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SET(phreeqc_ROOT
NOTICE
README
RELEASE
)
SET(phreeqc_DOC
Phreeqc_2_1999_manual.pdf
Phreeqc_3_2013_manual.pdf
phreeqc3.chm
phreeqc.txt
wrir02-4172.pdf
)
IF(WIN32)
foreach(file ${phreeqc_ROOT})
install (FILES ${file} DESTINATION ${CMAKE_INSTALL_PREFIX} RENAME ${file}.txt)
endforeach()
ELSE()
install (FILES ${phreeqc_ROOT} DESTINATION ${CMAKE_INSTALL_DOCDIR})
ENDIF()
install (FILES ${phreeqc_DOC} DESTINATION ${CMAKE_INSTALL_DOCDIR})

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EXTRA_DIST = CMakeLists.txt
# Docs
#
dist_doc_DATA = $(DOCS)
DOCS= \
NOTICE \
Phreeqc_2_1999_manual.pdf \
Phreeqc_3_2013_manual.pdf \
phreeqc.txt \
phreeqc3.chm \
README \
RELEASE \
wrir02-4172.pdf

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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.
Although this software program has been used by the U.S. Geological
Survey (USGS), no warranty, expressed or implied, is made by the USGS
or the U.S. Government as to the accuracy and functioning of the
program and related program material nor shall the fact of distribution
constitute any such warranty, and no responsibility is assumed by the
USGS in connection therewith.
The authors, the USGS, and the United States Government 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
IPhreeqc--Modules Based on the Geochemical Model PHREEQC for Use
in Scripting and Programming Languages
This file describes how to compile the IPhreeqc library and use
it in C++, C, and Fortran programs. The library may be compiled
after generating either a Visual Studio solution for Windows with
CMake or a Makefile for Linux with configure. All source and
compilation-related files are available at the following web site:
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.
-----------------------------------------------------------------------------------
TABLE OF CONTENTS
-----------------------------------------------------------------------------------
A. Distribution file
B. Documentation
C. Installing Windows COM versions
D. Downloading and unzipping the distribution file
E. Linux compiling, testing, and installing the IPhreeqc library
F. Windows compiling, testing, and installing the IPhreeqc library
G. Using the library
H. Contacts
-----------------------------------------------------------------------------------
A. Distribution file
-----------------------------------------------------------------------------------
The following distribution packages (containing the software,
compilation-related files, and an advection example in
C++, C, and Fortran) are available for Linux and Windows:
IPhreeqcCOM-@VERSION@-@REVISION@-win32.msi Windows
IPhreeqcCOM-@VERSION@-@REVISION@-x64.msi Windows
iphreeqc-@VERSION@-@REVISION@.zip Windows
iphreeqc-@VERSION@-@REVISION@.tar.gz Linux
-----------------------------------------------------------------------------------
B. Documentation
-----------------------------------------------------------------------------------
Descriptions and examples of IPhreeqc methods for C++, C, and Fortran
are available in HTML format in the doc directory of the distribution.
Charlton, S.R., and Parkhurst, D.L., 2011, Modules based on the geochemical model
PHREEQC for use in scripting and programming languages: Computers & Geosciences,
vol. 37, no. 10, p. 1653-1663.
*The following two user's guides are available in electronic format. Portable
Document Format (PDF) files are included in the doc subdirectory of all
PHREEQC program distributions.
Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples
for PHREEQC version 3--A computer program for speciation, batch-reaction,
one- dimensional transport, and inverse geochemical calculations: U.S.
Geological Survey Techniques and Methods, book 6, chap. A43, 497 p.
http://pubs.usgs.gov/tm/06/a43/.
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.
http://pubs.er.usgs.gov/publication/wri994259.
*The following two reports document the theory and implementation of
isotopes in PHREEQC. Portable Document Format (PDF) of Thorstenson and
Parkhurst (2002) is included in the doc subdirectory of the PHREEQC program
distribution.
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.
http://pubs.er.usgs.gov/publication/wri024172.
Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope
equilibrium constants for geochemical reactions: Geochimica et Cosmochimica
Acta, v. 68, no. 11, p. 2449-2465.
*Brief description of the program PhreeqcI.
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.
-----------------------------------------------------------------------------------
C. Installing Windows COM versions
-----------------------------------------------------------------------------------
For 64-bit computers, download both 32- and 64-bit versions:
IPhreeqcCOM-@VERSION@-@REVISION@-win32.msi
IPhreeqcCOM-@VERSION@-@REVISION@-x64.msi
Double click on each .msi file and follow the instructions.
IPhreeqcCOM is installed and ready to use for 32- and 64-bit applications.
To test the COM, you can open the Excel file and run the "runphreeqc" macro
(view->macros):
C:\Program Files\USGS\IPhreeqcCOM 3.2.0-9755\examples\com\excel\runphreeqc.xls
-----------------------------------------------------------------------------------
D. Downloading and unzipping the distribution file
-----------------------------------------------------------------------------------
Follow the steps using gunzip, 7zip, or other compression program that can unzip a tar.gz/zip file:
Steps in extracting files Explanation
---------------------------------------- -----------------------------------
gunzip iphreeqc-@VERSION@-@REVISION@.tar.gz Uncompress the tar.gz file.
tar -xvpof iphreeqc-@VERSION@-@REVISION@.tar Extract files from the tar file.
The directory iphreeqc-@VERSION@-@REVISION@ is created when the files are
extracted; if this directory already exists, you may want to delete or rename
it before extracting the files. The following directory structure is created
(the contents of each directory are shown to the right):
iphreeqc-@VERSION@-@REVISION@ Source code and configure/CMake files
./config More configure files
./database Database files for PHREEQC
./doc Documentation files
./examples Advection example for Fortran, C++, and C
./src Source code for IPhreeqc
./tests Tests that check that C++, C, and Fortran(optional)
are able to compile, link and run.
Note: A compiled executable is not included in the distribution.
-----------------------------------------------------------------------------------
E. Linux compiling, testing, and installing the IPhreeqc library
-----------------------------------------------------------------------------------
In general, to compile the software, you will need:
(a) a C++ compiler, and
(b) knowledge of configure, Make,
the compiler, and the Linux operating system.
A Makefile is generated by configure, and the Makefile is used to
compile, test, and install the software.
E.1. Change directory to the directory that was extracted from the tar file.
cd iphreeqc-@VERSION@-@REVISION@
E.2. Make a directory, for example, build.
mkdir build
E.3. Change directory to build.
cd build
E.4. Run configure
Many of the options for configure can be seen by typing:
../configure --help
Most common options:
--prefix=dir specifies the directory for installation of the
library. Default is /usr/local, $HOME would install
to your home directory.
