README.TXT
PHREEQC
A program for speciation, batch-reaction, one-dimensional
transport, and inverse geochemical calculations
NOTE: This file describes the batch version of PHREEQC. However, a
graphical user interface, PhreeqcI, is available that runs under
Windows operating systems. This interactive program 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. A brief description of the program
has been published as a Fact Sheet:
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.
PHREEQC - Version 2.14.3 November 17, 2007
Instructions for installation, execution, and testing are provided
below. After installation, see the file doc\phreeqc.txt in the PHREEQC
installation directory for summary information on PHREEQC.
For assistance, enhancement requests, or to report bugs, contact the
Hydrologic Analysis Software Support Program by sending e-mail to
h2osoft@usgs.gov or dlpark@usgs.gov.
For all versions of Microsoft Windows, this Windows console version of
PHREEQC must be run by using an MS-DOS Command Prompt window.
TABLE OF CONTENTS
A. SYSTEM REQUIREMENTS
B. DISTRIBUTION FILE
C. DOCUMENTATION
D. INSTALLING
o Installing PHREEQC
o PHREEQC directory structure
E. COMPILING
F. RUNNING THE SOFTWARE
o Out of environment space error
G. TESTING
H. CONTACTS
A. SYSTEM REQUIREMENTS
For installation of PHREEQC, 10 megabytes of free disk space is needed.
To run PHREEQC, the following are necessary:
- Windows 98/Me, Windows NT 4.0, Windows 2000, Windows XP, Windows Vista
- processor running at 100 megahertz or faster
- 8 megabytes RAM
- 20 megabytes free disk space
B. DISTRIBUTION FILE
The following distribution file (containing the software, test data sets,
and information files) is currently available.
phreeqc-2.14.3-2411.exe - Compiled using Microsoft Visual C++ 2005, includes source code
C. DOCUMENTATION
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.
This user's guide is available in electronic format. A Portable
Document Format (PDF) file is included in the doc subdirectory of
the PHREEQC program distribution. An online HTML version of the
User's Guide can also be found at
http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/
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.
This report documents the theory and implementation of isotopes
in PHREEQC. Portable Document Format (PDF) is included in the
doc subdirectory of the PHREEQC program distribution.
D. INSTALLING
Installing 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-2.14.3-2411.exe 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.
By default, the software is installed in the directory
C:\Program Files\USGS\phreeqc-2.14.3. 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 that any components damaged by, for example, being
inadvertently overwritten, can be quickly reinstalled by double-clicking
phreeqc-2.14.3-2411.exe--a maintenance version of the installation program
will be executed.
PHREEQC directory structure
---------------------------
The following directory structure will be created (the contents of each
directory are shown to the right):
phreeqc-2.14.3 files NOTICE.TXT, RELEASE.TXT, and this README.TXT;
batch file to run PHREEQC, database files
`-----doc documentation files
`-----examples examples from user's guide--used in verification tests
`-----src Makefile and source code
| `-----release compiled executable
`-----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 source code is provided so that users can generate the 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:
(a) a C compiler,
(b) familiarity with the compiler and the Windows operating system.
A Makefile used to compile the program under Linux is provided as an example
in the phreeqc-2.14.3-2411.exe distribution,
F. RUNNING THE SOFTWARE
If the option to modify the PATH environment variable was chosen
during installation, then the following commands may be used to run
PHREEQC from an MS-DOS Command Prompt window.
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.
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-2.14.3\phreeqc".
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-2.14.3\src\release\phreeqc.exe) may be
copied to the current directory; further, the default database file
must be in the current directory and named "phreeqc.dat". The default
database file is installed in phreeqc-2.14.3\database\phreeqc.dat.
The environment variable PHREEQC_DATABASE can be used to specify the
default database for a DOS window session. This environment variable
can be set with the command:
set PHREEQC_DATABASE=c:\mydirectory\myproject\mydata.dat
This environment 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 environment variable or the default database.
Out of environment space error
------------------------------
This error can occur in earlier Windows operating systems when assigning
a value to the PHREEQC_DATABASE environment variable or running PHREEQC,
including when running the verification tests. The error occurs when
there is insufficient space to hold a new environment variable definition.
You can avoid this error by initiating a new command shell and specifying
how much environment space you need. For example, in an MS-DOS Command
Prompt window, typing
command /e:1024
will initiate a new command shell with 1024 bytes of environment space.
Environment space can be between 256 and 32768 bytes.
The above command will increase the environment space for only the
current Command Prompt window. To permanently increase your
environment space, on Windows 9x/Me machines, click the MS-DOS
icon in the upper-left corner of the Command Prompt window and select
Properties. Select the Memory tab and increase the value in the
Initial environment field.
G. TESTING
Test data sets 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 tests are run in the phreeqc-2.14.3\test directory. The directory
phreeqc-2.14.3\examples contains the PHREEQC input data and expected results
for each test.
