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README.Win.txt
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@ -5,21 +5,21 @@ README.TXT
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
NOTE: This file describes the batch version of PHREEQC version 3 for Windows
operating systems. Also available for Windows operating systems is a graphical
user interface (GUI), PhreeqcI. This GUI can be downloaded from
NOTE: This file describes installing the GUI PhreeqcI and installing, compiling,
and testing the batch version of PHREEQC version 3 on Windows operating systems.
The GUI and batch versioin can be downloaded from
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html. PhreeqcI has
internal documentation for all PHREEQC data input and is a complete interface
to PHREEQC. Alternatively, a Notepad++ interface is available at
http://www.hydrochemistry.eu/downl.html.
screens for most PHREEQC keywords and allows input files that use any of PHREEQC
version 3 capabilities. Alternatively, a Notepad++ interface for PHREEQC version
3 is available at http://www.hydrochemistry.eu/downl.html.
PHREEQC - Version @VERSION@ @VER_DATE@
Instructions for installation, execution, and testing on Windows operating
Instructions for installating, executing, and testing on Windows operating
systems are provided below. After installation, see the phreeqc.txt file in the
doc directory of the PHREEQC installation for summary information on PHREEQC
and the RELEASE.TXT file for new features and bug fixes.
and the RELEASE.TXT file in the root directory for new features and bug fixes.
TABLE OF CONTENTS
@ -28,20 +28,22 @@ and the RELEASE.TXT file for new features and bug fixes.
B. Documentation
C. Installing and running the GUI PhreeqcI
D. Installing the batch version of PHREEQC
E. Compilation (optional)
F. Running the batch program
E. Compiling the batch version (optional)
F. Running the batch version
G. Testing and examples
H. Contacts
A. Distribution files
The following distribution files (containing the software, test data sets,
and information files) are currently available.
The following distribution files (containing the software, test data sets, and
information files) are available at
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.
phreeqci-@VERSION@.@REVISION@.msi--GUI compiled by using Microsoft Visual C++
2005
phreeqci-@VERSION@-@REVISION@.msi--GUI compiled by using Microsoft Visual C++
2005
phreeqc-@VERSION@.@REVISION@.msi--Batch version compiled by using Microsoft
phreeqc-@VERSION@-@REVISION@.msi--Batch version compiled by using Microsoft
Visual C++ 2005, includes source code
B. Documentation
@ -84,26 +86,29 @@ 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.
C. Installing and running of the GUI PhreeqcI
Note that if the software is to be installed on a server system,
the person installing the software generally must have administrator
rights.
To install the GUI, double-click phreeqci-@VERSION@.@REVISION@.msi to execute
To install the GUI, double-click phreeqci-@VERSION@-@REVISION@.msi to execute
the installation program and follow the directions on the screen. The GUI is
completely independent from the batch version.
To execute the GUI, access the program through the start menus of Windows.
By default, the software is installed in the directory C:\Program
Files\USGS\phreeqci-@VERSION@. This is the recommended installation directory,
but you may use other directories or disk drives.
Files\USGS\phreeqci-@VERSION@.@REVISION@ for 32-bit operating systems or
C:\Program Files (x86)\USGS\phreeqci-@VERSION@.@REVISION@ for 64-bit operating
systems. This is the recommended installation directory, but you may use other
directories or disk drives.
Note that program components not installed initially can be installed later,
and any components damaged (for example, by inadvertently overwriting the
directory) can be quickly reinstalled by double-clicking
phreeqci-@VERSION@.@REVISION@.msi--a maintenance version of the installation
phreeqci-@VERSION@-@REVISION@.msi--a maintenance version of the installation
program will be executed.
@ -112,16 +117,19 @@ D. Installing and running the batch version of PHREEQC
Note that if the software is to be installed on a server system, the person
installing the software generally must have administrator rights.
To install the software, double-click phreeqc-@VERSION@-@REVISION@.msi to
execute the installation program and follow the directions on the screen. The
installation program optionally will modify the PATH environment variable so
that the PHREEQC program can be executed from any directory, without needing to
type the full pathname of the program's location. The batch version is
completely independent from teh GUI version.
