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Reworked both from.SHE and as.SHE to resolve

the aforementioned bug and also some inconsistent behaviour when submitting a vector of potentials for certain electrode scales.
Both issues should be fixed now.
master
Taha Ahmed 4 years ago
parent
commit
bee42f9fd9
  1. 9
      DESCRIPTION
  2. 539
      R/unit-converters-electrochemical.R
  3. 6
      README.md

9
DESCRIPTION

@ -1,13 +1,14 @@
Package: common
Type: Package
Title: chepec common
Version: 0.0.0.9011
Version: 0.0.0.9012
Description: Commonly used functions and scripts.
Authors@R: person("Taha", "Ahmed", email = "taha@chepec.se", role = c("aut", "cre"))
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
Imports:
Imports:
stats,
knitr,
xtable,
utils,
knitr
utils

539
R/unit-converters-electrochemical.R

@ -89,7 +89,7 @@ RefCanonicalName <- function(refname) {
"Mg/Mg2+",
"Magnesium")
# if no argument or empty string supplied as arg, return the the entire list as df
# if no argument or empty string supplied as arg, return the entire list as df
# to give the user a nice overview of all available options
if (missing(refname) || refname == "") {
max.row.length <- 0
@ -185,60 +185,61 @@ potentials.as.SHE <- function() {
# all potentials vs SHE
potentials <-
as.data.frame(matrix(data =
# electrode # electrolyte # conc/M # conc label # temp # pot vs SHE # set id # ref
c("AgCl/Ag", "NaCl(aq)", "5.9", "saturated", "25", "0.2630", "9", "CRC 97th ed., 97-05-22",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "10", "0.215", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "15", "0.212", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "20", "0.208", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "25", "0.205", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "30", "0.201", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "35", "0.197", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "40", "0.193", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "10", "0.214", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "15", "0.209", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "20", "0.204", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "25", "0.199", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "30", "0.194", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "35", "0.189", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "40", "0.184", "2", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "10", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "15", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "20", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "25", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "30", "0.335", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "35", "0.334", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "40", "0.334", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "10", "0.287", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "20", "0.284", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "25", "0.283", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "30", "0.282", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "40", "0.278", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "10", "0.256", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "15", "0.254", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "20", "0.252", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "25", "0.250", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "30", "0.248", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "35", "0.246", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "40", "0.244", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "10", "0.254", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "15", "0.251", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "20", "0.248", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "25", "0.244", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "30", "0.241", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "35", "0.238", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "40", "0.234", "6", "Sawyer1995",
"AVS", "", "", "", "25", "-4.44", "7", "Trasatti1986",
"SHE", "", "", "", "-273.15", "0.00", "8", "Inzelt2013",
"SHE", "", "", "", "0", "0.00", "8", "Inzelt2013",
"SHE", "", "", "", "25", "0.00", "8", "Inzelt2013",
# arbitrary max T=580C (temp at which sodalime glass loses rigidity)
"SHE", "", "", "", "580", "0.00", "8", "Inzelt2013",
"Li", "", "1.0", "1.0M at 25C", "25", "-3.0401", "10", "CRC 97th ed., 97-05-22",
"Na", "", "1.0", "1.0M at 25C", "25", "-2.71", "11", "CRC 97th ed., 97-05-22",
"Mg", "", "1.0", "1.0M at 25C", "25", "-2.372", "12", "CRC 97th ed., 97-05-22"),
ncol = 8,
byrow = TRUE), stringsAsFactors = FALSE)
as.data.frame(
matrix(data =
