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User Rights Notice
This software and related material (data and (or) documentation),
contained in or furnished in connection with PHREEQC, are made available
by the U.S. Geological Survey (USGS) to be used in the public interest
and in the advancement of science. You may, without any fee or cost,
use, copy, modify, or distribute this software, and any derivative works
thereof, and its supporting documentation, subject to the following
restrictions and understandings.
If you distribute copies or modifications of the software and related
material, make sure the recipients receive a copy of this notice and
receive or can get a copy of the original distribution. If the software
and (or) related material are modified and distributed, it must be
made clear that the recipients do not have the original and they must
be informed of the extent of the modifications. For example, modified
files must include a prominent notice stating the modifications made, the
author of the modifications, and the date the modifications were made.
This restriction is necessary to guard against problems introduced in the
software by others, reflecting negatively on the reputation of the USGS.
The software is public property and you therefore have the right to
the source code, if desired.
You may charge fees for distribution, warranties, and services provided
in connection with the software or derivative works thereof. The name
USGS can be used in any advertising or publicity to endorse or promote
any products or commercial entity using this software if specific
written permission is obtained from the USGS.
The user agrees to appropriately acknowledge the authors and the USGS
in publications that result from the use of this software or in products
that include this software in whole or in part.
Because the software and related material are free (other than nominal
materials and handling fees) and provided "as is," the authors, the
USGS, and the United States Government have made no warranty, express
or implied, as to accuracy or completeness and are not obligated to
provide the user with any support, consulting, training or assistance
of any kind with regard to the use, operation, and performance of
this software nor to provide the user with any updates, revisions,
new versions, or "bug fixes."
The user assumes all risk for any damages whatsoever resulting from
loss of use, data, or profits arising in connection with the access,
use, quality, or performance of this software.

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README.TXT
PHREEQC
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
NOTE: This file describes the batch version of PHREEQC. However, a
graphical user interface, PhreeqcI, is available that runs under
Windows operating systems. This interactive program can be downloaded
from http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.
PhreeqcI has internal documentation for all PHREEQC data input and is a
complete interface to PHREEQC. A brief description of the program has
been published as a Fact Sheet:
Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user
interface to the geochemical model PHREEQC: U.S. Geological Survey
Fact Sheet FS-031-02, 2 p.
PHREEQC - Version @VERSION@ @VER_DATE@
Instructions for installation, execution, and testing are provided
below. After installation, see the phreeqc.txt file in the doc directory
of the PHREEQC installation for summary information on PHREEQC.
For assistance, enhancement requests, or to report bugs, contact
dlpark@usgs.gov.
TABLE OF CONTENTS
A. DISTRIBUTION FILES
B. DOCUMENTATION
C. EXTRACTING FILES
D COMPILING
E. INSTALLING
F. RUNNING THE PROGRAM
G. TESTING
H. CONTACTS
A. DISTRIBUTION FILES
The following distribution packages (containing the software, test data sets,
and information files) are currently available for UNIX systems:
phreeqc-@VERSION@-@REVISION@.Linux.tar.gz - Compiled with @GCC_VER@
kernel @KERNEL_VER@
phreeqc-@VERSION@-@REVISION@.source.tar.gz - Source code but no executable
B. DOCUMENTATION
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,
312 p.
This user's guide is available in electronic format. Portable Document
Format (PDF) files are included in the doc subdirectory of the
PHREEQC program distribution. An online HTML version of the User's
Guide can also be found at
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/
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
Investigations Report 02-4172, 129 p.
This report documents the theory and implementation of isotopes
in PHREEQC. Portable Document Format (PDF) is included in the
doc subdirectory of the PHREEQC program distribution.
C. EXTRACTING FILES
Compressed tar files are used to distribute the source code and
versions of the software compiled for selected UNIX operating systems.
All of the PHREEQC files needed to install and test the program are
contained in the file phreeqc-@VERSION@.@REVISION@-OS.tar.gz (where OS is a
string indicating the intended operating system.) If there is not a
tar file for your operating system or you want to compile the
software, the source version of the tar file contains all of the
PHREEQC files needed to compile and install the program on a
UNIX-based computer. For all of these distributions, the directory
phreeqc-@VERSION@ is created (or overwritten) when the files are extracted
from the tar file; if this directory already exists, you may want to
delete or rename it before extracting the files.
