Computer Programs

NAME, COMPUTER, PROBLEM, SOLUTION, RESTRICTIONS, CPU, FEATURES, AUXILIARIES, STATUS, REFERENCES, REQUIREMENTS, LANGUAGE, OPERATING SYSTEM, AUTHOR, MATERIAL, CATEGORIES

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To submit a request, click below on the link of the version you wish to order. Rules for end-users are
available here.

Program name | Package id | Status | Status date |
---|---|---|---|

PHRQCGRF | USCD1207/09 | Arrived | 06-MAY-2002 |

PHRQCGRF | USCD1207/20 | Tested | 06-JUL-2004 |

PHREEQCI 2.11.0.148 | USCD1207/25 | Tested | 25-APR-2005 |

PHREEQC 2.11 | USCD1207/26 | Tested | 25-APR-2005 |

PHREEQC 2.11 | USCD1207/27 | Tested | 25-APR-2005 |

Machines used:

Package ID | Orig. computer | Test computer |
---|---|---|

USCD1207/09 | IBM PC | |

USCD1207/20 | PC Windows | PC Pentium |

USCD1207/25 | PC Windows | PC Windows |

USCD1207/26 | Linux-based PC,UNIX W.S. | Linux-based PC,UNIX W.S. |

USCD1207/27 | IBM PC | PC Windows |

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3. DESCRIPTION OF PROGRAM OR FUNCTION

PHREEQC is a computer program written in the C programming language that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations, (2) reaction-path and advective-transport calculations involving specified irreversible reactions, mixing of solutions, mineral and gas equilibria, surface- complexation reactions, and ion-exchange reactions, and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for composition differences between waters, within specified compositional uncertainties.

PHREEQC is derived from the Fortran program PHREEQE, but it has been completely rewritten in C with the addition of many new capabilities. New features include the capabilities to use redox couples to distribute redox elements among their valence states in speciation calculations; to model ion-exchange and surface-complexation reactions; to model reactions with a fixed-pressure, multicomponent gas phase (that is, a gas bubble); to calculate the mass of water in the aqueous phase during reaction and transport calculations; to keep track of the moles of minerals present in the solid phases and determine automatically the thermodynamically stable phase assemblage; to simulate advective transport in combination with PHREEQC's reaction-modeling capability; and to make inverse modeling calculations that allow for uncertainties in the analytical data. The user interface is improved through the use of a simplified approach to redox reactions, which includes explicit mole-balance equations for hydrogen and oxygen; the use of a revised input that is modular and completely free format; and the use of mineral names and standard chemical symbolism rather than index numbers. The use of C eliminates nearly all limitations on array sizes, including numbers ofelements, aqueous species, solutions, phases, and lengths of character strings. A new equation solver that optimizes a set of equalities subject to both equality and inequality constraints is used to determine the thermodynamically stable set of phases in equilibrium with a solution. A more complete Newton-Raphson formulation, master-species switching, and scaling of the algebraic equations reduce the number of failures of the numerical method in PHREEQC relative to PHREEQE.

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PHRQCGRF is a separate code available for WINDOWS95 and MS-DOS that can be used to create a variety of graphs from the data generated by PHREEQC. The output data from PHREEQC may be plotted against distance, time, or other data listed in the PHREEQC selected output file, and a series of data versus distance graphs can be animated. PHRQCGRF can also extract the data of interest from the PHREEQC transport results and write the data sets to an external file.

PHRQCGRF helps visualize PHREEQC transport output files generated by using the - SELECTED_OUTPUT - keyword in a PHREEQC simulation. PHREEQC does not perform any geochemical modeling, but uses these files as the starting point for its various features. Once a file is specified, several options allow the user to choose exactly how to extract the data of interest. Data may be plotted against distance at a particular time, against time at a particular distance, against other data at a particular time or distance, or several data versus distance plots can be animated within a specified time interval. Additionally, results of PHREEQC transport simulations can be compared to measured field data, or PHREEQC simulations can be compared to other PHREEQC simulations. As an alternative to graphing, the extracted data sets may be written to an external file. Except for the extracting feature, the result of PHRQCGRF s data processing is the presentation of a graph reflecting the user s choices.

