phreeqc: R Interface to Geochemical Modeling Software

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A geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of aqueous geochemical calculations, including speciation, batch-reaction, one-dimensional reactive-transport, and inverse geochemical calculations.

Author
S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh, R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Date of publication
2015-10-01 13:18:54
Maintainer
S.R. Charlton <charlton@usgs.gov>
License
GPL-3 + file LICENSE
Version
3.3.1
URLs

View on CRAN

Man pages

Amm.dat
The Amm.dat database.
ex1
Example 1-Speciation Calculation
ex10
Example 10-Aragonite-Strontianite Solid Solution
ex11
Example 11-Transport and Cation Exchange
ex12
Example 12-Advective and Diffusive Flux of Heat and Solutes
ex13
Example 13-Aragonite-Strontianite Solid Solution
ex14
Example 14-Advective Transport, Cation Exchange, Surface...
ex15
Example 15-1D Transport: Kinetic Biodegradation, Cell Growth,...
ex15.dat
The ex15.dat database
ex16
Example 16-Inverse Modeling of Sierra Spring Waters
ex17
Example 17-Inverse Modeling With Evaporation
ex18
Example 18-Inverse Modeling of the Madison Aquifer
ex19
Example 19-Modeling Cd+2 Sorption With Linear, Freundlich,...
ex2
Example 2-Equilibration With Pure Phases
ex20
Example 20-Distribution of Isotopes Between Water and Calcite
ex21
Example 21-Modeling Diffusion of HTO, 36Cl-, 22Na+, and Cs+...
ex22
Example 22-Modeling Gas Solubilities: CO2 at High Pressures
ex3
Example 3-Mixing
ex4
Example 4-Evaporation and Homogeneous Redox Reactions
ex5
Example 5-Irreversible Reactions
ex6
Example 6-Reaction-Path Calculations
ex7
Example 7-Gas-Phase Calculations
ex8
Example 8-Surface Complexation
ex9
Example 9-Kinetic Oxidation of Dissolved Ferrous Iron With...
iso.dat
The iso.dat database.
llnl.dat
The llnl.dat database.
minteq.dat
The minteq.dat database.
minteq.v4.dat
The minteq.v4.dat database.
phrAccumulateLine
Accumulate line(s) for input to phreeqc.
phrClearAccumulatedLines
Clear the accumulated input buffer.
phreeqc.dat
The phreeqc.dat database
phreeqc-package
R interface to the PHREEQC geochemical modeling program.
phrGetAccumulatedLines
Retrieve the accumulated input.
phrGetComponentList
Retrieve a list containing the current list of components.
phrGetDumpFileName
Retrieve the name of the dump file.
phrGetDumpFileOn
Retrieve the current value of the dump file switch.
phrGetDumpStrings
Retrieve DUMP strings.
phrGetDumpStringsOn
Retrieve the current value of the dump strings switch.
phrGetErrorFileName
Retrieve the name of the error file.
phrGetErrorFileOn
Retrieve the current value of the error file switch.
phrGetErrorStrings
Retrieve error string messages.
phrGetErrorStringsOn
Retrieve the current value of the error strings switch.
phrGetLogFileName
Retrieve the name of the log file.
phrGetLogFileOn
Retrieve the current value of the log file switch.
phrGetLogStrings
Retrieve log output.
phrGetLogStringsOn
Retrieve the current value of the log strings switch.
phrGetOutputFileName
Retrieve the name of the output file.
phrGetOutputFileOn
Retrieve the current value of the output file switch.
phrGetOutputStrings
Retrieve standard phreeqc output.
phrGetOutputStringsOn
Retrieve the current value of the output strings switch.
phrGetSelectedOutput
Returns the contents of the selected output as a list of data...
phrGetSelectedOutputFileName
Retrieve the name of the selected_output file.
phrGetWarningStrings
Retrieve warning messages.
phrLoadDatabase
Load a phreeqc database file
phrLoadDatabaseString
Load a phreeqc database as a string or a list of strings.
phrRunAccumulated
Runs the accumulated input.
phrRunFile
Run phreeqc input file
phrRunString
Runs phreeqc using the given string as input.
phrSetDumpFileName
Set the name of the dump file.
phrSetDumpFileOn
Set the dump file on/off.
phrSetDumpStringsOn
Set dump strings on/off.
phrSetErrorFileName
Set the name of the error file.
phrSetErrorFileOn
Set error file on/off.
phrSetErrorStringsOn
Set error strings on/off.
phrSetLogFileName
Set the name of the log file.
phrSetLogFileOn
Set log file on/off.
phrSetLogStringsOn
Set log strings on/off.
phrSetOutputFileName
Set the name of the output file.
phrSetOutputFileOn
Set output file on/off.
phrSetOutputStringsOn
Set output strings on/off.
phrSetSelectedOutputFileName
Set the name of the selected_output file.
phrSetSelectedOutputFileOn
Set selected_output file on/off.
pitzer.dat
The pitzer.dat database.
sit.dat
The sit.dat database.
wateq4f.dat
The wateq4f.dat database.

