MARIO´ ABELGON ¸CALVES Faculdade de Ciˆencias da Universidade de Lisoba Lisoba, Portugal
An important share of geochemical studies increasingly relies on the use of computer programs1 to model
diverse geochemical systems. Most of these programs are freely available to the general public, or at a symbolic cost for educational and research purposes. Although developing open source and/or precompiled codes is 1We will use the term ‘‘computer code’’ as a set of written instructions aiming at solving a set of specific problems, and computer program to a compiled code to be executed as a stand- alone application under a given operating system.
markedly important, their regular maintenance should not be dismissed. Programming languages evolve, as well as operating systems and computer hardware, which means that codes without regular revision become outdated and eventually useless as their compiled versions may stop working properly under new operating systems.
All geochemical models rely very much on the availability of good quality, self-consistent thermodynamic data. This data is stored in database files that are accessed by the program while it is executed, making it one of its core elements. In the absence of specific data in the database for the problem to be modeled, some programs allow the incorporation of the data in simulations or, alternatively, the database can be modified by incorporation of new data. As new and improved experimental thermodynamic measurements are continuously being made, thermodynamic databases should also be regularly revised and updated.
The description that follows is meant to address mainly those computer programs most readily accessible and does not pretend to be an exhaustive list of all available programs. Although presenting the address of websites where these programs and codes are stored and may be obtained, one should be aware that this information will potentially become out of date rather quickly.
USGS CODES
The USGS supports various projects for developing soft- ware, including aqueous geochemistry computer pro- grams, which include the chemical speciation program WATEQ4F (1), well suited for processing large numbers of water analyses. The most recent upgrades include the revision of the thermodynamic data on uranium and arsenic species. The most complete computer programs available are the ones from the PHREEQC (2) family (http://wwwbrr.cr.usgs.gov/projects/GWC coupled/). PHREEQC is a program that performs chemical specia- tion calculations, reaction-path modeling, one-dimensional transport, and inverse geochemical calculations. Cur- rently, it contains a basic interpreter allowing a very flexible use of the program, meeting each one’s needs, especially for modeling kinetic data. The latest revi- sions (February–April 2003) include isotope fractiona- tion modeling (3). PHREEQC uses its own thermody- namic database, and also the LLNL and WATEQ4F databases, which are still updated and corrected regu- larly. Two graphical user interfaces (GUI) were devel- oped: PHREEQCI by USGS and PHREEQC for Windows by Vincent Post from the Vrije Universiteit Amster- dam (http://www.geo.vu.nl/users/posv/phreeqc). The latter allows the graphical display of the output, which is unavailable in the original program, which is rather achieved by using the PHRQCGRF program. PHAST is a three-dimensional multicomponent reaction-transport model that simulates transient groundwater flow, that may or may not include geochemical reactions. PHAST combines the HST3D simulator (4) for the transport cal- culations with PHREEQC for geochemical calculations. PHRQPITZ is specially designed to use with brines, as it implements Pitzer’s equation for the calculation of activity coefficients.
GEOCHEMICAL MODELING-COMPUTER CODES 141 Other computer programs include OTIS (5), used for
the geochemical modeling solute transport in streams and rivers. Recently, Bowser and Jones (6) presented a Microsoft Excel spreadsheet for a mineral-solute mass-balance model in order to study and under- stand the mineralogical controls on water compo- sition in surface and groundwater systems domi- nated by silicate lithologies. All of these programs, and others, are available from USGS webpages at http://water.usgs.gov/software/geochemical.html.
USEPA CODES
The USEPA has a series of supported computer codes, the most popular of which is the MINTEQA2/PRODEFA2 (last release in 1999 is version 4.0), widely used in environmental geochemistry problems (7), which is a chemical equilibrium computer model that is able to calculate chemical speciation, solubility equilibrium, titration, and surface complexation modeling. It also includes the Gaussian model for the interaction of dissolved organic matter (DOM) with cations. However, it lacks database maintenance. Gustafsson (8) has been developing VisualMINTEQ, a GUI version of this program that also presents other improvements, such as the NIST database, adsorption with five surface complexation models, ion-exchange, and inclusion of both the Stockholm Humic Model and the NICA-Donnan model for metal-DOM complexation to name only a few.
