Rphree: Interface to the geochemical modelling program PHREEQC

Interface and utility functions for the geochemical simulator PHREEQC. PHREEQC (version 2.17) itself is shipped in this package and compiled as shared library to achieve online calculations. Some functions for visualization and database manipulations are included.

AuthorMarco De Lucia
Date of publication2015-01-24 21:20:55
MaintainerMarco De Lucia <delucia@gfz-potsdam.de>
LicenseMIT + file LICENSE
Version0.1-6

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Man pages

AddProp: Add a new property (species, pure phase, ...) to an input...

Distribute: Distribute properties in an input buffer.

DistributeKin: DistributeKin

DS_CO2sol: Duan and Sun model for solubility of CO2 in NaCl solutions

DS_PhiCO2: Fugacity coefficient of CO2

DS_SI_CO2: Saturation Index for solubility of CO2(g) using Duan equation...

DS_ZCO2: Compressibility Z of CO2 by the Duan and Sun (2003) model

DS_ZCO2_var: Compressibility Z of CO2 by the Duan and Sun (2003) model

PlotMinDelta: Barplot of mineral deltas of an Rphree solution

RepSol: Replicate a SOLUTION

RGetPhases: Workhorse function for extraction of

RInputFromList: Transform a (formatted) solution in a new input buffer.

RKS_SI_CO2: Calculate the Saturation Index of CO2(g) by...

Rphree: Run online PHREEQC with the shipped 2.17 version

RPhreeCheckSel: Generate and/or check the selection of output from Rphree

RPhreeExt: Workhorse function for extraction of informations from a...

RPhreeFile: Read a normal PHREEQC input file and prepare it for Rphree

RPhreeFormatOut: Format the output returned by PHREEQC

Rphree-package: Rphree: R interface to the PHREEQC geochemical modeling...

RPhreeWriteInp: RPhreeWriteInp

RPinfo: Extract specific values from an Rphree output

RReadOut: RReadOut

RReadOutKin: RReadOutKin, import the output file of a kinetic simulation...

RReadPhases: extract the phases from a Rphree solution

SuppressSim: Suppress a simulation from an input buffer

VizAct: Plots activities or activity coefficients of a set of...

VizMinDelta: Plots mineral deltas of a set of solutions

VizSol: Visualize barplot of total solute concentrations of...

Functions

AddProp Man page
Distribute Man page
DistributeKin Man page
DS_CO2sol Man page
DS_PhiCO2 Man page
DS_SI_CO2 Man page
DS_ZCO2 Man page
DS_ZCO2_var Man page
PlotMinDelta Man page
RepSol Man page
RGetPhases Man page
RInputFromList Man page
RKS_SI_CO2 Man page
Rphree Man page
RPhreeCheckSel Man page
RPhreeExt Man page
RPhreeFile Man page
RPhreeFormatOut Man page
Rphree-package Man page
Rphreeqc Man page
RPhreeWriteInp Man page
RPinfo Man page
RReadOut Man page
RReadOutKin Man page
RReadPhases Man page
SuppressSim Man page
VizAct Man page
VizMinDelta Man page
VizSol Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/Rphree_Main.R R/Rphree_Pkg.R R/Rphree_Solub.R R/Rphree_Utils.R R/Rphree_Viz.R
inst
inst/CITATION
inst/extdata
inst/extdata/ex1.phrq
inst/extdata/iso.dat
inst/extdata/llnl_rphree.dat
inst/extdata/phreeqc.dat
inst/extdata/pitzer_rphree.dat
inst/extdata/wateq4f.dat
man
man/AddProp.Rd man/DS_CO2sol.Rd man/DS_PhiCO2.Rd man/DS_SI_CO2.Rd man/DS_ZCO2.Rd man/DS_ZCO2_var.Rd man/Distribute.Rd man/DistributeKin.Rd man/PlotMinDelta.Rd man/RGetPhases.Rd man/RInputFromList.Rd man/RKS_SI_CO2.Rd man/RPhreeCheckSel.Rd man/RPhreeExt.Rd man/RPhreeFile.Rd man/RPhreeFormatOut.Rd man/RPhreeWriteInp.Rd man/RPinfo.Rd man/RReadOut.Rd man/RReadOutKin.Rd man/RReadPhases.Rd man/RepSol.Rd man/Rphree-package.Rd man/Rphree.Rd man/SuppressSim.Rd man/VizAct.Rd man/VizMinDelta.Rd man/VizSol.Rd
src
src/Makevars.win
src/RPhree.c
src/RPhree.h
src/advection.c
src/basic.c
src/basic.h
src/basicsubs.c
src/cl1.c
src/cvdense.c
src/cvdense.h
src/cvode.c
src/cvode.h
src/dense.c
src/dense.h
src/dw.c
src/global.h
src/global_structures.h
src/input.c
src/input.h
src/integrate.c
src/inverse.c
src/isotopes.c
src/kinetics.c
src/kinetics.h
src/main.c
src/mainsubs.c
src/model.c
src/nvector.c
src/nvector.h
src/nvector_serial.c
src/nvector_serial.h
src/output.c
src/output.h
src/p2c.h
src/p2clib.c
src/parse.c
src/phqalloc.c
src/phqalloc.h
src/phreeqc_files.c
src/phrqproto.h
src/phrqtype.h
src/pitzer.c
src/pitzer.h
src/pitzer_structures.c
src/pitzer_structures.h
src/prep.c
src/print.c
src/read.c
src/readtr.c
src/sit.c
src/smalldense.c
src/smalldense.h
src/spread.c
src/step.c
src/step.h
src/structures.c
src/sundialsmath.c
src/sundialsmath.h
src/sundialstypes.h
src/tally.c
src/tidy.c
src/transport.c
src/utilities.c

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.