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iphreeqc/R/phreeqc.R.in
Scott R Charlton f625b45d93 working on build automation 
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8716 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-07 04:00:21 +00:00

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##' R interface to the phreeqc geochemical modeling program.
##'
##' Provides an interface to PHREEQC (Version 3)--A Computer Program for
##' Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse
##' Geochemical Calculations.
##'
##' \tabular{ll}{Package: \tab phreeqc\cr Type: \tab Package\cr Version: \tab 1.0-@REVISION_SVN@\cr Date: \tab @RELEASE_DATE@\cr License: \tab Unlimited\cr}
##'
##' @name phreeqc-package
##' @aliases phreeqc-package phreeqc
##' @docType package
##' @author David L. Parkhurst \email{dlpark@@usgs.gov}\cr C.A.J. Appelo
##' \email{appt@@hydrochemistry.eu}\cr Maintainer: Scott R. Charlton
##' \email{charlton@@usgs.gov}
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf} \url{http://computation.llnl.gov/casc/sundials/main.html}
##' @keywords package
##' @examples
##'
##' #########################################################################
##' # Run ex2 and plot results
##' #########################################################################
##'
##' # load the phreeqc.dat database
##' phrLoadDatabaseString(phreeqc.dat)
##'
##' # run example 2
##' phrRunString(ex2)
##'
##' # retrieve selected_output as a list of data.frame
##' so <- phrGetSelectedOutput()
##'
##' # plot the results
##' attach(so$n1)
##' title <- "Gypsum-Anhydrite Stability"
##' xlabel <- "Temperature, in degrees celcius"
##' ylabel <- "Saturation index"
##' plot(temp.C., si_gypsum, main = title, xlab = xlabel, ylab = ylabel,
##' col = "darkred", xlim = c(25, 75), ylim = c(-0.4, 0.0))
##' points(temp.C., si_anhydrite, col = "darkgreen")
##' legend("bottomright", c("Gypsum", "Anhydrite"),
##' col = c("darkred", "darkgreen"), pch = c(1, 1))
NULL
# Package Functions
##' Accumulate line(s) for input to phreeqc.
##'
##' Appends a line of text to the input buffer in order to be run using
##' \code{\link{phrRunAccumulated}}.
##'
##' @export phrAccumulateLine
##' @useDynLib phreeqc
##' @param line the line(s) to add for input to phreeqc.
##' @return NULL
##' @family Accumulate
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # this example loads the phreeqc.dat database, accumulates input, and
##' # runs it
##' phrLoadDatabaseString(phreeqc.dat)
##' phrAccumulateLine("TITLE Example 2.--Temperature dependence of solubility")
##' phrAccumulateLine(" of gypsum and anhydrite")
##' phrAccumulateLine("SOLUTION 1 Pure water")
##' phrAccumulateLine(" pH 7.0")
##' phrAccumulateLine(" temp 25.0")
##' phrAccumulateLine("EQUILIBRIUM_PHASES 1")
##' phrAccumulateLine(" Gypsum 0.0 1.0")
##' phrAccumulateLine(" Anhydrite 0.0 1.0")
##' phrAccumulateLine("REACTION_TEMPERATURE 1")
##' phrAccumulateLine(" 25.0 75.0 in 51 steps")
##' phrAccumulateLine("SELECTED_OUTPUT")
##' phrAccumulateLine(" -file ex2.sel")
##' phrAccumulateLine(" -temperature")
##' phrAccumulateLine(" -si anhydrite gypsum")
##' phrAccumulateLine("END")
##' phrSetOutputFileOn(TRUE)
##' if (is.null(phrRunAccumulated())) {
##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep = ""))
##' }
##'
phrAccumulateLine <-
function(line) {
invisible(.Call("accumLineLst", as.character(line), PACKAGE = .packageName))
}
##' Clear the accumulated input buffer.
##'
##' Clears the accumulated input buffer. The input buffer is accumulated from
##' calls to the \code{\link{phrAccumulateLine}} method.
##'
##' @export phrClearAccumulatedLines
##' @useDynLib phreeqc
##' @return NULL
##' @family Accumulate
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example loads some keyword input, clears the input, and displays
##' # the results.
##' phrAccumulateLine("SOLUTION 1")
##' phrAccumulateLine("END")
##' cat("The accumulated input is:", phrGetAccumulatedLines(), sep = "\n")
##' phrClearAccumulatedLines()
##' cat("The accumulated input now is:\n", phrGetAccumulatedLines(), sep = "\n")
##'
phrClearAccumulatedLines <-
function() {
invisible(.Call("clearAccum", PACKAGE = .packageName))
}
##' Retrieve the accumulated input.
##'
##' Returns the accumulated input as a character vector.
##'
##' @export phrGetAccumulatedLines
##' @useDynLib phreeqc
##' @return A character vector containing the accumulated input.
##' @family Accumulate
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example loads some keyword input and displays the contents.
##' phrAccumulateLine("SOLUTION 1")
##' phrAccumulateLine("END")
##' cat("The accumulated input is:", phrGetAccumulatedLines(), sep = "\n")
##'
phrGetAccumulatedLines <-
function() {
return(.Call("getAccumLines", PACKAGE = .packageName))
}
##' Retrieve a list containing the current list of components.
##'
##' @export phrGetComponentList
##' @useDynLib phreeqc
##' @return A list containing the names of the components defined in the current system.
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example runs the ex2 input file and echos the list of components.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrRunString(ex2)
##' cat("components:\n")
##' for (comp in phrGetComponentList()) {
##' cat(comp, "\n")
##' }
##'
phrGetComponentList <-
function() {
return(.Call("listComps", PACKAGE = .packageName))
}
##' Retrieve the name of the dump file.
##'
##' Retrieves the name of the dump file. This file name is used if not
##' specified within DUMP input. The default value is dump.0.out.
##'
##' @export phrGetDumpFileName
##' @useDynLib phreeqc
##' @return The name of the dump file as a string.
##' @family Dump
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetDumpFileOn(TRUE)
##'
##' input <- "SOLUTION 1 Pure water \n"
##' input <- paste(input, "EQUILIBRIUM_PHASES 1 \n")
##' input <- paste(input, " Calcite 0 10 \n")
##' input <- paste(input, "SAVE solution 1 \n")
##' input <- paste(input, "SAVE equilibrium_phases 1 \n")
##' input <- paste(input, "DUMP \n")
##' input <- paste(input, " -solution 1 \n")
##' input <- paste(input, " -equilibrium_phases 1\n")
##'
##' if (!is.null(phrRunString(input))) {
##' cat(phrGetErrorStrings())
##' }
##' cat(paste("see ", phrGetDumpFileName(), "."))
##'
##'
phrGetDumpFileName <-
function() {
return(.Call("getDumpFileName", PACKAGE = .packageName))
}
##' Retrieve DUMP strings.
##'
##' Retrieves the string buffer containing DUMP output as a character
##' vector.
##'
##' @export phrGetDumpStrings
##' @useDynLib phreeqc
##' @return The dump output as a character vector.
##' @family Dump
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetDumpStringsOn(TRUE)
##'
##' input <- "SOLUTION 1 Pure water \n"
##' input <- paste(input, "EQUILIBRIUM_PHASES 1 \n")
##' input <- paste(input, " Calcite 0 10 \n")
##' input <- paste(input, "SAVE solution 1 \n")
##' input <- paste(input, "SAVE equilibrium_phases 1 \n")
##' input <- paste(input, "DUMP \n")
##' input <- paste(input, " -solution 1 \n")
##' input <- paste(input, " -equilibrium_phases 1 \n")
##'
##' if (!is.null(phrRunString(input))) {
##' cat(phrGetErrorStrings(), sep = "\n")
##' }
##' cat(phrGetDumpStrings(), sep = "\n")
##'
phrGetDumpStrings <-
function() {
return(.Call("getDumpStrings", PACKAGE = .packageName))
}
##' Retrieve the name of the error file.