Files in this package

phreeqc
phreeqc/inst
phreeqc/inst/CITATION
phreeqc/src
phreeqc/src/Makevars
phreeqc/src/IPhreeqc.h
phreeqc/src/Debug.h
phreeqc/src/CSelectedOutput.cpp
phreeqc/src/ErrorReporterhxx.h
phreeqc/src/Var.h
phreeqc/src/IPhreeqc.cpp
phreeqc/src/CVarhxx.h
phreeqc/src/R.cpp
phreeqc/src/CSelectedOutputhxx.h
phreeqc/src/thread.h
phreeqc/src/Var.c
phreeqc/src/Version.h
phreeqc/src/phreeqcpp
phreeqc/src/phreeqcpp/cxxMix.h
phreeqc/src/phreeqcpp/Use.cpp
phreeqc/src/phreeqcpp/sundialstypes.h
phreeqc/src/phreeqcpp/SScomp.h
phreeqc/src/phreeqcpp/basicsubs.cpp
phreeqc/src/phreeqcpp/SS.cpp
phreeqc/src/phreeqcpp/dense.h
phreeqc/src/phreeqcpp/SurfaceCharge.h
phreeqc/src/phreeqcpp/parse.cpp
phreeqc/src/phreeqcpp/ExchComp.h
phreeqc/src/phreeqcpp/ReadClass.cpp
phreeqc/src/phreeqcpp/read.cpp
phreeqc/src/phreeqcpp/CurveObject.cpp
phreeqc/src/phreeqcpp/ExchComp.cpp
phreeqc/src/phreeqcpp/nvector_serial.cpp
phreeqc/src/phreeqcpp/readtr.cpp
phreeqc/src/phreeqcpp/System.h
phreeqc/src/phreeqcpp/Utils.h
phreeqc/src/phreeqcpp/ChartObject.cpp
phreeqc/src/phreeqcpp/tally.cpp
phreeqc/src/phreeqcpp/SelectedOutput.cpp
phreeqc/src/phreeqcpp/global_structures.h
phreeqc/src/phreeqcpp/StorageBinList.h
phreeqc/src/phreeqcpp/Parser.h
phreeqc/src/phreeqcpp/SSassemblage.h
phreeqc/src/phreeqcpp/SurfaceCharge.cpp
phreeqc/src/phreeqcpp/PHRQ_base.cpp
phreeqc/src/phreeqcpp/cvdense.h
phreeqc/src/phreeqcpp/pitzer_structures.cpp
phreeqc/src/phreeqcpp/ChartHandler.h
phreeqc/src/phreeqcpp/Solution.h
phreeqc/src/phreeqcpp/spread.cpp
phreeqc/src/phreeqcpp/cvdense.cpp
phreeqc/src/phreeqcpp/NA.h
phreeqc/src/phreeqcpp/runner.cpp
phreeqc/src/phreeqcpp/pitzer.cpp
phreeqc/src/phreeqcpp/Keywords.cpp
phreeqc/src/phreeqcpp/smalldense.cpp
phreeqc/src/phreeqcpp/Temperature.cpp
phreeqc/src/phreeqcpp/SS.h
phreeqc/src/phreeqcpp/PPassemblageComp.h
phreeqc/src/phreeqcpp/StorageBinList.cpp
phreeqc/src/phreeqcpp/PHRQ_base.h
phreeqc/src/phreeqcpp/mainsubs.cpp
phreeqc/src/phreeqcpp/ISolution.h
phreeqc/src/phreeqcpp/cvode.cpp
phreeqc/src/phreeqcpp/PBasic.h
phreeqc/src/phreeqcpp/Reaction.cpp
phreeqc/src/phreeqcpp/SSassemblage.cpp
phreeqc/src/phreeqcpp/step.cpp
phreeqc/src/phreeqcpp/ISolutionComp.h
phreeqc/src/phreeqcpp/dense.cpp
phreeqc/src/phreeqcpp/Exchange.cpp
phreeqc/src/phreeqcpp/Temperature.h
phreeqc/src/phreeqcpp/NumKeyword.h
phreeqc/src/phreeqcpp/PBasic.cpp
phreeqc/src/phreeqcpp/phqalloc.h
phreeqc/src/phreeqcpp/phqalloc.cpp
phreeqc/src/phreeqcpp/Surface.cpp
phreeqc/src/phreeqcpp/ChartObject.h
phreeqc/src/phreeqcpp/dw.cpp
phreeqc/src/phreeqcpp/SurfaceComp.cpp
phreeqc/src/phreeqcpp/integrate.cpp
phreeqc/src/phreeqcpp/advection.cpp
phreeqc/src/phreeqcpp/GasPhase.h
phreeqc/src/phreeqcpp/Pressure.cpp
phreeqc/src/phreeqcpp/cl1.cpp
phreeqc/src/phreeqcpp/nvector_serial.h
phreeqc/src/phreeqcpp/cxxKinetics.cpp
phreeqc/src/phreeqcpp/StorageBin.h
phreeqc/src/phreeqcpp/ISolutionComp.cpp
phreeqc/src/phreeqcpp/NumKeyword.cpp
phreeqc/src/phreeqcpp/Phreeqc.h
phreeqc/src/phreeqcpp/KineticsComp.cpp
phreeqc/src/phreeqcpp/cvode.h
phreeqc/src/phreeqcpp/Keywords.h
phreeqc/src/phreeqcpp/CurveObject.h
phreeqc/src/phreeqcpp/Use.h
phreeqc/src/phreeqcpp/transport.cpp
phreeqc/src/phreeqcpp/Reaction.h
phreeqc/src/phreeqcpp/dumper.h
phreeqc/src/phreeqcpp/StorageBin.cpp
phreeqc/src/phreeqcpp/nvector.h
phreeqc/src/phreeqcpp/print.cpp
phreeqc/src/phreeqcpp/runner.h
phreeqc/src/phreeqcpp/Surface.h
phreeqc/src/phreeqcpp/Utils.cpp
phreeqc/src/phreeqcpp/NameDouble.cpp
phreeqc/src/phreeqcpp/PPassemblageComp.cpp
phreeqc/src/phreeqcpp/GasComp.cpp
phreeqc/src/phreeqcpp/PPassemblage.cpp
phreeqc/src/phreeqcpp/nvector.cpp
phreeqc/src/phreeqcpp/kinetics.cpp
phreeqc/src/phreeqcpp/input.cpp
phreeqc/src/phreeqcpp/smalldense.h
phreeqc/src/phreeqcpp/Solution.cpp
phreeqc/src/phreeqcpp/PHRQ_io.h
phreeqc/src/phreeqcpp/sundialsmath.h
phreeqc/src/phreeqcpp/PHRQ_io.cpp
phreeqc/src/phreeqcpp/model.cpp
phreeqc/src/phreeqcpp/UserPunch.h
phreeqc/src/phreeqcpp/System.cpp
phreeqc/src/phreeqcpp/ISolution.cpp
phreeqc/src/phreeqcpp/Phreeqc.cpp
phreeqc/src/phreeqcpp/Parser.cpp
phreeqc/src/phreeqcpp/SolutionIsotope.cpp
phreeqc/src/phreeqcpp/GasComp.h
phreeqc/src/phreeqcpp/ChartHandler.cpp
phreeqc/src/phreeqcpp/PHRQ_io_output.cpp
phreeqc/src/phreeqcpp/phrqtype.h
phreeqc/src/phreeqcpp/sundialsmath.cpp
phreeqc/src/phreeqcpp/SelectedOutput.h
phreeqc/src/phreeqcpp/structures.cpp
phreeqc/src/phreeqcpp/prep.cpp
phreeqc/src/phreeqcpp/dumper.cpp
phreeqc/src/phreeqcpp/utilities.cpp
phreeqc/src/phreeqcpp/Pressure.h
phreeqc/src/phreeqcpp/sit.cpp
phreeqc/src/phreeqcpp/SolutionIsotope.h
phreeqc/src/phreeqcpp/GasPhase.cpp
phreeqc/src/phreeqcpp/SurfaceComp.h
phreeqc/src/phreeqcpp/isotopes.cpp
phreeqc/src/phreeqcpp/tidy.cpp
phreeqc/src/phreeqcpp/gases.cpp
phreeqc/src/phreeqcpp/inverse.cpp
phreeqc/src/phreeqcpp/cxxMix.cpp
phreeqc/src/phreeqcpp/KineticsComp.h
phreeqc/src/phreeqcpp/NameDouble.h
phreeqc/src/phreeqcpp/UserPunch.cpp
phreeqc/src/phreeqcpp/SScomp.cpp
phreeqc/src/phreeqcpp/Exchange.h
phreeqc/src/phreeqcpp/PPassemblage.h
