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manual.pdf → Phreeqc_2_1999_manual.pdf
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368
README.TXT
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@ -5,17 +5,12 @@ README.TXT
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.
NOTE: This file describes the batch version of PHREEQC version 3. 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.
PHREEQC - Version @VERSION@ @VER_DATE@
@ -30,72 +25,108 @@ 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. Documentation
B. Windows: Installing and running PhreeqcI
C. Windows: Installing the batch version of PHREEQC
D. Linux: Extracting, compiling (optional), and installing
the batch version of PHREEQC
D.1. Extracting files
D.2. Compiling (optional)
D.3. Installing
E. Windows and Linux: Running the batch program
F. Testing
F.1. Windows
F.2. Linux
F.3. Example problems
G. Contacts
A. 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., 2012, 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/06A43/.
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.
A. DISTRIBUTION FILES
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.
The following distribution packages (containing the software, test data sets,
and information files) are currently available for UNIX systems:
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.
phreeqc-@VERSION@-@REVISION@.Linux.tar.gz - Compiled with @GCC_VER@
kernel @KERNEL_VER@
phreeqc-@VERSION@-@REVISION@.source.tar.gz - Source code but no executable
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.
B. Windows installation and running of the GUI PhreeqcI
Download and run the file phreeqci-@VERSION@.@REVISION@.msi. PhreeqcI will be installed
in the selected directory, C:\Program Files (x86)\USGS\Phreeqc Interactive
@VERSION@.@REVISION@ by default. The program can be executed from the Start menu.
C. Windows: installing and running PhreeqcI
B. DOCUMENTATION
Download and run the file phreeqc-@VERSION@.@REVISION@.msi. All of the files
needed to install and test PHREEQC will be installed in the selected
directory, C:\Program Files (x86)\USGS\phreeqc-@VERSION@.@REVISION@ by
default.
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.
The following directory structure is created (the contents of each
directory are shown to the right):
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/
phreeqc-@VERSION@ files NOTICE.TXT, RELEASE.TXT, and this README.TXT
`-----bin compiled executable, template for execution script
`-----database database files required during execution
`-----doc documentation files
`-----examples examples from user's guide--used in verification tests
`-----src Makefile and source code
`-----test scripts to run verification tests
Notes: 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.
D. Linux: Extracting, compiling (optional), and installing the batch version of 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.
D.1. Linux: Extracting files
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
Compressed tar files are used to distribute the source code and
versions of the software compiled for selected UNIX operating systems.
All of the PHREEQC files needed to install and test the program are
contained in the file phreeqc-@VERSION@.@REVISION@-OS.tar.gz (where OS is a
string indicating the intended operating system.) If there is not a
tar file for your operating system or you want to compile the
software, the source version of the tar file contains all of the
PHREEQC files needed to compile and install the program on a
UNIX-based computer. For all of these distributions, the directory
phreeqc-@VERSION@ is created (or overwritten) when the files are extracted
from the tar file; if this directory already exists, you may want to
delete or rename it before extracting the files.
Compressed tar files are used to distribute the source code and versions of the software
compiled for Linux operating systems. All of the files needed to install and test
PHREEQC are contained in the file phreeqc-@VERSION@.@REVISION@.Linux.tar.gz. A Linux
executable file is included, which is compiled with @GCC_VER@ kernel @KERNEL_VER@. If
you want to compile the program for another operating system, the file
phreeqc-@VERSION@.@REVISION@.source.tar.gz contains all of the files needed to compile
and install PHREEQC. For all tar files, the directory phreeqc-@VERSION@ is created when
the files are extracted; if this directory already exists, you may want to delete or
rename it before extracting the files.
Follow the steps below to extract the files from a distribution tar
file.
Steps in extracting files explanation
Steps in extracting files Explanation
---------------------------------------- -----------------------------------
gunzip phreeqc-@VERSION@-@REVISION@.OS.tar.gz Uncompress the distribution file.
gunzip phreeqc-@VERSION@-@REVISION@.Linux.tar.gz Uncompress the distribution file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.OS.tar Extract files from the tar file.
tar -xvpof phreeqc-@VERSION@-@REVISION@.Linux.tar Extract files from the tar file.
The following directory structure is created (the contents of each
directory are shown to the right):
@ -114,8 +145,9 @@ Notes: (a) A compiled executable is not included in the source
directory structure. If you plan to put files in the PHREEQC
directory structure, do so only by creating subdirectories.