##'
##' Retrieves the name of the error file. The default value is phreeqc.0.err.
##'
##' The error file switch must be set using the \code{\link{phrSetErrorFileOn}} function.
##'
##' @export phrGetErrorFileName
##' @useDynLib phreeqc
##' @return The name of the error file as a string.
##' @family Error
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetErrorFileName <-
function() {
return(.Call("getErrorFileName", PACKAGE = .packageName))
}
##' Retrieve the current value of the dump file switch.
##'
##' @export phrGetDumpFileOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Dump
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetDumpFileOn <-
function() {
return(.Call("getDumpFileOn", PACKAGE = .packageName))
}
##' Retrieve the current value of the dump strings switch.
##'
##' @export phrGetDumpStringsOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Dump
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetDumpStringsOn <-
function() {
return(.Call("getDumpStringOn", PACKAGE = .packageName))
}
##' Retrieve the current value of the error file switch.
##'
##' @export phrGetErrorFileOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Error
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetErrorFileOn <-
function() {
return(.Call("getErrorFileOn", PACKAGE = .packageName))
}
##' Retrieve the current value of the error strings switch.
##'
##' @export phrGetErrorStringsOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Error
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetErrorStringsOn <-
function() {
return(.Call("getErrorStringOn", PACKAGE = .packageName))
}
##' Retrieve the current value of the log file switch.
##'
##' @export phrGetLogFileOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Log
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetLogFileOn <-
function() {
return(.Call("getLogFileOn", PACKAGE = .packageName))
}
##' Retrieve the current value of the log strings switch.
##'
##' @export phrGetLogStringsOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Log
##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##'
phrGetLogStringsOn <-
function() {
return(.Call("getLogStringOn", PACKAGE = .packageName))
}
##' Retrieve the current value of the output file switch.
##'
##' @export phrGetOutputFileOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetOutputFileOn <-
function() {
return(.Call("getOutputFileOn", PACKAGE = .packageName))
}
##' Retrieve the current value of the output strings switch.
##'
##' @export phrGetOutputStringsOn
##' @useDynLib phreeqc
##' @return TRUE if errors are currently being written to file.
##' @family Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##'
phrGetOutputStringsOn <-
function() {
return(.Call("getOutputStringOn", PACKAGE = .packageName))
}
##' Retrieve error string messages.
##'
##' Retrieves a character vector containing any error messages that were generated
##' during the last invocation of the following methods:
##' \code{\link{phrAccumulateLine}}, \code{\link{phrLoadDatabase}},
##' \code{\link{phrLoadDatabaseString}}, \code{\link{phrRunAccumulated}},
##' \code{\link{phrRunFile}}, \code{\link{phrRunString}}
##'
##' This routine is rarely needed when running interactively since the error
##' string is displayed when it occurs.
##'
##' @export phrGetErrorStrings
##' @useDynLib phreeqc
##' @return The error messages as a character vector.
##' @family Error
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # loaddatabase should fail
##' n <- try(phrLoadDatabase("missing.dat"), silent = TRUE)
##' # if n is non-NULL display error string
##' if (!is.null(n)) phrGetErrorStrings()
##'
phrGetErrorStrings <-
function() {
return(.Call("getErrorStrings", PACKAGE = .packageName))
}
##' Retrieve the name of the log file.
##'
##' Retrieves the name of the log file. The default name is phreeqc.0.log.
##'
##' @export phrGetLogFileName
##' @useDynLib phreeqc
##' @return The name of the log file as a string.
##' @family Log
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example checks to see if the log file is turned on
##' # and prints the appropriate message
##' if (phrGetLogFileOn()) {
##' cat("The name of the log file (is/will be):", phrGetLogFileName(), "\n")
##' } else {
##' cat("The log file is not turned on\n")
##' }
##'
phrGetLogFileName <-
function() {
return(.Call("getLogFileName", PACKAGE = .packageName))
}
##' Retrieve log output.
##'
##' Retrieves the string buffer containing phreeqc log output.
##'
##' @export phrGetLogStrings
##' @useDynLib phreeqc
##' @return A character vector containing phreeqc log output.
##' @family Log
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with gypsum with the output file on.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputFileOn(TRUE)
##'
##' input <- vector(mode="character")
##' input <- c(input, "SOLUTION 1 Pure water ")
##' input <- c(input, "EQUILIBRIUM_PHASES 1 ")
##' input <- c(input, " Gypsum 0 10 ")
##' input <- c(input, "KNOBS ")
##' input <- c(input, " -logfile TRUE ")
##'
##' if (is.null(phrRunString(input))) {
##' log <- phrGetLogStrings()
##' }
##'
phrGetLogStrings <-
function() {
return(.Call("getLogStrings", PACKAGE = .packageName))
}
##' Retrieve the name of the output file.
##'
##' Retrieves the name of the output file. The default name is phreeqc.0.out.
##'
##' @export
##' @useDynLib phreeqc
##' @return The name of the output file as a string.
##' @family Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with gypsum with the output file on.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputFileOn(TRUE)
##'
##' input <- vector(mode="character")
##' input <- c(input, "SOLUTION 1 Pure water ")
##' input <- c(input, "EQUILIBRIUM_PHASES 1 ")
##' input <- c(input, " Gypsum 0 10 ")
##'
##' if (is.null(phrRunString(input))) {
##' output <- readLines(phrGetOutputFileName())
##' unlink(phrGetOutputFileName()) # tidy up
##' }
##'
phrGetOutputFileName <-
function() {
return(.Call("getOutputFileName", PACKAGE = .packageName))
}
##' Retrieve standard phreeqc output.
##'
##' Retrieves the phreeqc output as a character vector.
##'
##' A NULL value is returned when there is no selected-output.
##'
##' @export phrGetOutputStrings
##' @useDynLib phreeqc
##' @return A character vector containing phreeqc output.
##' @family Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and displays
##' # the results
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##'
##' input <- vector(mode="character")
##' input <- c(input, "SOLUTION 1 Pure water ")
##' input <- c(input, "EQUILIBRIUM_PHASES 1 ")
##' input <- c(input, " Gypsum 0 10 ")
##'
##' if (is.null(phrRunString(input))) {
##' cat(phrGetOutputStrings(), sep = "\n")
##' }
##'
phrGetOutputStrings <-
function() {
return(.Call("getOutputStrings", PACKAGE = .packageName))
}
##' Returns the contents of the selected output as a list of data frames.
##'
##' phrGetSelectedOutput returns a named list containing the resultant
##' selected output blocks. The names of each data frame are creating by
##' concatenating the letter 'n' and the user number of the selected output
##' block.
##'
##' phrGetSelectedOutput uses the \code{\link{make.names}} function to create
##' valid column names. The allow_ variable is passed to
##' \code{\link{make.names}} and is used for backward compatibility.
##'
##' @export phrGetSelectedOutput
##' @useDynLib phreeqc
##' @param allow_ used for compatibility with R prior to 1.9.0 (default is TRUE).
##' @return Returns a named list of data frames containing the selected_output from the previous run.
