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Need to use i686 and x86_64 in tar file names.

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Still need to work on description of "source".

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7326 1feff8c3-07ed-0310-ac33-dd36852eb9cd
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David L Parkhurst 2013-01-15 00:41:36 +00:00
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README.Linux.txt
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@ -5,30 +5,36 @@ README.TXT
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
This file describes the batch version of PHREEQC version 3 for Linux. No
graphical user interface exits for Linux.
This file describes batch versions of PHREEQC version 3 for Linux. The "Linux"
versions (32- and 64-bit) contain an executable file compiled for Linux,
whereas the "source" version has no executable file, but has the files
necessary to configure and compile PHREEQC on any Unix operating system.
(For Windows, a graphical user interface, PhreeqcI, is available at
Instructions for installing, executing, and testing on Windows 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.)
PHREEQC - Version @VERSION@ @VER_DATE@
Instructions for installing, executing, and testing are provided below. After
installation, see the phreeqc.txt file in the doc directory of the PHREEQC
installation for summary information on PHREEQC and the RELEASE.TXT file for
new features and bug fixes.
TABLE OF CONTENTS
A. Distribution files
B. Documentation
C. Extracting files
D. Compiling and installing PHREEQC
E. Running the batch program
F. Testing and example problems
G. Contacts
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
@ -36,9 +42,11 @@ 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@.Linux.tar.gz--Compiled with @GCC_VER@
phreeqc-@VERSION@-@REVISION@.Linux.tar.gz --Compiled with @GCC_VER@
kernel @KERNEL_VER@
phreeqc-@VERSION@-@REVISION@.source.tar.gz--Source code, but no executable
phreeqc-@VERSION@-@REVISION@.Linux.x84_64.tar.gz--Compiled with @GCC_VER_64@
kernel @KERNEL_VER_64@
phreeqc-@VERSION@-@REVISION@.source.tar.gz --Source code, but no executable
B. Documentation
@ -81,68 +89,197 @@ Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user interface
FS-031-02, 2 p.
C. Extracting files
C. Linux versions (with executable)
Compressed tar files are used to distribute the source code and versions of the
software compiled for Linux operating systems. All of the files needed to
install and test PHREEQC are contained in the file
phreeqc-@VERSION@-@REVISION@.Linux.tar.gz. A Linux executable file is included,
which is compiled with @GCC_VER@ kernel @KERNEL_VER@. If you want to compile
the program for another operating system, the file
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@.source.tar.gz contains all of the files needed to
compile and install PHREEQC. For all tar files, 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.
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
---------------------------------------- -----------------------------------
gunzip phreeqc-@VERSION@-@REVISION@.Linux.tar.gz Uncompress the
tar.gz file.
Steps in extracting files Explanation
---------------------------------------- -----------------------------------
For the 32-bit version:
tar -xvpof phreeqc-@VERSION@-@REVISION@.Linux.tar Extract files from the tar
file.
gunzip phreeqc-@VERSION@-@REVISION@.Linux.tar.gz
Uncompress the tar.gz file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.Linux.tar
Extract files from the tar file.
or, for the 64-bit version:
gunzip phreeqc-@VERSION@-@REVISION@.Linux.x86_64.tar.gz
Uncompress the tar.gz file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.Linux.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@ files NOTICE.TXT, RELEASE.TXT, and this README.Linux.txt
`--bin compiled executable, template for execution script
`--database database files required during execution
`--doc documentation files
`--examples examples from user's guide--used in verification tests
`--src Makefile and source code
`--test scripts to run verification tests
phreeqc-@VERSION@-@REVISION@ Files NOTICE.TXT, RELEASE.TXT, and this README.Linux.txt
`--bin Compiled executable
`--database Database files (one is required for execution)
`--doc Documentation files
`--examples Examples from user's guide--used in verification tests
`--src Source code
`--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 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@/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@.source.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
Notes: (a) A compiled executable is not included in the source
distribution.
(b) It is recommended that no user files be kept in the PHREEQC
directory structure. If you plan to put files in the PHREEQC
directory structure, do so only by creating subdirectories.
directory structure.
D.2. Compiling, testing, installing
D. Compiling and installing 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:
If you can use the executable in the Linux.tar.gz version of the distribution
of the software, skip to the Installing section below.
If a compiled version of the software is not available for your computer or you
want to build the executable yourself, follow the instructions in this section.
The source distribution is provided for those users who want the source code.
Little or no support is provided for users generating their own versions of the
software. In general, to compile a new version of the software, you will need:
(a) a C compiler, and
(a) a C++ compiler, and
(b) a minimal level of knowledge of configure, Make, the compiler, and
the Linux operating system.
As provided in the source distribution, a Makefile can be generated by
configure, and the Makefile can be used to compile the software.
A Makefile can be generated by configure, and the Makefile can be used to
compile, test, and install the software.
To compile PHREEQC, do the following:
To compile, test, and install PHREEQC, do the following:
1. Change directory to the directory that was extracted from the tar file.
@ -168,19 +305,48 @@ To compile PHREEQC, do the following:
make
6. Check that compiled version runs the test cases
6. Check that compiled version runs the test cases. Check may take several
minutes.
make check
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, /usr/local/lib, etc. You can specify an sstallation prefix
other than "/usr/local" by using the"--prefix", --prefix=$HOME for
example.
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/databases
(b) $HOME/share/doc/phreeqc/databases
Example input files:
(a) /usr/local/share/doc/phreeqc/examples
(b) $HOME/share/doc/phreeqc/examples
E. Running the program
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.
@ -207,10 +373,9 @@ program can be executed with any of the commands below.
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. The executable is
normally phreeqc-@VERSION@/bin/phreeqcpp. In addition the default database
file, phreeqc.dat, may need to be in the current directory. Phreeqc.dat is
installed in phreeqc-@VERSION@/database/phreeqc.dat.
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 installed in phreeqc-@VERSION@/database/phreeqc.dat.
The shell variable PHREEQC_DATABASE can be used to specify the default
database. In the C shell, this variable can be set with the command:
@ -228,57 +393,10 @@ in the script in the installation directory to
phreeqc-@VERSION@/database/phreeqc.dat. It is possible to specify a different
default database by editing the script.
F. Testing and example problems
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.
On Linux, you should copy the directory phreeqc-@VERSION@/test to an area where
you have write access; the examples can be run from the copied directory.
Change to the directory that you copied 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 are compared to the expected results
(found in the examples directory). See the file check.log; if all goes well,
there should be few or no differences. Differences in path names and run times
are insignificant.
To clean up after the tests, type the command:
./clean.sh
Notes: The output data files for phreeqc-@VERSION@.@REVISION@.source.tar.gz
were created on a Linux system. You may notice slight numeric
differences in the results. These are generally due to different round-
off algorithms and the different architecture of the central processing
unit chip. Slight differences in output formats may occur on other
computers, particularly for the value 0.0.
Problem 9 generates a warning message that indicates negative
concentrations were generated in a kinetic run. The numerical method
automatically reduces the step size until negative concentrations are
eliminated and an accurate kinetic integration is obtained.
Problems 11, 12, 13, and 15 generate warning messages. The messages
simply indicate a shorthand method for defining cell lengths and cell
dispersivities was used.
========================================
E. Description of test cases
The tests are described in the table below, where 'test' corresponds
to the example number in the PHREEQC manual.
@ -338,7 +456,7 @@ test description of test and files
22 Modeling gas solubilities: CO2 at high pressures
G. CONTACTS
F. CONTACTS
Inquiries about this software distribution should be directed to:

2
README.Win.txt
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@ -165,7 +165,7 @@ 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,
(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