PHRQCGRF also offers flexibility in how an extracted data set is displayed. For example, both the x-axis and y-axis value ranges can be specified. Various plot appearances, such as colors, symbols, and line styles, can also be set according to the user s preferences.

USCD1207/24: PHREEQC graphic interactive version for Windows

VERSION 2.10.03 (released December 14th, 2004): It is now possible to specify the width of the tab stops for the input, output and database editor under Edit | Preferences.

USCD1207/25: This package is the version 2.11.0.148 (2005/02/07) of PhreeqcI, the interactive Windows program of PHREEQC. No source files are included in this package.

PhreeqcI Version 2.11-148 contains the batch version of PHREEQC, version 2.11-136.

This version of PhreeqcI has the bug fixes related to PHREEQC version 2.11.

Version 2.11 Date: February 7, 2005: A new database, minteq.v4.dat has been translated from version 4.02 of MINTEQA2. An older version of the MINTEQA2 database is retained in file minteq.dat.

Subversion has been introduced for version control system. The number included in distribution files (for example, "148" in phreeqc-2.11.0.148) is the Subversion revision number corresponding to the set of files used to build the current version. Subversion revision numbers change whenever any repository file is changed, so the number uniquely defines all files used in the current version.

USCD1207/26: Version 2.11 Date: February 7, 2005

PHREEQC version 2.11 has been released, including batch versions for Unix, Linux, and SunOS.

A new database, minteq.v4.dat has been translated from version 4.02 of MINTEQA2. An older version of the MINTEQA2 database is retained in file minteq.dat.

Subversion has been introduced for version control system. The number included in distribution files (for example, "136" in phreeqc-2.11-136.Linux.tar.gz) is the Subversion revision number corresponding to the set of files used to build the current version. Subversion revision numbers change whenever any repository file is changed, so the number uniquely defines all files used in the current version.

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4. METHODS

For speciation, reactions, and transport calculations, the code solves a reduced set of simultaneous non-linear equations that define equilibrium for a water, solute, gas, mineral, ion-exchanger, and surface-complexer chemical system. Equilibrium is based on an ion-association model for the aqueous phase and mass-action equations for mineral, gases, exchangers, and surface complexers. The complete set of equations includes a mole balance equation for each element in the system; mass-action equations for each aqueous species, each gas component, each mineral, each exchange species, and each surface complex; an activity coefficient equation for each aqueous species; a charge balance-equation for the aqueous phase; a charge-balance or charge-potential equation for each surface complexer; an equation for the activity of water; and an equation for the ionic strength of a solution. Subsets of this set of equations are solved for a particular geochemical calculation. The equations are solved by a modified Newton-Raphson calculation. The modification involves the use of an optimization routine based on linear programming. During the iterative Newton-Raphson process, some of the equations are included as objective functions rather than strict equalities. This approach is useful for determining the stable set of minerals and the presence or absence of a gas phase in a chemical system, it also makes the numerical algorithm more robust. The solution to the equations provides the activities and molalities of each aqueous species, the moles of each mineral, gas component, exchange species, and surface species present in the system.

In inverse modeling, one aqueous solution is assumed to react with minerals and gases to produce the observed composition of a second aqueous solution. The inverse model calculates the amounts of these gases and minerals from the difference in elemental concentrations between the two aqueous solutions. It is also possible to determine mixing fractions for two or more aqueous solutions and the mole transfers of minerals necessary to produce the composition of another aqueous solution. Inverse modeling is based strictly on a mole-balance approach and does not rely on the ion-association model except to determine the total number of moles of each element and redox state in each aqueous solution. The inverse model is formulated including uncertainty in each analytical datum. A linear set of equations is formulated including: mole balance for each element and element redox state in the system, a charge-balance equation for each aqueous solution, and a water-balance equation. In addition, inequality constraints are included to ensure that any adjustments to the analytical data are smaller than the uncertainties and to constrain the sign of mole transfers of mineral (if specified). The system of equalities and inequalities is solved by an optimization routine based on the Simplex method. An additional algorithm is used to find all sets of minerals that are feasible solutions to the inverse problems.

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5. RESTRICTIONS ON THE COMPLEXITY OF THE PROBLEM

PHREEQC is a general geochemical program and is applicable to many hydrochemical environments. However, several limitations need to be considered.