##' @family Selected Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # Load database and run ex2
##' phrLoadDatabaseString(phreeqc.dat)
##' phrRunString(ex2)
##'
##' # display a summary of the results
##' df <- phrGetSelectedOutput()
##' summary(df$n1)
##'
phrGetSelectedOutput <-
function(allow_ = TRUE) {
sel_outs <- .Call("getSelOutLst", PACKAGE = .packageName)
if (!is.null(sel_outs)) {
for (t in names(sel_outs)) {
if (!is.null(sel_outs[[t]])) {
names(sel_outs[[t]]) <- make.names(names(sel_outs[[t]]), unique = TRUE,
allow_ = allow_)
}
}
}
return(sel_outs)
}
##' Retrieve warning messages.
##'
##' Returns a character vector containing any warning messages that were
##' generated during the last invocation of the following methods:
##' \code{\link{phrAccumulateLine}}, \code{\link{phrLoadDatabase}},
##' \code{\link{phrLoadDatabaseString}}, \code{\link{phrRunAccumulated}},
##' \code{\link{phrRunFile}}, \code{\link{phrRunString}}.
##'
##' A NULL value is returned if there are no warnings.
##'
##' @export phrGetWarningStrings
##' @useDynLib phreeqc
##' @return A character vector containing warning messages or NULL.
##' @family Warning
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example loads the phreeqc.dat database and attempts to use the
##' # DATABASE keyword to set the database to wateq4f.dat. A warning is
##' # displayed stating that the DATABASE keyword is ignored in the 'R'
##' # implementation.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrAccumulateLine("DATABASE wateq4f.dat")
##' phrAccumulateLine("SOLUTION 1")
##' phrRunAccumulated()
##' if (!is.null(phrGetWarningStrings())) {
##' cat(phrGetWarningStrings(), sep = "\n")
##' }
##'
phrGetWarningStrings <-
function() {
return(.Call("getWarningStrings", PACKAGE = .packageName))
}
##' Load a phreeqc database file
##'
##' Loads the given phreeqc database into phreeqc. Returns NULL if successful.
##'
##'
##' @export phrLoadDatabase
##' @useDynLib phreeqc
##' @param filename The name of the database file.
##' @return This function returns NULL.
##' @family Load Database
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # create temporary database file
##' tf <- tempfile()
##' writeLines(phreeqc.dat, tf)
##'
##' if (is.null(phrLoadDatabase(tf))) {
##' cat("database ok\n")
##' } else {
##' cat("database contains errors\n")
##' }
##'
##' # delete temporary database file
##' unlink(tf)
##'
phrLoadDatabase <-
function(filename) {
invisible(.Call("loadDB", as.character(filename), PACKAGE = .packageName))
}
##' Load a phreeqc database as a string or a list of strings.
##'
##' Load the specified string(s) as a database into phreeqc. Returns NULL if
##' successful.
##'
##' All previous definitions are cleared.
##'
##' @export phrLoadDatabaseString
##' @useDynLib phreeqc
##' @param input String containing data to be used as the phreeqc database.
##' @return This function returns NULL.
##' @family Load Database
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @keywords interface
##' @examples
##'
##' # this example loads the phreeqc.dat database, turns on the
##' # output file and runs ex2 as a string
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputFileOn(TRUE)
##' if (is.null(phrRunString(ex2))) {
##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep = ""))
##' }
##'
phrLoadDatabaseString <-
function(input) {
invisible(.Call("loadDBLst", as.character(input), PACKAGE = .packageName))
}
##' Runs the accumulated input.
##'
##' Runs the input buffer as defined by calls to \code{\link{phrAccumulateLine}}.
##'
##' After calling \code{phrRunAccumulated} \code{\link{phrGetAccumulatedLines}} can
##' be used in case of errors. The accumulated lines will be cleared on the next call
##' to \code{\link{phrAccumulateLine}}.
##'
##' The \code{phrAccumulateLine} method cannot be called until a database
##' has been successfully loaded by calls to either
##' \code{\link{phrLoadDatabase}} or \code{\link{phrLoadDatabaseString}}.
##'
##' @export phrRunAccumulated
##' @useDynLib phreeqc
##' @return This function returns NULL on success.
##' @family Accumulate
##' @family Run
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # turn on the output file
##' phrSetOutputFileOn(TRUE)
##'
##' # load the phreeqc.dat database
##' phrLoadDatabaseString(phreeqc.dat)
##'
##' # accumulate the input
##' phrAccumulateLine("TITLE Example 2.--Temperature dependence of solubility")
##' phrAccumulateLine(" of gypsum and anhydrite")
##' phrAccumulateLine("SOLUTION 1 Pure water")
##' phrAccumulateLine(" pH 7.0")
##' phrAccumulateLine(" temp 25.0")
##' phrAccumulateLine("EQUILIBRIUM_PHASES 1")
##' phrAccumulateLine(" Gypsum 0.0 1.0")
##' phrAccumulateLine(" Anhydrite 0.0 1.0")
##' phrAccumulateLine("REACTION_TEMPERATURE 1")
##' phrAccumulateLine(" 25.0 75.0 in 51 steps")
##' phrAccumulateLine("SELECTED_OUTPUT")
##' phrAccumulateLine(" -file ex2.sel")
##' phrAccumulateLine(" -temperature")
##' phrAccumulateLine(" -si anhydrite gypsum")
##' phrAccumulateLine("END")
##'
##' # run it and echo the name of the output file
##' if (is.null(phrRunAccumulated())) {
##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep = ""))
##' }
phrRunAccumulated <-
function() {
invisible(.Call("runAccum", PACKAGE = .packageName))
}
##' Run phreeqc input file
##'
##' phrRunFile executes a phreeqc run using a file as input
##'
##' @export phrRunFile
##' @useDynLib phreeqc
##' @param filename The file name of the phreeqc input file.
##' @return This function returns NULL on success.
##' @family Run
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # load the phreeqc.dat database
##' phrLoadDatabaseString(phreeqc.dat)
##'
##' # create ex2 if it doesn't exist
##' if (!file.exists("ex2")) writeLines(ex2, "ex2")
##'
##' # run ex2
##' if (is.null(phrRunFile("ex2"))) {
##' cat("use phrGetSelectedOutput() to see results.")
##' }
##'
##' unlink("ex2") # tidy up
##'
phrRunFile <-
function(filename) {
invisible(.Call("runFile", as.character(filename), PACKAGE = .packageName))
}
##' Runs phreeqc using the given string as input.
##'
##' Runs phreeqc using the given string as input. Returns the number of
##' errors encountered during the run.
##'
##' The \code{RunString} method cannot be called until a database has
##' been successfully loaded by one of the following the LoadDatabase
##' methods \code{\link{phrLoadDatabase}}, \code{\link{phrLoadDatabaseString}}.
##'
##' @export phrRunString
##' @useDynLib phreeqc
##' @param input character vector containing phreeqc input
##' @return This function returns NULL on success.
##' @family Run
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @keywords interface
##' @examples
##'
##' #
##' # This example accumulates phreeqc input into a character vector
##' # and runs it.
##' #
##'
##' # load phreeqc.dat file
##' phrLoadDatabaseString(phreeqc.dat)
##'
##' # create input
##' input <- vector()
##' input <- c(input, "SOLUTION 1")
##' input <- c(input, " temp 25.0")
##' input <- c(input, " pH 7.0")
##'
##' # turn on output
##' phrSetOutputFileOn(TRUE)
##'
##' # run input
##' phrRunString(input)
##' cat(paste("see", phrGetOutputFileName(), "."))
##'
phrRunString <-
function(input) {
invisible(.Call("runStringLst", as.character(input), PACKAGE = .packageName))
}
##' Set the name of the dump file.
##'
##' Sets the name of the dump file. This file name is used if not specified
##' within the DUMP keyword block. The default value is dump.0.out.
##'
##' @export phrSetDumpFileName
##' @useDynLib phreeqc
##' @param filename the name of the file.
