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README.Phreeqc.TXT
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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
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A. Distribution files
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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
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B. Documentation
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*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.
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C. Installing the Windows batch version of PHREEQC with executable
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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.
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D. Compiling and installing the Windows batch version of PHREEQC without executable
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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
ColdChem.dat
core10.dat
frezchem.dat
iso.dat
llnl.dat minteq.dat
minteq.v4.dat
phreeqc.dat
pitzer.dat
sit.dat
Tipping_Hurley.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 Documentation 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.
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E. Compiling and installing the Linux batch version of PHREEQC
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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
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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 Documentation 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
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F. Running PHREEQC
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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
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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.
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G. Description of test cases
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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
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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
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H. Contacts
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Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov