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Working on phreeqc readme.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9733 1feff8c3-07ed-0310-ac33-dd36852eb9cd
This commit is contained in:
David L Parkhurst
parent
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commit
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@ -5,14 +5,12 @@ README.TXT
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A program for speciation, batch-reaction, one-dimensional
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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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transport, and inverse geochemical calculations
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This file describes compilation of the batch version of PHREEQC version 3 for
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This file describes three batch versions of PHREEQC for Windows and Linux: (1) A
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Linux. No executable file is included. The distribution contains all files
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Windows version with a compiled executable, (2) A Windows version that has source
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necessary to configure and compile PHREEQC on any Unix operating system.
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code that can be compiled with Visual Studio solutions that are generated by CMake,
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and (3) A Linux version with source code that can be compiled by a Makefile generated
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Instructions for configuring, compiling, installing, executing, and testing
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by configure. For Linux, there is no version with an executable, and compilation is
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on Linux operating systems are provided below. After installation, see the
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required.
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root or doc directory of the PHREEQC installation for summary information on
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PHREEQC in phreeqc.txt and the new features and bug fixes in RELEASE.TXT.
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No graphical user interface exists for Linux. (For Windows, a graphical user
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No graphical user interface exists for Linux. (For Windows, a graphical user
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interface, PhreeqcI, is available at
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interface, PhreeqcI, is available at
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@ -24,19 +22,24 @@ Notepad++ interface is available at http://www.hydrochemistry.eu/downl.html.)
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A. Distribution files
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A. Distribution files
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B. Documentation
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B. Documentation
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C. Extracting files (for Unix compilation)
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C. Installing the Windows executable version
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D. Compiling, testing, installing
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E. Running PHREEQC
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D. Compiling, testing, installing for Linux
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E. Compiling, testing, installing for Windows
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F. Running PHREEQC
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F. Description of test cases
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F. Description of test cases
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G. Contacts
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G. Contacts
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-----------------------------------------------------------------------------------
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-----------------------------------------------------------------------------------
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A. Distribution file
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A. Distribution files
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-----------------------------------------------------------------------------------
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-----------------------------------------------------------------------------------
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The following distribution package (containing the source code, configure
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The following distribution packages of the batch version of PHREEQC are available
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files, examples, and documentation) is available for Linux systems:
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for Windows and Linux:
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phreeqc-@VERSION@-@REVISION@.msi 64-bit batch version with executable
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compiled by using Microsoft Visual C++ 2005
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phreeqc-@VERSION@-@REVISION@.zip For compilation on Windows
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phreeqc-@VERSION@-@REVISION@.tar.gz For compilation on Linux
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phreeqc-@VERSION@-@REVISION@.tar.gz For compilation on Linux
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-----------------------------------------------------------------------------------
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-----------------------------------------------------------------------------------
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@ -81,44 +84,137 @@ Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user interface
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FS-031-02, 2 p.
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FS-031-02, 2 p.
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-----------------------------------------------------------------------------------
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-----------------------------------------------------------------------------------
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C. Extracting files (for Unix compilation)
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C. Installing the batch version of PHREEQC with executable
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-----------------------------------------------------------------------------------
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-----------------------------------------------------------------------------------
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A compressed tar file, phreeqc-@VERSION@-@REVISION@.tar.gz, is used to
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Note: the person installing the software generally must have administrator
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distribute the source code and other files necessary to compile, test, install,
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rights.
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and run PHREEQC on Unix operating systems.
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Follow the steps below to extract the files from a distribution tar
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To install the batch version, double-click phreeqc-@VERSION@-@REVISION@.msi to
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file.
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execute the installation program and follow the directions on the screen. The batch
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version is completely independent from the GUI version.
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-----------------------------------------------------------------------------------
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D. Compiling and installing the Windows batch version of PHREEQC without executable
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-----------------------------------------------------------------------------------
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Steps in extracting files Explanation
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In general, to compile the IPhreeqc library, you will need:
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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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(a) CMake (build process manager)
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(b) a C++ compiler,
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(c) familiarity with the compiler and the Windows operating system.
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D.1. Download and install CMake
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The directory phreeqc-@VERSION@-@REVISION@ is created when the files are
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CMake can be downloaded from http://www.cmake.org/. If you download the
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extracted; if this directory already exists, you may want to delete or rename
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executable, CMake is installed when you execute it.
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it before extracting the files.
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D.2. Unzip the distribution file phreeqc-@VERSION@-@REVISION@.zip
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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 it
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before extracting the files.
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The following directory structure is created (the contents of each directory
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The following directory structure is created (the contents of each directory are
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are shown to the right):
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shown to the right):
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phreeqc-@VERSION@-@REVISION@ Files related to configure
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phreeqc-@VERSION@-@REVISION@ Files related to CMake
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`--config More configure files
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`--database Database files required during execution
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`--database Database files required during execution
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`--doc Documentation files
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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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`--examples Examples from user's guide--used in verification tests
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`--src Source code
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`--src Source code
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`--test Files used to test the compilation
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`--test Files used to test the compilation
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D.3. Generate a Visual Studio solution
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CMake has many options other than Visual Studio, but here we assume that you are
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using some version of Visual Studio. On the first use of CMake, it may be
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necessary to close all Visual Studio instances.