Follow the steps below to extract the files from a distribution tar
file.
Steps in extracting files explanation
---------------------------------------- -----------------------------------
gunzip phreeqc-@VERSION@-@REVISION@.OS.tar.gz Uncompress the distribution file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.OS.tar Extract files from the tar file.
The following directory structure is created (the contents of each
directory are shown to the right):
phreeqc-@VERSION@ files NOTICE.TXT, RELEASE.TXT, and this README.TXT
`-----bin compiled executable, template for execution script
`-----database database files required during execution
`-----doc documentation files
`-----examples examples from user's guide--used in verification tests
`-----src Makefile and source code
`-----test scripts to run verification tests
Notes: (a) A compiled executable is not included in the source
distribution.
(b) It is recommended that no user files be kept in the PHREEQC
directory structure. If you plan to put files in the PHREEQC
directory structure, do so only by creating subdirectories.
D. COMPILING
If you have retrieved a pre-compiled distribution of the software, skip to
the Installing section below.
If a compiled version of the software is not available for your computer
or you want to build the executable yourself, follow the instructions in
this section. The source distribution is provided for those users who
want the source code. Little or no support is provided for users
generating their own versions of the software. In general, to compile a
new version of the software, you will need:
(a) a C compiler, and
(b) a minimal level of knowledge of Make, the compiler, and
the UNIX operating system.
As provided in the source distribution, the software is set up to be
compiled under Linux with gcc.
To generate a new executable, do the following:
1. Change directory to the source directory:
cd phreeqc-@VERSION@/src
2. Modify the beginning of the file named Makefile to correctly specify
system-dependent variables:
CC C compiler name
CCFLAGS C compiler flags
LOADFLAGS linker flags
INVERSE_CL1MP remove definition if gmp package
is not available on your system
3. Run make in the src directory to compile the source:
make
make will:
a. compile the source code, and
b. place the program executable in the PHREEQC bin directory.
E. INSTALLING
To make PHREEQC easy to use, a link to the script that runs PHREEQC
should be placed in a directory that is included in each user's search
path. Run make in the PHREEQC src subdirectory to create the link:
make install BINDIR=directory_for_links
A script for running the executable is placed in the PHREEQC installation
directory and a link to that script is placed in the directory defined
by BINDIR. If each user's search path consists of
/usr/bin:/usr/opt/bin:/usr/local/bin
using the command
make install BINDIR=/usr/local/bin
will make PHREEQC accessible from any directory without requiring the full
pathname of the executable. Note that to create and delete links to the
PHREEQC script, the installer must have sufficient rights to the BINDIR
directory. By default, BINDIR is $HOME/bin.
F. RUNNING THE PROGRAM
If PHREEQC has been installed in a directory included in the users'
PATH (as described above), the program can be executed with any of the
commands below.
command to execute PHREEQC explanation
----------------------------- -----------------------------------------
phreeqc The program will query for each of the
needed files.
phreeqc input The input file is named input, the output
file will be named input.out and the
default database file will be used.
phreeqc input output The input file is named input, the output
file is named output, and the default
database file will be used.
phreeqc input output database All file names are specified explicitly.
phreeqc input output database screen_output
All file names are specified explicitly,
and screen output is directed to the
file screen_output.
If the "make install" command described above has not been executed,
the executable must be copied to the current directory. The executable
is normally phreeqc-@VERSION@/bin/phreeqc. In addition the default database
file will be phreeqc.dat in the current directory. Phreeqc.dat is
installed in phreeqc-@VERSION@/database/phreeqc.dat.
The shell variable PHREEQC_DATABASE can be used to specify the default
database. In the C shell, this variable can be set with the command:
setenv PHREEQC_DATABASE /home/jdoe/local/project/mydata.dat
In the Bourne or Korn shell, this variable can be set with the command:
export PHREEQC_DATABASE=/home/jdoe/local/project/mydata.dat
The shell variable can be set permanently by including the appropriate
command in a file that is read when the shell is initiated, frequently
$HOME/.login or $HOME/.profile. If this shell variable is not set,
the default database is set in the script in the installation directory
to phreeqc-@VERSION@/database/phreeqc.dat. It is possible to specify a
different default database by editing the script.
