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iphreeqc/R/valgrind.R
Mike Taves 31af15ae73
Fix typos
2024-12-02 15:28:05 +13:00

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pkgname <- "phreeqc"
source(file.path(R.home("share"), "R", "examples-header.R"))
options(warn = 1)
base::assign(".ExTimings", "phreeqc-Ex.timings", pos = 'CheckExEnv')
base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
base::assign(".format_ptime",
function(x) {
if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
options(OutDec = '.')
format(x[1L:3L], digits = 7L)
},
pos = 'CheckExEnv')
### * </HEADER>
library('phreeqc')
base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
cleanEx()
nameEx("ex1")
### * ex1
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex1
### Title: Example 1-Speciation Calculation
### Aliases: ex1
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex1)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex1", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex10")
### * ex10
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex10
### Title: Example 10-Aragonite-Strontianite Solid Solution
### Aliases: ex10
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex10)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex10", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex11")
### * ex11
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex11
### Title: Example 11-Transport and Cation Exchange
### Aliases: ex11
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex11)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex11", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex12")
### * ex12
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex12
### Title: Example 12-Advective and Diffusive Flux of Heat and Solutes
### Aliases: ex12
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex12)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex12", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex13")
### * ex13
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex13a
### Title: Example 13-Aragonite-Strontianite Solid Solution
### Aliases: ex13a ex13b ex13c
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex13a)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex13", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex14")
### * ex14
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex14
### Title: Example 14-Advective Transport, Cation Exchange, Surface
### Complexation, and Mineral Equilibria
### Aliases: ex14
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex14)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex14", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex15")
### * ex15
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex15
### Title: Example 15-1D Transport: Kinetic Biodegradation, Cell Growth,
### and Sorption
### Aliases: ex15
### Keywords: dataset
### ** Examples
# this example takes longer than 5 seconds
phrLoadDatabaseString(ex15.dat)
phrSetOutputStringsOn(TRUE)
## Not run: phrRunString(ex15)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex15", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex16")
### * ex16
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex16
### Title: Example 16-Inverse Modeling of Sierra Spring Waters
### Aliases: ex16
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex16)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex16", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex17")
### * ex17
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex17
### Title: Example 17-Inverse Modeling With Evaporation
### Aliases: ex17
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(pitzer.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex17)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex17", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex18")
### * ex18
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex18
### Title: Example 18-Inverse Modeling of the Madison Aquifer
### Aliases: ex18
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex18)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex18", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex19")
### * ex19
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### 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
### Aliases: ex19
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex19)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex19", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex2")
### * ex2
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex2
### Title: Example 2-Equilibration With Pure Phases
### Aliases: ex2
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex2)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex2", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex20")
### * ex20
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex20a
### Title: Example 20-Distribution of Isotopes Between Water and Calcite
### Aliases: ex20a ex20b
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(iso.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex20a)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex20", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex21")
### * ex21
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex21
### Title: Example 21-Modeling Diffusion of HTO, 36Cl-, 22Na+, and Cs+ in a
### Radial Diffusion Cell
### Aliases: ex21
### 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
## Not run: phrRunString(ex21)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex21", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex22")
### * ex22
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex22
### Title: Example 22-Modeling Gas Solubilities: CO2 at High Pressures
### Aliases: ex22
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex22)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex22", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex3")
### * ex3
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex3
### Title: Example 3-Mixing
### Aliases: ex3
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex3)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex3", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex4")
### * ex4
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex4
### Title: Example 4-Evaporation and Homogeneous Redox Reactions
### Aliases: ex4
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex4)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex4", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex5")
### * ex5
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex5
### Title: Example 5-Irreversible Reactions
### Aliases: ex5
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex5)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex5", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex6")
### * ex6
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex6
### Title: Example 6-Reaction-Path Calculations
### Aliases: ex6
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex6)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex6", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex7")
### * ex7
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex7
### Title: Example 7-Gas-Phase Calculations
### Aliases: ex7
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex7)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex7", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex8")
### * ex8
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex8
### Title: Example 8-Surface Complexation
### Aliases: ex8
### 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()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex8", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("ex9")
### * ex9
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: ex9
### Title: Example 9-Kinetic Oxidation of Dissolved Ferrous Iron With
### Oxygen
### Aliases: ex9
### Keywords: dataset
### ** Examples
phrLoadDatabaseString(phreeqc.dat)
phrSetOutputStringsOn(TRUE)
phrRunString(ex9)
phrGetOutputStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("ex9", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrAccumulateLine")
### * phrAccumulateLine
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrAccumulateLine
### Title: Accumulate line(s) for input to phreeqc.
### Aliases: phrAccumulateLine
### ** 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 = ""))
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrAccumulateLine", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrClearAccumulatedLines")
### * phrClearAccumulatedLines
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrClearAccumulatedLines
### Title: Clear the accumulated input buffer.
### Aliases: phrClearAccumulatedLines
### ** 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")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrClearAccumulatedLines", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetAccumulatedLines")
### * phrGetAccumulatedLines
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetAccumulatedLines
### Title: Retrieve the accumulated input.
### Aliases: phrGetAccumulatedLines
### ** Examples
# This example loads some keyword input and displays the contents.
phrAccumulateLine("SOLUTION 1")
phrAccumulateLine("END")
cat("The accumulated input is:", phrGetAccumulatedLines(), sep = "\n")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetAccumulatedLines", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetComponentList")
### * phrGetComponentList
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetComponentList
### Title: Retrieve a list containing the current list of components.
### Aliases: phrGetComponentList
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetComponentList", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetDumpFileName")
### * phrGetDumpFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetDumpFileName
### Title: Retrieve the name of the dump file.
### Aliases: phrGetDumpFileName
### ** 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(), "."))
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetDumpFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetDumpStrings")
### * phrGetDumpStrings
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetDumpStrings
### Title: Retrieve DUMP strings.
### Aliases: phrGetDumpStrings
### ** 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")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetDumpStrings", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetErrorStrings")
### * phrGetErrorStrings
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetErrorStrings
### Title: Retrieve error string messages.
### Aliases: phrGetErrorStrings
### ** Examples
# loaddatabase should fail
n <- try(phrLoadDatabase("missing.dat"), silent = TRUE)
# if n is non-NULL display error string
if (!is.null(n)) phrGetErrorStrings()
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetErrorStrings", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetLogFileName")
### * phrGetLogFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetLogFileName
### Title: Retrieve the name of the log file.
### Aliases: phrGetLogFileName
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetLogFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetLogStrings")
### * phrGetLogStrings
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetLogStrings
### Title: Retrieve log output.
### Aliases: phrGetLogStrings
### ** 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()
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetLogStrings", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetOutputFileName")
### * phrGetOutputFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetOutputFileName
### Title: Retrieve the name of the output file.
### Aliases: phrGetOutputFileName
### ** 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
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetOutputFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetOutputStrings")
### * phrGetOutputStrings
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetOutputStrings
### Title: Retrieve standard phreeqc output.
### Aliases: phrGetOutputStrings
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetOutputStrings", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetSelectedOutput")
### * phrGetSelectedOutput
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetSelectedOutput
### Title: Returns the contents of the selected output as a list of data
### frames.
### Aliases: phrGetSelectedOutput
### ** Examples
# Load database and run ex2
phrLoadDatabaseString(phreeqc.dat)
phrRunString(ex2)
# display a summary of the results
df <- phrGetSelectedOutput()
summary(df$n1)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetSelectedOutput", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetSelectedOutputFileName")
### * phrGetSelectedOutputFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetSelectedOutputFileName
### Title: Retrieve the name of the selected_output file.
### Aliases: phrGetSelectedOutputFileName
### ** 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))
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetSelectedOutputFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrGetWarningStrings")
### * phrGetWarningStrings
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrGetWarningStrings
### Title: Retrieve warning messages.
### Aliases: phrGetWarningStrings
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrGetWarningStrings", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrLoadDatabase")
### * phrLoadDatabase
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrLoadDatabase
### Title: Load a phreeqc database file
### Aliases: phrLoadDatabase
### ** 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)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrLoadDatabase", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrLoadDatabaseString")
### * phrLoadDatabaseString
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrLoadDatabaseString
### Title: Load a phreeqc database as a string or a list of strings.
### Aliases: phrLoadDatabaseString
### 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 = ""))
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrLoadDatabaseString", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrRunAccumulated")
### * phrRunAccumulated
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrRunAccumulated
### Title: Runs the accumulated input.
### Aliases: phrRunAccumulated
### ** 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 = ""))
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrRunAccumulated", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrRunFile")
### * phrRunFile
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrRunFile
### Title: Run phreeqc input file
### Aliases: phrRunFile
### ** 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
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrRunFile", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrRunString")
### * phrRunString
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrRunString
### Title: Runs phreeqc using the given string as input.
### Aliases: phrRunString
### 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(), "."))
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrRunString", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetDumpFileName")
### * phrSetDumpFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetDumpFileName
### Title: Set the name of the dump file.
### Aliases: phrSetDumpFileName
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetDumpFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetDumpFileOn")
### * phrSetDumpFileOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetDumpFileOn
### Title: Set the dump file on/off.
### Aliases: phrSetDumpFileOn
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetDumpFileOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetDumpStringsOn")
### * phrSetDumpStringsOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetDumpStringsOn
### Title: Set dump strings on/off.
### Aliases: phrSetDumpStringsOn
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetDumpStringsOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetErrorFileName")
### * phrSetErrorFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetErrorFileName
### Title: Set the name of the error file.
### Aliases: phrSetErrorFileName
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetErrorFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetErrorFileOn")
### * phrSetErrorFileOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetErrorFileOn
### Title: Set error file on/off.
### Aliases: phrSetErrorFileOn
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetErrorFileOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetErrorStringsOn")
### * phrSetErrorStringsOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetErrorStringsOn
### Title: Set error strings on/off.
### Aliases: phrSetErrorStringsOn
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetErrorStringsOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetLogFileName")
### * phrSetLogFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetLogFileName
### Title: Set the name of the log file.
### Aliases: phrSetLogFileName
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetLogFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetLogFileOn")
### * phrSetLogFileOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetLogFileOn
### Title: Set log file on/off.
### Aliases: phrSetLogFileOn
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetLogFileOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetLogStringsOn")
### * phrSetLogStringsOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetLogStringsOn
### Title: Set log strings on/off.
### Aliases: phrSetLogStringsOn
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetLogStringsOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetOutputFileName")
### * phrSetOutputFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetOutputFileName
### Title: Set the name of the output file.
### Aliases: phrSetOutputFileName
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetOutputFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetOutputFileOn")
### * phrSetOutputFileOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetOutputFileOn
### Title: Set output file on/off.
### Aliases: phrSetOutputFileOn
### ** 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)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetOutputFileOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetOutputStringsOn")
### * phrSetOutputStringsOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetOutputStringsOn
### Title: Set output strings on/off.
### Aliases: phrSetOutputStringsOn
### ** 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")
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetOutputStringsOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetSelectedOutputFileName")
### * phrSetSelectedOutputFileName
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetSelectedOutputFileName
### Title: Set the name of the selected_output file.
### Aliases: phrSetSelectedOutputFileName
### ** 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))
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetSelectedOutputFileName", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phrSetSelectedOutputFileOn")
### * phrSetSelectedOutputFileOn
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phrSetSelectedOutputFileOn
### Title: Set selected_output file on/off.
### Aliases: phrSetSelectedOutputFileOn
### ** 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))
}
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phrSetSelectedOutputFileOn", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("phreeqc-package")
### * phreeqc-package
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: phreeqc-package
### Title: R interface to the PHREEQC geochemical modeling program.
### Aliases: phreeqc phreeqc-package
### 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 celsius"
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))
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("phreeqc-package", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
### * <FOOTER>
###
options(digits = 7L)
base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')
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