ConvertRefPot() now handles AVS scale too.

CHI.R

@@ -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 = ","),
+               data.frame(stringsAsFactors = FALSE,
-                  ncol = 2, byrow = T)))
+               sampleid, matrix(scan(zz, what = numeric(), sep = ","),
+               ncol = 2, byrow = T)))
       close(zz)
    }
    names(ff) <- c("sampleid", "time", "potential")

common.R

@@ -2,17 +2,21 @@
 # General-purpose functions
 # Taha Ahmed, Jan 2011
 
-# CONTENTS
+# CONTENTS              Status      Depends on
-# >>>> LinearBaseline (deprecated)
+# --------              ------      ----------
-# >>>> int2padstr
+# >>>> LinearBaseline   deprecated  ?
-# >>>> It2charge **** STOP USING THIS FUNCTION ***
+# >>>> int2padstr                   ?
-# >>>> ProvideSampleId
+# >>>> It2charge        deprecated  ?
-# >>>> ConvertRefPot
+# >>>> ProvideSampleId              ?
-# >>>> Celsius2Kelvin
+# >>>> Celsius2Kelvin               ?
-# >>>> Kelvin2Celsius
+# >>>> Kelvin2Celsius               ?
-# >>>> as.radians
+# >>>> as.radians                   ?
-# >>>> as.degrees
+# >>>> as.degrees                   ?
-# >>>> molarity2mass
+# >>>> 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)
+}

xrdtf.R

@@ -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)