AQUEOUS MODEL: PHREEQC uses ion-association and Debye-Hueckel expressions to account for the non-ideality of aqueous solutions. This type of aqueous model is adequate at low ionic strength but may break down at higher ionic strengths (in the range of seawater and above). An attempt has been made to extend the range of applicability of the aqueous model through the use of an ionic-strength term in the Debye-Hueckel expressions. These terms have been fitted for the major ions using chloride mean-salt activity-coefficient data (Truesdell and Jones, 1974). Thus, in sodium chloride dominated systems, the model may be reliable to higher ionic strengths. For high ionic strength waters, the specific interaction approach to thermodynamic properties of aqueous solutions should be used (for example, Pitzer, 1979, Harvie and Weare, 1980, Harvie and others, 1984, Plummer and others, 1988).

The other limitation of the aqueous model is lack of internal consistency in the data in the database. Most of the log K's and enthalpies of reaction have been taken from various literature sources. No systematic attempt has been made to determine the aqueous model that was used to develop the log K's or whether the aqueous model defined by the current database file is consistent with the original experimental data. The database files provided with the program should be considered to be preliminary. Careful selection of aqueous species and thermodynamic data is left to the users of the program.

ION EXCHANGE: The ion exchange model assumes that the thermodynamic activity of an exchange species is equal to its equivalent fraction. Other formulations use other definitions of activity, mole fraction for example, or additional activity coefficients to convert equivalentfraction to activity (Appelo,1994). No attempt has been made to include other or more complicated exchange models. In many field studies, ion-exchange modeling requires experimental data on material from the study site for appropriate model application.

SURFACE COMPLEXATION: PHREEQC incorporates the Dzombak and Morel (1990) diffuse double-layer and a non-electrostatic surface- complexation model (Davis and Kent, 1990). Other models, including isotherms and triple- and quadruple-layer models have not been included in PHREEQC.

Davis and Ken (1990) reviewed surface-complexation modeling and note theoretical problems with the standard state for sorbed species. Other uncertainties occur in determining the number of sites, the surface area, the composition of sorbed species, and the appropriate log K's. In many field studies, surface-complexation modeling requires experimental data on material from the study site for appropriate model application.

The capability of PHREEQC to calculate the composition of the diffuse layer (-diffuse_layer option) is ad hoc and should be used only as a preliminary sensitivity analysis.

CONVERGENCE PROBLEMS: PHREEQC tries to identify input errors, but it is not capable of detecting some physical impossibilities in the chemical system that is modeled. For example, PHREEQC allows a solution to be charge balanced by addition or removal of an element. If this element has no charged species or if charge imbalance remains even after the concentration of the element has been reduced to zero, then the numerical method will appear to have failed to converge. Other physical impossibilities that have been encountered are (1) when a base is added to attain a fixed pH, but in fact an acid is needed (or vice versa) and (2) when noncarbonate alkalinity exceeds the total alkalinity given on input.

At present, the numerical method has proved to be relatively robust. Known convergence problems--cases when the numerical method fails to find a solution to the non-linear algebraic equations--have occurred only when physically impossible equilibria have been posed and when trying to find the stable phase assemblage among a large number (approximately 25) minerals, each with a large number of moles (5 moles or more). It is suspected that the latter case is caused by loss of numerical precision in working with sparingly soluble minerals (that is, small aqueous concentrations) in systems with large total concentrations (on the order of 100 moles).

Occasionally it has been necessary to use the scaling features of the KNOBS keyword. The scaling features appear to be necessary when total dissolved concentrations fall below approximately 10-15 molal.

INVERSE MODELING: Inclusion of uncertainties in the process of identifying inverse models is a major advance. However, the numerical method has shown some lack of robustness due to the way the solver handles small numbers. The option to change the tolerance used by the solver is an attempt to remedy this problem. In addition, the inability to include isotopic information in the modeling process is a serious limitation.

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6. TYPICAL RUNNING TIME

For speciation, initial exchange composition, initial surface composition, and simple mixing and chemical reaction calculations, the program will run in seconds on 486 and faster machines. Large inverse calculations may take several minutes to complete. Transport calculations may take minutes to hours depending on the number of the cells and the complexity of the chemistry that is simulated.

USCD1207/25: Interactive program.