To install the software, double-click phreeqc-@VERSION@-@REVISION@.msi to execute
the installation program and follow the directions on the screen. The
installation program will modify the PATH environment variable so that
the PHREEQC program can be executed from a command prompt window from any
directory without needing to type the full pathname of the program's location.
The batch version is completely independent from the GUI version.
By default, the software is installed in the directory C:\Program
Files\USGS\phreeqc-@VERSION@. This is the recommended installation directory,
but you may use other directories or disk drives.
Files\USGS\phreeqc-@VERSION@.@REVISION@ (32-bit operating system) or C:\Program
Files (x86)\USGS\phreeqc-@VERSION@.@REVISION@ (64-bit operating system). This is
the recommended installation directory, but you may use other directories or
disk drives. The following documentation assumes default installation for a 64-
bit operating system.
Note that program components not installed initially can be installed later,
and any components damaged (for example, by inadvertently overwriting the
@ -132,40 +140,43 @@ program will be executed.
The following directory structure will be created (the contents of each
directory are shown to the right):
phreeqc-@VERSION@ files NOTICE.TXT, RELEASE.TXT, and this
README.Win.TXT; batch file to run PHREEQC
--database database files
--doc documentation files
--examples examples from user's guide--used in verification tests
--src Makefile and source code
--ClrClass_release phreeqcpp.exe, executable with charting
--Class_release phreeqcpp.exe, executable without charting
--test batch files to run verification tests
C:\Program Files (x86)\USGS\phreeqc-@VERSION@.@REVISION@
Files NOTICE.TXT, RELEASE.TXT, this file
(README.TXT), and Visual Studio project files
--bin phreeqc.bat, batch file for executing PHREEQC
--ClrRelease phreeqc.exe, executable with charting
--Release phreeqc.exe, executable without charting (runs faster)
--database Database files
--doc Documentation files
--examples Examples from user's guide--used in verification tests
--src Source code
--test Batch files to run verification tests
Note: It is recommended that no user files be kept in the PHREEQC
directory structure. If you plan to put files in the PHREEQC
directory structure, do so only by creating subdirectories.
E. Compiling
E. Compiling the batch version
The source code is provided so that users can generate the executable
The source code is provided so that users can generate an executable
themselves. Little or no support is provided for users generating
their own versions of the software. In general, to compile a new
version of the software, you will need:
version of PHREEQC, you will need:
(a) a C compiler,
(b) familiarity with the compiler and the Windows operating system.
A Visual Studio project (phreeqcpp.sln) is included in the top-level directory
A Visual Studio project (phreeqc.sln) is included in the top-level directory
for compilation on Windows operating systems.
F. Running the batch program
F. Running the batch version
If PHREEQC has been installed in a directory included in the users' PATH, the
batch program can be executed with any of the commands below.
batch program can be executed from a command-prompt window with any of the
commands below.
command to execute PHREEQC explanation
----------------------------- -----------------------------------------
@ -188,28 +199,36 @@ batch program can be executed with any of the commands below.
and screen output is directed to the
file screen_output.
If the option to modify the PATH environment variable was not chosen during
installation, then two options exist: (1) the full pathname to the script that
runs phreeqc can be used in place of "phreeqc" in the above commands (for
example "c:\program files\usgs\phreeqc-@VERSION@\phreeqcpp". Note that because
of the space present in "program files", quotation marks must be used to enter
the full pathname.), or, (2) the executable (installed in
phreeqc-@VERSION@\src\release\phreeqcpp.exe) may be copied to the current
directory; further, the default database file may need to be in the current
directory and named "phreeqc.dat". The default database file is installed in
phreeqc-@VERSION@\database\phreeqc.dat.
Two alternative options exist for running the program: (1) the full pathname to
the batch file that runs phreeqc can be used in place of "phreeqc" in the above
commands ("C:\Program Files (x86)
\USGS\phreeqc-@VERSION@.@REVISION@\bin\phreeqc.bat". Note that because of the
space present in "Program Files", quotation marks must be used to enter the full
pathname); or, (2) the executable (charting version is installed in C:\Program
Files (x86)\USGS\phreeqc-@VERSION@.@REVISION@\ bin\ClrRelease\phreeqc.exe) may be
copied to the current directory; further, the default database file may need to
be in the current directory and named "phreeqc.dat". The default database file is
installed in C:\Program Files (x86)
\USGS\phreeqc-@VERSION@.@REVISION@\database\phreeqc.dat.