G. TESTING
Test data sets are provided to verify that the program is correctly installed
and running on the system. The tests execute the examples presented in
the user's guide, which demonstrate most of the program's capabilities.
The PHREEQC test directory contains the script to run the tests. The PHREEQC
examples directory contains the input data and the expected results for
each test.
To test the installation, change to the phreeqc-@VERSION@/test directory and type
the command:
./test.sh [start [stop]]
where: start = the number of the first test to perform, default = 1
stop = the number of the last test to perform, default = 18
For example:
command what happens
---------------------------------- --------------------------------
./test.sh runs all of the tests
./test.sh 1 1 runs the first test
./test.sh 2 3 runs tests 2 and 3
./test.sh 4 runs test 4 through the last test
After the tests are completed, the results are compared to the expected
results (found in the PHREEQC examples directory). See the file check.log;
if all goes well, there should be no differences.
To clean up after the tests, type the command:
./clean.sh
Notes: The output data files for phreeqc-@VERSION@.@REVISION@.source.tar.gz
were created on a Linux system. You may notice slight numeric differences
in the results. These are generally due to different round-off algorithms
and the different architecture of the central processing unit chip.
Slight differences in output formats may occur on other computers,
particularly for the value 0.0.
Problem 9 generates a warning message that indicates negative
concentrations were generated in a kinetic run. The numerical
method automatically reduces the step size until negative
concentrations are eliminated and an accurate kinetic integration
is obtained.
Problems 11, 12, 13, and 15 generate warning messages. The
messages simply indicate a shorthand method for defining cell
lengths and cell dispersivities was used.
The tests are described in the table below, where 'test' is the test
number and the 'usage' column indicates how a file is used, with i for
input and o for output.
test description of test and files file name & usage
---- -------------------------------------------- -----------------
1 Add uranium and speciate seawater
PHREEQC input file ex1 i
Printed results of calculation ex1.out o
2 Temperature dependence of solubility
of gypsum and anhydrite
PHREEQC input file ex2 i
Printed results of calculation ex2.out o
Results written to the selected-output file ex2.sel o
3 A. Calcite equilibrium at log Pco2 = -2.0 and 25C
B. Definition of seawater
C. Mix 70% ground water, 30% seawater
D. Equilibrate mixture with calcite and dolomite
E. Equilibrate mixture with calcite only
PHREEQC input file ex3 i
Printed results of calculation ex3.out o
4 A. Rain water evaporation
B. Factor of 20 more solution
PHREEQC input file ex4 i
Printed results of calculation ex4.out o
5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
PHREEQC input file ex5 i
Printed results of calculation ex5.out o
Results written to the selected-output file ex5.sel o
6 6A. React to phase boundaries
6A1.--Find amount of k-feldspar dissolved to
reach gibbsite saturation
6A2.--Find amount of k-feldspar dissolved to
reach kaolinite saturation
6A3.--Find amount of k-feldspar dissolved to
reach K-mica saturation
6A4.--Find amount of k-feldspar dissolved to
reach k-feldspar saturation
6A5.--Find point with kaolinite present,
but no gibbsite
6A6.--Find point with K-mica present,
but no kaolinite
6B. Path between phase boundaries
6C. Kinetic calculation
PHREEQC input file ex6 i
Printed results of calculation ex6.out o
Results written to the selected-output file ex6A-B.sel o
Results written to the selected-output file ex6C.sel o
7 Organic decomposition with fixed-pressure and
fixed-volume gas phases
PHREEQC input file ex7 i
Printed results of calculation ex7.out o
Results written to the selected-output file ex7.sel o
8 Sorption of zinc on hydrous iron oxides
PHREEQC input file ex8 i
Printed results of calculation ex8.out o
Results written to the selected-output file ex8.sel o
9 Kinetically controlled oxidation of ferrous iron.
Decoupled valence states of iron.