# electrode # electrolyte # conc/M # conc label # temp # pot vs SHE # set id # ref
c("AgCl/Ag", "NaCl(aq)", "5.9", "saturated", "25", "0.2630", "9", "CRC 97th ed., 97-05-22",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "10", "0.215", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "15", "0.212", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "20", "0.208", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "25", "0.205", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "30", "0.201", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "35", "0.197", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "3.5", "3.5M at 25C", "40", "0.193", "1", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "10", "0.214", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "15", "0.209", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "20", "0.204", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "25", "0.199", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "30", "0.194", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "35", "0.189", "2", "Sawyer1995",
"AgCl/Ag", "KCl(aq)", "4.2", "saturated", "40", "0.184", "2", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "10", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "15", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "20", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "25", "0.336", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "30", "0.335", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "35", "0.334", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "0.1", "0.1M at 25C", "40", "0.334", "3", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "10", "0.287", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "20", "0.284", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "25", "0.283", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "30", "0.282", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "1.0", "1.0M at 25C", "40", "0.278", "4", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "10", "0.256", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "15", "0.254", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "20", "0.252", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "25", "0.250", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "30", "0.248", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "35", "0.246", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "3.5", "3.5M at 25C", "40", "0.244", "5", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "10", "0.254", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "15", "0.251", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "20", "0.248", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "25", "0.244", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "30", "0.241", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "35", "0.238", "6", "Sawyer1995",
"Hg2Cl2/Hg", "KCl(aq)", "4.2", "saturated", "40", "0.234", "6", "Sawyer1995",
"AVS", "", "", "", "25", "-4.44", "7", "Trasatti1986",
"SHE", "", "", "", "-273.15", "0.00", "8", "Inzelt2013",
"SHE", "", "", "", "0", "0.00", "8", "Inzelt2013",
"SHE", "", "", "", "25", "0.00", "8", "Inzelt2013",
# arbitrary max T=580C (temp at which sodalime glass loses rigidity)
"SHE", "", "", "", "580", "0.00", "8", "Inzelt2013",
"Li", "", "1.0", "1.0M at 25C", "25", "-3.0401", "10", "CRC 97th ed., 97-05-22",
"Na", "", "1.0", "1.0M at 25C", "25", "-2.71", "11", "CRC 97th ed., 97-05-22",
"Mg", "", "1.0", "1.0M at 25C", "25", "-2.372", "12", "CRC 97th ed., 97-05-22"),
ncol = 8,
byrow = TRUE), stringsAsFactors = FALSE)
colnames(potentials) <-
c("electrode",
@ -297,24 +298,23 @@ as.SHE <- function(potential,
# if the supplied temperature does not exist in the data, this function will attempt to interpolate
# note that concentration has to match, no interpolation is attempted for conc
# make this work for arbitrary-length vectors of potential and scale
# make sure potential and scale args have the same length
# potential and scale vectors supplied by user could have arbitrary length
# just make sure potential and scale args have the same length (or length(scale) == 1)
if (length(potential) == 0 | length(scale) == 0) {
stop("Arguments potential or scale cannot be empty!")
stop("Potential or scale arguments cannot be empty!")
} else if (length(potential) != length(scale)) {
# stop, unless length(scale) == 1 where we will assume it should be recycled
if (length(scale) == 1) {
message("Argument <scale> has unit length. Recycling it to match length of <potential>. ")
message("Arg <scale> has unit length. We'll recycle it to match length of <potential>.")
scale <- rep(scale, length(potential))
} else {
stop(paste0("Correspondence between the supplied potentials and scales could not be worked out.\n",
"Please make sure the number of elements in each match, or make <scale> unit length."))
stop("Length of <potential> and <scale> must be equal OR <scale> may be unit length.")
