Package: phreeqc 3.8.0

phreeqc: R Interface to Geochemical Modeling Software

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.

Authors:S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb], R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUNDIALS

phreeqc_3.8.0.tar.gz
phreeqc_3.8.0.zip(r-4.5)phreeqc_3.8.0.zip(r-4.4)phreeqc_3.8.0.zip(r-4.3)
phreeqc_3.8.0.tgz(r-4.4-x86_64)phreeqc_3.8.0.tgz(r-4.4-arm64)phreeqc_3.8.0.tgz(r-4.3-x86_64)phreeqc_3.8.0.tgz(r-4.3-arm64)
phreeqc_3.8.0.tar.gz(r-4.5-noble)phreeqc_3.8.0.tar.gz(r-4.4-noble)
phreeqc_3.8.0.tgz(r-4.4-emscripten)phreeqc_3.8.0.tgz(r-4.3-emscripten)
phreeqc.pdf |phreeqc.html✨
phreeqc/json (API)

# Install 'phreeqc' in R:
install.packages('phreeqc', repos = c('https://scharlton2.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/usgs-coupled/iphreeqc/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • Amm.dat - The Amm.dat database.
  • ColdChem.dat - The ColdChem.dat database.
  • Kinec.v2.dat - Thermodynamic and rates database from Oelkers and coworkers.
  • PHREEQC_ThermoddemV1.10_15Dec2020.dat - Thermochemical Database from the BRGM institute
  • Tipping_Hurley.dat - The Tipping_Hurley.dat database
  • core10.dat - The core10.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
  • ex13a - Example 13-Aragonite-Strontianite Solid Solution
  • ex13b - Example 13-Aragonite-Strontianite Solid Solution
  • ex13c - Example 13-Aragonite-Strontianite Solid Solution
  • ex14 - Example 14-Advective Transport, Cation Exchange, Surface Complexation, and Mineral Equilibria
  • ex15 - Example 15-1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
  • 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, and Langmuir Isotherms, and With a Deterministic Distribution of Sorption Sites for Organic Matter, Clay Minerals, and Iron Oxyhydroxides
  • ex2 - Example 2-Equilibration With Pure Phases
  • ex20a - Example 20-Distribution of Isotopes Between Water and Calcite
  • ex20b - Example 20-Distribution of Isotopes Between Water and Calcite
  • ex21 - Example 21-Modeling Diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a Radial Diffusion Cell
  • 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 Oxygen
  • frezchem.dat - The frezchem.dat database
  • 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.
  • phreeqc.dat - The phreeqc.dat database
  • phreeqc_rates.dat - Thermodynamic and rates database
  • pitzer.dat - The pitzer.dat database.
  • sit.dat - The sit.dat database.
  • wateq4f.dat - The wateq4f.dat database.

On CRAN:

3.03 score 9 stars 60 scripts 633 downloads 42 exports 0 dependencies

Last updated 4 months agofrom:8eabf69a0f. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-win-x86_64OKNov 16 2024
R-4.5-linux-x86_64OKNov 16 2024
R-4.4-win-x86_64OKNov 16 2024
R-4.4-mac-x86_64OKNov 16 2024
R-4.4-mac-aarch64OKNov 16 2024
R-4.3-win-x86_64OKNov 16 2024
R-4.3-mac-x86_64OKNov 16 2024
R-4.3-mac-aarch64OKNov 16 2024

Exports:phrAccumulateLinephrClearAccumulatedLinesphrGetAccumulatedLinesphrGetComponentListphrGetDumpFileNamephrGetDumpFileOnphrGetDumpStringsphrGetDumpStringsOnphrGetErrorFileNamephrGetErrorFileOnphrGetErrorStringsphrGetErrorStringsOnphrGetLogFileNamephrGetLogFileOnphrGetLogStringsphrGetLogStringsOnphrGetOutputFileNamephrGetOutputFileOnphrGetOutputStringsphrGetOutputStringsOnphrGetSelectedOutputphrGetSelectedOutputFileNamephrGetWarningStringsphrLoadDatabasephrLoadDatabaseStringphrRunAccumulatedphrRunFilephrRunStringphrSetDumpFileNamephrSetDumpFileOnphrSetDumpStringsOnphrSetErrorFileNamephrSetErrorFileOnphrSetErrorStringsOnphrSetLogFileNamephrSetLogFileOnphrSetLogStringsOnphrSetOutputFileNamephrSetOutputFileOnphrSetOutputStringsOnphrSetSelectedOutputFileNamephrSetSelectedOutputFileOn

