From cd12e1bb0a2b595e6d5b11faaa7f20a473017543 Mon Sep 17 00:00:00 2001 From: Scott R Charlton Date: Tue, 19 May 2015 21:17:15 +0000 Subject: [PATCH] Move http://internalbrr.cr.usgs.gov/svn_GW/IPhreeqc/trunk/README.IPhreeqc.TXT to http://internalbrr.cr.usgs.gov/svn_GW/phreeqc3/trunk/doc/README.IPhreeqc.TXT git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9672 1feff8c3-07ed-0310-ac33-dd36852eb9cd --- README.IPhreeqc.TXT | 355 -------------------------------------------- 1 file changed, 355 deletions(-) delete mode 100644 README.IPhreeqc.TXT diff --git a/README.IPhreeqc.TXT b/README.IPhreeqc.TXT deleted file mode 100644 index 3f24a09f..00000000 --- a/README.IPhreeqc.TXT +++ /dev/null @@ -1,355 +0,0 @@ -README - - IPhreeqc--Modules Based on the Geochemical Model PHREEQC for Use - in Scripting and Programming Languages - -This file describes how to compile the IPhreeqc library and use -it in C++, C, and Fortran programs. The library may be compiled -after generating either a Visual Studio solution for Windows with -CMake or a Makefile for Linux with configure. All source and -compilation-related files are available at the following web site: - -http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html. - ------------------------------------------------------------------------------------ -TABLE OF CONTENTS ------------------------------------------------------------------------------------ - - A. Distribution file - B. Documentation - C. Downloading and unzipping the distribution file - D. Linux compiling, testing, and installing the IPhreeqc library - E. Windows compiling, testing, and installing the IPhreeqc library - F. Using the library - G. Contacts - ------------------------------------------------------------------------------------ -A. Distribution file ------------------------------------------------------------------------------------ - - The following distribution package (containing the software, - compilation-related files, and an advection example in - C++, C, and Fortran) is available for Linux and Windows: - - iphreeqc-@VERSION@-@REVISION@.tar.gz Linux - iphreeqc-@VERSION@-@REVISION@.zip Windows - - ------------------------------------------------------------------------------------ -B. Documentation ------------------------------------------------------------------------------------ - - Descriptions and examples of IPhreeqc methods for C++, C, and Fortran - are available in HTML format in the doc directory of the distribution. - - Charlton, S.R., and Parkhurst, D.L., 2011, Modules based on the geochemical model - PHREEQC for use in scripting and programming languages: Computers & Geosciences, - vol. 37, no. 10, p. 1653-1663. - - *The following two user's guides are available in electronic format. Portable - Document Format (PDF) files are included in the doc subdirectory of all - PHREEQC program distributions. - - Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples - for PHREEQC version 3--A computer program for speciation, batch-reaction, - one- dimensional transport, and inverse geochemical calculations: U.S. - Geological Survey Techniques and Methods, book 6, chap. A43, 497 p. - http://pubs.usgs.gov/tm/06/a43/. - - Parkhurst, D.L., and Appelo, C.A.J., 1999, User's guide to PHREEQC (Version - 2)-- A computer program for speciation, batch-reaction, one-dimensional - transport, and inverse geochemical calculations: U.S. Geological Survey - Water-Resources Investigations Report 99-4259, 312 p. - http://pubs.er.usgs.gov/publication/wri994259. - - *The following two reports document the theory and implementation of - isotopes in PHREEQC. Portable Document Format (PDF) of Thorstenson and - Parkhurst (2002) is included in the doc subdirectory of the PHREEQC program - distribution. - - Thorstenson, D.C., and Parkhurst, D.L., 2002, Calculation of individual isotope - equilibrium constants for implementation in geochemical models: U.S. - Geological Survey Water-Resources Investigations Report 02-4172, 129 p. - http://pubs.er.usgs.gov/publication/wri024172. - - Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope - equilibrium constants for geochemical reactions: Geochimica et Cosmochimica - Acta, v. 68, no. 11, p. 2449-2465. - - *Brief description of the program PhreeqcI. - - Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user interface - to the geochemical model PHREEQC: U.S. Geological Survey Fact Sheet - FS-031-02, 2 p. - - ------------------------------------------------------------------------------------ -C. Downloading and unzipping the distribution file ------------------------------------------------------------------------------------ - - Follow the steps using gunzip, 7zip, or other compression program that can unzip a tar.gz/zip file: - - Steps in extracting files Explanation - ---------------------------------------- ----------------------------------- - gunzip iphreeqc-@VERSION@-@REVISION@.tar.gz Uncompress the tar.gz file. - tar -xvpof iphreeqc-@VERSION@-@REVISION@.tar Extract files from the tar file. - - The directory iphreeqc-@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): - - iphreeqc-@VERSION@-@REVISION@ Source code and configure/CMake files - ./config More configure files - ./database Database files for PHREEQC - ./doc Documentation files - ./src Source code for IPhreeqc - ./tests Tests that check that C++, C, and Fortran(optional) - are able to compile, link and run. - - Note: A compiled executable is not included in the distribution. - ------------------------------------------------------------------------------------ -D. Linux compiling, testing, and installing the IPhreeqc library ------------------------------------------------------------------------------------ - - In general, to compile the software, you will need: - - (a) a C++ compiler, and - (b) a minimal level of knowledge of configure or CMake, Make, - the compiler, and the Linux operating system. - - A Makefile is generated by configure, and the Makefile is used to - compile, test, and install the software. - - D.1. Change directory to the directory that was extracted from the tar file. - - cd iphreeqc-@VERSION@-@REVISION@ - - D.2. Make a directory, for example, build. - - mkdir build - - D.3. Change directory to build. - - cd build - - D.4. Run configure - - Many of the options for configure can be seen by typing: - - ../configure --help - - Most common options: - --prefix=dir--specifies the directory for installation of the - library. Default is /usr/local, $HOME would install - to your home directory. - --disable-fortran--specifies that you do not want to include the Fortran test - files during "make check", which compiles, links, and runs programs that - use IPhreeqc. - - Run configure as follows: - - ../configure [options] - - D.5. Compile the IPhreeqc library - - make [-j 4] - - Optionally, use -j n--where n is the number of compilations make runs in parallel. - - D.6. Compile and run the test cases. The files in the directory tests are compiled and linked - to the IPhreeqc library. The Fortran files are optionally included (--enable-fortran - configure option). - - make check - - D.7. Install the IPhreeqc library. By default the program is installed in /usr/local/bin - and /usr/local/share/doc/iphreeqc-@VERSION@-@REVISION@. Alternatively, the directory defined - by --prefix in the configure command is used. - - make install - - The locations of various files are given for default installation (no - --prefix definition). - - Libraries: - /usr/local/lib/libiphreeqc.a (Static library) - /usr/local/lib/libiphreeqc.so (Shared object library) - /usr/local/lib/libiphreeqc.la (libtool library file) - - Include files: - C++ and C headers for user's code: - /usr/local/include/IPhreeqc.h (C header) - /usr/local/include/IPhreeqc.hpp (C++ header) - - Optionally, user's code may need one or more of the following: - /usr/local/include/Var.h (IPhreeqc VAR structure) - /usr/local/include/IPhreeqcCallbacks.h (IPhreeqc callbacks) - - Documentation (PDFs, IPhreeqc API(html)): - /usr/local/share/doc/iphreeqc-@VERSION@-@REVISION@ - - Databases: - /usr/local/share/doc/iphreeqc-@VERSION@-@REVISION@/database - - Fortran interfaces - /usr/local/share/doc/iphreeqc-@VERSION@-@REVISION@/src - ------------------------------------------------------------------------------------ -E. Windows compiling, testing, and installing the IPhreeqc library ------------------------------------------------------------------------------------ - - In general, to compile the IPhreeqc library, you will need: - - (a) CMake (build process manager) - (b) a C++ compiler, - (c) familiarity with the compiler and the Windows operating system. - - E.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. - - E.2 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) BUILD_SHARED_LIBS--If checked, .dll files will be - created. If not checked, a .lib file will be created. - Note that .dll files have a .lib file associated with them, - but it is not the same .lib generated when - BUILD_SHARED_LIBS is not checked. - (2) 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. - (4) IPHREEQC_FORTRAN_TESTING--Sets whether the test calculations - (tests directory) will include Fortran test files. A Fortran - compiler is required. - - 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. - - E.3. Compile and install IPhreeqc - - Open the Visual Studio solution in the build directory defined in CMake. - - 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. - - Libraries that can be installed: - IPhreeqc.lib - IPhreeqcd.lib - IPhreeqc.dll - IPhreeqcd.dll - - Include files: - C++ and C headers for user's code: - IPhreeqc.hpp (C++ header) - IPhreeqc.h (C header) - - Optionally, may need one or more of the following: - Var.h (IPhreeqc VAR structure) - IPhreeqcCallbacks.h (IPhreeqc callbacks) - - Src files: - To use IPhreeqc in Fortran: - IPhreeqc_interface.F90 - - Database files: - Amm.dat - frezchem.dat - iso.dat - llnl.dat - minteq.dat - minteq.v4.dat - phreeqc.dat - pitzer.dat - sit.dat - wateq4f.dat - - Documentation files: - html/index.html (IPhreeqc API documentation) - ------------------------------------------------------------------------------------ -F. Using the library ------------------------------------------------------------------------------------ - - F.1. C++ - - In C++, you will include the IPhreeqc.hpp header file and - create an IPhreeqc instance: - - #include "IPhreeqc.hpp" - IPhreeqc iphreeqc; - - or - - IPhreeqc *iphreeqc = new IPhreeqc(); - - You will need to link to the IPhreeqc.lib that you installed. - - F.2. C - - In C, you will include the C interface header, IPhreeqc.h, and - create an IPhreeqc instance. - - #include "IPhreeqc.h" - int id; - id = CreateIPhreeqc(); - - You will need to link to the IPhreeqc.lib that you installed. - - F.3. Fortran - - In Fortran, you will need to include the source file IPhreeqc_interface.F90 - in your project files. This file defines the IPhreeqc Fortran module. - - USE IPhreeqc - INTEGER(KIND=4) id - id = CreateIPhreeqc() - - You will need to link to the IPhreeqc.lib that you installed. - ------------------------------------------------------------------------------------ -G. CONTACTS ------------------------------------------------------------------------------------ - -Inquiries about this software distribution should be directed to: - -e-mail: h2osoft@usgs.gov or dlpark@usgs.gov -