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Open CMake.
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Fill in the top two lines:
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Where is the source code:
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The top level directory (ie c:/iphreeqc-@VERSION@-@REVISION@).
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Where to build the binaries:
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A new directory. It is suggested that the name of the directory include
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the characteristics of the library that is built, including the VS
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version, 32/64 bit, dll/lib. for example, vs2012_64_dll.
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Click Configure.
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From the pulldown menu select the 64-bit version for your Visual Studio.
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Normally, the default radio button should be sufficient. Click Finish.
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Options in the top panel:
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(1) CMAKE_INSTALL_PREFIX--Sets the the install directory where the
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library and header files will be saved. It is suggested that
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an INSTALL directory be defined inside the directory chosen
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for the binaries.
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Click Configure until the screen is not red. If the screen remains red, you will
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have to deal with the CMake error messages.
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Click Generate.
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You should now have a Visual Studio solution file (.sln) in the directory chosen
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for the binaries (second line of CMake screen). At any point, you can delete the
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contents of the directory and start over. You can make solutions for different
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Visual Studios, or different options in other directories.
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D.4. Compile and install PHREEQC
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Open the Visual Studio solution in the build directory defined in CMake.
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The default configuration is "Debug". If you want a release libraries
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(or dlls) and examples, change the configuration to "Release".
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Build ALL_BUILD.
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IPhreeqc is compiled.
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Build RUN_TESTS. Programs that test IPhreeqc are compiled and run, and optionally
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(CMake IPHREEQC_FORTRAN_TESTING option) the Fortran test project.
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Build INSTALL.
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The libraries, header files, Fortran module source files, PHREEQC database
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files, and documentation are installed in the install directory selected in
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CMake.
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Install\library directory (lib or dll) may include:
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Notes: (a) A compiled executable is not included in the source
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Install\Database files:
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distribution.
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Amm.dat
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(b) It is recommended that no user files be kept in the PHREEQC
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frezchem.dat
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directory structure.
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iso.dat
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llnl.dat
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-----------------------------------------------------------------------------------
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minteq.dat
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D. Compiling, testing, installing
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minteq.v4.dat
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phreeqc.dat
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pitzer.dat
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sit.dat
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wateq4f.dat
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Install\doc files:
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Phreeqc_3_2013_manual.pdf Manual for PHREEQC version 3
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Phreeqc_2_1999_manual.pdf Manual for PHREEQC version 2
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phreeqc.txt Short explanation for PHREEQC
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RELEASE Release notes
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README this readme file
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NOTICE User rights notice
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phreeqc3.chm Latest PHREEQC documentation
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Install\examples files:
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Input files for the 22 examples described in the version 3 manual
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Note: In order to use the CLR version (Charting) the Zedgraph.dll file
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must be registered either by installing the Phreeqc or the PhreeqcI MSI,
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or through the use of the Visual Studio Tool gacutil.
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-----------------------------------------------------------------------------------
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E. Compiling and installing the Linux batch version of PHREEQC
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-----------------------------------------------------------------------------------
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-----------------------------------------------------------------------------------
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No support beyond this README file is provided for users compiling their own
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No support beyond this README file is provided for users compiling their own
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@ -131,74 +227,98 @@ versions of the software. In general, to compile the software, you will need:
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A Makefile can be generated by configure, and the Makefile can be used to
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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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compile, test, and install the software.
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To compile, test, and install PHREEQC, do the following:
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E.1. Extracting the files
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D.1. Change directory to the directory that was extracted from the tar file.
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Follow the steps below to extract the files from a distribution tar file.
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cd phreeqc-@VERSION@-@REVISION@
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Steps in extracting files Explanation
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---------------------------------------- -----------------------------------
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D.2. Make a directory, for example, Release.
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gunzip phreeqc-@VERSION@-@REVISION@.source.tar.gz Uncompress the tar.gz file.
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mkdir Release
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tar -xvpof phreeqc-@VERSION@-@REVISION@.source.tar Extract files from the tar file.
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D.3. Change directory to Release.
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cd Release
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D.4. Run configure
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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 it
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Many of the options for configure can be seen by typing:
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before extracting the files.
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../configure --help
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The following directory structure is created (the contents of each directory are
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shown to the right):
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The most common option:
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--prefix=dir specifies the directory for installation of the
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phreeqc-@VERSION@-@REVISION@ Files related to configure
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library. Default is /usr/local, $HOME would install
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`--config More configure files
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to your home directory.
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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 distribution.
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Run configure as follows:
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(b) It is recommended that no user files be kept in the PHREEQC directory
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structure.