--enable-fortran-test=yes specifies that you do want to include the Fortran test
files during "make check", which compiles, links, and runs programs
that use IPhreeqc.
Run configure as follows:
../configure [options]
E.5. Compile the IPhreeqc library
make [-j 4]
Optionally, use -j n--where n is the number of compilations make runs in parallel.
E.6. Compile and run the test cases. The files in the directory tests are compiled
and linked to the IPhreeqc library. The Fortran files are optionally included
(--enable-fortran-test configure option).
make check
E.7. Install the IPhreeqc library. By default the program is installed in /usr/local/bin
and /usr/local/share/doc/iphreeqc. Alternatively, the directory defined by --prefix
in the configure command is used.
make install
The locations of various files are given for default installation (no
--prefix definition).
Libraries:
/usr/local/lib/libiphreeqc.a (Static library)
/usr/local/lib/libiphreeqc.so (Shared object library)
/usr/local/lib/libiphreeqc.la (libtool library file)
Include files:
C++ and C headers for user's code:
/usr/local/include/IPhreeqc.h (C header)
/usr/local/include/IPhreeqc.hpp (C++ header)
Optionally, user's code may need one or more of the following:
/usr/local/include/Var.h
/usr/local/include/IPhreeqcCallbacks.h
/usr/local/include/Keywords.h
/usr/local/include/PHRQ_io.h
Documentation:
/usr/local/share/doc/iphreeqc/IPhreeqc.pdf
/usr/local/share/doc/iphreeqc/html/index.html (IPhreeqc API)
/usr/local/share/doc/iphreeqc/RELEASE (Release notes)
/usr/local/share/doc/iphreeqc/README (this readme file)
/usr/local/share/doc/iphreeqc/NOTICE (User rights notice)
Databases:
/usr/local/share/doc/iphreeqc/database
Amm.dat
frezchem.dat
iso.dat
llnl.dat
minteq.dat
minteq.v4.dat
phreeqc.dat
pitzer.dat
sit.dat
wateq4f.dat
Advection example for Fortran, C++, and C:
/usr/local/share/doc/iphreeqc/examples
Fortran interface
/usr/local/share/doc/iphreeqc/src/IPhreeqc_interface.F90
-----------------------------------------------------------------------------------
F. Windows compiling, testing, and installing the IPhreeqc library
-----------------------------------------------------------------------------------
In general, to compile the IPhreeqc library, you will need:
(a) CMake (build process manager)
(b) a C++ compiler,
(c) familiarity with the compiler and the Windows operating system.
F.1. Download and install CMake
CMake can be downloaded from http://www.cmake.org/. If you download
the executable, CMake is installed when you execute it.
F.2 Generate a Visual Studio solution
CMake has many options other than Visual Studio, but here we assume
that you are using some version of Visual Studio. On the first use
of CMake, it may be necessary to close all Visual Studio instances.
Open CMake. Fill in the top two lines.
Where is the source code:
The top level directory (ie c:/iphreeqc-@VERSION@-@REVISION@).
Where to build the binaries:
A new directory. It is suggested that the name
of the directory include the characteristics of
the library that is built, including the VS
version, 32/64 bit, dll/lib.
for example, vs2012_64_dll.
Click Configure. From the pulldown menu select the 64-bit version
for your Visual Studio. Normally, the default radio button should
be sufficient. Click Finish.
Options in the top panel:
(1) BUILD_SHARED_LIBS--If checked, .dll files will be
created. If not checked, a .lib file will be created.
Note that .dll files have a .lib file associated with them,
but it is not the same .lib generated when
BUILD_SHARED_LIBS is not checked.
(2) CMAKE_INSTALL_PREFIX--Sets the the install directory where the
library and header files will be saved. It is suggested that
an INSTALL directory be defined inside the directory chosen
for the binaries.
(3) BUILD_CLR_LIBS--If checked, will compile the CLR version of the
library. This will enable the charting capabilities of
phreeqc through the use of Zedgraph. This option is only
available if BUILD_SHARED_LIBS is checked.
(4) IPHREEQC_ENABLE_MODULE--Uncheck if you want to
use the deprecated (old-style) include file (IPhreeqc.f90.inc
or IPhreeqc.f.inc) to define IPhreeqc in Fortran files.
Leave checked to use IPhreeqc as a Fortran module (USE IPhreeqc),
which is recommended. Leave checked if not using Fortran.
(5) IPHREEQC_FORTRAN_TESTING--Sets whether the test calculations
(tests directory) will include Fortran test files. A Fortran
compiler is required.
Click Configure until the screen is not red. If the screen remains
red, you will have to deal with the CMake error messages.
Click Generate.
You should now have a Visual Studio solution file (.sln) in the
directory chosen for the binaries (second line of CMake screen).
At any point, you can delete the contents of the directory and
start over. You can make solutions for different Visual Studios,
or different options in other directories.
F.3. Compile and install IPhreeqc
Open the Visual Studio solution in the build directory defined in CMake.
The default configuration is "Debug". If you want a release libraries
(or dlls) and examples, change the configuration to "Release".
Build ALL_BUILD. IPhreeqc is compiled.
Build RUN_TESTS. Programs that test IPhreeqc are compiled and run,
and optionally (CMake IPHREEQC_FORTRAN_TESTING option) the Fortran test
project.
Build INSTALL. The libraries, header files, Fortran module source
files, phreeqc database files, and documentation are installed in the
install directory selected in CMake.
Install\library directory (lib or dll) may include:
IPhreeqc.lib (Release)
IPhreeqcd.lib (Debug)
IPhreeqcmsr.lib (MinSizeRel)
IPhreeqcrwdi.lib (RelWithDebInfo)
IPhreeqc.dll (Release Shared)
IPhreeqcd.dll (Debug Shared)
IPhreeqcmsr.dll (MinSizeRel Shared)
IPhreeqcrwdi.dll (RelWithDebInfo Shared)
ZedGraph.dll (CLR/Charting)
Install\include files:
C++ and C headers for user's code:
IPhreeqc.hpp (C++ header)
IPhreeqc.h (C header)
Optionally, you may need one or more of the following:
Var.h
IPhreeqcCallbacks.h
Keywords.h
PHRQ_io.h
Install\src files:
To use IPhreeqc in Fortran:
IPhreeqc_interface.F90
Install\Database files:
Amm.dat
frezchem.dat
iso.dat
llnl.dat
minteq.dat
minteq.v4.dat
phreeqc.dat
pitzer.dat
sit.dat
wateq4f.dat
Install\doc files:
IPhreeqc.pdf IPhreeqc journal article
html\index.html IPhreeqc API documentation
NOTICE User rights notice
README This readme file
RELEASE Release notes
Install\examples files:
c, cpp, fortran Advection example
Note: In order to use the CLR version (Charting) the Zedgraph.dll file
must be registered either by installing the Phreeqc or the PhreeqcI MSI,
or through the use of the Visual Studio Tool gacutil.
-----------------------------------------------------------------------------------
G. Using the library
-----------------------------------------------------------------------------------
G.1. C++
In C++, you will include the IPhreeqc.hpp header file and
create an IPhreeqc instance:
#include "IPhreeqc.hpp"
IPhreeqc iphreeqc;
or
IPhreeqc *iphreeqc = new IPhreeqc();
You will need to link to the IPhreeqc.lib that you installed.
G.2. C
In C, you will include the C interface header, IPhreeqc.h, and
create an IPhreeqc instance.
#include "IPhreeqc.h"
int id;
id = CreateIPhreeqc();
You will need to link to the IPhreeqc.lib that you installed.
G.3. Fortran
In Fortran, you will need to include the source file IPhreeqc_interface.F90
in your project files. This file defines the IPhreeqc Fortran module.
USE IPhreeqc
INTEGER(KIND=4) id
id = CreateIPhreeqc()
You will need to link to the IPhreeqc.lib that you installed.
-----------------------------------------------------------------------------------
H. CONTACTS
-----------------------------------------------------------------------------------
Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov

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README.TXT
PHREEQC
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
This file describes batch versions of PHREEQC version 3 for Linux. The @M32@
(32-bit) and @M64@ (64-bit) versions, referred to as "Linux" versions, contain
an executable file compiled for Linux, whereas the plain .tar.gz version,
referred to as the "source" version, has no executable file, but has the files
necessary to configure and compile PHREEQC on any Unix operating system.
Instructions for installing, executing, and testing on Linux operating
systems are provided below. After installation, see the root or doc directory
of the PHREEQC installation for summary information on PHREEQC in phreeqc.txt
and the new features and bug fixes in RELEASE.TXT.
No graphical user interface exits for Linux. (For Windows, a graphical user
interface, PhreeqcI, is available at
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html and a
Notepad++ interface is available at http://www.hydrochemistry.eu/downl.html.)
TABLE OF CONTENTS
A. Distribution files
B. Documentation
C. Linux versions (with executable)
C.1. Extracting files
C.2. Running
C.2. Testing
D. Source version (for Unix compilation)
D.1. Extracting files
D.2. Compiling, testing, installing
D.3. Running
E. Description of test cases
F. Contacts
A. Distribution files
The following distribution packages (containing the software, test data
sets, and information files) are currently available for Linux systems:
phreeqc-@VERSION@-@REVISION@.@M32@.tar.gz--Compiled with @GCC_VER@
kernel @KERNEL_VER@
phreeqc-@VERSION@-@REVISION@.@M64@.tar.gz--Compiled with @GCC_VER_64@
kernel @KERNEL_VER_64@
phreeqc-@VERSION@-@REVISION@.tar.gz --Source code, but no executable
B. Documentation
*The following two user's guides are available in electronic format. Portable
Document Format (PDF) files are included in the doc subdirectory of the
PHREEQC program distribution.
Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples
for PHREEQC version 3--A computer program for speciation, batch-reaction,
one- dimensional transport, and inverse geochemical calculations: U.S.
Geological Survey Techniques and Methods, book 6, chap. A43, 497 p.
http://pubs.usgs.gov/tm/06/a43/.
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.
http://pubs.er.usgs.gov/publication/wri994259.
*The following two reports document the theory and implementation of
isotopes in PHREEQC. Portable Document Format (PDF) of Thorstenson and
Parkhurst (2002) is included in the doc subdirectory of the PHREEQC program
distribution.
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.
http://pubs.er.usgs.gov/publication/wri024172.
Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope
equilibrium constants for geochemical reactions: Geochimica et Cosmochimica
Acta, v. 68, no. 11, p. 2449-2465.
*Brief description of the program PhreeqcI.
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.
C. Linux versions (with executable)
Compressed tar files, phreeqc-@VERSION@-@REVISION@.Linux.tar.gz and
phreeqc-@VERSION@-@REVISION@.Linux.x86_64.tar.gz, are used to distribute the
source code and the compiled executable for Linux operating systems. The 32-bit
Linux executable file is compiled with
@GCC_VER@ kernel @KERNEL_VER_64@
and the 64-bit Linux executable file is compiled with
@GCC_VER_64@ kernel @KERNEL_VER@.
All of the files needed to run and test PHREEQC are contained in each tar file.
(If you want to compile the program yourself, the file
phreeqc-@VERSION@-@REVISION@.tar.gz contains all of the files needed to
configure, compile, test, and install PHREEQC. See Section D for details.)
C.1. Extracting files
Follow the steps below to extract the files from a distribution tar
file.
Steps in extracting files Explanation
---------------------------------------- -----------------------------------
For the 32-bit version:
gunzip phreeqc-@VERSION@-@REVISION@.i686.tar.gz Uncompress the tar.gz file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.i686.tar Extract files from the tar file.
or, for the 64-bit version:
gunzip phreeqc-@VERSION@-@REVISION@.x86_64.tar.gz Uncompress the tar.gz file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.x86_64.tar Extract files from the tar file.
The directory phreeqc-@VERSION@-@REVISION@ is created when the files are
extracted; if this directory already exists, you may want to delete or rename
it before extracting the files.
The following directory structure is created (the contents of each
directory are shown to the right):
phreeqc-@VERSION@-@REVISION@ Files NOTICE.TXT, RELEASE, and (this file) README
`--bin Compiled executable
`--database Database files (one is required for execution)
`--doc Documentation files
`--examples Examples from user's guide--used in verification tests
`--test Scripts to run verification tests
Notes: 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.
C.2. Running
If PHREEQC has been installed in a directory included in the users' PATH, 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 directory containing the executable file is not included in the PATH
environmental variable, you can (1) use the complete path name to the
executable in place of "phreeqc" above, or (2) copy the executable to the
current directory. The executable is phreeqc-@VERSION@-@REVISION@/bin/phreeqc.
In addition a database file may need to be in the current directory.