PHREEQC input file ex9 i
Printed results of calculation ex9.out o
Results written to the selected-output file ex9.sel o
10 Solid solution of strontianite and aragonite.
PHREEQC input file ex10 i
Printed results of calculation ex10.out o
Results written to the selected-output file ex10.sel o
11 Transport and ion exchange.
PHREEQC input file ex11 i
Printed results of calculation ex11.out o
Results written to the selected-output file ex11adv.sel o
Results written to the selected-output file ex11trn.sel o
12 Advective and diffusive transport of heat and solutes. Constant
boundary condition at one end, closed at other. The problem is
designed so that temperature should equal Na-conc (in mmol/kgw)
after diffusion.
PHREEQC input file ex12 i
Printed results of calculation ex12.out o
Results written to the selected-output file ex12.sel o
13 A. 1 mmol/l NaCl/NO3 enters column with stagnant zones. Implicit
definition of first-order exchange model.
B. 1 mmol/l NaCl/NO3 enters column with stagnant zones. Explicit
definition of first-order exchange factors.
C. 1 mmol/l NaCl/NO3 enters column with stagnant zones. 5 layer
stagnant zone with finite differences.
PHREEQC input file ex13a i
Printed results of calculation ex13a.out o
Results written to the selected-output file ex13a.sel o
PHREEQC input file ex13b i
Printed results of calculation ex13b.out o
Results written to the selected-output file ex13b.sel o
PHREEQC input file ex13c i
Printed results of calculation ex13c.out o
Results written to the selected-output file ex13c.sel o
14 Transport with equilibrium_phases, exchange, and surface reactions
PHREEQC input file ex14 i
Printed results of calculation ex14.out o
Results written to the selected-output file ex14.sel o
15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
PHREEQC input file ex15 i
database file ex15.dat i
Printed results of calculation ex15.out o
Results written to the selected-output file ex15.sel o
16 Inverse modeling of Sierra springs
PHREEQC input file ex16 i
Printed results of calculation ex16.out o
17 Inverse modeling of Black Sea water evaporation
PHREEQC input file ex17 i
Printed results of calculation ex17.out o
18 Inverse modeling of Madison aquifer
PHREEQC input file ex18 i
Printed results of calculation ex18.out o
H. CONTACTS
Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov

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U.S. Geological Survey phreeqc(1)
NAME
phreeqc - A program for speciation, batch-reaction, one-
dimensional transport, and inverse geochemical calculations
SYNOPSIS
phreeqc [infile [outfile [database [screen_output]]]
OPTIONS
infile the name of the PHREEQC input file
outfile the name of the file to which PHREEQC output
will be written
database the name of the PHREEQC database
screen_output the name of the file to which screen output
will be directed
If no arguments are specified, the program prompts for the
input, output, and database file names.
If only infile is specified, then outfile defaults to
infile.out. If no database file is specified, the
phreeqc.dat database distributed with PHREEQC will be used.
ABSTRACT
PHREEQC is a computer program written in the C programming
language that is designed to perform a wide variety of low-
temperature aqueous geochemical calculations. PHREEQC is
based on an ion-association aqueous model and has
capabilities for (1) speciation and saturation-index
calculations; (2) batch-reaction and one-dimensional (1D)
transport calculations involving reversible reactions, which
include aqueous, mineral, gas, solid-solution, surface-
complexation, and ion-exchange equilibria, and irreversible
reactions, which include specified mole transfers of
reactants, kinetically controlled reactions, mixing of
solutions, and temperature changes; and (3) inverse
modeling, which finds sets of mineral and gas mole transfers
that account for differences in composition between waters,
within specified compositional uncertainty limits.
METHOD
For speciation and batch-reaction calculations, PHREEQC
solves sets of nonlinear mole-balance and mass-action
equations that define an ion-association model. A Newton-
Raphson formulation is used to iteratively arrive at a
solution to the equations. A robust numerical method is
provided by using an optimizing solver that allows both
equality and inequality equations. The solver is used to
obtain the intermediate estimates of changes in the unknowns
at each iteration.
For inverse modeling, a set of linear mole-balance equations
are solved. The equations contain additional unknowns that
account for uncertainty in the analytical data. The
optimizing solver is used to solve the linear equations
while maintaining the uncertainty terms within specified
limits.