D.2. Linux: Compiling (optional)
D. COMPILING
XXXXXXXXXXXXXXX need to describe confinure here XXXXXXXXXXXXXXXXXX
If you have retrieved a pre-compiled distribution of the software, skip to
the Installing section below.
@ -129,7 +161,7 @@ new version of the software, you will need:
(a) a C compiler, and
(b) a minimal level of knowledge of Make, the compiler, and
the UNIX operating system.
the Linux operating system.
As provided in the source distribution, the software is set up to be
compiled under Linux with gcc.
@ -145,7 +177,8 @@ To generate a new executable, do the following:
CC C compiler name
CCFLAGS C compiler flags
LOADFLAGS linker flags
INVERSE_CL1MP remove definition if gmp package
MULTICHART Requires WINE and zedgraph .NET control
INVERSE_CL1MP Do not define if the gmp package
is not available on your system
3. Run make in the src directory to compile the source:
@ -158,11 +191,11 @@ To generate a new executable, do the following:
b. place the program executable in the PHREEQC bin directory.
E. INSTALLING
D.3. Linux: Installing
To make PHREEQC easy to use, a link to the script that runs PHREEQC
should be placed in a directory that is included in each user's search
path. Run make in the PHREEQC src subdirectory to create the link:
path. Run make in the PHREEQC src subdirectory to create the link:
make install BINDIR=directory_for_links
@ -182,11 +215,10 @@ PHREEQC script, the installer must have sufficient rights to the BINDIR
directory. By default, BINDIR is $HOME/bin.
F. RUNNING THE PROGRAM
E. Linux and Windows: Running the batch program
If PHREEQC has been installed in a directory included in the users'
PATH (as described above), the program can be executed with any of the
commands below.
If PHREEQC has been installed in a directory included in the users' PATH, the program can
be executed with any of the commands below.
command to execute PHREEQC explanation
----------------------------- -----------------------------------------
@ -209,8 +241,8 @@ commands below.
and screen output is directed to the
file screen_output.
If the "make install" command described above has not been executed,
the executable must be copied to the current directory. The executable
For Linux, if the "make install" command described above has not been executed,
the executable may be copied to the current directory. The executable
is normally phreeqc-@VERSION@/bin/phreeqc. In addition the default database
file will be phreeqc.dat in the current directory. Phreeqc.dat is
installed in phreeqc-@VERSION@/database/phreeqc.dat.
@ -232,22 +264,24 @@ to phreeqc-@VERSION@/database/phreeqc.dat. It is possible to specify a
different default database by editing the script.
G. TESTING
F. 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 PHREEQC test directory contains the script to run the tests. The PHREEQC
examples directory contains the input data and the expected results for
each test.
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. On Windows operating systems, the "examples" and "Win" directories have
been copied to My Documents\xxx, and the examples can be run from Win.
To test the installation, change to the phreeqc-@VERSION@/test directory and type
the command:
F.1. Windows
./test.sh [start [stop]]
On Windows operating systems, the "examples" and "Win" directories from
phreeqc-@VERSION@ have been copied to My Documents\xxx, and the examples can be
run from Win. Either double click the test.bat file from Windows Explorer or cd
to the directory in a command-prompt window and type ./test.sh [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
stop = the number of the last test to perform, default = 22
For example:
@ -259,9 +293,40 @@ For example:
./test.sh 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.
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.
To clean up after the tests, double click on clean.bat in Windows Explorer or
type the command ./clean.bat from a command prompt.
F.2. Linux
On Linux, you should copy the directory phreeqc-@VERSION@/test to an area where
you have write access; the examples can be run from the copied directory. Change
to the directory that you copied and type the command:
./test.sh [start [stop]]
where: start = the number of the first test to perform, default = 1
stop = the number of the last test to perform, default = 22
For example:
command what happens
---------------------------------- --------------------------------
./test.sh runs all of the tests
./test.sh 1 1 runs the first test
./test.sh 2 3 runs tests 2 and 3
./test.sh 4 runs test 4 through the last test
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.
To clean up after the tests, type the command:
@ -284,155 +349,66 @@ Notes: The output data files for phreeqc-@VERSION@.@REVISION@.source.tar.gz
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.
