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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.
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TABLE OF CONTENTS
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A. Distribution file
B. Documentation
C. Installing Windows COM versions
D. Downloading and unzipping the distribution file
E. Linux compiling, testing, and installing the IPhreeqc library
F. Windows compiling, testing, and installing the IPhreeqc library
G. Using the library
H. Contacts
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A. Distribution file
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The following distribution packages (containing the software,
compilation-related files, and an advection example in
C++, C, and Fortran) are available for Linux and Windows:
IPhreeqcCOM-@VERSION@-@REVISION@-win32.msi Windows
IPhreeqcCOM-@VERSION@-@REVISION@-x64.msi Windows
iphreeqc-@VERSION@-@REVISION@.zip Windows
iphreeqc-@VERSION@-@REVISION@.tar.gz Linux
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B. Documentation
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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.
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C. Installing Windows COM versions
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For 64-bit computers, download both 32- and 64-bit versions:
IPhreeqcCOM-@VERSION@-@REVISION@-win32.msi
IPhreeqcCOM-@VERSION@-@REVISION@-x64.msi
Double click on each .msi file and follow the instructions.
IPhreeqcCOM is installed and ready to use for 32- and 64-bit applications.
To test the COM, you can open the Excel file and run the "runphreeqc" macro
(view->macros):
C:\Program Files\USGS\IPhreeqcCOM 3.2.0-9755\examples\com\excel\runphreeqc.xls
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D. Downloading and unzipping the distribution file
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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
./examples Advection example for Fortran, C++, and C
./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.
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E. Linux compiling, testing, and installing the IPhreeqc library
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In general, to compile the software, you will need:
(a) a C++ compiler, and
(b) knowledge of configure, 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.
E.1. Change directory to the directory that was extracted from the tar file.
cd iphreeqc-@VERSION@-@REVISION@
E.2. Make a directory, for example, build.
mkdir build
E.3. Change directory to build.
cd build
E.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.
--enable-fortran-test=yes specifies that you do 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]
E.5. Compile the IPhreeqc library
make [-j 4]
Optionally, use -j n--where n is the number of compilations make runs in parallel.
E.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-test configure option).
make check
E.7. Install the IPhreeqc library. By default the program is installed in /usr/local/bin
and /usr/local/share/doc/iphreeqc. 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
/usr/local/include/IPhreeqcCallbacks.h
/usr/local/include/Keywords.h
/usr/local/include/PHRQ_io.h
Documentation:
/usr/local/share/doc/iphreeqc/IPhreeqc.pdf
/usr/local/share/doc/iphreeqc/html/index.html (IPhreeqc API)
/usr/local/share/doc/iphreeqc/RELEASE (Release notes)
/usr/local/share/doc/iphreeqc/README (this readme file)
/usr/local/share/doc/iphreeqc/NOTICE (User rights notice)
Databases:
/usr/local/share/doc/iphreeqc/database
Amm.dat
ColdChem.dat
core10.dat
frezchem.dat
iso.dat
llnl.dat
minteq.dat
minteq.v4.dat
phreeqc.dat
pitzer.dat
sit.dat
stimela.dat
Tipping_Hurley.dat
wateq4f.dat
Advection example for Fortran, C++, and C:
/usr/local/share/doc/iphreeqc/examples
Fortran interface
/usr/local/share/doc/iphreeqc/src/IPhreeqc_interface.F90
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F. 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.
F.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.
F.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.
(3) BUILD_CLR_LIBS--If checked, will compile the CLR version of the
library. This will enable the charting capabilities of
phreeqc through the use of Zedgraph. This option is only
available if BUILD_SHARED_LIBS is checked.
(4) IPHREEQC_ENABLE_MODULE--Uncheck if you want to
use the deprecated (old-style) include file (IPhreeqc.f90.inc
or IPhreeqc.f.inc) to define IPhreeqc in Fortran files.
Leave checked to use IPhreeqc as a Fortran module (USE IPhreeqc),
which is recommended. Leave checked if not using Fortran.
(5) 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.
F.3. Compile and install IPhreeqc
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:
IPhreeqc.lib (Release)
IPhreeqcd.lib (Debug)
IPhreeqcmsr.lib (MinSizeRel)
IPhreeqcrwdi.lib (RelWithDebInfo)
IPhreeqc.dll (Release Shared)
IPhreeqcd.dll (Debug Shared)
IPhreeqcmsr.dll (MinSizeRel Shared)
IPhreeqcrwdi.dll (RelWithDebInfo Shared)
ZedGraph.dll (CLR/Charting)
Install\include files:
C++ and C headers for user's code:
IPhreeqc.hpp (C++ header)
IPhreeqc.h (C header)
Optionally, you may need one or more of the following:
Var.h
IPhreeqcCallbacks.h
Keywords.h
PHRQ_io.h
Install\src files:
To use IPhreeqc in Fortran:
IPhreeqc_interface.F90
Install\Database files:
Amm.dat
frezchem.dat
iso.dat
llnl.dat
minteq.dat
minteq.v4.dat
phreeqc.dat
pitzer.dat
sit.dat
stimela.dat
wateq4f.dat
Install\doc files:
IPhreeqc.pdf IPhreeqc journal article
html\index.html IPhreeqc API documentation
NOTICE User rights notice
README This readme file
RELEASE Release notes
Install\examples files:
c, cpp, fortran Advection example
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.
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G. Using the library
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G.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.
G.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.
G.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.
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H. CONTACTS
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Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov
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