}
}
arglength <- length(potential)
# make the args concentration, temperature and electrolyte this same length,
# unless the user supplied them (only necessary for > 1)
# unless the user supplied them (only necessary for length > 1)
if (arglength > 1) {
# handle two cases:
# 1. user did not touch concentration, temperature and electrolyte args.
@ -327,7 +327,7 @@ as.SHE <- function(potential,
identical(electrolyte, formals(as.SHE)$electrolyte)) {
# case 1
# message("NOTE: default concentration and temperature values used for all potentials and scales.")
message(paste0("Default concentration (", formals(as.SHE)$concentration, "), temperature (", formals(as.SHE)$temperature, "C) used for all supplied potential and scale values."))
message(paste0("The default concentration (", formals(as.SHE)$concentration, ") and temperature (", formals(as.SHE)$temperature, "C) will be assumed for all your potential/scale values."))
concentration <- rep(concentration, arglength)
temperature <- rep(temperature, arglength)
electrolyte <- rep(electrolyte, arglength)
@ -340,7 +340,7 @@ as.SHE <- function(potential,
## we can now safely assume that length(<args>) == arglength
# place args into a single dataframe
# this way, we can correlate columns to each other by row
df <-
dfargs <-
data.frame(potential = potential,
scale = common::RefCanonicalName(scale),
electrolyte = electrolyte,
@ -348,139 +348,155 @@ as.SHE <- function(potential,
temperature = temperature,
stringsAsFactors = FALSE)
# add column to keep track of vacuum scale
df$vacuum <- as.logical(FALSE)
# dfargs$vacuum <- as.logical(FALSE)
# add column to hold calc potential vs SHE
df$SHE <- as.numeric(NA)
dfargs$SHE <- as.numeric(NA)
## From here on, ONLY access the arguments via this dataframe
## That is, use dfargs$electrolyte, NOT electrolyte
# SHE scale special considerations
# 1. concentration is constant
if (any(df$scale == common::RefCanonicalName("SHE"))) {
df$concentration[which(df$scale == common::RefCanonicalName("SHE"))] <- ""
df$electrolyte[which(df$scale == common::RefCanonicalName("SHE"))] <- ""
# 1. concentration is constant for SHE
if (any(dfargs$scale == common::RefCanonicalName("SHE"))) {
dfargs$concentration[which(dfargs$scale == common::RefCanonicalName("SHE"))] <- ""
dfargs$electrolyte[which(dfargs$scale == common::RefCanonicalName("SHE"))] <- ""
}
# AVS scale special considerations
# 1. concentration is meaningless
# 2. direction is opposite of electrochemical scales, requiring change of sign
if (any(df$scale == common::RefCanonicalName("AVS"))) {
# concentration is meaningless for AVS (no electrolyte)
# so for those rows, we'll reset it
df$concentration[which(df$scale == common::RefCanonicalName("AVS"))] <- ""
df$electrolyte[which(df$scale == common::RefCanonicalName("AVS"))] <- ""
df$vacuum[which(df$scale == common::RefCanonicalName("AVS"))] <- TRUE
# 1. concentration is meaningless for AVS
if (any(dfargs$scale == common::RefCanonicalName("AVS"))) {
# concentration is meaningless for AVS (no electrolyte) so for those rows, we'll reset it
dfargs$concentration[which(dfargs$scale == common::RefCanonicalName("AVS"))] <- ""
dfargs$electrolyte[which(dfargs$scale == common::RefCanonicalName("AVS"))] <- ""
# dfargs$vacuum[which(dfargs$scale == common::RefCanonicalName("AVS"))] <- TRUE
}
# now just work our way through df, line-by-line to determine potential as SHE
# all necessary conditions should be recorded right here in df
for (p in 1:dim(df)[1]) {
# Fixed a bug 2018-03-04
# Issue: if scale was {Li,Na,Mg} the default electrolyte string "saturated" caused
# zero rows to be returned in the subset.SHE.data match, with error returned to user.
# Fixed by making the matching more step-wise:
# + first, subset against electrode scale. If only one row, done. If more,
# + subset against either conc.string or conc.num. Stop if zero rows (error), otherwise proceed.
subset.scale <- subset(as.SHE.data, electrode == df$scale[p])
