. Johnsen, D.A. Bruce, and M.J. Byle, eds ASCE Publications, Reston, Virginia pp. 1454-1465doi:10.1061/40663(2003)123
• Borden, R.C. 2007. “Concurrent Bioremediation of Perchlorate and 1,1,1-Trichloroethane in an Emulsified Oil Barrier.” J. Contam. Hydrol. 941-213-33
• Cadotte M.L. Deschênes R. Samson. 2007. “Selection of a Remediation Scenario for a Diesel-Contaminated Site Using LCA.” Intnl. J. LCA 124239-251
• Clayton, M.H.R.C. Borden. 2009. “Numerical Modeling of Emulsified Oil Distribution in Heterogeneous Aquifers.” Ground Water 472246-258
• Clement, T.P.Y. Sun B.S. Hooker J.N. Petersen. 1997. “Modeling Natural Attenuation of Contaminants in Saturated Groundwater.” In Situ and On-Site Bioremediation:  Volume 1 A. Leeson and B.C. Alleman, eds Battelle Press, Columbus, Ohio pp. 37-42 (Presented at the Fourth International In Situ and On-Site Bioremediation Symposium, New Orleans, Louisiana, April 28-May 1, 1997.)
• Clement, T.P.Y. Sun C. Zheng. 1998. “RT3D - A Modflow-Family Reactive Transport Simulator.” Proceedings of MODFLOW '98 International Conference, Volume 1 E.P. Poeter, C. Zheng, and M.C. Hill, eds International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado pp. 397-403
• Clement, T.P.C.D. Johnson Y. Sun G.M. Klecka C. Bartlett. 1999. “Modeling Natural Attenuation of Chlorinated Solvent Plumes at the Dover Air Force Base Site.” Natural Attenuation of Chlorinated Solvents, Petroleum Hydrocarbons, and Other Organic Compounds A. Leeson and B.C. Alleman, eds Battelle Press, Columbus, Ohio pp. 29-34(Presented at the Fifth International In Situ and On-Site Bioremediation Symposium, San Diego, California, April 19-22, 1999.)
• Clement, T.P.C.D. Johnson . Sun G.M. Klecka C. Bartlett. 2000. “Natural Attenuation of Chlorinated Solvent Compounds:  Model Development and Field-Scale Application at the Dover Site.” J. Contam. Hydrol. 422-4113-140
• Clement, T.P.T.R. Gautam K.K. Lee M.J. Truex G.B. Davis. 2004. “Modeling of DNAPL-Dissolution, Rate-Limited Sorption and Biodegradation Reactions in Groundwater Systems.” Bioremediation J. 81-247-64
• Coulibaly, K.M.C.M. Long R.C. Borden. 2006. “Transport of Edible Oil Emulsions in Clayey Sands:  One-Dimensional Column Results and Model Development.” J. Hydrologic Engrg.113230-237
• Davis, J.H. 2003. Fate and Transport Modeling of Selected Chlorinated Organic Compounds at Hangar 1000, U.S. Naval Air Station, Jacksonville, Florida. Water Resources Investigations Report 03-4089. U.S. Geological Survey, Tallahassee, Florida
• Di Molfetta, A.R. Sethi. 2006. “Clamshell Excavation of a Permeable Reactive Barrier.” Environ. Geol. 503361-369
• Geistlinger, H.D. Eisermann M. Schirmer U. Mayer T.P. Clement. 2003. “Development of New Modeling Tools for Simulating and Designing Reactive Gas Walls.” Groundwater Quality Modeling and Management Under Uncertainty S. Mishra, ed ASCE Publications, Reston, Virginia pp. 192-203 doi:10.1061/40696(2003)18
• Gödeke, S.H-H. Richnow H. Wei ßA. Fischer C. Vogt H. Borsdorf M. Schirmer. 2006. “Multi Tracer Test for the Implementation of Enhanced In-Situ Bioremediation at a BTEX-Contaminated Megasite.” J. Contam. Hydrol. 873-4211-236
• Gomez, D.E.P.C. de Blanc W.G. Rixey P.B. Bedient P.J.J. Alvarez. 2008. “Modeling Benzene Plume Elongation Mechanisms Exerted by Ethanol Using RT3D with a General Substrate Interaction Module.” Water Resour. Res. 445W05405doi:10.1029/2007WR006184
• Huang, J.J.A. Christ M.N. Goltz. 2008. “An Assembly Model for Simulation of Large-Scale Ground Water Flow and Transport.” Ground Water 466882-892
• Johnson, C.D.R.S. Skeen D.P. Leigh T.P. Clement Y. Sun. 1998. “Modeling Natural Attenuation of Chlorinated Ethenes Using the RT3D Code.” Proceedings of the Water Environment Federation 71st Annual Conference and Exposition, WEFTEC '98, Volume 3Water Environment Federation, Alexandria, Virginia pp. 225-247
• Khadam, I.M.J.J. Kaluarachchi. 2003. “Multi-criteria Decision Analysis with Probabilistic Risk Assessment for the Management of Contaminated Ground Water.” Environmental Impact Assessment Review. 236683-721