F.3. Example problems
test description of test and files file name & usage
---- -------------------------------------------- -----------------
The tests are described in the table below, where 'test' corresponds
to the example number in the PHREEQC manual.
test description of test and files
---- --------------------------------------------
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
3 Mixing seawater and groundwater
4 A. Rain water evaporation
B. Factor of 20 more solution
PHREEQC input file ex4 i
Printed results of calculation ex4.out o
4 Evaporation and solution volume
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
6 Reaction path calculations with K-feldspar to phase boundaries
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
13 1D Transport in a Dual Porosity Column With Cation Exchange
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
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
PHREEQC input file ex18 i
Printed results of calculation ex18.out o
22 Modeling gas solubilities: CO2 at high pressures
H. CONTACTS
G. CONTACTS
Inquiries about this software distribution should be directed to:

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@ -30,11 +30,10 @@ OPTIONS
infile.out. If no database file is specified, the
phreeqc.dat database distributed with PHREEQC will be used.
ABSTRACT
PHREEQC is a computer program written in the C programming
language that is designed to perform a wide variety of low-
temperature aqueous geochemical calculations. PHREEQC is
based on an ion-association aqueous model and has
ABSTRACT PHREEQC is a computer program written in the C
programming language that is designed to perform a wide
variety of low- temperature aqueous geochemical calculations.
PHREEQC is based on an ion-association aqueous model and has
capabilities for (1) speciation and saturation-index
calculations; (2) batch-reaction and one-dimensional (1D)
transport calculations involving reversible reactions, which
@ -42,10 +41,10 @@ ABSTRACT
complexation, and ion-exchange equilibria, and irreversible
reactions, which include specified mole transfers of
reactants, kinetically controlled reactions, mixing of
solutions, and temperature changes; and (3) inverse
modeling, which finds sets of mineral and gas mole transfers
that account for differences in composition between waters,
within specified compositional uncertainty limits.
solutions, and pressure and temperature changes; and (3)
inverse modeling, which finds sets of mineral and gas mole
transfers that account for differences in composition between
waters, within specified compositional uncertainty limits.
METHOD
For speciation and batch-reaction calculations, PHREEQC
@ -88,13 +87,13 @@ DATA REQUIREMENTS
For speciation modeling, analytical data for a solution
composition (SOLUTION keyword) are needed.
For batch-reaction modeling, the initial solution
composition is required (SOLUTION or MIX data block). Other
equilibrium reactants may be defined with
EQUILIBRIUM_PHASES, EXCHANGE, SURFACE, GAS_PHASE, and
SOLID_SOLUTION data blocks. Nonequilibrium reactions may be
defined with KINETICS and RATES, REACTION, and
REACTION_TEMPERATURE data blocks.
For batch-reaction modeling, the initial solution composition
is required (SOLUTION or MIX data block). Other equilibrium
reactants may be defined with EQUILIBRIUM_PHASES, EXCHANGE,
SURFACE, GAS_PHASE, and SOLID_SOLUTION data blocks.
Nonequilibrium reactions may be defined with KINETICS and
RATES, REACTION, REACTION_PRESSURE, and REACTION_TEMPERATURE
data blocks.
For 1D transport modeling, the data for batch-reaction
modeling are needed for each cell in the modeled system. In
@ -130,7 +129,15 @@ SYSTEM REQUIREMENTS
computers with processors running at 100 megahertz or
faster.
DOCUMENTATION
DOCUMENTATION
Parkhurst, D.L., and Appelo, C.A.J., 2012, 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/06A43/.
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
@ -141,6 +148,11 @@ DOCUMENTATION
individual isotope equilibrium constants for implementation in
geochemical models: U.S. Geological Survey Water-Resources
Investigations Report 02-4172, 129 p.
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.
RELATED DOCUMENTATION
@ -177,9 +189,10 @@ RELATED DOCUMENTATION
Report 94-4169, 130 p.
REFERENCES
Appelo, C.A.J., and Postma, D., 1993, Geochemistry,
groundwater and pollution: Rotterdam, Netherlands, and
Brookfield, Vermont, A.A. Balkema.
Appelo, C.A.J., and Postma, D., 2005, Geochemistry,
groundwater and pollution (2nd ed.): Rotterdam,
Netherlands, and Brookfield, Vermont, A.A. Balkema.
Appelo, C.A.J., and Willemsen, A., 1987, Geochemical
calculations and observations on salt water intrusions.

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