phreeqc/src/phreeqcpp/cxxKinetics.h
phreeqc/src/IPhreeqchpp.h
phreeqc/src/IPhreeqcLib.cpp
phreeqc/src/IPhreeqcCallbacks.h
phreeqc/NAMESPACE
phreeqc/data
phreeqc/data/databases.rda
phreeqc/data/examples.rda
phreeqc/R
phreeqc/R/phreeqc.R
phreeqc/MD5
phreeqc/DESCRIPTION
phreeqc/man
phreeqc/man/ex17.Rd
phreeqc/man/ex3.Rd
phreeqc/man/ex16.Rd
phreeqc/man/ex12.Rd
phreeqc/man/phrGetDumpFileOn.Rd
phreeqc/man/phrGetErrorFileOn.Rd
phreeqc/man/phrGetDumpStrings.Rd
phreeqc/man/phrSetErrorFileName.Rd
phreeqc/man/phrSetErrorStringsOn.Rd
phreeqc/man/phrLoadDatabaseString.Rd
phreeqc/man/phrSetSelectedOutputFileName.Rd
phreeqc/man/ex8.Rd
phreeqc/man/phrRunFile.Rd
phreeqc/man/phrGetErrorStrings.Rd
phreeqc/man/phrGetOutputFileName.Rd
phreeqc/man/ex15.dat.Rd
phreeqc/man/phrGetErrorStringsOn.Rd
phreeqc/man/ex15.Rd
phreeqc/man/phrSetOutputFileName.Rd
phreeqc/man/phrAccumulateLine.Rd
phreeqc/man/phrGetComponentList.Rd
phreeqc/man/phrRunString.Rd
phreeqc/man/phreeqc-package.Rd
phreeqc/man/phrGetLogFileOn.Rd
phreeqc/man/phrSetDumpFileName.Rd
phreeqc/man/ex2.Rd
phreeqc/man/sit.dat.Rd
phreeqc/man/phrGetSelectedOutputFileName.Rd
phreeqc/man/phrGetWarningStrings.Rd
phreeqc/man/phrGetSelectedOutput.Rd
phreeqc/man/phrRunAccumulated.Rd
phreeqc/man/ex7.Rd
phreeqc/man/phrGetLogFileName.Rd
phreeqc/man/phrSetLogFileName.Rd
phreeqc/man/phrClearAccumulatedLines.Rd
phreeqc/man/ex19.Rd
phreeqc/man/ex4.Rd
phreeqc/man/phrSetOutputFileOn.Rd
phreeqc/man/ex1.Rd
phreeqc/man/phrSetDumpStringsOn.Rd
phreeqc/man/phrSetDumpFileOn.Rd
phreeqc/man/phrGetOutputFileOn.Rd
phreeqc/man/phrLoadDatabase.Rd
phreeqc/man/phrGetDumpStringsOn.Rd
phreeqc/man/ex21.Rd
phreeqc/man/phrGetAccumulatedLines.Rd
phreeqc/man/phrGetErrorFileName.Rd
phreeqc/man/wateq4f.dat.Rd
phreeqc/man/ex20.Rd
phreeqc/man/phrGetOutputStringsOn.Rd
phreeqc/man/minteq.v4.dat.Rd
phreeqc/man/phrGetLogStrings.Rd
phreeqc/man/ex13.Rd
phreeqc/man/phrGetDumpFileName.Rd
phreeqc/man/ex5.Rd
phreeqc/man/phrSetErrorFileOn.Rd
phreeqc/man/iso.dat.Rd
phreeqc/man/ex10.Rd
phreeqc/man/ex22.Rd
phreeqc/man/phrGetLogStringsOn.Rd
phreeqc/man/phrSetSelectedOutputFileOn.Rd
phreeqc/man/ex6.Rd
phreeqc/man/phrGetOutputStrings.Rd
phreeqc/man/phreeqc.dat.Rd
phreeqc/man/phrSetLogFileOn.Rd
phreeqc/man/phrSetLogStringsOn.Rd
phreeqc/man/pitzer.dat.Rd
phreeqc/man/minteq.dat.Rd
phreeqc/man/ex18.Rd
phreeqc/man/Amm.dat.Rd
phreeqc/man/llnl.dat.Rd
phreeqc/man/ex14.Rd
phreeqc/man/ex9.Rd
phreeqc/man/ex11.Rd
phreeqc/man/phrSetOutputStringsOn.Rd
phreeqc/LICENSE