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459 lines
18 KiB
Plaintext
459 lines
18 KiB
Plaintext
README.TXT
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PHREEQC
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A program for speciation, batch-reaction, one-dimensional
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transport, and inverse geochemical calculations
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This file describes batch versions of PHREEQC version 3 for Linux. The @M32@
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(32-bit) and @M64@ (64-bit) versions, referred to as "Linux" versions, contain
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an executable file compiled for Linux, whereas the plain .tar.gz version,
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referred to as the "source" version, has no executable file, but has the files
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necessary to configure and compile PHREEQC on any Unix operating system.
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Instructions for installing, executing, and testing on Linux operating
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systems are provided below. After installation, see the root or doc directory
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of the PHREEQC installation for summary information on PHREEQC in phreeqc.txt
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and the new features and bug fixes in RELEASE.TXT.
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No graphical user interface exits for Linux. (For Windows, a graphical user
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interface, PhreeqcI, is available at
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http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html and a
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Notepad++ interface is available at http://www.hydrochemistry.eu/downl.html.)
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TABLE OF CONTENTS
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A. Distribution files
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B. Documentation
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C. Linux versions (with executable)
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C.1. Extracting files
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C.2. Running
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C.2. Testing
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D. Source version (for Unix compilation)
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D.1. Extracting files
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D.2. Compiling, testing, installing
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D.3. Running
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E. Description of test cases
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F. Contacts
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A. Distribution files
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The following distribution packages (containing the software, test data
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sets, and information files) are currently available for Linux systems:
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phreeqc-@VERSION@-@REVISION@.@M32@.tar.gz--Compiled with @GCC_VER@
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kernel @KERNEL_VER@
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phreeqc-@VERSION@-@REVISION@.@M64@.tar.gz--Compiled with @GCC_VER_64@
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kernel @KERNEL_VER_64@
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phreeqc-@VERSION@-@REVISION@.tar.gz --Source code, but no executable
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B. Documentation
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*The following two user's guides are available in electronic format. Portable
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Document Format (PDF) files are included in the doc subdirectory of the
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PHREEQC program distribution.
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Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples
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for PHREEQC version 3--A computer program for speciation, batch-reaction,
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one- dimensional transport, and inverse geochemical calculations: U.S.
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Geological Survey Techniques and Methods, book 6, chap. A43, 497 p.
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http://pubs.usgs.gov/tm/06/a43/.
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Parkhurst, D.L., and Appelo, C.A.J., 1999, User's guide to PHREEQC (Version
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2)-- A computer program for speciation, batch-reaction, one-dimensional
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transport, and inverse geochemical calculations: U.S. Geological Survey
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Water-Resources Investigations Report 99-4259, 312 p.
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http://pubs.er.usgs.gov/publication/wri994259.
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*The following two reports document the theory and implementation of
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isotopes in PHREEQC. Portable Document Format (PDF) of Thorstenson and
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Parkhurst (2002) is included in the doc subdirectory of the PHREEQC program
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distribution.
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Thorstenson, D.C., and Parkhurst, D.L., 2002, Calculation of individual isotope
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equilibrium constants for implementation in geochemical models: U.S.
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Geological Survey Water-Resources Investigations Report 02-4172, 129 p.
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http://pubs.er.usgs.gov/publication/wri024172.
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Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope
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equilibrium constants for geochemical reactions: Geochimica et Cosmochimica
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Acta, v. 68, no. 11, p. 2449-2465.
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*Brief description of the program PhreeqcI.
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Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user interface
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to the geochemical model PHREEQC: U.S. Geological Survey Fact Sheet
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FS-031-02, 2 p.
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C. Linux versions (with executable)
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Compressed tar files, phreeqc-@VERSION@-@REVISION@.Linux.tar.gz and
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phreeqc-@VERSION@-@REVISION@.Linux.x86_64.tar.gz, are used to distribute the
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source code and the compiled executable for Linux operating systems. The 32-bit
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Linux executable file is compiled with
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@GCC_VER@ kernel @KERNEL_VER_64@
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and the 64-bit Linux executable file is compiled with
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@GCC_VER_64@ kernel @KERNEL_VER@.
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All of the files needed to run and test PHREEQC are contained in each tar file.
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(If you want to compile the program yourself, the file
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phreeqc-@VERSION@-@REVISION@.tar.gz contains all of the files needed to
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configure, compile, test, and install PHREEQC. See Section D for details.)
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C.1. Extracting files
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Follow the steps below to extract the files from a distribution tar
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file.
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Steps in extracting files Explanation
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---------------------------------------- -----------------------------------
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For the 32-bit version:
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gunzip phreeqc-@VERSION@-@REVISION@.i686.tar.gz Uncompress the tar.gz file.
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tar -xvpof phreeqc-@VERSION@-@REVISION@.i686.tar Extract files from the tar file.
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or, for the 64-bit version:
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gunzip phreeqc-@VERSION@-@REVISION@.x86_64.tar.gz Uncompress the tar.gz file.
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tar -xvpof phreeqc-@VERSION@-@REVISION@.x86_64.tar Extract files from the tar file.
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The directory phreeqc-@VERSION@-@REVISION@ is created when the files are
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extracted; if this directory already exists, you may want to delete or rename
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it before extracting the files.
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The following directory structure is created (the contents of each
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directory are shown to the right):
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phreeqc-@VERSION@-@REVISION@ Files NOTICE.TXT, RELEASE, and (this file) README
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`--bin Compiled executable
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`--database Database files (one is required for execution)
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`--doc Documentation files
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`--examples Examples from user's guide--used in verification tests
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`--test Scripts to run verification tests
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Notes: It is recommended that no user files be kept in the PHREEQC directory
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structure. If you plan to put files in the PHREEQC directory
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structure, do so only by creating subdirectories.
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C.2. Running
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If PHREEQC has been installed in a directory included in the users' PATH, the
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program can be executed with any of the commands below.
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command to execute PHREEQC explanation
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----------------------------- -----------------------------------------
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phreeqc The program will query for each of the
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needed files.
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phreeqc input The input file is named input, the output
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file will be named input.out and the
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default database file will be used.
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phreeqc input output The input file is named input, the output
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file is named output, and the default
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database file will be used.
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phreeqc input output database All file names are specified explicitly.
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phreeqc input output database screen_output
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All file names are specified explicitly,
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and screen output is directed to the
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file screen_output.
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If the directory containing the executable file is not included in the PATH
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environmental variable, you can (1) use the complete path name to the
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executable in place of "phreeqc" above, or (2) copy the executable to the
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current directory. The executable is phreeqc-@VERSION@-@REVISION@/bin/phreeqc.
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In addition a database file may need to be in the current directory.
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Phreeqc.dat is generally used by default and is found at
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phreeqc-@VERSION@-@REVISION@/database/phreeqc.dat.
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The shell variable PHREEQC_DATABASE can be used to specify the default database.
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In the C shell, this variable can be set (assuming the tar file was extracted in
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the directory /home/jdoe) with a command such as:
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setenv PHREEQC_DATABASE /home/jdoe/phreeqc-@VERSION@-@REVISION@/database/phreeqc.dat
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In the Bourne or Korn shell, this variable can be set with the command:
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export PHREEQC_DATABASE=/home/jdoe/phreeqc-@VERSION@-@REVISION@/database/phreeqc.dat
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The shell variable can be set permanently by including the appropriate command
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in a file that is read when the shell is initiated, frequently $HOME/.login or
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$HOME/.profile. If this shell variable is not set, the default database is
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assumed to be phreeqc.dat in the current directory.
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C.3. Testing
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Input files are provided to verify that the program is correctly installed and
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running on the system. The tests execute the examples presented in the user's
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guide, which demonstrate most of the program's capabilities. The directory
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phreeqc-@VERSION@-@REVISION@/examples contains the input data for each test.
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Provided that the directory phreeqc-@VERSION@-@REVISION@/test is a directory where
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you have write access; the examples can be run from that directory.
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Change to the directory and type the command:
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./test.sh [start [stop]]
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where: start = the number of the first test to perform, default = 1
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stop = the number of the last test to perform, default = 22
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For example:
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command what happens
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---------------------------------- --------------------------------
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./test.sh runs all of the tests
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./test.sh 1 1 runs the first test
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./test.sh 2 3 runs tests 2 and 3
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./test.sh 4 runs test 4 through the last test
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After the tests are completed, the results can be found in the test directory.
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To clean up after the tests, type the command:
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./clean.sh
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D. Source version (for compilation)
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A compressed tar file, phreeqc-@VERSION@-@REVISION@.tar.gz, is used to
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distribute the source code and other files necessary to compile, test, install,
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and run PHREEQC on Unix operating systems. (A compiled executable for Linux is
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distributed in the Linux versions. See section C.)
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D.1. Extracting files
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Follow the steps below to extract the files from a distribution tar
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file.
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Steps in extracting files Explanation
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---------------------------------------- -----------------------------------
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gunzip phreeqc-@VERSION@-@REVISION@.source.tar.gz Uncompress the tar.gz file.
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tar -xvpof phreeqc-@VERSION@-@REVISION@.source.tar Extract files from the tar file.
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The directory phreeqc-@VERSION@-@REVISION@ is created when the files are
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extracted; if this directory already exists, you may want to delete or rename
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it before extracting the files.
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The following directory structure is created (the contents of each directory
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are shown to the right):
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phreeqc-@VERSION@-@REVISION@ Files related to configure
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`--config More configure files
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`--database Database files required during execution
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`--doc Documentation files
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`--examples Examples from user's guide--used in verification tests
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`--src Source code
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`--test Files used to test the compilation
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Notes: (a) A compiled executable is not included in the source
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distribution.
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(b) It is recommended that no user files be kept in the PHREEQC
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directory structure.
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D.2. Compiling, testing, installing
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No support beyond this README file is provided for users compiling their own
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versions of the software. In general, to compile the software, you will need:
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(a) a C++ compiler, and
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(b) a minimal level of knowledge of configure, Make, the compiler, and
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the Linux operating system.