##' @return NULL
##' @family Dump
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and writes the
##' # dump results to file.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetDumpFileOn(TRUE)
##' phrSetDumpFileName("phreeqc.dump")
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0 10 ',
##' 'SAVE solution 1 ',
##' 'SAVE equilibrium_phases 1 ',
##' 'DUMP ',
##' ' -solution 1 ',
##' ' -equilibrium_phases 1 '
##' )
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetDumpFileName(), "\n")
##' }
##'
phrSetDumpFileName <-
function(filename) {
invisible(.Call("setDumpFileName", as.character(filename), PACKAGE = .packageName))
}
##' Set the dump file on/off.
##'
##' Sets the dump file switch on or off. This switch controls whether or
##' not phreeqc writes to the dump file. The initial setting is off.
##'
##' @export phrSetDumpFileOn
##' @useDynLib phreeqc
##' @param value if TRUE, captures output normally sent to the dump file into a buffer.
##' @return NULL
##' @family Dump
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and writes the
##' # dump results to file.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetDumpFileOn(TRUE)
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0 10 ',
##' 'SAVE solution 1 ',
##' 'SAVE equilibrium_phases 1 ',
##' 'DUMP ',
##' ' -solution 1 ',
##' ' -equilibrium_phases 1 '
##' )
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetDumpFileName(), "\n")
##' }
##'
phrSetDumpFileOn <-
function(value) {
invisible(.Call("setDumpFileOn", as.logical(value), PACKAGE = .packageName))
}
##' Set dump strings on/off.
##'
##' Sets the dump strings switch on or off. This switch controls whether or
##' not the data normally sent to the dump file are stored in a buffer for
##' retrieval. The initial setting is off.
##'
##' @export phrSetDumpStringsOn
##' @useDynLib phreeqc
##' @param value if TRUE, captures output normally sent to the error file into a buffer.
##' @return NULL
##' @family Dump
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and echos the
##' # dump strings.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetDumpStringsOn(TRUE)
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0 10 ',
##' 'SAVE solution 1 ',
##' 'SAVE equilibrium_phases 1 ',
##' 'DUMP ',
##' ' -solution 1 ',
##' ' -equilibrium_phases 1 '
##' )
##'
##' if (is.null(phrRunString(input))) {
##' cat("Dump:\n")
##' cat(phrGetDumpStrings(), sep = "\n")
##' }
##'
phrSetDumpStringsOn <-
function(value) {
invisible(.Call("setDumpStringOn", as.logical(value), PACKAGE = .packageName))
}
##' Set the name of the error file.
##'
##' Sets the name of the error file. The default value is phreeqc.0.err.
##'
##' @export phrSetErrorFileName
##' @useDynLib phreeqc
##' @param filename the name of the file.
##' @return NULL
##' @family Error
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and displays
##' # the log file name.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetLogFileOn(TRUE)
##' phrSetLogFileName("phreeqc.log")
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0 10 '
##' )
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetErrorFileName(), "\n")
##' }
##'
phrSetErrorFileName <-
function(filename) {
invisible(.Call("setErrorFileName", as.character(filename), PACKAGE = .packageName))
}
##' Set error file on/off.
##'
##' Sets the error file switch on or off. This switch controls whether
##' or not phreeqc writes to the error file. The initial setting is off.
##'
##' The try is necessary to keep the error message from displaying immediately.
##'
##' @export phrSetErrorFileOn
##' @useDynLib phreeqc
##' @param value if TRUE, writes output to the the error file.
##' @return NULL
##' @family Error
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example attempts to run ex1, fails, and writes the error
##' # message to the error file (no database is loaded).
##' phrSetErrorFileOn(TRUE)
##' phrSetErrorFileName("phreeqc.errors")
##' if (!is.null(try(phrRunString(ex1), silent=TRUE))) {
##' cat("see", phrGetErrorFileName(), "\n")
##' }
##'
phrSetErrorFileOn <-
function(value) {
invisible(.Call("setErrorFileOn", as.logical(value), PACKAGE = .packageName))
}
##' Set error strings on/off.
##'
##' Sets the error strings switch on or off. This switch controls whether or
##' not the data normally sent to the error file are stored in a buffer for
##' retrieval. The initial setting is on.
##'
##' The try is necessary to keep the error message from displaying immediately.
##'
##' @export phrSetErrorStringsOn
##' @useDynLib phreeqc
##' @param value if TRUE, captures output normally sent to the error file into a buffer.
##' @return NULL
##' @family Error
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example attempts to run ex1, fails, and displays the error message
##' # (no database is loaded).
##' phrSetErrorStringsOn(TRUE)
##' if (!is.null(try(phrRunString(ex1), silent=TRUE))) {
##' cat(phrGetErrorStrings(), "\n")
##' }
##'
phrSetErrorStringsOn <-
function(value) {
invisible(.Call("setErrorStringOn", as.logical(value), PACKAGE = .packageName))
}
##' Set the name of the log file.
##'
##' Sets the name of the log file. The default value is phreeqc.0.log
##'
##' Logging must be enabled through the use of the KNOBS -logfile
##' option in order to receive any log messages.
##'
##' @export phrSetLogFileName
##' @useDynLib phreeqc
##' @param filename the name of the file.
##' @return NULL
##' @family Log
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and displays
##' # the log file name.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetLogFileOn(TRUE)
##' phrSetLogFileName("phreeqc.log")
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0 10 ',
##' 'KNOBS ',
##' ' -logfile true '
##' )
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetLogFileName(), "\n")
##' }
##'
phrSetLogFileName <-
function(filename) {
invisible(.Call("setLogFileName", as.character(filename), PACKAGE = .packageName))
}
##' Set log file on/off.
##'
##' Sets the log file switch on or off. This switch controls whether
##' or not phreeqc writes log messages to the log file. The initial
##' setting is off.
##'
##' Logging must be enabled through the use of the KNOBS -logfile
##' option in order to receive an log messages.
##'
##' @export phrSetLogFileOn
##' @useDynLib phreeqc
##' @param value if TRUE, writes output to the the log file.
##' @return NULL
##' @family Log
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example runs ex2 with the log file turned on.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetLogStringsOn(TRUE)
##'
##' # turn logging on
##' phrAccumulateLine("KNOBS; -logfile true")
##' phrRunAccumulated()
##'
##' if (is.null(phrRunString(ex2))) {
##' cat("see", phrGetLogFileName(), "\n")
##' }
##'
phrSetLogFileOn <-
function(value) {
invisible(.Call("setLogFileOn", as.logical(value), PACKAGE = .packageName))
}
##' Set log strings on/off.
##'
##' Sets the log strings switch on or off. This switch controls whether or
##' not the data normally sent to the log file are stored in a buffer for
##' retrieval. The initial setting is off.
##'
##' @export phrSetLogStringsOn
##' @useDynLib phreeqc
##' @param value if TRUE, captures output normally sent to the log file into a buffer.
##' @return NULL
##' @family Log
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example runs ex2 with log strings turned on.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetLogStringsOn(TRUE)
##'
##' # turn logging on
##' phrAccumulateLine("KNOBS; -logfile true")
##' phrRunAccumulated()
##'
##' if (is.null(phrRunString(ex2))) {
##' cat(phrGetLogStrings(), sep = "\n")
##' }
##'
phrSetLogStringsOn <-
function(value) {
invisible(.Call("setLogStringOn", as.logical(value), PACKAGE = .packageName))
}
##' Set the name of the output file.
##'
##' Sets the name of the output file. The default value is phreeqc.0.out.
##'
##' The output file must be turned on using the \code{\link{phrSetOutputFileOn}} function.