The program BIOPLUME III (9) is a 2-D finite dif- ference model that accounts for advection, diffusion, adsorption, and biodegradation in groundwater sys- tems to model natural attenuation of organic contami- nants. BIOCHLOR (10) and BIOSCREEN (11) are both Microsoft Excel spreadsheet-based codes that model natural attenuation of chlorinated solvents and petroleum- derived hydrocarbons in water systems, respectively.
CHEMFLO-2000 (12) is a model that simulates water flow and chemical transport and fate in the vadose zone. CHEMFLO-2000 is a program that is written in Java, which makes it platform- independent. All of these programs can be obtained from http://www.epa.gov/ada/csmos/models.
OTHER CODES
The set of computer codes known as EQ3/6 (13) supported by Lawrence Livermore National Laboratory (LLNL) was originally developed to model water-rock interactions in hydrothermal systems. It is currently one of the most complete programs applied to several problems, including municipal and industrial waste situations, and has been used to assess natural and engineered remediation processes. Unlike the programs presented until now, it must be purchased from LLNL. Closely related but mostly used for a range of high temperature and pressure is SUPCRT92 (14). This program has been discontinued, but still available on request to the authors.
The Geochemist Workbench (15) is a commercial software with a range of capabilities similar to EQ3/6 and PHREEQC. It is available for Windows only, but taking advantage of this environment makes it user friendly, with
graphical capabilities included that are normally absent from most of these programs.
The Windermere Humic Aqueous Model (WHAM) ver- sion 6 (16) models the ion–humic substances interaction in surface waters using surface complexation. It also incor- porates cation exchange on clays. However, precipitation and dissolution of solids as well as oxidation-reduction reactions cannot be simulated. This program must also be purchased for use. Alternatively, WinHumicV is a freely available GUI version of WHAM with model V imple- mented (17).
Steefel and Yabusaki (18) developed the GIMRT/OS3D codes for 2-D and 3-D multicomponent coupled reactive- transport modeling for flow in porous media. Both of these programs were superseded by the program CRUNCH (http://www.csteefel.com/CrunchPublic/WebCrunch.html), which can be obtained from the developer (C. I. Steefel) on request.
ORCHESTRA (19) (http://www.meeussen.nl/orchestra/) represents a new class of computer programs for use in geochemical reactive-transport modeling. This pro- gram is actually a framework where chemical speci- ation models can be implemented by the user and combine them with kinetic and transport processes. It is written in Java and takes advantage of object- oriented programming. In the same class of programs is MEDIA (http://www.nioo.knaw.nl/homepages/meysman/), to simulate the biogeochemistry of marine and estuar- ine sediments.
BIBLIOGRAPHY
1. Ball, J.W. and Nordstrom, D.K. (1991). User’s Manual for WATEQ4F, with Revised Thermodynamic Data Base and Test Cases for Calculating Speciation of Major, Trace, and Redox Elements in Natural Waters. U.S. Geological Survey, Open-File Report 91-183, Washington, DC.
2. Parkhurst, D.L. and Appelo, C.A.J. (1999). User’s Guide to PHREEQC (Version 2)—A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse Geochemical Calculations. U.S. Geological Survey Water- Resources Investigations Report 99-4259. Washington, DC, p. 312.
3. Thorstenson, D.C. and Parkhurst, D.L. (2002). Calculation of Individual Isotope Equilibrium Constants for Implementation in Geochemical Models. U.S. Geological Survey Water- Resources Investigation Report 02-4172. Washington, DC, p. 129.
4. Kipp, K.L. (1987). HST3D—A Computer Code for Simulation of Heat and Solute Transport in Three-dimensional Ground- water Flow Systems. U.S. Geological Survey Water-Resources Investigations Report 86-4095. Washington, DC, p. 517. 5. Runkel, R.L. (1998). One Dimensional Transport with Inflow
and Storage (OTIS): A Solute Transport Model for Streams and Rivers. U.S. Geological Survey Water-Resources Investi- gation Report 98-4018. Washington, DC, p. 73.
6. Bowser, C.J. and Jones, B.F. (2002). Mineralogic controls on the composition of natural waters dominated by silicate hydrolysis. Amer. J. Sci. 302: 582–662.
7. Allison, J.D., Brown, D.S., and Novo-Gradac, K.J. (1991). MINTEQA2/PRODEFA2, A Geochemical Assessment Model for Environmental Systems: Version 3.0 User’s Manual. U. S. Environmental Protection Agency, Washington, DC, p. 107.
142 GEOCHEMICAL MODELING—COMPUTER CODE CONCEPTS 8. Gustafsson, J.P. (2004). Visual MINTEQ ver. 2.30. Available:
http://www.lwr.kth.se/english/OurSoftware/Vminteq/index. htm.
9. Rafai, H.S., Newel, C.J., Gonzales, J.R., Dendrou, S., Kennedy, L., and Wilson, J.T. (1998). BIOPLUME III—Natural Attenuation Decision Support System, User’s Manual Version 1.0. EPA/600/R-98/010. USEPA, Washington, DC, p. 282.
10. Aziz, C.E., Newel, C.J., Gonzales, J.R., Haas, P., Clement, T.P., and Sun, Y. (2000). BIOCHLOR—Natural Attenuation Decision Support System, User’s Manual, Version 1.0. EPA/600/R-00/008. USEPA, Washington, DC, p. 46.
11. Newel, C.J., McLoed, R.K., and Gonzales, J.R. (1996). BIO- SCREEN—Natural Attenuation Decision Support System, User’s Manual, Version 1.3. EPA/600/R-96/087. USEPA, Washington, DC, p. 65.
12. Nofziger, D.L. and Wu, J. (2003). CHEMFLO-2000—Interac- tive Software for Simulating Water and Chemical Movement in Unsatured Soils. EPA/600/R-03/008. USEPA, Washington, DC, p. 69.
13. Wolery, T.J. (1992). EQ3/6, A Software Package for Geo- chemical Modeling of Aqueous Systems: Package Overview and Installation Guide (Version 7.0). (UCRL-MA-110662 PT I).
14. Johnson, J.W., Oelkers, E.H., and Helgeson, H.C. (1992). SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000◦C. Comput. Geosci. 18: 899–947.
15. Bethke, C.M. (1996). Geochemical Reaction Modeling, Con- cepts and Applications. Oxford University Press, New York. 16. Tipping, E. (1998). Humic ion-binding model VI: an improved
description of the interactions of protons and metal ions with humic substances. Aqua. Geochem. 4: 3–48.
17. Gustafsson, J.P. (1999). WinHumicV. http://www.lwr.kth. se/english/OurSoftWare/WinHumicV/.
18. Steefel, C.I. and Yabusaki, S.B. (1996). OS3D/GIMRT, Soft- ware for Multicomponent—Multidimensional Reactive Trans- port. User manual and programmer’s guide. PNL-11166. Battelle, Richland, WA.
19. Meeussen, J.C.L. (2003). ORCHESTRA: An object-oriented framework for implementing chemical equilibrium models. Environment. Sci. Technol. 37: 1175–1182.
READING LIST
Plummer, L.N., Parkhurst, D.L., Fleming, G.W., and Dun- kle, S.A. (1988). A Computer Program Incorporating Pitzer’s Equations for Calculation of Geochemical Reactions in Brines: U.S. Geological Survey Water-Resources Investigations Report 88-4153. Washington, DC, p. 310.