mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-16 00:28:23 +01:00
Updated README file for CMake
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9667 1feff8c3-07ed-0310-ac33-dd36852eb9cd
This commit is contained in:
Scott R Charlton
parent
94cb927c67
commit
dfde36d5d4
374
README
374
README
@ -1,27 +1,355 @@
|
||||
Building Static Libraries
|
||||
=========================
|
||||
./configure
|
||||
make LDFLAGS=-all-static check
|
||||
|
||||
This will attemp to link ALL libraries statically. To be successful all libraries must have .a files.
|
||||
|
||||
README.TXT
|
||||
|
||||
Building Static iphreeqc Library
|
||||
================================
|
||||
./configure
|
||||
make LDFLAGS=-static check
|
||||
|
||||
This will link the iphreeqc library statically. All required additional libraries may be linked to
|
||||
shared libraries.
|
||||
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
|
||||
|
||||
|
||||
Building shared and static iphreeqc Library (linking tests statically)
|
||||
======================================================================
|
||||
./configure
|
||||
make
|
||||
make LDFLAGS=-static check # static to iphreeqc
|
||||
or
|
||||
make LDFLAGS=-all-static check # completely static (if possible)
|
||||
-----------------------------------------------------------------------------------
|
||||
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++
|
||||
|
||||
This configuration will create both static and shared (if supported) iphreeqc libraries. But
|
||||
test programs (created during make check) will be statically linked to iphreeqc library
|
||||
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