##'
##' @export phrSetOutputFileName
##' @useDynLib phreeqc
##' @param filename the name of the file.
##' @return NULL
##' @family Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and displays
##' # the resulting file name.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputFileOn(TRUE)
##' phrSetOutputFileName("phreeqc.output")
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0 10 '
##' )
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetOutputFileName(), "\n")
##' }
##'
phrSetOutputFileName <-
function(filename) {
invisible(.Call("setOutputFileName", as.character(filename), PACKAGE = .packageName))
}
##' Set output file on/off.
##'
##' Sets the output file switch on or off. This switch controls whether
##' or not phreeqc writes to the output file. This is the output normally
##' generated when phreeqc is run. The initial setting is off.
##'
##' @export phrSetOutputFileOn
##' @useDynLib phreeqc
##' @param value if TRUE, writes output to the the output file.
##' @return NULL
##' @family Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example runs ex2 with the output file turned on.
##'
##' # write temporary input file
##' tf <- tempfile()
##' writeLines(ex2, tf)
##'
##' # load database and run input file
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputFileOn(TRUE)
##' if (is.null(phrRunFile(tf))) {
##' cat("see", phrGetOutputFileName(), "\n")
##' }
##'
##' # delete temporary input file
##' unlink(tf)
##'
phrSetOutputFileOn <-
function(value) {
invisible(.Call("setOutputFileOn", as.logical(value), PACKAGE = .packageName))
}
##' Set output strings on/off.
##'
##' Set the output string switch on or off. This switch controls whether or
##' not the data normally sent to the output file are stored in a buffer for
##' retrieval. The initial setting is off.
##'
##' The output strings setting is only used by the Run methods:
##' \code{\link{phrRunAccumulated}}, \code{\link{phrRunFile}},
##' \code{\link{phrRunString}}.
##'
##' @export phrSetOutputStringsOn
##' @useDynLib phreeqc
##' @param value if TRUE, captures output normally sent to the output file into a buffer.
##' @return NULL
##' @family Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite and displays
##' # the results.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0 10 '
##' )
##'
##' if (is.null(phrRunString(input))) {
##' cat(phrGetOutputStrings(), sep = "\n")
##' }
##'
phrSetOutputStringsOn <-
function(value) {
invisible(.Call("setOutputStringOn", as.logical(value), PACKAGE = .packageName))
}
##' Retrieve the name of the selected_output file.
##'
##' Retrieves the name of the selected_output file. The default value is selected_{nuser}.0.out.
##'
##' The selected_output file must be turned on using the \code{\link{phrSetSelectedOutputFileOn}} function.
##'
##' @export phrGetSelectedOutputFileName
##' @useDynLib phreeqc
##' @param nuser the user number specified in the SELECTED_OUTPUT block.
##' @return The name of the selected_output file as a string.
##' @family Selected Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite at various temperatures
##' # and displays the name of the selected_output file.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetSelectedOutputFileOn(1, TRUE)
##' phrSetSelectedOutputFileName(1, "ex2.sel")
##'
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0.0 1.0 ',
##' 'REACTION_TEMPERATURE 1 ',
##' ' 25.0 75.0 in 51 steps ',
##' 'SELECTED_OUTPUT 1 ',
##' ' -temperature ',
##' ' -si calcite '
##' )
##'
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetSelectedOutputFileName(1))
##' }
##'
phrGetSelectedOutputFileName <-
function(nuser) {
invisible(.Call("getSelectedOutputFileName", as.integer(nuser), PACKAGE = .packageName))
}
##' Set the name of the selected_output file.
##'
##' Sets the name of the selected_output file. The default value is selected_{nuser}.0.out.
##'
##' The selected_output file must be turned on using the \code{\link{phrSetSelectedOutputFileOn}} function.
##'
##' @export phrSetSelectedOutputFileName
##' @useDynLib phreeqc
##' @param nuser the user number specified in the SELECTED_OUTPUT block.
##' @param filename the name of the selected_output file.
##' @return NULL
##' @family Selected Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite at various temperatures
##' # and displays the name of the selected_output file.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetSelectedOutputFileOn(1, TRUE)
##' phrSetSelectedOutputFileName(1, "ex2.sel")
##'
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0.0 1.0 ',
##' 'REACTION_TEMPERATURE 1 ',
##' ' 25.0 75.0 in 51 steps ',
##' 'SELECTED_OUTPUT 1 ',
##' ' -temperature ',
##' ' -si calcite '
##' )
##'
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetSelectedOutputFileName(1))
##' }
##'
phrSetSelectedOutputFileName <-
function(nuser, filename) {
invisible(.Call("setSelectedOutputFileName", as.integer(nuser), as.character(filename), PACKAGE = .packageName))
}
##' Set selected_output file on/off.
##'
##' Sets the output file switch on or off. This switch controls whether
##' or not phreeqc writes to the output file. This is the output normally
##' generated when phreeqc is run. The initial setting is off.
##'
##' @export phrSetSelectedOutputFileOn
##' @useDynLib phreeqc
##' @param nuser the user number specified in the SELECTED_OUTPUT block.
##' @param value if TRUE, writes output to the the selected_output file.
##' @return NULL
##' @family Selected Output
##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
##' @examples
##'
##' # This example equilibrates pure water with calcite at various temperatures
##' # and displays the name of the selected_output file.
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetSelectedOutputFileOn(1, TRUE)
##' phrSetSelectedOutputFileName(1, "ex2.sel")
##'
##' input <- c(
##' 'SOLUTION 1 Pure water ',
##' 'EQUILIBRIUM_PHASES 1 ',
##' ' Calcite 0.0 1.0 ',
##' 'REACTION_TEMPERATURE 1 ',
##' ' 25.0 75.0 in 51 steps ',
##' 'SELECTED_OUTPUT 1 ',
##' ' -temperature ',
##' ' -si calcite '
##' )
##'
##'
##' if (is.null(phrRunString(input))) {
##' cat("see", phrGetSelectedOutputFileName(1))
##' }
##'
phrSetSelectedOutputFileOn <-
function(nuser, value) {
invisible(.Call("setSelectedOutputFileOn", as.integer(nuser), as.logical(value), PACKAGE = .packageName))
}
##' @name phreeqc.dat
##' @title The phreeqc.dat database
##' @description phreeqc.dat is a phreeqc database file derived from PHREEQE,
##' which is consistent with wateq4f.dat, but has a smaller set of elements and
##' aqueous species. The database has been reformatted for use by
##' \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage phreeqc.dat # phrLoadDatabaseString(phreeqc.dat)
##' @keywords dataset
NULL
##' @name ex15.dat
##' @title The ex15.dat database
##' @description ex15.dat is a database used by example 15 (\code{\link{ex15}}).
##' The database has been reformatted for use by
##' \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage ex15.dat # phrLoadDatabaseString(ex15.dat)
##' @keywords dataset
NULL
##' @name Amm.dat
##' @title The Amm.dat database.
##' @description Amm.dat is the same as phreeqc.dat, except that ammmonia redox
##' state has been decoupled from the rest of the nitrogen system; that is,
##' ammonia has been defined as a separate component. The database has been
##' reformatted for use by \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage Amm.dat # phrLoadDatabaseString(Amm.dat)
##' @keywords dataset
NULL
##' @name wateq4f.dat
##' @title The wateq4f.dat database.
##' @description wateq4f.dat is a database derived from WATEQ4F. The database
##' has been reformatted for use by \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage wateq4f.dat # phrLoadDatabaseString(wateq4f.dat)
##' @keywords dataset
NULL
##' @name llnl.dat
##' @title The llnl.dat database.