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../configure [options]
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D.5. Compile the program
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E.2. Change directory to the directory that was extracted from the tar file.
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cd phreeqc-@VERSION@-@REVISION@
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E.3. Make a directory, for example, Release.
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mkdir Release
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E.4. Change directory to Release.
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cd Release
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E.5. Run 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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The most common option: --prefix=dir specifies the directory for installation of
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the library. Default is /usr/local, $HOME would install to your home directory.
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Run configure as follows:
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../configure [options]
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E.6. Compile the program
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make [-j 4]
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make [-j 4]
|
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Optionally, use -j n--where n is the number of compilations make runs in parallel.
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Optionally, use -j n--where n is the number of compilations make runs in parallel.
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D.6. Check that compiled version runs the test cases.
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E.7. Check that compiled version runs the test cases.
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Check may take several minutes.
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Check may take several minutes.
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make check
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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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Results of running the test cases are stored in the directory Release/test
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Release/test
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D.7. Install the program.
|
E.8. Install the program.
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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
|
By default the program is installed in /usr/local/bin and
|
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other than "/usr/local" by using the prefix option, prefix=$HOME for
|
/usr/local/share/doc/phreeqc. You can specify an installation prefix other than
|
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example.
|
"/usr/local" by using the prefix option, prefix=$HOME for example.
|
||||||
|
|
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make install
|
make install
|
||||||
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|
||||||
The locations of various files are given below, where "install" is the
|
The locations of various files are given below, where "install" is the
|
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installation directory, /usr/local by default, or the value given
|
installation directory, /usr/local by default, or the value given by the --prefix
|
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by the --prefix option to configure.
|
option to configure.
|
||||||
|
|
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Executable:
|
Executable:
|
||||||
install/bin/phreeqc
|
install/bin/phreeqc
|
||||||
|
|
||||||
Documentation:
|
Documentation:
|
||||||
|
|
||||||
install/share/doc/phreeqc
|
install/share/doc/phreeqc
|
||||||
Phreeqc_3_2013_manual.pdf Manual for Phreeqc version 3
|
Phreeqc_3_2013_manual.pdf Manual for Phreeqc version 3
|
||||||
Phreeqc_2_1999_manual.pdf Manual for Phreeqc version 2
|
Phreeqc_2_1999_manual.pdf Manual for Phreeqc version 2
|
||||||
phreeqc.txt Short explanation for Phreeqc
|
phreeqc.txt Short explanation for Phreeqc
|
||||||
RELEASE Release notes
|
RELEASE Release notes
|
||||||
README this readme file
|
README this readme file
|
||||||
NOTICE User rights notice
|
NOTICE User rights notice
|
||||||
???phreeqc3.chm
|
???phreeqc3.chm
|
||||||
|
|
||||||
Databases:
|
Databases:
|
||||||
@ -221,11 +341,11 @@ D.7. Install the program.
|
|||||||
Input files for 22 examples documented in the Phreeqc 3 manual
|
Input files for 22 examples documented in the Phreeqc 3 manual
|
||||||
|
|
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-----------------------------------------------------------------------------------
|
-----------------------------------------------------------------------------------
|
||||||
E. Running PHREEQC
|
F. Running PHREEQC
|
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-----------------------------------------------------------------------------------
|
-----------------------------------------------------------------------------------
|
||||||
|
|
||||||
If PHREEQC has been installed in a directory included in the users' PATH, the
|
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
|
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
|
and screen output is directed to the
|
||||||
file screen_output.
|
file screen_output.
|
||||||
|
|
||||||
For Linux, if the "make install" command described above has not been
|
If phreeqc is not located in a directory in PATh, the executable may be copied to the
|
||||||
executed, the executable may be copied to the current directory. In addition
|
current directory. In addition the default database file, phreeqc.dat, or another
|
||||||
the default database file, phreeqc.dat, or another desired database may need
|
desired database may need to be in the current directory.
|
||||||
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
|
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:
|
is named /home/jdoe/local/project/mydata.dat) with the command:
|
||||||
|
|
||||||
setenv PHREEQC_DATABASE /home/jdoe/local/project/mydata.dat
|
setenv PHREEQC_DATABASE /home/jdoe/local/project/mydata.dat
|
||||||
@ -269,7 +389,10 @@ In the Bourne or Korn shell, this variable can be set with the command:
|
|||||||
The shell variable can be set permanently by including the appropriate command
|
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
|
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
|
$HOME/.profile. If this shell variable is not set, the default database is
|
||||||
assumed to be phreeqc.dat in the current directory.
|
assumed to be phreeqc.dat in the current directory.
|
||||||
|
|
||||||
|
For Windows:
|
||||||
|
???
|
||||||
|
|
||||||
-----------------------------------------------------------------------------------
|
-----------------------------------------------------------------------------------
|
||||||
F. Description of test cases
|
F. Description of test cases
|
||||||
|
|||||||
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Reference in New Issue
Block a user