Phreeqc.dat is generally used by default and is found at
phreeqc-@VERSION@-@REVISION@/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 (assuming the tar file was extracted in
the directory /home/jdoe) with a command such as:
setenv PHREEQC_DATABASE /home/jdoe/phreeqc-@VERSION@-@REVISION@/database/phreeqc.dat
In the Bourne or Korn shell, this variable can be set with the command:
export PHREEQC_DATABASE=/home/jdoe/phreeqc-@VERSION@-@REVISION@/database/phreeqc.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
assumed to be phreeqc.dat in the current directory.
C.3. Testing
Input files 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 directory
phreeqc-@VERSION@-@REVISION@/examples contains the input data for each test.
Provided that the directory phreeqc-@VERSION@-@REVISION@/test is a directory where
you have write access; the examples can be run from that directory.
Change to the 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 = 22
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 can be found in the test directory.
To clean up after the tests, type the command:
./clean.sh
D. Source version (for compilation)
A compressed tar file, phreeqc-@VERSION@-@REVISION@.tar.gz, is used to
distribute the source code and other files necessary to compile, test, install,
and run PHREEQC on Unix operating systems. (A compiled executable for Linux is
distributed in the Linux versions. See section C.)
D.1. Extracting files
Follow the steps below to extract the files from a distribution tar
file.
Steps in extracting files Explanation
---------------------------------------- -----------------------------------
gunzip phreeqc-@VERSION@-@REVISION@.source.tar.gz Uncompress the tar.gz file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.source.tar Extract files from the tar file.
The directory phreeqc-@VERSION@-@REVISION@ is created when the files are
extracted; if this directory already exists, you may want to delete or rename
it before extracting the files.
The following directory structure is created (the contents of each directory
are shown to the right):
phreeqc-@VERSION@-@REVISION@ Files related to configure
`--config More configure files
`--database Database files required during execution
`--doc Documentation files
`--examples Examples from user's guide--used in verification tests
`--src Source code
`--test Files used to test the compilation
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.
D.2. Compiling, testing, installing
No support beyond this README file is provided for users compiling their own
versions of the software. In general, to compile the software, you will need:
(a) a C++ compiler, and
(b) a minimal level of knowledge of configure, Make, the compiler, and
the Linux operating system.
A Makefile can be generated by configure, and the Makefile can be used to
compile, test, and install the software.
To compile, test, and install PHREEQC, do the following:
1. Change directory to the directory that was extracted from the tar file.
cd phreeqc-@VERSION@-@REVISION@
2. Make a directory, for example, Release.
mkdir Release
3. Change directory to Release.
cd Release
4. Run configure
../configure
Many of the options for configure can be seen by typing:
../configure --help
5. Compile the program
make
6. Check that compiled version runs the test cases. Check may take several
minutes.
make check
Results of running the test cases are stored in the directory
Release/test
7. Install the program. By default the program is installed in /usr/local/bin
and /usr/local/share/doc/phreeqc. You can specify an installation prefix
other than "/usr/local" by using the prefix option, prefix=$HOME for
example.
make install
The locations of various files are given (a) for default installation (make
install), and (b) if prefix is defined to be $HOME (make install prefix=
$HOME). $HOME is used to represent your home directory in the following
pathnames.
Executable:
(a) /usr/local/bin/phreeqc
(b) $HOME/bin/phreeqc
Documentation (PDFs, README, NOTICE, phreeqc.txt):
(a) /usr/local/share/doc/phreeqc
(b) $HOME/share/doc/phreeqc
Databases:
(a) /usr/local/share/doc/phreeqc/database
(b) $HOME/share/doc/phreeqc/database
Example input files:
(a) /usr/local/share/doc/phreeqc/examples
(b) $HOME/share/doc/phreeqc/examples
D.3. Running
If PHREEQC has been installed in a directory included in the users' PATH, 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.
For Linux, if the "make install" command described above has not been executed,
the executable may be copied to the current directory. In addition the default
database file, phreeqc.dat, may need to be in the current directory.
Phreeqc.dat is in phreeqc-@VERSION@-@REVISION@/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 (assuming your database
is named /home/jdoe/local/project/mydata.dat) 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
assumed to be phreeqc.dat in the current directory.
E. Description of test cases
The tests are described in the table below, where 'test' corresponds
to the example number in the PHREEQC manual.
test description of test and files
---- --------------------------------------------
1 Add uranium and speciate seawater
2 Temperature dependence of solubility
of gypsum and anhydrite
3 Mixing seawater and groundwater
4 Evaporation and solution volume
5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
6 Reaction path calculations with K-feldspar to phase boundaries
7 Organic decomposition with fixed-pressure and
fixed-volume gas phases
8 Sorption of zinc on hydrous iron oxides
9 Kinetically controlled oxidation of ferrous iron.
Decoupled valence states of iron.
10 Solid solution of strontianite and aragonite.
11 Transport and ion exchange.
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.
13 1D Transport in a Dual Porosity Column With Cation Exchange
14 Transport with equilibrium_phases, exchange, and surface reactions
15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
16 Inverse modeling of Sierra springs
17 Inverse modeling of Black Sea water evaporation
18 Inverse modeling of Madison aquifer
19 Modeling Cd+2 sorption with Linear, Freundlich, and Langmuir isotherms,
and with a deterministic distribution of sorption sites for organic
matter, clay minerals, and iron oxyhydroxides
20 Distribution of isotopes between water and calcite
21 Modeling diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a radial diffusion
cell
22 Modeling gas solubilities: CO2 at high pressures
F. CONTACTS
Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov

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README.TXT
PHREEQC
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
This file describes three batch versions of PHREEQC for Windows and Linux: (1) A
Windows version with a compiled executable, (2) A Windows version that has source
code that can be compiled with Visual Studio solutions that are generated by CMake,
and (3) A Linux version with source code that can be compiled by a Makefile generated
by configure. For Linux, there is no version with an executable, and compilation is
required.
No graphical user interface exists for Linux. (For Windows, a graphical user
interface, PhreeqcI, is available at
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html and a
Notepad++ interface is available at http://www.hydrochemistry.eu/downl.html.)
TABLE OF CONTENTS
A. Distribution files
B. Documentation
C. Installing the Windows batch version of PHREEQC with executable
D. Compiling and installing the Windows batch version of PHREEQC without executable
E. Compiling and installing the Linux batch version of PHREEQC
F. Running PHREEQC
G. Description of test cases
H. Contacts
-----------------------------------------------------------------------------------
A. Distribution files
-----------------------------------------------------------------------------------
The following distribution packages of the batch version of PHREEQC are available
for Windows and Linux:
phreeqc-@VERSION@-@REVISION@.msi 64-bit batch version with executable
compiled by using Microsoft Visual C++ 2005
phreeqc-@VERSION@-@REVISION@.zip For compilation on Windows
phreeqc-@VERSION@-@REVISION@.tar.gz For compilation on Linux
-----------------------------------------------------------------------------------
B. Documentation
-----------------------------------------------------------------------------------
*The following two user's guides are available in electronic format. Portable
Document Format (PDF) files are included in the doc subdirectory of the
PHREEQC program distribution.
Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples
for PHREEQC version 3--A computer program for speciation, batch-reaction,
one- dimensional transport, and inverse geochemical calculations: U.S.
Geological Survey Techniques and Methods, book 6, chap. A43, 497 p.
http://pubs.usgs.gov/tm/06/a43/.
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.
http://pubs.er.usgs.gov/publication/wri994259.
*The following two reports document the theory and implementation of
isotopes in PHREEQC. Portable Document Format (PDF) of Thorstenson and
Parkhurst (2002) is included in the doc subdirectory of the PHREEQC program
distribution.
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.
http://pubs.er.usgs.gov/publication/wri024172.
Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope
equilibrium constants for geochemical reactions: Geochimica et Cosmochimica
Acta, v. 68, no. 11, p. 2449-2465.
*Brief description of the program PhreeqcI.
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.
-----------------------------------------------------------------------------------
C. Installing the Windows batch version of PHREEQC with executable
-----------------------------------------------------------------------------------
Note: the person installing the software generally must have administrator
rights.
To install the batch version, double-click phreeqc-@VERSION@-@REVISION@.msi to
execute the installation program and follow the directions on the screen. The batch
version is completely independent from the GUI version.
Default installation is in the directory:
C:\Program Files\USGS\phreeqc-@VERSION@-@REVISION@-x64
which includes subdirectories:
bin\
database\
doc\
examples\
src\
test\
The installation sets environmental variables PATH, PATH_PHREEQC, and PHREEQC_ROOT.
-----------------------------------------------------------------------------------
D. Compiling and installing the Windows batch version of PHREEQC without executable
-----------------------------------------------------------------------------------
In general, to compile the IPhreeqc library, you will need:
(a) CMake (build process manager)
(b) a C++ compiler,
(c) familiarity with the compiler and the Windows operating system.
D.1. Download and install CMake
CMake can be downloaded from http://www.cmake.org/. If you download the
executable, CMake is installed when you execute it.
D.2. Unzip the distribution file phreeqc-@VERSION@-@REVISION@.zip
The directory phreeqc-@VERSION@-@REVISION@ is created when the files are
extracted; if this directory already exists, you may want to delete or rename it
before extracting the files.
The following directory structure is created (the contents of each directory are
shown to the right):
phreeqc-@VERSION@-@REVISION@ Files related to CMake
`--database Database files required during execution
`--doc Documentation files
`--examples Examples from user's guide--used in verification tests
`--src Source code
`--test Files used to test the compilation
D.3. Generate a Visual Studio solution
CMake has many options other than Visual Studio, but here we assume that you are
using some version of Visual Studio. On the first use of CMake, it may be
necessary to close all Visual Studio instances.
Open CMake.
Fill in the top two lines:
Where is the source code:
The top level directory (ie c:/phreeqc-@VERSION@-@REVISION@).
Where to build the binaries:
A new directory. It is suggested that the name of the directory include
the characteristics of the library that is built, including the VS
version, and 32/64 bit, such as VS2012_x64.
Click Configure.
From the pulldown menu of the cmake-gui popup, select the 64-bit version
for your Visual Studio. Normally, the default radio button should be
sufficient. Click Finish.
Options in the top panel:
(1) CMAKE_INSTALL_PREFIX--Sets the the install directory where the
library and header files will be saved. It is suggested that
an INSTALL directory be defined inside the directory chosen
for the binaries.
Click Configure until the screen is not red. If the screen remains red, you will
have to deal with the CMake error messages.
Click Generate.
You should now have a Visual Studio solution file (.sln) in the directory chosen
for the binaries (second line of CMake screen). At any point, you can delete the
contents of the directory and start over. You can make solutions for different
Visual Studios, or different options in other directories.
D.4. Compile and install PHREEQC
Open the Visual Studio solution in the build directory defined in CMake.
The default configuration is "Debug". If you want a release libraries
(or dlls) and examples, change the configuration to "Release".
Build ALL_BUILD.
IPhreeqc is compiled.
Build RUN_TESTS. Programs that test IPhreeqc are compiled and run, and optionally
(CMake IPHREEQC_FORTRAN_TESTING option) the Fortran test project.
Build INSTALL.
The executables, PHREEQC database files, and documentation are installed in the
install directory selected in CMake (denoted "install" in the following
descriptions).
Install:
RELEASE.txt Release notes
README.txt this readme file
NOTICE.txt User rights notice
Install\bin directory:
Subdirectories with executables
Install\Database files:
Amm.dat
frezchem.dat
iso.dat
llnl.dat
minteq.dat
minteq.v4.dat
phreeqc.dat
pitzer.dat
sit.dat
wateq4f.dat
Install\doc files:
Phreeqc_3_2013_manual.pdf Manual for PHREEQC version 3
Phreeqc_2_1999_manual.pdf Manual for PHREEQC version 2
phreeqc.txt Short explanation for PHREEQC
phreeqc3.chm Latest PHREEQC documentation
wrir02-4172.pdf Documenation of isotope calculations
Install\examples files:
Input files for the 22 examples described in the version 3 manual
Note: In order to use the CLR version (Charting) the Zedgraph.dll file must be
registered either by installing the Phreeqc batch version with executable or the
PhreeqcI MSI, or through the use of the Visual Studio Tool gacutil.
-----------------------------------------------------------------------------------
E. Compiling and installing the Linux batch version of PHREEQC
-----------------------------------------------------------------------------------
No support beyond this README file is provided for users compiling their own
versions of the software. In general, to compile the software, you will need:
(a) a C++ compiler, and
(b) a minimal level of knowledge of configure, Make, the compiler, and
the Linux operating system.
A Makefile can be generated by configure, and the Makefile can be used to
compile, test, and install the software.
E.1. 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@.source.tar.gz Uncompress the tar.gz file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.source.tar Extract files from the tar file.
The directory phreeqc-@VERSION@-@REVISION@ is created when the files are
extracted; if this directory already exists, you may want to delete or rename it
before extracting the files.
The following directory structure is created (the contents of each directory are
shown to the right):
phreeqc-@VERSION@-@REVISION@ Files related to configure
`--config More configure files
`--database Database files required during execution
`--doc Documentation files
`--examples Examples from user's guide--used in verification tests
`--src Source code
`--test Files used to test the compilation
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.