##' @description llnl.dat is a database derived from databases for EQ3/6 and
##' Geochemist's Workbench that uses thermodynamic data compiled by the
##' Lawrence Livermore National Laboratory. The database has been reformatted
##' for use by \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @usage llnl.dat # phrLoadDatabaseString(llnl.dat)
##' @keywords dataset
NULL
##' @name minteq.dat
##' @title The minteq.dat database.
##' @description minteq.dat is a database derived from the databases for the
##' program MINTEQA2. The database has been reformatted for use by
##' \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage minteq.dat # phrLoadDatabaseString(minteq.dat)
##' @keywords dataset
NULL
##' @name minteq.v4.dat
##' @title The minteq.v4.dat database.
##' @description minteq.v4.dat is a database derived from MINTEQA2 version 4.
##' The database has been reformatted for use by
##' \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage minteq.v4.dat # phrLoadDatabaseString(minteq.v4.dat)
##' @keywords dataset
NULL
##' @name pitzer.dat
##' @title The pitzer.dat database.
##' @description pitzer.dat is a database for the specific-ion-interaction model
##' of Pitzer as implemented in PHRQPITZ. The database has been reformatted for
##' use by \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage pitzer # phrLoadDatabaseString(pitzer.dat)
##' @keywords dataset
NULL
##' @name sit.dat
##' @title The sit.dat database.
##' @description sit.dat is a database derived from databases for EQ3/6 and
##' Geochemist's Workbench that uses thermodynamic data compiled by the
##' Lawrence Livermore National Laboratory. The database has been reformatted
##' for use by \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage sit.dat # phrLoadDatabaseString(sit.dat)
##' @keywords dataset
NULL
##' @name iso.dat
##' @title The iso.dat database.
##' @description iso.dat is a partial implementation of the individual component
##' approach to isotope calculations as described by Thorstenson and Parkhurst.
##' The database has been reformatted for use by
##' \code{\link{phrLoadDatabaseString}}.
##' @docType data
##' @family Databases
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @usage iso.dat # phrLoadDatabaseString(iso.dat)
##' @keywords dataset
NULL
##' @name ex1
##' @title Example 1--Speciation Calculation
##' @description This example calculates the distribution of aqueous species in
##' seawater and the saturation state of seawater relative to a set of minerals.
##' To demonstrate how to expand the model to new elements, uranium is added to
##' the aqueous model defined by \code{\link{phreeqc.dat}}. The example can be
##' run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex1)
##' phrGetOutputStrings()
##'
NULL
##' @name ex2
##' @title Example 2--Equilibration With Pure Phases
##' @description This example shows how to calculate the solubility and relative
##' thermodynamic stability of two minerals, gypsum and anhydrite. The example
##' can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex2)
##' phrGetOutputStrings()
##'
NULL
##' @name ex3
##' @title Example 3--Mixing
##' @description This example demonstrates the capabilities of PHREEQC to
##' perform a series of geochemical simulations, with the final simulations
##' relying on results from previous simulations within the same run. The
##' example investigates diagenetic reactions that may occur in zones where
##' seawater mixes with carbonate groundwater. The example is divided into five
##' simulations, labeled part A through part E. (A) Carbonate groundwater is
##' defined by equilibrating pure water with calcite at a of 10-2.0 atm. (B)
##' Seawater is defined by using the major-ion data given in table.9. (C) The
##' two solutions are mixed together in the proportions 70 percent groundwater
##' and 30 percent seawater. (D) The mixture is equilibrated with calcite and
##' dolomite. (E) The mixture is equilibrated with calcite only to investigate
##' the chemical evolution if dolomite precipitation is assumed to be
##' negligible. The example can be run using the \code{\link{phrRunString}}
##' routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex3)
##' phrGetOutputStrings()
##'
NULL
##' @name ex4
##' @title Example 4--Evaporation and Homogeneous Redox Reactions
##' @description Evaporation is accomplished by removing water from the chemical
##' system. Water can be removed by several methods: (1) water can be specified
##' as an irreversible reactant with a negative reaction coefficient in the
##' REACTION keyword input, (2) the solution can be mixed with pure water which
##' is given a negative mixing fraction in MIX, or (3) "H2O" can be specified as
##' the alternative reaction in EQUILIBRIUM_PHASES keyword input, in which case
##' water is removed or added to the aqueous phase to attain equilibrium with a
##' specified phase. This example uses the first method; the REACTION data block
##' is used to simulate concentration of rainwater by approximately 20-fold by
##' removing 95 percent of the water. The resulting solution contains only about
##' 0.05 kg of water. In a subsequent simulation, the MIX keyword is used to
##' generate a solution that has the same concentrations as the evaporated
##' solution, but has a total mass of water of approximately 1 kg. The example
##' can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex4)
##' phrGetOutputStrings()
##'
NULL
##' @name ex5
##' @title Example 5--Irreversible Reactions
##' @description This example demonstrates the irreversible reaction
##' capabilities of PHREEQC in modeling the oxidation of pyrite. Oxygen (O2) and
##' NaCl are added irreversibly to pure water in six amounts (0.0, 0.001, 0.005,
##' 0.01, 0.03, and 0.05 mol); the relative proportion of O2 to NaCl in the
##' irreversible reaction is 1.0 to 0.5. Pyrite, calcite, and goethite are
##' allowed to dissolve to equilibrium and the carbon dioxide partial pressure
##' is maintained at 10-3.5 (atmospheric partial pressure). In addition, gypsum
##' is allowed to precipitate if it becomes supersaturated. The example can be
##' run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex5)
##' phrGetOutputStrings()
##'
NULL
##' @name ex6
##' @title Example 6--Reaction-Path Calculations
##' @description In this example, the precipitation of phases as a result of
##' incongruent dissolution of K-feldspar (microcline) is investigated. Only the
##' four phases originally addressed by Helgeson and others (1969)--K-feldspar,
##' gibbsite, kaolinite, and K-mica (muscovite)--are considered. The
##' thermodynamic data for the phases (PHASES keyword) are derived from Robie
##' and others (1978) and are the same as for test problem 5 in the PHREEQE
##' manual (Parkhurst and others, 1980). The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex6)
##' phrGetOutputStrings()
##'
NULL
##' @name ex7
##' @title Example 7--Gas-Phase Calculations
##' @description This example demonstrates the capabilities of PHREEQC to model
##' the evolution of gas compositions in equilibrium with a solution with a
##' fixed (total) pressure or a fixed volume of the gas phase. In the case of a
##' fixed-pressure gas phase, a gas bubble forms as soon as the sum of the
##' partial pressures of the component gases exceeds the specified pressure of
##' the gas phase. Once the bubble forms, its volume and composition will vary
##' with the extent of reactions. This case applies to gas bubbles forming in
##' surface water or groundwater at a given depth, where the total pressure is
##' constant. With a fixed-volume gas phase, the aqueous solution is in contact
##' with a head space of a fixed volume, which is typical for a laboratory
##' experiment with a closed bottle. The gas phase always exists in this head
##' space, but its pressure and composition will vary with the reactions.