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
R interface to the PHREEQC geochemical modeling program.phreeqc-package phreeqc
The Amm.dat database.Amm.dat
The ColdChem.dat database.ColdChem.dat
The core10.dat databasecore10.dat
Example 1-Speciation Calculationex1
Example 10-Aragonite-Strontianite Solid Solutionex10
Example 11-Transport and Cation Exchangeex11
Example 12-Advective and Diffusive Flux of Heat and Solutesex12
Example 13-Aragonite-Strontianite Solid Solutionex13a ex13b ex13c
Example 14-Advective Transport, Cation Exchange, Surface Complexation, and Mineral Equilibriaex14
Example 15-1D Transport: Kinetic Biodegradation, Cell Growth, and Sorptionex15
The ex15.dat databaseex15.dat
Example 16-Inverse Modeling of Sierra Spring Watersex16
Example 17-Inverse Modeling With Evaporationex17
Example 18-Inverse Modeling of the Madison Aquiferex18
Example 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 Oxyhydroxidesex19
Example 2-Equilibration With Pure Phasesex2
Example 20-Distribution of Isotopes Between Water and Calciteex20a ex20b
Example 21-Modeling Diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a Radial Diffusion Cellex21
Example 22-Modeling Gas Solubilities: CO2 at High Pressuresex22
Example 3-Mixingex3
Example 4-Evaporation and Homogeneous Redox Reactionsex4
Example 5-Irreversible Reactionsex5
Example 6-Reaction-Path Calculationsex6
Example 7-Gas-Phase Calculationsex7
Example 8-Surface Complexationex8
Example 9-Kinetic Oxidation of Dissolved Ferrous Iron With Oxygenex9
The frezchem.dat databasefrezchem.dat
The iso.dat database.iso.dat
Thermodynamic and rates database from Oelkers and coworkers.Kinec.v2.dat
The llnl.dat database.llnl.dat
The minteq.dat database.minteq.dat
The minteq.v4.dat database.minteq.v4.dat
Accumulate line(s) for input to phreeqc.phrAccumulateLine
Clear the accumulated input buffer.phrClearAccumulatedLines
Thermodynamic and rates databasephreeqc_rates.dat
Thermochemical Database from the BRGM institute (French Geological Survey)PHREEQC_ThermoddemV1.10_15Dec2020.dat
The phreeqc.dat databasephreeqc.dat
Retrieve the accumulated input.phrGetAccumulatedLines
Retrieve a list containing the current list of components.phrGetComponentList
Retrieve the name of the dump file.phrGetDumpFileName
Retrieve the current value of the dump file switch.phrGetDumpFileOn
Retrieve DUMP strings.phrGetDumpStrings
Retrieve the current value of the dump strings switch.phrGetDumpStringsOn
Retrieve the name of the error file.phrGetErrorFileName
Retrieve the current value of the error file switch.phrGetErrorFileOn
Retrieve error string messages.phrGetErrorStrings
Retrieve the current value of the error strings switch.phrGetErrorStringsOn
Retrieve the name of the log file.phrGetLogFileName
Retrieve the current value of the log file switch.phrGetLogFileOn
Retrieve log output.phrGetLogStrings
Retrieve the current value of the log strings switch.phrGetLogStringsOn
Retrieve the name of the output file.phrGetOutputFileName
Retrieve the current value of the output file switch.phrGetOutputFileOn
Retrieve standard phreeqc output.phrGetOutputStrings
Retrieve the current value of the output strings switch.phrGetOutputStringsOn
Returns the contents of the selected output as a list of data frames.phrGetSelectedOutput
Retrieve the name of the selected_output file.phrGetSelectedOutputFileName
Retrieve warning messages.phrGetWarningStrings
Load a phreeqc database filephrLoadDatabase
Load a phreeqc database as a string or a list of strings.phrLoadDatabaseString
Runs the accumulated input.phrRunAccumulated
Run phreeqc input filephrRunFile
Runs phreeqc using the given string as input.phrRunString
Set the name of the dump file.phrSetDumpFileName
Set the dump file on/off.phrSetDumpFileOn
Set dump strings on/off.phrSetDumpStringsOn
Set the name of the error file.phrSetErrorFileName
Set error file on/off.phrSetErrorFileOn
Set error strings on/off.phrSetErrorStringsOn
Set the name of the log file.phrSetLogFileName
Set log file on/off.phrSetLogFileOn
Set log strings on/off.phrSetLogStringsOn
Set the name of the output file.phrSetOutputFileName
Set output file on/off.phrSetOutputFileOn
Set output strings on/off.phrSetOutputStringsOn
Set the name of the selected_output file.phrSetSelectedOutputFileName
Set selected_output file on/off.phrSetSelectedOutputFileOn
The pitzer.dat database.pitzer.dat
The sit.dat database.sit.dat
The Tipping_Hurley.dat databaseTipping_Hurley.dat
The wateq4f.dat database.wateq4f.dat