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README.TXT
PHREEQC
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
This file describes compilation of the batch version of PHREEQC version 3 for
Linux. No executable file is included. The distribution contains all files
necessary to configure and compile PHREEQC on any Unix operating system.
Instructions for configuring, compiling, 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 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. Extracting files (for Unix compilation)
D. Compiling, testing, installing
E. Running PHREEQC
F. Description of test cases
G. Contacts
-----------------------------------------------------------------------------------
A. Distribution file
-----------------------------------------------------------------------------------
The following distribution package (containing the source code, configure
files, examples, and documentation) is available for Linux systems:
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. Extracting files (for Unix 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.
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. 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:
D.1. Change directory to the directory that was extracted from the tar file.
cd phreeqc-@VERSION@-@REVISION@
D.2. Make a directory, for example, Release.
mkdir Release
D.3. Change directory to Release.
cd Release
D.4. 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, $HOME would install
to your home directory.
Run configure as follows:
../configure [options]
D.5. Compile the program
make [-j 4]
Optionally, use -j n--where n is the number of compilations make runs in parallel.
D.6. Check that compiled version runs the test cases.
Check may take several minutes.
make check
Results of running the test cases are stored in the directory
Release/test
D.7. Install the program.
By default the program is installed in /usr/local/bin
and /usr/local/share/doc/phreeqc. You can specify an installation prefix
other than "/usr/local" by using the prefix option, prefix=$HOME for
example.
make install
The locations of various files are given 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
phreeqc.txt Short explanation for Phreeqc
RELEASE Release notes
README this readme file
NOTICE User rights notice
???phreeqc3.chm
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
-----------------------------------------------------------------------------------
E. Running PHREEQC
-----------------------------------------------------------------------------------
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, or another desired database may need
to be in the current directory.
Databases are phreeqc-@VERSION@-@REVISION@/database and, if installed,
install/share/doc/phreeqc/database.
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.
-----------------------------------------------------------------------------------
F. 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
-----------------------------------------------------------------------------------
G. Contacts
-----------------------------------------------------------------------------------
Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov