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ConvertRefPot() now handles AVS scale too.

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master
Taha Ahmed 14 years ago
parent 1d0dd666b0
commit b687e77eb5
3 changed files with 167 additions and 65 deletions
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5
CHI.R
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@ -82,8 +82,9 @@ ocp2df <- function(datafilename) {
for (s in 1:length(starts)) {
zz <- textConnection(chifile[starts[s]:ends[s]], "r")
ff <- rbind(ff,
data.frame(sampleid, matrix(scan(zz, what = numeric(), sep = ","),
ncol = 2, byrow = T)))
data.frame(stringsAsFactors = FALSE,
sampleid, matrix(scan(zz, what = numeric(), sep = ","),
ncol = 2, byrow = T)))
close(zz)
}
names(ff) <- c("sampleid", "time", "potential")

223
common.R
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@ -2,17 +2,21 @@
# General-purpose functions
# Taha Ahmed, Jan 2011
# CONTENTS
# >>>> LinearBaseline (deprecated)
# >>>> int2padstr
# >>>> It2charge **** STOP USING THIS FUNCTION ***
# >>>> ProvideSampleId
# >>>> ConvertRefPot
# >>>> Celsius2Kelvin
# >>>> Kelvin2Celsius
# >>>> as.radians
# >>>> as.degrees
# >>>> molarity2mass
# CONTENTS Status Depends on
# -------- ------ ----------
# >>>> LinearBaseline deprecated ?
# >>>> int2padstr ?
# >>>> It2charge deprecated ?
# >>>> ProvideSampleId ?
# >>>> Celsius2Kelvin ?
# >>>> Kelvin2Celsius ?
# >>>> as.radians ?
# >>>> as.degrees ?
# >>>> molarity2mass ?
# >>>> AVS2SHE -
# >>>> SHE2AVS -
# >>>> ConvertRefPotEC -
# >>>> ConvertRefPot ConvertRefPotEC, SHE2AVS, AVS2SHE
@ -132,56 +136,6 @@ ProvideSampleId <- function (fullpathwithfilename) {
##################################################
################# ConvertRefPot ##################
##################################################
ConvertRefPot <- function(argpotential, argrefscale, valuerefscale) {
# Converts from some reference potential scale into another
# SHE: standard hydrogen electrode scale
# Ag/AgCl: silver silver-chloride electrode scale
# SCE: standard calomel scale
#
##### Add more reference electrodes here >>
refpotatSHEzero <- c( 0, -0.21, -0.24, 3)
refrownames <- c( "SHE", "Ag/AgCl", "SCE", "Li/Li+")
refcolnames <- c("SHE0", "AgCl0", "SCE0", "Li0")
##### Add more reference electrodes here <<
#
SHE0 <- data.frame(matrix(refpotatSHEzero, ncol=length(refpotatSHEzero), byrow=T))
refpotmtx <- matrix(NA, length(SHE0), length(SHE0))
refpotmtx[,1] <- matrix(as.matrix(SHE0), ncol=1, byrow=T)
for (c in 2:length(SHE0)) {
# loop over columns (except the first)
for (r in 1:length(SHE0)) {
# loop over rows
refpotmtx[r, c] <- refpotmtx[r, 1] - refpotmtx[c, 1]
}
}
refpotdf <- as.data.frame(refpotmtx)
names(refpotdf) <- refcolnames
row.names(refpotdf) <- refrownames
## So far we have made a matrix of all the possible combinations,
## given the vector refpotatSHEzero. The matrix is not strictly necessary,
## but it may prove useful later. It does.
#
# Match argrefscale to the refrownames
argmatch <- match(argrefscale, refrownames, nomatch = 0)
# Match valuerefscale to the refrownames
valuematch <- match(valuerefscale, refrownames, nomatch = 0)
# We simply assume that the match was well-behaved
valuepotential <- argpotential + refpotdf[valuematch, argmatch]
# Check that arg and value electrodes are within bounds for a match
if (argmatch == 0 || valuematch == 0) {
# No match
# Perform suitable action
message("Arg out of bounds in call to ConvertRefPot")
valuepotential <- NA
}
return(valuepotential)
}
##################################################
############### Celsius2Kelvin ###################
##################################################
@ -224,6 +178,7 @@ as.radians <- function(degrees) {
}
##################################################
################# as.degrees #####################
##################################################
@ -234,6 +189,7 @@ as.degrees <- function(radians) {
}
##################################################
############### molarity2mass ####################
##################################################
@ -250,3 +206,148 @@ molarity2mass <- function(formulamass, volume, molarity) {
# [g * mol-1] * [liter] * [mole * liter-1] = [g]
return(mass)
}
##################################################
#################### AVS2SHE #####################
##################################################
AVS2SHE <- function(avs) {
# Converts from absolute vacuum scale (AVS) to SHE scale
she <- -(4.5 + avs)
return(she)
}
##################################################
#################### SHE2AVS #####################
##################################################
SHE2AVS <- function(she) {
# Converts from SHE scale to absolute vacuum (AVS) scale
avs <- -(4.5 + she)
return(avs)
}
##################################################
############### ConvertRefPotEC ##################
##################################################
ConvertRefPotEC <- function(argpotential, argrefscale, valuerefscale) {
# Converts from an electrochemical reference potential scale into another
# SHE: standard hydrogen electrode scale
# Ag/AgCl: silver silver-chloride electrode scale
# SCE: standard calomel scale
#
##### Add more reference electrodes here >>
refpotatSHEzero <- c( 0, -0.21, -0.24, 3)
refrownames <- c( "SHE", "Ag/AgCl", "SCE", "Li/Li+")
refcolnames <- c("SHE0", "AgCl0", "SCE0", "Li0")
##### Add more reference electrodes here <<
#
SHE0 <- data.frame(matrix(refpotatSHEzero, ncol=length(refpotatSHEzero), byrow=T))
refpotmtx <- matrix(NA, length(SHE0), length(SHE0))
refpotmtx[,1] <- matrix(as.matrix(SHE0), ncol=1, byrow=T)
for (c in 2:length(SHE0)) {
# loop over columns (except the first)
for (r in 1:length(SHE0)) {
# loop over rows
refpotmtx[r, c] <- refpotmtx[r, 1] - refpotmtx[c, 1]
}
}
refpotdf <- as.data.frame(refpotmtx)
names(refpotdf) <- refcolnames
row.names(refpotdf) <- refrownames
## So far we have made a matrix of all the possible combinations,
## given the vector refpotatSHEzero. The matrix is not strictly necessary,
## but it may prove useful later. It does.
#
# Match argrefscale to the refrownames
argmatch <- match(argrefscale, refrownames, nomatch = 0)
# Match valuerefscale to the refrownames
valuematch <- match(valuerefscale, refrownames, nomatch = 0)
# We simply assume that the match was well-behaved
valuepotential <- argpotential + refpotdf[valuematch, argmatch]
# Check that arg and value electrodes are within bounds for a match
if (argmatch == 0 || valuematch == 0) {
# No match
# Perform suitable action
message("Arg out of bounds in call to ConvertRefPot")
valuepotential <- NA
}
return(valuepotential)
}
##################################################
################# ConvertRefPot ##################
##################################################
ConvertRefPot <- function(argpotential, argrefscale, valuerefscale) {
# Check that argpotential is valid numeric
# IDEA: make a matrix out of these (scale names and flags)
# Valid scales
scale.names <- list()
scale.names[["SHE"]] <- c("SHE", "NHE", "she", "nhe")
scale.names[["AgCl"]] <- c("Ag/AgCl", "AgCl", "ag/agcl", "agcl")
scale.names[["SCE"]] <- c("SCE", "sce")
scale.names[["Li"]] <- c("Li/Li+", "Li", "Li+", "li", "li+", "li/li+")
scale.names[["AVS"]] <- c("AVS", "avs")
# Set flags
bool.flags <- as.data.frame(matrix(0, nrow = length(scale.names), ncol = 2))
names(bool.flags) <- c("argref", "valueref")
row.names(bool.flags) <- names(scale.names)
# argrefscale
# Check that argrefscale is valid character mode
# ...
for (j in 1:length(row.names(bool.flags))) {
if (any(scale.names[[row.names(bool.flags)[j]]] == argrefscale)) {
bool.flags[row.names(bool.flags)[j], "argref"] <- j
}
}
# valuerefscale
# Check that valuerefscale is valid character mode
# ...
for (k in 1:length(row.names(bool.flags))) {
if (any(scale.names[[row.names(bool.flags)[k]]] == valuerefscale)) {
bool.flags[row.names(bool.flags)[k], "valueref"] <- k
}
}
# Depending on which flags are set, call the corresponding function
decision.vector <- colSums(bool.flags)
# Check if both scales are the same (no conversion needed). If so, abort gracefully.
# ...
if (decision.vector["argref"] == 5 || decision.vector["valueref"] == 5) {
# AVS is requested, deal with it it
if (decision.vector["argref"] == 5) {
# Conversion _from_ AVS
rnpotential <- ConvertRefPotEC(AVS2SHE(argpotential),
"SHE",
scale.names[[decision.vector["valueref"]]][1])
}
if (decision.vector["valueref"] == 5) {
# Conversion _to_ AVS
rnpotential <- SHE2AVS(ConvertRefPotEC(argpotential,
scale.names[[decision.vector["argref"]]][1],
"SHE"))
}
} else {
rnpotential <- ConvertRefPotEC(argpotential,
scale.names[[decision.vector["argref"]]][1],
scale.names[[decision.vector["valueref"]]][1])
}
return(rnpotential)
}

4
xrdtf.R
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@ -110,7 +110,7 @@ scherrer <- function(integralbreadth, thth, wavelength = 1.54056, shapeconstant
# Function for calculating crystallite grain size from reflection data
# ARGS: integralbreadth - vector with integral breadth of reflections (in degrees)
# thth - vector with 2theta values of reflections (in degrees)
# wavelength - X-ray wavelength used (default 1.54056 Å, Cu Ka)
# wavelength - X-ray wavelength used (default 1.54056 A, Cu Ka)
# shapeconstant - Scherrer constant (default spherical, ~0.9)
# VALUE: vector with size parameters
## REQUIRES: as.radians(), source("/home/taha/chepec/chetex/common/R/common.R")
@ -127,7 +127,7 @@ scherrer <- function(integralbreadth, thth, wavelength = 1.54056, shapeconstant
##################################################
pdf2df <- function(pdffile) {
# Function for extracting information from ICDD PDF XML-files
# For example the PDF files produced by the PDF database at Ångström's X-ray lab
# For example the PDF files produced by the PDF database at Angstrom's X-ray lab
# NOTE: sometimes intensity values are specified as less than some value.
# In those cases, this function simply strips the less-than character.
# ARGS: pdffile (complete path and filename to PDF file)

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