E.2. Change directory to the directory that was extracted from the tar file.
cd phreeqc-@VERSION@-@REVISION@
E.3. Make a directory, for example, Release.
mkdir Release
E.4. Change directory to Release.
cd Release
E.5. Run configure
Many of the options for configure can be seen by typing:
../configure --help
The most common option: --prefix=dir specifies the directory for installation of
the library. Default is /usr/local, $HOME would install to your home directory.
Run configure as follows:
../configure [options]
E.6. Compile the program
make [-j n]
Optionally, use -j n--where n is the number of compilations make runs in parallel.
E.7. Check that compiled version runs the test cases.
Check may take several minutes.
make check
Results of running the test cases are stored in the directory Release/test
E.8. Install the program.
By default the program is installed in /usr/local/bin and
/usr/local/share/doc/phreeqc. You can specify an installation prefix other than
"/usr/local" by using the prefix option, prefix=$HOME for example.
make install
The locations of various files are given below, where "install" is the
installation directory, /usr/local by default, or the value given by the --prefix
option to configure.
Executable:
install/bin/phreeqc
Documentation:
install/share/doc/phreeqc
Phreeqc_3_2013_manual.pdf Manual for Phreeqc version 3
Phreeqc_2_1999_manual.pdf Manual for Phreeqc version 2
wrir02-4172.pdf Documenation of isotope calculations
phreeqc.txt Short explanation for Phreeqc
RELEASE Release notes
README this readme file
NOTICE User rights notice
phreeqc3.chm Compiled HTML documentation
Databases:
install/share/doc/phreeqc/database
Amm.dat
frezchem.dat
iso.dat
llnl.dat
minteq.dat
minteq.v4.dat
phreeqc.dat
pitzer.dat
sit.dat
wateq4f.dat
Example input files:
install/share/doc/phreeqc/examples
Input files for 22 examples documented in the Phreeqc 3 manual
-----------------------------------------------------------------------------------
F. Running PHREEQC
-----------------------------------------------------------------------------------
If PHREEQC has been installed in a directory included in the users' PATH, the
program can be executed from a command line 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 phreeqc is not located in a directory in PATH, the executable may be copied to the
current directory. In addition the default database file, phreeqc.dat, or another
desired database may need to be in the current directory.
PHREEQC is run by a script on Linux and a batch file on Windows. The environmental
variable PHREEQC_DATABASE can be used to specify a default database.
-----------------------------------------------------------------------------------
G. Description of test cases
-----------------------------------------------------------------------------------
The tests are described in the table below, where 'test' corresponds
to the example number in the PHREEQC manual.
test description of test and files
---- --------------------------------------------
1 Add uranium and speciate seawater
2 Temperature dependence of solubility
of gypsum and anhydrite
3 Mixing seawater and groundwater
4 Evaporation and solution volume
5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
6 Reaction path calculations with K-feldspar to phase boundaries
7 Organic decomposition with fixed-pressure and
fixed-volume gas phases
8 Sorption of zinc on hydrous iron oxides
9 Kinetically controlled oxidation of ferrous iron.
Decoupled valence states of iron.
10 Solid solution of strontianite and aragonite.
11 Transport and ion exchange.
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.
13 1D Transport in a Dual Porosity Column With Cation Exchange
14 Transport with equilibrium_phases, exchange, and surface reactions
15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
16 Inverse modeling of Sierra springs
17 Inverse modeling of Black Sea water evaporation
18 Inverse modeling of Madison aquifer
19 Modeling Cd+2 sorption with Linear, Freundlich, and Langmuir isotherms,
and with a deterministic distribution of sorption sites for organic
matter, clay minerals, and iron oxyhydroxides
20 Distribution of isotopes between water and calcite
21 Modeling diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a radial diffusion
cell
22 Modeling gas solubilities: CO2 at high pressures
-----------------------------------------------------------------------------------
H. Contacts
-----------------------------------------------------------------------------------
Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov

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README.PhreeqcI.txt
PhreeqcI Version @VERSION@ @VER_DATE@
A graphical user interface to:
PHREEQC--A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
This file describes installing the GUI PhreeqcI on Windows operating systems.
The GUI can be downloaded from
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.
PhreeqcI has screens for most PHREEQC keywords and allows input files that use any
of PHREEQC version 3 capabilities. Alternatively, a Notepad++ interface for
PHREEQC version 3 is available at http://www.hydrochemistry.eu/downl.html.
TABLE OF CONTENTS
A. Distribution file
B. Documentation
C. Installing and running the GUI PhreeqcI
D. Testing and examples
E. Contacts
-----------------------------------------------------------------------------------
A. Distribution files
-----------------------------------------------------------------------------------
The following distribution file (containing the software, databases, examples and
documentation) are available at
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.
phreeqci-@VERSION@-@REVISION@.msi--GUI compiled by using Microsoft Visual C++ 2005
-----------------------------------------------------------------------------------
B. Documentation
-----------------------------------------------------------------------------------
*Brief description of the program PhreeqcI.
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.
*The following two user's guides are available in electronic format. Portable
Document Format (PDF) files are included in the doc subdirectory of the
PHREEQC program distribution. Latest documentationis available from
the Help menu of PhreeqcI.
Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples
for PHREEQC version 3--A computer program for speciation, batch-reaction,
one- dimensional transport, and inverse geochemical calculations: U.S.
Geological Survey Techniques and Methods, book 6, chap. A43, 497 p.
http://pubs.usgs.gov/tm/06/a43/.
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.
http://pubs.er.usgs.gov/publication/wri994259.
*The following two reports document the theory and implementation of isotopes
in PHREEQC. Portable Document Format (PDF) of Thorstenson and Parkhurst
(2002) is included in the doc subdirectory of the PHREEQC program
distribution.
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.
http://pubs.er.usgs.gov/publication/wri024172.
Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope
equilibrium constants for geochemical reactions: Geochimica et Cosmochimica
Acta, v. 68, no. 11, p. 2449-2465.
-----------------------------------------------------------------------------------
C. Installing and running the GUI PhreeqcI
-----------------------------------------------------------------------------------
Note: the person installing the software generally must have administrator
rights.
To install the GUI, double-click phreeqci-@VERSION@-@REVISION@.msi to execute
the installation program and follow the directions on the screen. The GUI is
completely independent from the batch version.
To execute the GUI, access the program through the start menus of Windows.
By default, PhreeqcI is installed in the directory
C:\Program Files (x86)\USGS\phreeqci-@VERSION@-@REVISION@.
