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README.Phreeqc.TXT
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@ -5,14 +5,12 @@ README.TXT
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.
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
@ -24,19 +22,24 @@ Notepad++ interface is available at http://www.hydrochemistry.eu/downl.html.)
A. Distribution files
B. Documentation
C. Extracting files (for Unix compilation)
D. Compiling, testing, installing
E. Running PHREEQC
C. Installing the Windows executable version
D. Compiling, testing, installing for Linux
E. Compiling, testing, installing for Windows
F. Running PHREEQC
F. Description of test cases
G. Contacts
-----------------------------------------------------------------------------------
A. Distribution file
A. Distribution files
-----------------------------------------------------------------------------------
The following distribution package (containing the source code, configure
files, examples, and documentation) is available for Linux systems:
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
-----------------------------------------------------------------------------------
@ -81,44 +84,137 @@ Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user interface
FS-031-02, 2 p.
-----------------------------------------------------------------------------------
C. Extracting files (for Unix compilation)
C. Installing the batch version of PHREEQC with executable
-----------------------------------------------------------------------------------
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.
Note: the person installing the software generally must have administrator
rights.
Follow the steps below to extract the files from a distribution tar
file.
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.
Steps in extracting files Explanation
---------------------------------------- -----------------------------------
gunzip phreeqc-@VERSION@-@REVISION@.source.tar.gz Uncompress the tar.gz file.
-----------------------------------------------------------------------------------
D. Compiling and installing the Windows batch version of PHREEQC without executable
-----------------------------------------------------------------------------------
tar -xvpof phreeqc-@VERSION@-@REVISION@.source.tar Extract files from the tar file.
In general, to compile the IPhreeqc library, you will need:
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.
(a) CMake (build process manager)
(b) a C++ compiler,
(c) familiarity with the compiler and the Windows operating system.
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
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
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.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:/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) 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 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:
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
RELEASE Release notes
README this readme file
NOTICE User rights notice
phreeqc3.chm Latest PHREEQC documentation
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 or the PhreeqcI MSI,
or through the use of the Visual Studio Tool gacutil.
-----------------------------------------------------------------------------------
D. Compiling, testing, installing
E. Compiling and installing the Linux batch version of PHREEQC
-----------------------------------------------------------------------------------
No support beyond this README file is provided for users compiling their own
@ -131,61 +227,85 @@ versions of the software. In general, to compile the software, you will need:
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:
E.1. Extracting the files
D.1. Change directory to the directory that was extracted from the tar file.
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@
D.2. Make a directory, for example, Release.
E.3. Make a directory, for example, Release.
mkdir Release
D.3. Change directory to Release.
E.4. Change directory to Release.
cd Release
D.4. Run configure
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.
The most common option: --prefix=dir specifies the directory for installation of
the library. Default is /usr/local, $HOME would install to your home directory.
Run configure as follows:
../configure [options]
D.5. Compile the program
E.6. Compile the program
make [-j 4]
Optionally, use -j n--where n is the number of compilations make runs in parallel.
D.6. Check that compiled version runs the test cases.
E.7. Check that compiled version runs the test cases.
Check may take several minutes.
make check
Results of running the test cases are stored in the directory
Results of running the test cases are stored in the directory Release/test
Release/test
E.8. Install the program.
D.7. Install the program.
By default the program is installed in /usr/local/bin
and /usr/local/share/doc/phreeqc. You can specify an installation prefix
other than "/usr/local" by using the prefix option, prefix=$HOME for
example.
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.
installation directory, /usr/local by default, or the value given by the --prefix
option to configure.
Executable:
install/bin/phreeqc
@ -221,11 +341,11 @@ D.7. Install the program.
Input files for 22 examples documented in the Phreeqc 3 manual
-----------------------------------------------------------------------------------
E. Running PHREEQC
F. 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.
program can be executed from a command line with any of the commands below.
command to execute PHREEQC explanation
----------------------------- -----------------------------------------
@ -248,16 +368,16 @@ program can be executed with any of the commands below.
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.
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.
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
database.
For Linux:
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
@ -271,6 +391,9 @@ 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.
For Windows:
???
-----------------------------------------------------------------------------------
F. Description of test cases
-----------------------------------------------------------------------------------