• Langenhoff, A.A.M.J.J.M. Staps C. Pijls A. Alphenaar G. Zwiep H.H.M. Rijnaarts. 2002. “Intrinsic and Stimulated In Situ Biodegradation of Hexachlorocyclohexane (HCH).” Water, Air, and Soil Pollution: Focus 23171-181
• Lee, M-S. K-K. Lee Y. Hyun T.P. Clement D. Hamilton. 2006. “Nitrogen Transformation and Transport Modeling in Groundwater Aquifers.” Ecolog. Model. 1921-2143-159
• Li, L.C.H. Benson E.M. Lawson. 2005. “Impact of Mineral Fouling on Hydraulic Behavior of Permeable Reactive Barriers.” Ground Water. 434582-596
• Li, L.C.H. Benson E.M. Lawson. 2006. “Modeling Porosity Reductions Caused by Mineral Fouling in Continuous-Wall Permeable Reactive Barriers.” J. Contam. Hydrol. 831-289-121
• Lim, M-S.I.W. Yeo T.P. Clement Y. Roh K-K. Lee. 2007. “Mathematical Model for Predicting Microbial Reduction and Transport of Arsenic in Groundwater Systems.” Water Res.41102079-2088
• Ling, M.H.S. Rifai. 2007. “Modeling Natural Attenuation with Source Control at a Chlorinated Solvents Dry Cleaner Site.” Ground Water Monitor. Remed. 271108-121
• Lu, G.T.P. Clement C. Zheng T.H. Wiedemeier. 1999. “Natural Attenuation of BTEX Compounds: Model Development and Field-Scale Application.” Ground Water 375707-717
• Lu, G.C. Zheng A. Wolfsberg. 2005. “Effect of Uncertain Hydraulic Conductivity on the Simulated Fate and Transport of BTEX Compounds at a Field Site.” J. Environ. Engr.1315767-776
• Mailloux, M.B. Tartakovsky D. Milette S.R. Guiot A. Peisajovich L. Olivier C. Bélanger M-J. Lorrain. 2002. “Evaluation of a Carbon-Source Stimulated Bioremediation Technology for the Remediation of a Nitrate-Contaminated Aquifer at an Airport Site.” Ground and Water:  Theory to Practice D. Stolle, A.R. Piggott and J.J. Crowder, eds Southern Ontario Section of the Canadian Geotechnical Society, Toronto, Ontario, Canada pp. 919-925(Presented at the 55th Canadian Geotechnical and 3rd Joint IAH-CNC and CGS Groundwater Specialty Conferences, Niagara Falls, Ontario, October 20-23, 2002.)
• Phanikumar, M.S.D.W. Hyndman D.C. Wiggert M.J. Dybas M.E. Witt C.S. Criddle. 2002. “Simulation of Microbial Transport and Carbon Tetrachloride Biodegradation in Intermittently-Fed Aquifer Columns.” Water Resour. Res. 3841033 doi:10.1029/2001WR000289
• Phanikumar, M.S.D.W. Hyndman C.S. Criddle. 2002. “Biocurtain Design Using Reactive Transport Models.” Ground Water Monitor. Remed. 223113-123
• Phanikumar, M.S.D.W. Hyndman X. Zhao M.J. Dybas. 2005. “A Three-Dimensional Model of Microbial Transport and Biodegradation at the Schoolcraft, Michigan, Site.” Water Resour. Res. 415W05011 doi:10.1029/2004WR003376
• Reed, P.B. Minsker A.J. Valocchi. 2000. “Cost-effective Long-term Groundwater Monitoring Design Using a Genetic Algorithm and Global Mass Interpolation.” Water Resour. Res.36123731-3741
• Reed, P.B. Minsker D.E. Goldberg. 2000. “Designing a Competent Simple Genetic Algorithm for Search and Optimization.” Water Resour. Res. 36123757-3761
• Rolle, M.T.P. Clement R. Sethi A.D. Molfetta. 2008. “A Kinetic Approach for Simulating Redox-controlled Fringe and Core Biodegradation Processes in Groundwater:  Model Development and Application to a Landfill Site in Piedmont, Italy.” Hydrol. Proc. J.22254905-4921
• Sun, Y.J.N. Petersen T.P. Clement B.S. Hooker. 1998. “Effect of Reaction Kinetics on Predicted Concentration Profiles During Subsurface Bioremediation.” J. Contam. Hydrol.313-4359-372
• Sun, Y.J.N. Petersen J. Bear T.P. Clement B.S. Hooker. 1999. “Modeling Microbial Transport and Biodegradation in a Dual-Porosity System.” Transport in Porous Media35149-65
• Tartakovsky, B.D. Millette S. Delisle S.R. Guiot. 2002. “Ethanol-Stimulated Bioremediation of Nitrate-Contaminated Ground Water.” Ground Water Monitor. Remed. 22178-87
• Tenbus, F.J.W.B. Fleck. 2001. Simulation of Ground-Water Flow and Transport of Chlorinated Hydrocarbons at Graces Quarters, Aberdeen Proving Ground, Maryland. Water Resources Investigations Report 01-4106. U.S. Geological Survey, Baltimore, Maryland
• Truex, M.J.C.D. Johnson J.R. Spencer T.P. Clement B.B. Looney. 2007. “A Deterministic Approach to Evaluate and Implement Monitored Natural Attenuation for Chlorinated Solvents.” Remediation J. 17423-40