To test the installation, in an MS-DOS Command Prompt window change to
the phreeqc-2.14.3\test directory:
c:
cd "program files"
cd usgs\phreeqc-2.14.3\test
Execute the tests by typing the command:
test [start [stop]]
where: start = the number of the first test to perform, default = 1
stop = the number of the last test to perform, default = 18
For example:
command what happens
---------------------------------- --------------------------------
test runs all of the tests
test 1 1 runs the first test
test 2 3 runs tests 2 and 3
test 4 runs test 4 through the last test
After the tests are completed, the results are compared to the
expected results (found in the PHREEQC examples directory). See the
file check.log; if all goes well, there should be no differences.
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.
To clean up after the tests, type the command:
clean
The tests are described in the table below. Test is the test number and
the usage column indicates how a file is used, with i for input and o for
output.
test description of test and files file name & usage
---- -------------------------------------------- -----------------
1 Add uranium and speciate seawater
PHREEQC input file ex1 i
Printed results of calculation ex1.out o
2 Temperature dependence of solubility
of gypsum and anhydrite
PHREEQC input file ex2 i
Printed results of calculation ex2.out o
Results written to the selected-output file ex2.sel o
3 A. Calcite equilibrium at log Pco2 = -2.0 and 25C
B. Definition of seawater
C. Mix 70% ground water, 30% seawater
D. Equilibrate mixture with calcite and dolomite
E. Equilibrate mixture with calcite only
PHREEQC input file ex3 i
Printed results of calculation ex3.out o
4 A. Rain water evaporation
B. Factor of 20 more solution
PHREEQC input file ex4 i
Printed results of calculation ex4.out o
5 Add oxygen, equilibrate with pyrite, calcite, and goethite.
PHREEQC input file ex5 i
Printed results of calculation ex5.out o
Results written to the selected-output file ex5.sel o
6 6A. React to phase boundaries
6A1.--Find amount of k-feldspar dissolved to
reach gibbsite saturation
6A2.--Find amount of k-feldspar dissolved to
reach kaolinite saturation
6A3.--Find amount of k-feldspar dissolved to
reach K-mica saturation
6A4.--Find amount of k-feldspar dissolved to
reach k-feldspar saturation
6A5.--Find point with kaolinite present,
but no gibbsite
6A6.--Find point with K-mica present,
but no kaolinite
6B. Path between phase boundaries
6C. Kinetic calculation
PHREEQC input file ex6 i
Printed results of calculation ex6.out o
Results written to the selected-output file ex6A-B.sel o
Results written to the selected-output file ex6C.sel o
7 Organic decomposition with fixed-pressure and
fixed-volume gas phases
PHREEQC input file ex7 i
Printed results of calculation ex7.out o
Results written to the selected-output file ex7.sel o
8 Sorption of zinc on hydrous iron oxides
PHREEQC input file ex8 i
Printed results of calculation ex8.out o
Results written to the selected-output file ex8.sel o
9 Kinetically controlled oxidation of ferrous iron.
Decoupled valence states of iron.
PHREEQC input file ex9 i
Printed results of calculation ex9.out o
Results written to the selected-output file ex9.sel o
10 Solid solution of strontianite and aragonite.
PHREEQC input file ex10 i
Printed results of calculation ex10.out o
Results written to the selected-output file ex10.sel o
11 Transport and ion exchange.
PHREEQC input file ex11 i
Printed results of calculation ex11.out o
Results written to the selected-output file ex11adv.sel o
Results written to the selected-output file ex11trn.sel o
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.
PHREEQC input file ex12 i
Printed results of calculation ex12.out o
Results written to the selected-output file ex12.sel o
13 A. 1 mmol/l NaCl/NO3 enters column with stagnant zones. Implicit
definition of first-order exchange model.
B. 1 mmol/l NaCl/NO3 enters column with stagnant zones. Explicit
definition of first-order exchange factors.
C. 1 mmol/l NaCl/NO3 enters column with stagnant zones. 5 layer
stagnant zone with finite differences.
PHREEQC input file ex13a i
Printed results of calculation ex13a.out o
Results written to the selected-output file ex13a.sel o
PHREEQC input file ex13b i
Printed results of calculation ex13b.out o
Results written to the selected-output file ex13b.sel o
PHREEQC input file ex13c i
Printed results of calculation ex13c.out o
Results written to the selected-output file ex13c.sel o
14 Transport with equilibrium_phases, exchange, and surface reactions
PHREEQC input file ex14 i
Printed results of calculation ex14.out o
Results written to the selected-output file ex14.sel o
15 1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
PHREEQC input file ex15 i
database file ex15.dat i
Printed results of calculation ex15.out o
Results written to the selected-output file ex15.sel o
16 Inverse modeling of Sierra springs
PHREEQC input file ex16 i
Printed results of calculation ex16.out o
17 Inverse modeling of Black Sea water evaporation
PHREEQC input file ex17 i
Printed results of calculation ex17.out o
18 Inverse modeling of Madison aquifer
PHREEQC input file ex18 i
Printed results of calculation ex18.out o
H. CONTACTS
Inquiries about this software distribution should be directed to:
e-mail: h2osoft@usgs.gov or dlpark@usgs.gov