This is the recommended installation directory, but you may use other
directories or disk drives.
Note that program components not installed initially can be installed later,
and any components damaged (for example, by inadvertently overwriting the
directory) can be reinstalled by double-clicking
phreeqci-@VERSION@-@REVISION@.msi--a maintenance version of the installation
program will be executed.
-----------------------------------------------------------------------------------
D. Testing and examples
-----------------------------------------------------------------------------------
Input files are provided to verify that the program is correctly installed and
running on your system. The input files execute the examples presented in the
2013 user's guide, which demonstrate most of the program's capabilities. The
PHREEQC "examples" directory contains the input files.
To run the examples, copy the "examples" directory (C:\Program Files (x86)\USGS\
Phreeqc Interactive 3.1.4-8929\examples) to a location where you have
read/write access. The examples can be run from the new directory either by
double clicking one of the .pqi files from Windows Explorer or by the
File->Open menu of PhreeqcI.
The examples are described in the table below, where 'Num' corresponds
to the example number in the PHREEQC manual. Charts can be compared to charts
in the manual (Techniques and Methods 6-A43).
Num Description of example
---- --------------------------------------------
1 Add uranium species and speciate seawater
2 Temperature dependence of solubility
of gypsum and anhydrite
3 Mixing seawater and groundwater
4 Evaporation and solution volume
5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
6 Reaction path calculations with K-feldspar to phase boundaries
7 Organic decomposition with fixed-pressure and
fixed-volume gas phases
8 Sorption of zinc on hydrous iron oxides
9 Kinetically controlled oxidation of ferrous iron.
Decoupled valence states of iron.
10 Solid solution of strontianite and aragonite.
11 Transport and ion exchange.
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.
13 1D Transport in a Dual Porosity Column With Cation Exchange
14 Transport with equilibrium_phases, exchange, and surface reactions
15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
16 Inverse modeling of Sierra springs
17 Inverse modeling of Black Sea water evaporation
18 Inverse modeling of Madison aquifer
19 Modeling Cd+2 sorption with Linear, Freundlich, and Langmuir isotherms,
and with a deterministic distribution of sorption sites for organic
matter, clay minerals, and iron oxyhydroxides
20 Distribution of isotopes between water and calcite
21 Modeling diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a radial diffusion
cell
22 Modeling gas solubilities: CO2 at high pressures
-----------------------------------------------------------------------------------
E. CONTACTS
-----------------------------------------------------------------------------------
Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov

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README.TXT
PHREEQC
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
NOTE: This file describes installing the GUI PhreeqcI and installing, compiling,
and testing the batch version of PHREEQC version 3 on Windows operating systems.
The GUI and batch version can be downloaded from
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html. PhreeqcI has
screens for most PHREEQC keywords and allows input files that use any of PHREEQC
version 3 capabilities. Alternatively, a Notepad++ interface for PHREEQC version
3 is available at http://www.hydrochemistry.eu/downl.html.
PHREEQC - Version @VERSION@ @VER_DATE@
Instructions for installing, executing, and testing on Windows operating
systems are provided below. After installation, see the phreeqc.txt file in the
doc directory of the PHREEQC installation for summary information on PHREEQC
and the RELEASE.TXT file in the root directory for new features and bug fixes.
TABLE OF CONTENTS
A. Distribution files
B. Documentation
C. Installing and running the GUI PhreeqcI
D. Installing the batch version of PHREEQC
E. Compiling the batch version (optional)
F. Running the batch version
G. Testing and examples
H. Contacts
A. Distribution files
The following distribution files (containing the software, test data sets, and
information files) are available at
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.
phreeqci-@VERSION@-@REVISION@.msi--GUI compiled by using Microsoft Visual C++
2005
phreeqc-@VERSION@-@REVISION@.msi--Batch version compiled by using Microsoft
Visual C++ 2005, includes source code
B. Documentation
*Brief description of the program PhreeqcI.
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.
*The following two user's guides are available in electronic format. Portable
Document Format (PDF) files are included in the doc subdirectory of the
PHREEQC program distribution.
Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples
for PHREEQC version 3--A computer program for speciation, batch-reaction,
one- dimensional transport, and inverse geochemical calculations: U.S.
Geological Survey Techniques and Methods, book 6, chap. A43, 497 p.
http://pubs.usgs.gov/tm/06/a43/.
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.
http://pubs.er.usgs.gov/publication/wri994259.
*The following two reports document the theory and implementation of isotopes
in PHREEQC. Portable Document Format (PDF) of Thorstenson and Parkhurst
(2002) is included in the doc subdirectory of the PHREEQC program
distribution.
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.
http://pubs.er.usgs.gov/publication/wri024172.
Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope
equilibrium constants for geochemical reactions: Geochimica et Cosmochimica
Acta, v. 68, no. 11, p. 2449-2465.
C. Installing and running the GUI PhreeqcI
Note that if the software is to be installed on a server system,
the person installing the software generally must have administrator
rights.
To install the GUI, double-click phreeqci-@VERSION@-@REVISION@.msi to execute
the installation program and follow the directions on the screen. The GUI is
completely independent from the batch version.
To execute the GUI, access the program through the start menus of Windows.
By default, the software is installed in the directory C:\Program
Files\USGS\phreeqci-@VERSION@-@REVISION@ for 32-bit operating systems or
C:\Program Files (x86)\USGS\phreeqci-@VERSION@-@REVISION@ for 64-bit operating
systems. This is the recommended installation directory, but you may use other
directories or disk drives.
Note that program components not installed initially can be installed later,
and any components damaged (for example, by inadvertently overwriting the
directory) can be quickly reinstalled by double-clicking
phreeqci-@VERSION@-@REVISION@.msi--a maintenance version of the installation
program will be executed.
D. Installing and running the batch version of PHREEQC
Note that if the software is to be installed on a server system, the person
installing the software generally must have administrator rights.
To install the software, double-click phreeqc-@VERSION@-@REVISION@.msi to execute
the installation program and follow the directions on the screen. The
installation program will modify the PATH environment variable so that
the PHREEQC program can be executed from a command prompt window from any
directory without needing to type the full pathname of the program's location.
The batch version is completely independent from the GUI version.
By default, the software is installed in the directory C:\Program
Files\USGS\phreeqc-@VERSION@-@REVISION@ (32-bit operating system) or C:\Program
Files (x86)\USGS\phreeqc-@VERSION@-@REVISION@ (64-bit operating system). This is
the recommended installation directory, but you may use other directories or
disk drives. The following documentation assumes default installation for a 64-
bit operating system.