• Uçankuş, T.K. Ünlü. 2008. “The Effect of Aquifer Heterogeneity on Natural Attenuation Rate of BTEX.” Environ. Geol. 544759-776
• Wethasinghe, CS.T.S. Yuen J.J. Kaluarachchi R. Hughes. 2006. “Uncertainty in Biokinetic Parameters on Bioremediation:  Health Risks and Economic Implications.” Environ. Intnl.323312-323
• Wood, R.C.J. Huang M.N. Goltz. 2006. “Modeling Chlorinated Solvent Bioremediation Using Hydrogen Release Compound (HRC).” Bioremediation J. 103129-141
• Wriedt, GM. Rode. 2006. “Modelling Nitrate Transport and Turnover in a Lowland Catchment System.” J. Hydrol. 3281-2157-176
• Yan, S.B. Minsker. 2006. “Optimal Groundwater Remediation Design Using an Adaptive Neural Network Genetic Algorithm.” Water Resour. Res. 425W05407doi:10.1029/2005WR004303

Related Topics

These publications discuss topics related to RT3D or that are of potential interest to RT3D users. RT3D is typically ancillary to the main topic in these publications. The RT3D FAQ lists additional documents related to specific questions and may also be of interest to RT3D users (i.e., articles on topics, such as determination of dispersivity values). Sorted by author.

• Clement, T.P. 1998. “Remediation of Contaminated Ground Water - Lessons from U.S.A.” J. Indian Water Works Association 4241-247
• Clement, T.P. 2001. “A Generalized Analytical Method for Solving Multi-Species Transport Equations Coupled with a First-Order Reaction Network.” Water Resour. Res. 371157-163
• Clement, T.P.B.M. Peyton T.R. Ginn R.S. Skeen. 1999. “Modeling Microbial Transport and Accumulation Processes in Saturated Porous Media: A Review.” Advances in Nuclear Science and Technology:  Volume 26 J. Lewins and M. Becker, eds Kluwer Academic/Plenum Publishers, New York pp. 59-78
• Clement T.P.V. Srinivasan C.D. Johnson M.J. Truex. 2006. Development of a New Analytical Tool for Modeling the Fate and Transport of Chlorinated Solvent Species. WSRC-STI-2006-00076 Savannah River National Laboratory, Washington Savannah River Company, Aiken, South Carolina
• Davis, R.J.N.L. JonesT.P. Clement. 1998. “Efficient Tools for Building Multi-Component Transport Models.” Proceedings of MODFLOW '98 International Conference, Volume 1E.P. Poeter, C. Zheng, and M.C. Hill, eds International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado pp. 195-202
• Lu, X.Y. Sun. 2008. “A Solution of Transport in Porous Media with Equilibrium and Kinetic Reactions.” Transp. Porous Media 722199-206
• Magar, V.S.H.D. Stensel J.A. Puhakka J.F. Ferguson. 1999. “Sequential Anaerobic Dechlorination of Pentachlorophenol:  Competitive Inhibition Effects and a Kinetic Model.” Environ. Sci. Technol. 33101604-1611
• Matott, L.S.A.J. Rabideau. 2008. “Calibration of Subsurface Batch and Reactive-Transport Models Involving Complex Biogeochemical Processes.” Adv. Water Resour. 312269-286
• Palanichamy, J.T. Becker M. Spiller J. Köngeter S. Mohan. 2009. “Multicomponent Reaction Modelling Using a Stochastic Algorithm.” Comput. Visual. Sci. 12251-61
• Peyton, B.M.T.P Clement J.P. Connolly. 2000. “Modeling of Natural Remediation:  Contaminant Fate and Transport.” Chapter 5 in  Natural Remediation of Environmental Contaminants M. Swindoll, R.G. Stahl, and S.J. Ells, eds Society for Environmental and Toxicology and Chemistry, Pensacola, Florida pp. 79-120
• Phanikumar, M.S.J.T. McGuire. 2004. “A 3D Partial-Equilibrium Model to Simulate Coupled Hydrogeological, Microbiological, and Geochemical Processes.” in Subsurface Systems Geophys. Res. Letters 3111L11503 doi:10.1029/2004GL019468
• Sun, Y.T.P. Clement. 1999. “A Decomposition Method for Solving Coupled Multi-Species Reactive Transport Problems.” Transport in Porous Media 373327-346
• Sun, Y.J.N. Petersen T.P. Clement R.S. Skeen. 1999. “Development of Analytical Solutions for Multi-Species Transport with Serial and Parallel Reactions.” Water Resour. Res.351185-190
• Sun, Y.J.N. Petersen T.P. Clement. 1999. “Analytical Solutions for Multiple Species Reactive Transport in Multiple Dimensions.” J. Contam. Hydrol. 354429-440​​​​​​​