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 for use on
Apple Macintosh computers running OS X.
PHREEQC - Version 2.12.1 November 16, 2005
Instructions for installation, execution, and testing are provided
below. After installation, see the phreeqc.txt file in the doc directory
of the PHREEQC installation for summary information on PHREEQC.
For assistance, enhancement requests, or to report bugs, contact
dlpark@usgs.gov.
TABLE OF CONTENTS
A. DISTRIBUTION FILES
B. DOCUMENTATION
C. EXTRACTING FILES
D COMPILING
E. INSTALLING
F. RUNNING THE PROGRAM
G. TESTING
H. CONTACTS
A. DISTRIBUTION FILES
The following distribution package (containing the software, test data
sets, and information files) is currently available for Mac OS X:
phreeqc-2.12.1-669.dmg.gz - Compiled with Xcode 2.2 (gcc 4.01)
B. 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. Portable Document
Format (PDF) files are 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.
C. EXTRACTING FILES
PHREEQC for Mac OS X is distributed as a compressed disk image file; the
downloaded file may self expand or will expand to a disk image by double-
clicking it in the Finder. After the User Rights Notice is agreed to, the
image will mount and reveal the phreeqc-2.12.1 folder, which may be copied
into any directory. Note that if you copy it to the /Applications folder,
users without admin privileges will not be able run phreeqc because it
writes files back into its own directory. On multi-user systems, it may
be desirable to move copies of the phreeqc-2.12.1 folder into each user's
home directory.
The following directory structure is assumed (the contents of each
directory are shown to the right):
phreeqc-2.12.1 AppleScript applets
`-----bin compiled executable
`-----database database files required during execution
`-----doc documentation files
`-----examples examples from user's guide--used in verification
tests
`-----src source code for AppleScript scripts
Notes: (a) The PHREEQC source code is not included in the Mac
distribution, but is available by downloading the generic Unix
version.
(b) The "run phreeqc" applet assumes that the phreeqc executable
resides in the /bin directory relative to the path to the
"run phreeqc" application.
D. COMPILING
The Mac version is pre-compiled.
E. INSTALLING
No special installation is needed; if the software is run from a Terminal
window (by opening the file "/bin/phreeqc"), see the instructions
available for the generic unix version in order to resolve path problems.
F. RUNNING THE PROGRAM
By opening (double-clicking) the file "run phreeqc", the user is prompted
sequentially for the input, output and database files. These files can
reside in any directory; the database files are initially stored in
"/database/". Pressing the "Cancel" button in any file dialog
will halt execution of the script. Normally, no feedback is provided
because the applet simply calls the phreeqc executable. Any errors
or warnings will be written to the output file. The log file "phreeqc.log"
may be checked if results are not what was expected. Note that selected
output files and phreeqc.log will be stored in the directory with
"run phreeqc". After the output file is created, the user is given the
option of opening the output file in an application of his/her choosing.
Just be sure to choose an application that can open text files. If
desired, the AppleScript script could be changed to always open the
output file in the same application (i.e. TextEdit).
PHREEQC operates with generic text files; these files may be edited using
"TextEdit" or any program that can work with text files. An excellent text
editor is available from <http://www.barebones.com>. Because PHREEQC is
a Unix program, it expects the end-of-line character to be a line-feed
(ASCII 10). Many Mac programs generate text files using carriage-returns
(ASCII 13) as the end-of-line character.
A symptom of incorrect line-endings is that the output file will simply
echo the input with no calculations performed.
If you are using older input files from a Mac, or if your text editor
uses the older end-of-line character, then simply drop your input file(s)
onto the Mac2Unix droplet to convert them before using them as input to
PHREEQC. A companion droplet called Unix2Mac is included in case one needs
to reverse the process. Each time the file is converted a new file is
created that ends with either "LF" or "CR" as appropriate.
G. TESTING
The Mac OS X version of PHREEQC has been tested and the results are
comparable to the results on other Unix systems. The example files
are provided in the Examples directory.
Notes: The output data files were created on a Linux system. You may notice
slight numeric differences in the results. These are generally due
to different round-off algorithms and the different architecture of
the central processing unit chip. Slight differences in output
formats may occur on other computers, particularly for the value
0.0.
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.
The tests are described in the table below, where '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