For transport modeling, the partial differential equations
of transport are solved by an operator splitting scheme that
sequentially solves for advective and dispersive transport,
followed by chemical equilibration that is equivalent to
batch-reaction calculations for each cell. Time steps are
selected to maintain numerical accuracy. If kinetic
reactions are modeled, yet another splitting of operators is
implemented and a 5th order Runge-Kutta method is used to
integrate the ordinary differential equations of the kinetic
reactions.
HISTORY--See RELEASE.TXT
DATA REQUIREMENTS
Proper use of the program requires adequate knowledge of
geochemistry and a proper formulation of the problem. Input
is arranged in keyword data blocks, which can appear in any
order. Data fields for a keyword are read in a free format,
thus they are not column dependent.
For speciation modeling, analytical data for a solution
composition (SOLUTION keyword) are needed.
For batch-reaction modeling, the initial solution
composition is required (SOLUTION or MIX data block). Other
equilibrium reactants may be defined with
EQUILIBRIUM_PHASES, EXCHANGE, SURFACE, GAS_PHASE, and
SOLID_SOLUTION data blocks. Nonequilibrium reactions may be
defined with KINETICS and RATES, REACTION, and
REACTION_TEMPERATURE data blocks.
For 1D transport modeling, the data for batch-reaction
modeling are needed for each cell in the modeled system. In
addition, physical information is needed about column
dimensions, time steps, boundary conditions, and
dispersivity.
For inverse modeling, the solution composition of the final
solution and one or more initial solutions are needed
(SOLUTION data block). Uncertainty limits must be defined
explicitly or by default for each element and element redox
state in the solutions. In addition, the identity and
composition of a set of plausible reactants and products are
needed.
Three default databases are included that contain the
definition of aqueous species, exchange species, surface
species, and mineral and phases for a set of elements. The
database phreeqc.dat contains information for Al, B, Ba, Br,
C, Ca, Cd, Cl, Cu, F, Fe, H, K, Li, Mg, Mn, N, Na, O, P, S,
Si, Sr, Zn. The database wateq4f.dat contains the
additional constituents Ag, As, Cs, Fulvate, Humate, I, Ni,
Rb, Se, and U. The database minteq.dat is derived from the
thermodynamic data of the program MINTEQA2. If additional
elements, species, or phases are needed, then chemical
reactions, log K, and data for the temperature dependence of
log K are needed for each additional species and phase.
SYSTEM REQUIREMENTS
PHREEQC is written in ANSI C. Generally, the program is
easily installed on most computer systems. The code has
been used on UNIX-based computers and on IBM-compatible
computers with processors running at 100 megahertz or
faster.
DOCUMENTATION
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, 312 p.
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
Investigations Report 02-4172, 129 p.
RELATED DOCUMENTATION
Charlton, S.R., Macklin, C.L. and Parkhurst, D.L., 1997,
PHREEQCI--a graphical user interface for the geochemical
computer program PHREEQC: U.S. Geological Survey Water-
Resources Investigations Report 97-4222, 9 p.
Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user
interface to the geochemical model PHREEQC: U.S. Geological Survey
Fact Sheet FS-031-02, 2 p.
Parkhurst, D.L., Thorstenson, D.C., and Plummer, L.N., 1980,
PHREEQE--a computer program for geochemical calculations:
U.S. Geological Survey Water-Resources Investigations
Report 80-96, 195 p. (Revised and reprinted, 1990.)
Plummer, L.N., Parkhurst, D.L., Fleming, G.W., and Dunkle,
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, 310 p.
Plummer, L.N., Prestemon, E.C., and Parkhurst, D.L., 1991,
An interactive code (NETPATH) for modeling NET
geochemical reactions along a flow PATH: U.S.
Geological Survey Water-Resources Investigations Report
91-4078, 227 p.
Plummer, L.N., Prestemon, E.C., and Parkhurst, D.L., 1994,
An interactive code (NETPATH) for modeling NET
geochemical reactions along a flow PATH--version 2.0:
U.S. Geological Survey Water-Resources Investigations
Report 94-4169, 130 p.
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.
TRAINING
PHREEQC is taught as part of the courses Geochemistry for
Ground-Water Systems (GW3021TC) at the USGS National
Training Center.
CONTACTS
Operation:
U.S. Geological Survey
David Parkhurst
Denver Federal Center, MS 413
Lakewood, CO 80225
dlpark@usgs.gov

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