mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-13 07:08:23 +01:00
8de0e98ed9
git-subtree-dir: phreeqc3-doc git-subtree-mainline: f2026ac2d3748f57af8ed0764d3a2d77f9fcf84b git-subtree-split: 7a7c7c04dd3fc8605d421da7774d2b95225be7dc
345 lines
15 KiB
Plaintext
345 lines
15 KiB
Plaintext
README.TXT
|
|
|
|
PHREEQC
|
|
|
|
A program for speciation, batch-reaction, one-dimensional
|
|
transport, and inverse geochemical calculations
|
|
|
|
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 version can be downloaded from
|
|
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html. PhreeqcI has
|
|
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 installing, 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 in the root directory for new features and bug fixes.
|
|
|
|
|
|
TABLE OF CONTENTS
|
|
|
|
A. Distribution files
|
|
B. Documentation
|
|
C. Installing and running the GUI PhreeqcI
|
|
D. Installing the batch version of PHREEQC
|
|
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 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
|
|
|
|
phreeqc-@VERSION@-@REVISION@.msi--Batch version compiled by using Microsoft
|
|
Visual C++ 2005, includes source code
|
|
|
|
B. Documentation
|
|
|
|
*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.
|
|
|
|
|
|
*The following two user's guides are available in electronic format. Portable
|
|
Document Format (PDF) files are included in the doc subdirectory of the
|
|
PHREEQC program distribution.
|
|
|
|
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.
|
|
|
|
|
|
C. Installing and running 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
|
|
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@-@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
|
|
program will be executed.
|
|
|
|
|
|
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 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@-@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
|
|
directory) can be quickly reinstalled by double-clicking
|
|
phreeqc-@VERSION@-@REVISION@.msi--a maintenance version of the installation
|
|
program will be executed.
|
|
|
|
The following directory structure will be created (the contents of each
|
|
directory are shown to the right):
|
|
|
|
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 the batch version
|
|
|
|
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 PHREEQC, you will need:
|
|
|
|
(a) a C++ compiler,
|
|
(b) familiarity with the compiler and the Windows operating system.
|
|
|
|
A Visual Studio project (phreeqc.sln) is included in the top-level directory
|
|
for compilation on Windows operating systems.
|
|
|
|
|
|
F. Running the batch version
|
|
|
|
The batch program can be executed from a command-prompt window with any of the
|
|
commands below.
|
|
|
|
command to execute PHREEQC explanation
|
|
----------------------------- -----------------------------------------
|
|
phreeqc The program will query for each of the
|
|
needed files.
|
|
|
|
phreeqc input The input file is named input, the output
|
|
file will be named input.out and the
|
|
default database file will be used.
|
|
|
|
phreeqc input output The input file is named input, the output
|
|
file is named output, and the default
|
|
database file will be used.
|
|
|
|
phreeqc input output database All file names are specified explicitly.
|
|
|
|
phreeqc input output database screen_output
|
|
|
|
All file names are specified explicitly,
|
|
and screen output is directed to the
|
|
file screen_output.
|
|
|
|
Three alternative options exist for running the program: (1) the full pathname to
|
|
the batch file 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); (2) the full path to one of the executable
|
|
files can be used in place of "phreeqc" in the above commands
|
|
("C:\Program Files (x86)USGS\phreeqc-@VERSION@-@REVISION@\bin\Release\phreeqc.exe",
|
|
for example); or (3) an executable ("C:\Program Files (x86)\USGS\
|
|
phreeqc-@VERSION@-@REVISION@\bin\ClrRelease\phreeqc.exe, for example) may be
|
|
copied to the current directory and executed with .\phreeqc. The database file
|
|
may need to be in the current directory. The default database file is installed
|
|
in C:\Program Files (x86)\USGS\phreeqc-@VERSION@-@REVISION@\database\phreeqc.dat.
|
|
|
|
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
|
|
|
|
When using the batch file, phreeqc.bat, 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
|
|
running on the system. The tests execute the examples presented in the user's
|
|
guide, which demonstrate most of the program's capabilities. The PHREEQC
|
|
"examples" directory contains the input data and the expected results for each
|
|
test.
|
|
|
|
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 changing
|
|
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
|
|
no_chart is any alphanumeric string, which causes no charts to be
|
|
generated.
|
|
|
|
For example:
|
|
|
|
command what happens
|
|
--------------------------------- --------------------------------
|
|
test.bat runs all of the tests
|
|
test.bat 1 1 runs the first test
|
|
test.bat 2 3 runs tests 2 and 3
|
|
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 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.
|
|
|
|
The tests are described in the table below, where 'test' corresponds
|
|
to the example number in the PHREEQC manual. Charts can be compared to charts
|
|
in the manual (Techniques and Methods 6-A43).
|
|
|
|
test description of test and files
|
|
---- --------------------------------------------
|
|
1 Add uranium and speciate seawater
|
|
|
|
2 Temperature dependence of solubility
|
|
of gypsum and anhydrite
|
|
|
|
3 Mixing seawater and groundwater
|
|
|
|
4 Evaporation and solution volume
|
|
|
|
5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
|
|
|
|
6 Reaction path calculations with K-feldspar to phase boundaries
|
|
|
|
7 Organic decomposition with fixed-pressure and
|
|
fixed-volume gas phases
|
|
|
|
8 Sorption of zinc on hydrous iron oxides
|
|
|
|
9 Kinetically controlled oxidation of ferrous iron.
|
|
Decoupled valence states of iron.
|
|
|
|
10 Solid solution of strontianite and aragonite.
|
|
|
|
11 Transport and ion exchange.
|
|
|
|
12 Advective and diffusive transport of heat and solutes. Constant boundary
|
|
condition at one end, closed at other. The problem is designed so that
|
|
temperature should equal Na-conc (in mmol/kgw) after diffusion.
|
|
|
|
13 1D Transport in a Dual Porosity Column With Cation Exchange
|
|
|
|
14 Transport with equilibrium_phases, exchange, and surface reactions
|
|
|
|
15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
|
|
|
|
16 Inverse modeling of Sierra springs
|
|
|
|
17 Inverse modeling of Black Sea water evaporation
|
|
|
|
18 Inverse modeling of Madison aquifer
|
|
|
|
19 Modeling Cd+2 sorption with Linear, Freundlich, and Langmuir isotherms,
|
|
and with a deterministic distribution of sorption sites for organic
|
|
matter, clay minerals, and iron oxyhydroxides
|
|
|
|
20 Distribution of isotopes between water and calcite
|
|
|
|
21 Modeling diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a radial diffusion
|
|
cell
|
|
|
|
22 Modeling gas solubilities: CO2 at high pressures
|
|
|
|
|
|
H. CONTACTS
|
|
|
|
Inquiries about this software distribution should be directed to:
|
|
|
|
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov
|
|
|