##' Another way to model gas-liquid reactions in PHREEQC is to maintain a fixed
##' partial pressure by using the EQUILIBRIUM_PHASES data block. This
##' fixed-partial-pressure approach is illustrated in this example by fixing
##' the CO2 pressure for a SOLUTION. The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex7)
##' phrGetOutputStrings()
##'
NULL
##' @name ex8
##' @title Example 8--Surface Complexation
##' @description In all surface complexation models, sorption is a function of
##' both chemical and electrostatic energy as described by the free energy
##' relationship. Sorption is stronger when the Gibbs energy decreases. Thus, a
##' counter-ion that carries a charge opposite to the surface charge tends to be
##' sorbed electrostatically, while a co-ion that carries a charge with the same
##' sign as the surface tends to be rejected. The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' # example 8 requires the selected_output file to be turned on
##' phrSetSelectedOutputFileOn(1, TRUE)
##' phrRunString(ex8)
##' phrGetOutputStrings()
##'
NULL
##' @name ex9
##' @title Example 9--Kinetic Oxidation of Dissolved Ferrous Iron With Oxygen
##' @description Kinetic rate expressions can be defined in a completely general
##' way in PHREEQC by using Basic statements in the RATES data block. The rate
##' expressions can be used in batch-reaction and transport calculations with
##' the KINETICS data block. For transport calculations (ADVECTION or TRANSPORT),
##' kinetic reactions can be defined cell by cell by the number range following
##' the KINETICS keyword (KINETICS m-n). The rate expressions are integrated with
##' an embedded (up to) 5th-order Runge-Kutta-Fehlberg algorithm, or with a
##' stiff, variable-order, variable-step multistep solver (Cohen and Hindmarsh,
##' 1996). Equilibrium is calculated before a kinetic calculation is initiated
##' and again when a kinetic reaction increment is added. Equilibrium includes
##' solution species equilibrium; exchange-, equilibrium-phase-, solid-solution-,
##' and surface-assemblage equilibrium; and gas-phase equilibrium. A check is
##' performed to ensure that the difference between estimates of the integrated
##' rate over a time interval is smaller than a user-defined tolerance. If the
##' tolerance is not satisfied, then the integration over the time interval is
##' automatically restarted with a smaller time interval. The example can be run
##' using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex9)
##' phrGetOutputStrings()
##'
NULL
##' @name ex10
##' @title Example 10--Aragonite-Strontianite Solid Solution
##' @description PHREEQC has the capability to model multicomponent ideal and
##' binary nonideal solid solutions. For ideal solid solutions, the activity of
##' each end member solid is equal to its mole fraction. For nonideal solid
##' solutions, the activity of each end member is the product of the mole
##' fraction and an activity coefficient, which is determined from the mole
##' fraction and Guggenheim excess free-energy parameters. Example 10 considers
##' an aragonite (CaCO3)-strontianite (SrCO3) solid solution and demonstrates
##' how the composition of the solid solution and the aqueous phase change as
##' strontium carbonate is added to an initially pure calcium carbonate system.
##' The example can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex10)
##' phrGetOutputStrings()
##'
NULL
##' @name ex11
##' @title Example 11--Transport and Cation Exchange
##' @description The following example simulates the chemical composition of the
##' effluent from a column containing a cation exchanger (Appelo and Postma,
##' 2005). Initially, the column contains a sodium-potassium-nitrate solution
##' in equilibrium with the exchanger. The column is flushed with three pore
##' volumes of calcium chloride solution. Calcium, potassium, and sodium react
##' to equilibrium with the exchanger at all times. The problem is run two
##' ways--by using the ADVECTION data block, which models only advection, and by
##' using the TRANSPORT data block, which simulates advection and dispersive
##' mixing. The example can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex11)
##' phrGetOutputStrings()
##'
NULL
##' @name ex12
##' @title Example 12--Advective and Diffusive Flux of Heat and Solutes
##' @description This example demonstrates the capability of PHREEQC to
##' calculate transient transport of heat and solutes in a column or along a 1D
##' flowline. A column is initially filled with a dilute KCl solution at 25
##' degrees C in equilibrium with a cation exchanger. A KNO3 solution then
##' advects into the column and establishes a new temperature of 0 degrees C.
##' Subsequently, a sodium chloride solution at 24 degrees C is allowed to
##' diffuse from both ends of the column, assuming no heat is lost through the
##' column walls. At one end, a constant boundary condition is imposed, and at
##' the other end, the final cell is filled with the sodium chloride solution
##' and a closed boundary condition is prescribed. For the column end with a
##' constant boundary condition, an analytical solution is compared with PHREEQC
##' results, for unretarded Cl- (R = 1.0) and retarded Na+ and temperature
##' (R = 3.0). Finally, the second-order accuracy of the numerical method is
##' verified by increasing the number of cells by a factor of three and
##' demonstrating a decrease in the error of the numerical solution by
##' approximately one order of magnitude relative to the analytical solution.
##' The example can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex12)
##' phrGetOutputStrings()
##'
NULL
##' @rdname ex13
##' @name ex13a
##' @aliases ex13a ex13b ex13c
##' @title Example 13--Aragonite-Strontianite Solid Solution
##' @description PHREEQC has the capability to model multicomponent ideal and
##' binary nonideal solid solutions. For ideal solid solutions, the activity of
##' each end member solid is equal to its mole fraction. For nonideal solid
##' solutions, the activity of each end member is the product of the mole
##' fraction and an activity coefficient, which is determined from the mole
##' fraction and Guggenheim excess free-energy parameters. Example 10 considers
##' an aragonite (CaCO3)-strontianite (SrCO3) solid solution and demonstrates
##' how the composition of the solid solution and the aqueous phase change as
##' strontium carbonate is added to an initially pure calcium carbonate system.
##' The example can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex13a)
##' phrGetOutputStrings()
##'
NULL
##' @name ex14
##' @title Example 14--Advective Transport, Cation Exchange, Surface
##' Complexation, and Mineral Equilibria
##' @description This example uses the phase-equilibrium, cation-exchange, and
##' surface-complexation reaction capabilities of PHREEQC in combination with
##' advective-transport capabilities to model the evolution of water in the
##' Central Oklahoma aquifer. The geochemistry of the aquifer has been described
##' by Parkhurst and others (1996). Two predominant water types occur in the
##' aquifer: a calcium magnesium bicarbonate water with pH in the range of 7.0
##' to 7.5 in the unconfined part of the aquifer and a sodium bicarbonate water
##' with pH in the range of 8.5 to 9.2 in the confined part of the aquifer. In
##' addition, marine-derived sodium chloride brines exist below the aquifer and
##' presumably in fluid inclusions and dead-end pore spaces within the aquifer.
##' Large concentrations of arsenic, selenium, chromium, and uranium occur
##' naturally within the aquifer. Arsenic is associated almost exclusively with
##' the high-pH, sodium bicarbonate water type. The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex14)
##' phrGetOutputStrings()
##'
NULL
##' @name ex15
##' @title Example 15--1D Transport: Kinetic Biodegradation, Cell Growth, and
##' Sorption
##' @description A test problem for advective-dispersive-reactive transport was
##' developed by Tebes-Stevens and Valocchi (1997) and Tebes-Stevens and others
##' (1998). Although based on relatively simple speciation chemistry, the
##' solution to the problem demonstrates several interacting chemical processes
##' that are common to many environmental problems: bacterially mediated
##' degradation of an organic substrate; bacterial cell growth and decay; metal
##' sorption; and aqueous speciation, including metal-ligand complexation. In
##' this example, the test problem is solved with PHREEQC, which produces
##' results almost identical to those of Tebes-Stevens and Valocchi (1997) and
##' Tebes-Stevens and others (1998). The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' # this example takes longer than 5 seconds
##' phrLoadDatabaseString(ex15.dat)
##' phrSetOutputStringsOn(TRUE)
##' \dontrun{phrRunString(ex15)}
##' phrGetOutputStrings()
##'
NULL
##' @name ex16
##' @title Example 16--Inverse Modeling of Sierra Spring Waters
##' @description This example repeats the inverse modeling calculations of the
##' chemical evolution of spring-water compositions in the Sierra Nevada that
##' are described in a classic paper by Garrels and Mackenzie (1967). The same
##' example is described in the manual for the inverse-modeling program NETPATH
##' (Plummer and others, 1991 and 1994). The example uses two spring-water
##' compositions, one from an ephemeral spring, which is less chemically
##' evolved, and one from a perennial spring, which probably has had a longer
##' residence time in the subsoil. The differences in composition between the
##' ephemeral spring and the perennial spring are assumed to be caused by
##' reactions between the water and the minerals and gases it contacts. The
##' object of inverse modeling in this example is to find sets of minerals and
##' gases that, when reacted in appropriate amounts, account for the differences
##' in composition between the two solutions. The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex16)
##' phrGetOutputStrings()
##'
NULL
##' @name ex17
##' @title Example 17--Inverse Modeling With Evaporation
##' @description Evaporation is handled in the same manner as other
##' heterogeneous reactions for inverse modeling. To model evaporation (or
##' dilution), it is necessary to include a phase with the composition "H2O".
##' The important concept in modeling evaporation is the water mole-balance
##' equation (see Parkhurst and Appelo, 1999, "Equations and Numerical Method
##' for Inverse Modeling"). The moles of water in the initial solutions times
##' their mixing fractions, plus water gained or lost by dissolution or
##' precipitation of phases, plus water gained or lost through redox reactions,
##' must equal the moles of water in the final solution. The equation is still
##' approximate because it does not include the moles of water gained or lost in
##' hydrolysis and complexation reactions in the solutions. The results of
##' inverse modeling are compared with a forward model using Pitzer equations to
##' calculate the sequence of salts that precipitate during evaporation. The
##' example can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(pitzer.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex17)
##' phrGetOutputStrings()
##'
NULL
##' @name ex18
##' @title Example 18--Inverse Modeling of the Madison Aquifer
##' @description In this example, inverse modeling, including isotope
##' mole-balance modeling, is applied to the evolution of water in the Madison
##' aquifer in Montana. Plummer and others (1990) used mole-balance modeling to
##' quantify the extent of dedolomitization at locations throughout the aquifer.
##' In the dedolomitization process, anhydrite dissolution causes the
##' precipitation of calcite and dissolution of dolomite. Additional reactions
##' identified by mole-balance modeling include sulfate reduction, cation
##' exchange, and halite and sylvite dissolution (Plummer and others, 1990). Del
##' 13C and del 34S data were used to corroborate the mole-balance models and
##' carbon-14 was used to estimate groundwater ages (Plummer and others, 1990).
##' Initial and final water samples were selected from a flow path that extends
##' from north-central Wyoming northeast across Montana (Plummer and others,
##' 1990, flow path 3). This pair of water samples was selected specifically
##' because it was one of the few pairs that showed a relatively large
##' discrepancy between previous mole-balance approaches and the mole-balance
##' approach of PHREEQC, which includes uncertainties; results for most sample
##' pairs were not significantly different between the two approaches. In
##' addition, this pair of samples was selected because it was modeled in detail
##' in Plummer and others (1990) to determine the sensitivity of mole-balance
##' results to various model assumptions and was used as an example in the
##' NETPATH manual (Plummer and others, 1994, example 6). Results of PHREEQC
##' calculations are compared to NETPATH calculations. This example is also
##' discussed in Parkhurst (1997). The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex18)
##' phrGetOutputStrings()
##'
NULL
##' @name ex19
##' @title 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
##' @description Sorption of heavy metals and organic pollutants on natural
##' materials can be described by linear, Freundlich, or Langmuir isotherms. All
##' three isotherms can be calculated by PHREEQC, as shown in this example for
##' Cd+2 sorbing on a loamy soil (Christensen, 1984; Appelo and Postma, 2005). A
##' more mechanistic approach, also illustrated here, is to model the
##' distribution of Cd+2 over the sorbing components in the soil, in this case,
##' in and on organic matter, clay minerals, and iron oxyhydroxides. The example
##' can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex19)
##' phrGetOutputStrings()
##'
NULL
##' @rdname ex20
##' @name ex20a
##' @aliases ex20a ex20b
##' @title Example 20--Distribution of Isotopes Between Water and Calcite
##' @description The database \code{\link{iso.dat}} implements the approach to
##' isotope reactions described by Thorstenson and Parkhurst (2002, 2004), in
##' which minor isotopes are treated as individual thermodynamic components. The
##' aqueous and solid species of minor isotopes have slightly different
##' equilibrium constants than those of the major isotopes, which account for
##' fractionation processes. The treatment of isotopes in gases requires a
##' separate species for each isotopic variant of a gas; for example, the
##' isotopic variants of carbon dioxide are CO2, C18OO, C18O2, 13CO2, 13C18OO,
##' and 13C18O2. Similarly, every isotopic variant of a mineral must be included
##' as a component of a solid solution to represent completely the isotopic
##' composition of the solid. The equilibrium constants in iso.dat are derived
##' from empirical fractionation factors, from statistical mechanical theory,
##' or, where no data are available (the most common case), by assuming no
##' fractionation. However, the database is a framework that can be expanded as
##' additional isotopic thermodynamic data become available. The example can be
##' run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(iso.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex20a)
##' phrGetOutputStrings()
##'
NULL
##' @name ex21
##' @title Example 21--Modeling Diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a
##' Radial Diffusion Cell
##' @description This example illustrates how PHREEQC version 3 can simulate a
##' diffusion experiment, as is now often performed for assessing the properties
##' of a repository for nuclear waste in a clay formation. A sample is cut from
##' a core of clay, enveloped in filters, and placed in a diffusion cell (see
##' Van Loon and others, 2004, for details). Solutions with tracers are
##' circulated at the surfaces of the filters, the tracers diffuse into and out
##' of the clay, and the solutions are sampled and analyzed regularly in time.
##' The concentration changes are interpreted with Fick's diffusion equations to
##' obtain transport parameters for modeling the rates of migration of elements
##' away from a waste repository. Transport in clays is mainly diffusive because
##' of the low hydraulic conductivity, and solutes are further retarded by
##' sorption (cations) and by exclusion from part of the pore space (anions).
##' The example can be run using the \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' # example 21 requires the selected_output file to be turned on
##' phrSetSelectedOutputFileOn(1, TRUE)
##' phrSetOutputStringsOn(TRUE)
##' # this takes longer than 5 seconds
##' \dontrun{phrRunString(ex21)}
##' phrGetOutputStrings()
##'
NULL
##' @name ex22
##' @title Example 22--Modeling Gas Solubilities: CO2 at High Pressures
##' @description PHREEQC calculates the fugacity coefficient with the
##' Peng-Robinson equation of state (Peng and Robinson, 1976) from the critical
##' pressure and temperature, and the acentric factor of the gas in a gas
##' mixture to obtain the limiting volume and the attraction factor in the Van
##' der Waals equation. The fugacity coefficient is close to 1 when the total
##' pressure of the gas phase is less than about 10 atm, and it can be neglected
##' in the solubility calculation. At higher pressures, the effect can be
##' substantial. At low pressures, the concentration of CO2 increases
##' near-linearly with pressure. At 25 degrees C and pressures higher than 62
##' atm, the concentration increases more gradually because the fugacity
##' coefficient drops rapidly. The example can be run using the
##' \code{\link{phrRunString}} routine.
##' @docType data
##' @family Examples
##' @references \url{http://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
##' @keywords dataset
##' @examples
##'
##' phrLoadDatabaseString(phreeqc.dat)
##' phrSetOutputStringsOn(TRUE)
##' phrRunString(ex22)
##' phrGetOutputStrings()
##'
NULL
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