USCD1207/26: the tests ran in 38 seconds on Linux and in 17 min 42 seconds on SUN.

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7. UNUSUAL FEATURES OF THE PROGRAM

This program is excellent for speciation, mixing, mineral equilibration, ion-exchange, surface complexation, and reaction modelling. It also has the capability to include any of these types of chemical calculations in a 1D advective transport system. This transport capability is simple and relatively fast, so it is appropriate for initial investigations of the chemistry of a dynamic system, before effort is expended on an expensive multidimensional, multicomponent transport model. However, the program lacks true kinetics and the capability to model dispersion.

The capability to estimate the diffuse-layer composition in surface complexation calculations is unique among generally available codes.

The use of uncertainty in inverse modelling is unique to this code.

The code may also serve well as a geochemical module for coupled reaction and transport models.

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8. RELATED OR AUXILIARY PROGRAMS

This program supersedes PHREEQE, but not PHRQPITZ, which is based on a specific interaction aqueous model. PHREEQC has all of the capabilities of WATEQ4F and the WATEQ4F data base is included in the distribution. The use of uncertainties in inverse modelling makes it a valuable companion to the NETPATH code.

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Package ID | Status date | Status |
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USCD1207/09 | 06-MAY-2002 | Masterfiled Arrived |

USCD1207/20 | 06-JUL-2004 | Tested at NEADB |

USCD1207/25 | 25-APR-2005 | Tested at NEADB |

USCD1207/26 | 25-APR-2005 | Tested at NEADB |

USCD1207/27 | 25-APR-2005 | Tested at NEADB |

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10. REFERENCES

Appelo, C.A.J., and Postma, D., 1993, Geochemistry, groundwater and pollution: Rotterdam, Netherlands, and Brookfield, Vermont, A.A. Balkema.

Appelo, C.A.J., and Willemsen, A., 1987, Geochemical calculations and observations on salt water intrusions. I: A combined geochemical/mixing cell model: Journal of Hydrology, v. 94, p. 313-330.

Parkhurst, D.L., and Plummer, L.N., 1993, Geochemical models, in Alley, W.M., ed., Regional ground-water quality: New York, Van Nostrand Reinhold, chap. 9, p. 199-225.

Plummer, L.N., 1984, Geochemical modeling: A comparison of forward and inverse methods, in Hitchon, B., and Wallick, E.I., eds., Proceedings First Canadian/American Conference on hydrogeology--Practical Applications of Ground Water Geochemistry, Banff, Alberta, Canada: Worthington, Ohio, National Water Well Association, p. 149-177.

USCD1207/09, included references:

- J. Vrabel and P.D. Glynn:User's Guide to PHRQCGRF: A Computer Program for Graphical

Interpretation of PHREEQC Geochemical Transport Simulations.

U.S. Geological Survey Open File Report 98-281, 30p (1998)

USCD1207/20, included references:

- Joseph Vrabel and Pierre D. Glynn:User's Guide to PHRQCGRF - A Computer Program for Graphical Interpretation of

PHREEQC Geochemical Transport Simulations

Open File Report 98-281

USCD1207/25, included references:

- David L. Parkhurst and C.A.J. Appelo:User's Guide To PHREEQC (Version 2) - A Computer Program For Speciation,

Batch-Reaction, One-Dimensional Transport, And Inverse Geochemical Calculations

Water-Resources Investigations Report 99-4259 (1999)

- Donald C. Thorstenson and David L. Parkhurst:

Calculation of Individual Isotope Equilibrium Constants for Implementation in

Geochemical Models

Water-Resources Investigations Report 02-4172 (2002)

- PHREEQCI-A Graphical User Interface to the Geochemical Model PHREEQC

USGS Fact Sheet FS-031-02 (April 2002)

USCD1207/26, included references:

- David L. Parkhurst and C.A.J. Appelo:User's Guide To PHREEQC (Version 2) - A Computer Program For Speciation,

Batch-Reaction, One-Dimensional Transport, And Inverse Geochemical Calculations

Water-Resources Investigations Report 99-4259 (1999)

- Donald C. Thorstenson and David L. Parkhurst:

Calculation of Individual Isotope Equilibrium Constants for Implementation in

Geochemical Models

Water-Resources Investigations Report 02-4172 (2002)

