mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-16 16:44:49 +01:00
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
This commit is contained in:
Scott R Charlton
parent
5e3b593729
commit
cd12e1bb0a
@ -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
|
|
||||||
|
|
||||||
Loading…
x
Reference in New Issue
Block a user