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A Makefile can be generated by configure, and the Makefile can be used to
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compile, test, and install the software.
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To compile, test, and install PHREEQC, do the following:
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1. Change directory to the directory that was extracted from the tar file.
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cd phreeqc-@VERSION@-@REVISION@
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2. Make a directory, for example, Release.
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mkdir Release
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3. Change directory to Release.
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cd Release
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4. Run configure
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../configure
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Many of the options for configure can be seen by typing:
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../configure --help
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5. Compile the program
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make
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6. Check that compiled version runs the test cases. Check may take several
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minutes.
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make check
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Results of running the test cases are stored in the directory
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Release/test
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7. Install the program. By default the program is installed in /usr/local/bin
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and /usr/local/share/doc/phreeqc. You can specify an installation prefix
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other than "/usr/local" by using the prefix option, prefix=$HOME for
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example.
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make install
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The locations of various files are given (a) for default installation (make
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install), and (b) if prefix is defined to be $HOME (make install prefix=
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$HOME). $HOME is used to represent your home directory in the following
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pathnames.
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Executable:
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(a) /usr/local/bin/phreeqc
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(b) $HOME/bin/phreeqc
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Documentation (PDFs, README, NOTICE, phreeqc.txt):
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(a) /usr/local/share/doc/phreeqc
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(b) $HOME/share/doc/phreeqc
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Databases:
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(a) /usr/local/share/doc/phreeqc/database
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(b) $HOME/share/doc/phreeqc/database
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Example input files:
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(a) /usr/local/share/doc/phreeqc/examples
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(b) $HOME/share/doc/phreeqc/examples
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D.3. Running
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If PHREEQC has been installed in a directory included in the users' PATH, the
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program can be executed with any of the commands below.
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command to execute PHREEQC explanation
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----------------------------- -----------------------------------------
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phreeqc The program will query for each of the
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needed files.
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phreeqc input The input file is named input, the output
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file will be named input.out and the
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default database file will be used.
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phreeqc input output The input file is named input, the output
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file is named output, and the default
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database file will be used.
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phreeqc input output database All file names are specified explicitly.
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phreeqc input output database screen_output
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All file names are specified explicitly,
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and screen output is directed to the
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file screen_output.
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For Linux, if the "make install" command described above has not been executed,
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the executable may be copied to the current directory. In addition the default
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database file, phreeqc.dat, may need to be in the current directory.
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Phreeqc.dat is in phreeqc-@VERSION@-@REVISION@/database/phreeqc.dat.
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The shell variable PHREEQC_DATABASE can be used to specify the default
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database. In the C shell, this variable can be set (assuming your database
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is named /home/jdoe/local/project/mydata.dat) with the command:
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setenv PHREEQC_DATABASE /home/jdoe/local/project/mydata.dat
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In the Bourne or Korn shell, this variable can be set with the command:
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export PHREEQC_DATABASE=/home/jdoe/local/project/mydata.dat
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The shell variable can be set permanently by including the appropriate command
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in a file that is read when the shell is initiated, frequently $HOME/.login or
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$HOME/.profile. If this shell variable is not set, the default database is
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assumed to be phreeqc.dat in the current directory.
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E. Description of test cases
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The tests are described in the table below, where 'test' corresponds
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to the example number in the PHREEQC manual.
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test description of test and files
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---- --------------------------------------------
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1 Add uranium and speciate seawater
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2 Temperature dependence of solubility
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of gypsum and anhydrite
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3 Mixing seawater and groundwater
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4 Evaporation and solution volume
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5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
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6 Reaction path calculations with K-feldspar to phase boundaries
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7 Organic decomposition with fixed-pressure and
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fixed-volume gas phases
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8 Sorption of zinc on hydrous iron oxides
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9 Kinetically controlled oxidation of ferrous iron.
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Decoupled valence states of iron.
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10 Solid solution of strontianite and aragonite.
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11 Transport and ion exchange.
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12 Advective and diffusive transport of heat and solutes. Constant boundary
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condition at one end, closed at other. The problem is designed so that
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temperature should equal Na-conc (in mmol/kgw) after diffusion.
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13 1D Transport in a Dual Porosity Column With Cation Exchange
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14 Transport with equilibrium_phases, exchange, and surface reactions
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15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
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16 Inverse modeling of Sierra springs
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17 Inverse modeling of Black Sea water evaporation
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18 Inverse modeling of Madison aquifer
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19 Modeling Cd+2 sorption with Linear, Freundlich, and Langmuir isotherms,
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and with a deterministic distribution of sorption sites for organic
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matter, clay minerals, and iron oxyhydroxides
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20 Distribution of isotopes between water and calcite
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21 Modeling diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a radial diffusion
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cell
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22 Modeling gas solubilities: CO2 at high pressures
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F. CONTACTS
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Inquiries about this software distribution should be directed to:
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e-mail: h2osoft@usgs.gov or dlpark@usgs.gov
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