USCD1207/27, included references:

- David L. Parkhurst and C.A.J. Appelo:User's Guide To PHREEQC (Version 2) - A Computer Program For Speciation,

Batch-Reaction, One-Dimensional Transport, And Inverse Geochemical Calculations

Water-Resources Investigations Report 99-4259 (1999)

- Donald C. Thorstenson and David L. Parkhurst:

Calculation of Individual Isotope Equilibrium Constants for Implementation in

Geochemical Models

Water-Resources Investigations Report 02-4172 (2002)

- PHREEQCI-A Graphical User Interface to the Geochemical Model PHREEQC

USGS Fact Sheet FS-031-02 (April 2002)

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11. HARDWARE REQUIREMENTS

PHRQCGRF is written in Fortran to be run in Windows environment (W9X, NT, XP).

PHREEQCI is PC DOS Interactive program.

PHREEQC is written in ANSI C. Generally, the program is easily installed on most computer systems.

USCD1207/24: PHREEQC for Windows has been tested on platforms that run under Windows95, Windows98, Windows NT, Windows Me, Windows 2000 and Windows XP.

It requires 7.2 MB of free hard disk space.

Optional system requirements are:

A colour monitor with a recommended resolution of at least 800 by 600 pixels.

A powerful CPU to speed up calculations

USCD1207/25: Tested at the NEA Data Bank on a Dell Precision Workstation 650, Intel(R) Xeon(TM) CPU 2.66GHz, 1024Kb.

USCD1207/26: Tested at the NEA Data Bank on a Dell PowerEdge 1650 Bi-Pentium III 1.4 GHz SUN Ultra 5.

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Package ID | Computer language |
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USCD1207/09 | C-LANGUAGE |

USCD1207/20 | FORTRAN |

USCD1207/25 | C-LANGUAGE |

USCD1207/26 | C-LANGUAGE |

USCD1207/27 | C-LANGUAGE |

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13. SOFTWARE REQUIREMENTS

No restrictions are known for DOS and Unix operating systems. Some modifications are needed to setup a C program on a Macintosh.

PHRQCGRF needs MS-DOS.

The program has been compiled and run under DOS, Windows, and Linux, and on the following work stations: Data General, Sun, IBM.

USCD1207/20: Windows9X, Windows NT , XP

USCD1207/24: Windows95, Windows98, Windows NT, Windows Me, Windows 2000 and Windows XP.

USCD1207/25: Tested at the NEA Data Bank with Microsoft Windows XP Professional (5.1.2600). Storage size: about 6.5 Mbytes.

USCD1207/26: Tested at the NEA Data Bank with Linux RedHat 7.3 SunOS 5.8, GNU gcc 2.96 compiler.

USCD1207/27: Windows9X, Windows NT , XP

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USCD1207/09

readme.txt Information filePHRQCGRF.exe Main executable

DOSXMSF.exe Executable

DOSXNT.exe Executable

DOSXNT.386

HELVB.fon Executable

ROMAN.fon Executable

SAMPLESv1.smp PHREEQC Version 1 file format

SAMPLESv2.smp PHREEQC Version 2 file format

FIELDSdst.fldField file format for distance

FIELDtim.fld Field file format for time

MANPCGRF.ps Program doc. in ps format

MANPCGRF.pdf Program doc. in pdf format

PHRQCGRF.for FORTRAN source code

DIST2.for FORTRAN source code

TIME.for FORTRAN source code

SPVSP.for FORTRAN source code

MOVIE3.for FORTRAN source code

COMPARE.for FORTRAN source code

XTRACDAT.for FORTRAN source code

UTILITY2.for FORTRAN source code

PNTGRAF8.for FORTRAN source code

HELP.for FORTRAN source code

USCD1207/20

Files for PC Windows platforms:documentation, examples, source files, tests

USCD1207/25

Phreeqc Interactive 2.11 filesDocumentation

Examples

USCD1207/26

LINUX/SUN/Unix versions: database, documentation, examples, source files, testsUSCD1207/27

Phreeqc Interactive 2.11 filesDocumentation

Examples

Source files

Keywords: advection, chemical reactions, environmental transport, geochemistry, radioactive effluents, radionuclide migration, speciation.