The environment variable PHREEQC_DATABASE can be used to specify the
Two executables are distributed in subdirectories of the bin directory. The
executable (phreeqc.exe) in \bin\ClrRelease has charting capabilities. The
executable in \bin\Release does not have charting capabilities. The version
without charting will run up to two times faster than the charting version and
may be preferred for long calculations that do not require charting.
The environmental variable PHREEQC_DATABASE can be used to specify the
default database for a DOS window session. This environmental variable
can be set with the command:
set PHREEQC_DATABASE=c:\mydirectory\myproject\mydata.dat
set PHREEQC_DATABASE=C:\mydirectory\myproject\mydata.dat
This environmental variable takes precedence over any default definition
of the database file. If PHREEQC is invoked with at least three
arguments, the third argument is the database file and it takes
precedence over the environmental variable or the default database.
G. Testing and examples
Input files are provided to verify that the program is correctly installed and
@ -218,10 +237,13 @@ guide, which demonstrate most of the program's capabilities. The PHREEQC
"examples" directory contains the input data and the expected results for each
test.
The "examples" and "Win" directories from phreeqc-@VERSION@ have been copied to
My Documents\xxx, and the examples can be run from My Documents\Win. Either
double click the test.bat file from Windows Explorer or cd to the directory in
a command-prompt window and type test.bat [start [stop [no_chart]]]
to run the examples, copy the "test" directory (C:\Program Files (x86)
\USGS\phreeqc-@VERSION@.@REVISION@\test) to a location where you have read/write
access. The examples can be run from the new directory either by double clicking
the test.bat file from Windows Explorer or by chaning directories to the
new directory in a command-prompt window and typing the following:
test.bat [start [stop [no_chart]]]
where: start is the number of the first test to perform, default = 1
stop is the number of the last test to perform, default = 22
@ -238,36 +260,21 @@ For example:
test.bat 4 runs test 4 through the last test
test.bat 1 10 no runs tests 1 through 10 without charts
You will have to close chart windows after each chart has completed to proceed
to the remaining examples. After the tests are completed, the results are
compared to the expected results (found in the examples directory). See the
file check.log; if all goes well, there should be few or no differences.
Differences in path names and run times are insignificant.
You will have to close chart windows after each chart has completed to proceed to
the remaining examples. After the tests are completed, the results can be
compared to the expected results (found in the examples directory) by executing
the check.bat batch file. See the file check.log for differences. Differences in
path names and run times are insignificant. The results in the directory examples
were calculated with the charting version of PHREEQC. Comparing non-charting
results to charting results may produce a large number of differences in
check.log; however, in almost all cases, the differences are related to the
calculated pe. The pe may differ significantly and many aqueous species
concentrations may differ, but the concentrations of aqueous species should
differ by less than 1e-8 mol/kgw.
To clean up after the tests, double click on clean.bat in Windows Explorer or
type the command clean.bat from a command prompt.
Note: Sometimes different processors, or different compilers cause
minor numerical differences in the results or differences in
representation of exponents. In general, concentrations should
differ by less than about 1e-14 (mol/kg water) between two sets
of results. The pe may vary several units in some systems
without redox buffering; however, all concentrations should
still differ by only small amounts.
Problem 9 generates a warning message that indicates negative
concentrations were generated in a kinetic run. The numerical
method automatically reduces the step size until negative
concentrations are eliminated and an accurate kinetic integration
is obtained.
Problems 11, 12, 13, and 15 generate warning messages. The
messages simply indicate a shorthand method for defining cell
lengths and cell dispersivities was used in a transport
calculation.
The tests are described in the table below, where 'test' corresponds
to the example number in the PHREEQC manual.
@ -325,6 +332,7 @@ test description of test and files
22 Modeling gas solubilities: CO2 at high pressures
H. CONTACTS
Inquiries about this software distribution should be directed to: