mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-15 16:18:22 +01:00
IPhreeqc: moved all output files to tempdir(); Fixed some of the documentation
This commit is contained in:
Scott Charlton
parent
c60ec7be3e
commit
f3c1fcabb5
@ -79,6 +79,7 @@ NULL
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##' phrAccumulateLine(" -si anhydrite gypsum")
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##' phrAccumulateLine("END")
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##' phrSetOutputFileOn(TRUE)
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##' phrSetOutputFileName(file.path(tempdir(), "ex2.output"))
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##' if (is.null(phrRunAccumulated())) {
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##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep = ""))
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##' }
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@ -177,6 +178,7 @@ function() {
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##'
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetDumpFileOn(TRUE)
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##' phrSetDumpFileName(file.path(tempdir(), "dump.out"))
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##'
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##' input <- "SOLUTION 1 Pure water \n"
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##' input <- paste(input, "EQUILIBRIUM_PHASES 1 \n")
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@ -190,7 +192,7 @@ function() {
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##' if (!is.null(phrRunString(input))) {
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##' cat(phrGetErrorStrings())
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##' }
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##' cat(paste("see ", phrGetDumpFileName(), "."))
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##' cat(paste("see ", phrGetDumpFileName(), ".\n", sep = ""))
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##'
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##'
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phrGetDumpFileName <-
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@ -259,7 +261,7 @@ function() {
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##'
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##' @export phrGetDumpFileOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if output as defined by the DUMP data block are currently being written to file.
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##' @family Dump
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##'
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@ -274,7 +276,7 @@ function() {
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##'
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##' @export phrGetDumpStringsOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if output as defined by the DUMP data block are currently being stored as a character vector.
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##' @family Dump
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##'
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@ -289,7 +291,7 @@ function() {
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##'
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##' @export phrGetErrorFileOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if error messages are currently being written to file.
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##' @family Error
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##'
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@ -304,7 +306,7 @@ function() {
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##'
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##' @export phrGetErrorStringsOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if error messages are currently being stored as a character vector.
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##' @family Error
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##'
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@ -319,7 +321,7 @@ function() {
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##'
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##' @export phrGetLogFileOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if log messages are currently being written to file.
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##' @family Log
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##'
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@ -334,7 +336,7 @@ function() {
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##'
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##' @export phrGetLogStringsOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if log messages are currently being stored as a character vector.
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##' @family Log
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##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
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##'
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@ -349,7 +351,7 @@ function() {
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##'
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##' @export phrGetOutputFileOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if output messages are currently being written to file.
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##' @family Output
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##'
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@ -364,7 +366,7 @@ function() {
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##'
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##' @export phrGetOutputStringsOn
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return TRUE if errors are currently being written to file.
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##' @return TRUE if output messages are currently being stored as a character vector.
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##' @family Output
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##'
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@ -444,7 +446,7 @@ function() {
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##'
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##' # This example equilibrates pure water with gypsum with the output file on.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetOutputFileOn(TRUE)
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##' phrSetLogStringsOn(TRUE)
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##'
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##' input <- vector(mode="character")
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##' input <- c(input, "SOLUTION 1 Pure water ")
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@ -468,7 +470,7 @@ function() {
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##'
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##' Retrieves the name of the output file. The default name is phreeqc.0.out.
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##'
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##' @export
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##' @export phrGetOutputFileName
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##' @useDynLib phreeqc, .registration = TRUE
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##' @return The name of the output file as a string.
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##' @family Output
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@ -478,6 +480,7 @@ function() {
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##' # This example equilibrates pure water with gypsum with the output file on.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetOutputFileOn(TRUE)
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##' phrSetOutputFileName(file.path(tempdir(), "gypsum.out"))
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##'
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##' input <- vector(mode="character")
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##' input <- c(input, "SOLUTION 1 Pure water ")
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@ -662,6 +665,7 @@ function(filename) {
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##' # output file and runs ex2 as a string
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetOutputFileOn(TRUE)
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##' phrSetOutputFileName(file.path(tempdir(), "ex2.load-database.out"))
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##' if (is.null(phrRunString(ex2))) {
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##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep = ""))
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##' }
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@ -695,6 +699,7 @@ function(input) {
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##'
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##' # turn on the output file
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##' phrSetOutputFileOn(TRUE)
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##' phrSetOutputFileName(file.path(tempdir(), "ex2.out"))
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##'
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##' # load the phreeqc.dat database
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##' phrLoadDatabaseString(phreeqc.dat)
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@ -747,7 +752,7 @@ function() {
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##'
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##' # run ex2
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##' if (is.null(phrRunFile("ex2"))) {
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##' cat("use phrGetSelectedOutput() to see results.")
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##' cat("use phrGetSelectedOutput() to see results.\n")
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##' }
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##'
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##' unlink("ex2") # tidy up
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@ -793,10 +798,11 @@ function(filename) {
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##'
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##' # turn on output
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##' phrSetOutputFileOn(TRUE)
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##' phrSetOutputFileName(file.path(tempdir(), "pure_water.out"))
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##'
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##' # run input
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##' phrRunString(input)
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##' cat(paste("see", phrGetOutputFileName(), "."))
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##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep=""))
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##'
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phrRunString <-
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function(input) {
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@ -822,7 +828,7 @@ function(input) {
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##' # dump results to file.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetDumpFileOn(TRUE)
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##' phrSetDumpFileName("phreeqc.dump")
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##' phrSetDumpFileName(file.path(tempdir(), "phreeqc.dump"))
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##' input <- c(
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##' 'SOLUTION 1 Pure water ',
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##' 'EQUILIBRIUM_PHASES 1 ',
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@ -835,7 +841,7 @@ function(input) {
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##' )
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetDumpFileName(), "\n")
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##' cat(paste("see ", phrGetDumpFileName(), ".\n", sep = ""))
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##' }
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##'
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phrSetDumpFileName <-
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@ -874,7 +880,7 @@ function(filename) {
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##' )
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetDumpFileName(), "\n")
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##' cat(paste("see ", phrGetDumpFileName(), ".\n", sep = ""))
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##' }
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##'
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phrSetDumpFileOn <-
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@ -937,11 +943,10 @@ function(value) {
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##' @references \url{ftp://brrftp.cr.usgs.gov/pub/charlton/iphreeqc/IPhreeqc.pdf}
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##' @examples
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##'
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##' # This example equilibrates pure water with calcite and displays
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##' # the log file name.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetLogFileOn(TRUE)
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##' phrSetLogFileName("phreeqc.log")
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##' # This example attempts to run a input string, fails and writes
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##' # the error message to the error file (no database is loaded).
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##' phrSetErrorFileOn(TRUE)
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##' phrSetErrorFileName(file.path(tempdir(), "phreeqc.errors"))
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##' input <- c(
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##' 'SOLUTION 1 Pure water ',
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##' 'EQUILIBRIUM_PHASES 1 ',
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@ -949,7 +954,7 @@ function(value) {
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##' )
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetErrorFileName(), "\n")
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##' cat(paste("see ", phrGetErrorFileName(), ".\n", sep = ""))
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##' }
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##'
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phrSetErrorFileName <-
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@ -977,9 +982,9 @@ function(filename) {
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##' # This example attempts to run ex1, fails, and writes the error
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##' # message to the error file (no database is loaded).
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##' phrSetErrorFileOn(TRUE)
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##' phrSetErrorFileName("phreeqc.errors")
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##' phrSetErrorFileName(file.path(tempdir(), "phreeqc.errors"))
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##' if (!is.null(try(phrRunString(ex1), silent=TRUE))) {
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##' cat("see", phrGetErrorFileName(), "\n")
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##' cat(paste("see ", phrGetErrorFileName(), ".\n", sep = ""))
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##' }
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##'
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phrSetErrorFileOn <-
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@ -1038,7 +1043,7 @@ function(value) {
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##' # the log file name.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetLogFileOn(TRUE)
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##' phrSetLogFileName("phreeqc.log")
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##' phrSetLogFileName(file.path(tempdir(), "phreeqc.log"))
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##' input <- c(
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##' 'SOLUTION 1 Pure water ',
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##' 'EQUILIBRIUM_PHASES 1 ',
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@ -1048,7 +1053,7 @@ function(value) {
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##' )
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetLogFileName(), "\n")
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##' cat(paste("see ", phrGetLogFileName(), ".\n", sep = ""))
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##' }
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##'
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phrSetLogFileName <-
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@ -1077,14 +1082,15 @@ function(filename) {
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##'
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##' # This example runs ex2 with the log file turned on.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetLogStringsOn(TRUE)
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##' phrSetLogFileOn(TRUE)
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##' phrSetLogFileName(file.path(tempdir(), "ex2.log"))
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##'
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##' # turn logging on
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##' phrAccumulateLine("KNOBS; -logfile true")
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##' phrRunAccumulated()
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##'
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##' if (is.null(phrRunString(ex2))) {
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##' cat("see", phrGetLogFileName(), "\n")
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##' cat(paste("see ", phrGetLogFileName(), ".\n", sep = ""))
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##' }
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##'
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phrSetLogFileOn <-
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@ -1145,7 +1151,7 @@ function(value) {
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##' # the resulting file name.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetOutputFileOn(TRUE)
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##' phrSetOutputFileName("phreeqc.output")
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##' phrSetOutputFileName(file.path(tempdir(), "calcite.out"))
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##' input <- c(
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##' 'SOLUTION 1 Pure water ',
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##' 'EQUILIBRIUM_PHASES 1 ',
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@ -1153,7 +1159,7 @@ function(value) {
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##' )
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetOutputFileName(), "\n")
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##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep = ""))
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##' }
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##'
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phrSetOutputFileName <-
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@ -1186,8 +1192,9 @@ function(filename) {
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##' # load database and run input file
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetOutputFileOn(TRUE)
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##' phrSetOutputFileName(file.path(tempdir(), "ex2.out"))
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##' if (is.null(phrRunFile(tf))) {
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##' cat("see", phrGetOutputFileName(), "\n")
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##' cat(paste("see ", phrGetOutputFileName(), ".\n", sep = ""))
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##' }
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##'
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##' # delete temporary input file
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@ -1257,7 +1264,7 @@ function(value) {
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##' # and displays the name of the selected_output file.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetSelectedOutputFileOn(1, TRUE)
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##' phrSetSelectedOutputFileName(1, "ex2.sel")
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##' phrSetSelectedOutputFileName(1, file.path(tempdir(), "ex2.sel"))
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##'
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##' input <- c(
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##' 'SOLUTION 1 Pure water ',
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@ -1272,7 +1279,7 @@ function(value) {
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##'
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetSelectedOutputFileName(1))
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##' cat(paste("see ", phrGetSelectedOutputFileName(1), ".\n", sep = ""))
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##' }
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##'
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phrGetSelectedOutputFileName <-
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@ -1301,7 +1308,7 @@ function(nuser) {
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##' # and displays the name of the selected_output file.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetSelectedOutputFileOn(1, TRUE)
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##' phrSetSelectedOutputFileName(1, "ex2.sel")
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##' phrSetSelectedOutputFileName(1, file.path(tempdir(), "ex2.sel"))
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##'
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##' input <- c(
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##' 'SOLUTION 1 Pure water ',
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@ -1316,7 +1323,7 @@ function(nuser) {
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##'
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetSelectedOutputFileName(1))
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##' cat(paste("see ", phrGetSelectedOutputFileName(1), ".\n", sep = ""))
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##' }
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##'
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phrSetSelectedOutputFileName <-
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@ -1345,7 +1352,7 @@ function(nuser, filename) {
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##' # and displays the name of the selected_output file.
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##' phrLoadDatabaseString(phreeqc.dat)
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##' phrSetSelectedOutputFileOn(1, TRUE)
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##' phrSetSelectedOutputFileName(1, "ex2.sel")
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##' phrSetSelectedOutputFileName(1, file.path(tempdir(), "ex2.sel"))
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##'
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##' input <- c(
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##' 'SOLUTION 1 Pure water ',
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@ -1360,7 +1367,7 @@ function(nuser, filename) {
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##'
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##'
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##' if (is.null(phrRunString(input))) {
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##' cat("see", phrGetSelectedOutputFileName(1))
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##' cat(paste("see ", phrGetSelectedOutputFileName(1), ".\n", sep = ""))
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##' }
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##'
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phrSetSelectedOutputFileOn <-
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@ -1757,7 +1764,7 @@ NULL
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##' phrRunString(ex8)
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##' phrGetOutputStrings()
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##' # cleanup
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##' unlink(c("Zn1e_7", "Zn1e_4"))
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##' unlink(c("ex8.sel", "Zn1e_7", "Zn1e_4"))
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##'
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NULL
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