Note that program components not installed initially can be installed later,
and any components damaged (for example, by inadvertently overwriting the
directory) can be quickly reinstalled by double-clicking
phreeqc-@VERSION@-@REVISION@.msi--a maintenance version of the installation
program will be executed.
The following directory structure will be created (the contents of each
directory are shown to the right):
C:\Program Files (x86)\USGS\phreeqc-@VERSION@-@REVISION@
Files NOTICE.TXT, RELEASE.TXT, this file
(README.TXT), and Visual Studio project files
--bin phreeqc.bat, batch file for executing PHREEQC
--ClrRelease phreeqc.exe, executable with charting
--Release phreeqc.exe, executable without charting (runs faster)
--database Database files
--doc Documentation files
--examples Examples from user's guide--used in verification tests
--src Source code
--test Batch files to run verification tests
Note: 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.
E. Compiling the batch version
The source code is provided so that users can generate an executable
themselves. Little or no support is provided for users generating
their own versions of the software. In general, to compile a new
version of PHREEQC, you will need:
(a) a C++ compiler,
(b) familiarity with the compiler and the Windows operating system.
A Visual Studio project (phreeqc.sln) is included in the top-level directory
for compilation on Windows operating systems.
F. Running the batch version
The batch program can be executed from a command-prompt window 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.
Three alternative options exist for running the program: (1) the full pathname to
the batch file can be used in place of "phreeqc" in the above commands
("C:\Program Files (x86)USGS\phreeqc-@VERSION@-@REVISION@\bin\phreeqc.bat").
Note that because of the space present in "Program Files", quotation marks must
be used to enter the full pathname); (2) the full path to one of the executable
files can be used in place of "phreeqc" in the above commands
("C:\Program Files (x86)USGS\phreeqc-@VERSION@-@REVISION@\bin\Release\phreeqc.exe",
for example); or (3) an executable ("C:\Program Files (x86)\USGS\
phreeqc-@VERSION@-@REVISION@\bin\ClrRelease\phreeqc.exe, for example) may be
copied to the current directory and executed with .\phreeqc. The database file
may need to be in the current directory. The default database file is installed
in C:\Program Files (x86)\USGS\phreeqc-@VERSION@-@REVISION@\database\phreeqc.dat.
Two executables are distributed in subdirectories of the bin directory. The
executable (phreeqc.exe) in \bin\ClrRelease has charting capabilities. The
executable in \bin\Release does not have charting capabilities. The version
without charting will run up to two times faster than the charting version and
may be preferred for long calculations that do not require charting.
The environmental variable PHREEQC_DATABASE can be used to specify the
default database for a DOS window session. This environmental variable
can be set with the command:
set PHREEQC_DATABASE=C:\mydirectory\myproject\mydata.dat
When using the batch file, phreeqc.bat, this environmental variable takes
precedence over any default definition of the database file. If PHREEQC is
invoked with at least three arguments, the third argument is the database file
and it takes precedence over the environmental variable or the default
database.
G. Testing and examples
Input files 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
"examples" directory contains the input data and the expected results for each
test.
To run the examples, copy the "test" directory (C:\Program Files (x86)
\USGS\phreeqc-@VERSION@-@REVISION@\test) to a location where you have
read/write access. The examples can be run from the new directory either by
double clicking the test.bat file from Windows Explorer or by changing
directories to the new directory in a command-prompt window and typing the
following:
test.bat [start [stop [no_chart]]]
where: start is the number of the first test to perform, default = 1
stop is the number of the last test to perform, default = 22
no_chart is any alphanumeric string, which causes no charts to be
generated.
For example:
command what happens
--------------------------------- --------------------------------
test.bat runs all of the tests
test.bat 1 1 runs the first test
test.bat 2 3 runs tests 2 and 3
test.bat 4 runs test 4 through the last test
test.bat 1 10 no runs tests 1 through 10 without charts
You will have to close chart windows after each chart has completed to proceed
to the remaining examples. After the tests are completed, the results can be
compared to the expected results (found in the examples directory) by executing
the check.bat batch file. See the file check.log for differences. Differences
in path names and run times are insignificant. The results in the directory
examples were calculated with the charting version of PHREEQC. Comparing non-
charting results to charting results may produce a large number of differences
in check.log; however, in almost all cases, the differences are related to the
calculated pe. The pe may differ significantly and many aqueous species
concentrations may differ, but the concentrations of aqueous species should
differ by less than 1e-8 mol/kgw.
To clean up after the tests, double click on clean.bat in Windows Explorer or
type the command clean.bat from a command prompt.
The tests are described in the table below, where 'test' corresponds
to the example number in the PHREEQC manual. Charts can be compared to charts
in the manual (Techniques and Methods 6-A43).
test description of test and files
---- --------------------------------------------
1 Add uranium and speciate seawater
2 Temperature dependence of solubility
of gypsum and anhydrite
3 Mixing seawater and groundwater
4 Evaporation and solution volume
5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
6 Reaction path calculations with K-feldspar to phase boundaries
7 Organic decomposition with fixed-pressure and
fixed-volume gas phases
8 Sorption of zinc on hydrous iron oxides
9 Kinetically controlled oxidation of ferrous iron.
Decoupled valence states of iron.
10 Solid solution of strontianite and aragonite.
11 Transport and ion exchange.
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.
13 1D Transport in a Dual Porosity Column With Cation Exchange
14 Transport with equilibrium_phases, exchange, and surface reactions
15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
16 Inverse modeling of Sierra springs
17 Inverse modeling of Black Sea water evaporation
18 Inverse modeling of Madison aquifer
19 Modeling Cd+2 sorption with Linear, Freundlich, and Langmuir isotherms,
and with a deterministic distribution of sorption sites for organic
matter, clay minerals, and iron oxyhydroxides
20 Distribution of isotopes between water and calcite
21 Modeling diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a radial diffusion
cell
22 Modeling gas solubilities: CO2 at high pressures
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 pressure 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, REACTION_PRESSURE, 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., 2012, Description of
input and examples for PHREEQC version 3--A computer
program for speciation, batch-reaction, one- dimensional
transport, and inverse geochemical calculations: U.S.
Geological Survey Techniques and Methods, book 6, chap.
A43, 497 p. http://pubs.usgs.gov/tm/06A43/.
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.
Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of
individual isotope equilibrium constants for geochemical
reactions: Geochimica et Cosmochimica Acta, v. 68, no.
11, p. 2449-2465.
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., 2005, Geochemistry,
groundwater and pollution (2nd ed.): 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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