if (dim(subset.scale)[1] > 1) {
# now just work our way through dfargs, line-by-line to determine potential as SHE
# all necessary conditions should be recorded right here in dfargs
for (p in 1:dim(dfargs)[1]) {
## WE ARE NOW WORKING ROW-BY-ROW THROUGH THE SUPPLIED ARGUMENTS IN dfargs
# Step-wise matching:
# + first, we subset against electrode scale. If dataset only has one row, done. Else,
# + we subset against either conc.string or conc.num. Stop if zero rows in dataset (error), otherwise proceed.
# Our "dataset" is the literature data supplied via the argument as.SHE.data
this.data.scale <- subset(as.SHE.data, electrode == dfargs$scale[p])
# subset.scale <- subset(as.SHE.data, electrode == dfargs$scale[p])
if (dim(this.data.scale)[1] > 1) {
# continue matching, now against conc.string or conc.num
if (is.character(df$concentration[p])) {
subset.concentration <-
subset(subset.scale, conc.string == df$concentration[p])
if (is.character(dfargs$concentration[p])) {
this.data.concentration <-
# subset.concentration <-
subset(this.data.scale, conc.string == dfargs$concentration[p])
} else {
subset.concentration <-
subset(subset.scale, conc.num == df$concentration[p])
this.data.concentration <-
# subset.concentration <-
subset(this.data.scale, conc.num == dfargs$concentration[p])
}
# stop if the resulting dataframe after matching contains no rows
if (dim(subset.concentration)[1] == 0) {
stop("Sorry, it seems we failed to find any matching entries in potentials.as.SHE().")
if (dim(this.data.concentration)[1] == 0) {
stop(paste0("Failed to find any matching entries in dataset for ",
paste(dfargs[p, ], collapse = " ", sep = "")))
}
# Note: it's ok at this point if the resulting df contains more than one row as
# Note: it's ok at this point if the resulting dataset contains more than one row as
# more matching will be done below
# If we haven't had reason to stop(), we should be good
# just housekeeping: rename the variable so we don't have to edit code below
subset.SHE.data <- subset.concentration
this.SHE.data <- this.data.concentration
# subset.SHE.data <- subset.concentration
} else {
# just housekeeping: rename the variable so we don't have to change the code that follows
subset.SHE.data <- subset.scale
# just housekeeping again
this.SHE.data <- this.data.scale
# subset.SHE.data <- subset.scale
}
# use KCl(aq) as default to avoid aborting
# (good assumption at this point, as we always have KCl for the cases
# where an electrode system has more than one electrolyte)
default.electrolyte <- "KCl(aq)"
# If this subset contains more than one unique electrolyte (e.g., NaCl and KCl)
# the user MUST have made a choice (in the "electrolyte" argument) that results
# in a single electrolyte remaining, or else we will warn and abort
if (length(unique(subset.SHE.data$electrolyte)) > 1) {
# data (in subset.SHE.data) contains more than one electrolyte
# if user did not change electrolyte arg value, use default and issue warning
if (identical(electrolyte, formals(as.SHE)$electrolyte)) {
warning(paste0("You did not specify an electrolyte, but more than one ",
"is available for E = ", df$potential[p], " V vs ", df$scale[p], ".\n",
"Using electrolyte: ", default.electrolyte))
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == default.electrolyte)
## Electrolyte
# == We would like to transparently handle the following scenario:
# || if the user did not specify electrolyte solution (which we can check by using formals())
# || but the dataset (after subsetting against scale and concentration above) still contains
# || more than one electrolyte
# >> Approach: we'll specify a "fallback" electrolyte, KCl (usually that's what the user wants)
# >> and inform/warn about it
# KCl is a good assumption, as we always have KCl
# for the cases where an electrode system has more than one electrolyte
fallback.electrolyte <- "KCl(aq)"
if (length(unique(this.SHE.data$electrolyte)) > 1) {
if (formals(as.SHE)$electrolyte == "") {
warning(paste0("More than one electrolyte ",
"available for E(", dfargs$scale[p], ") in dataset. ",
"I'll assume you want ", fallback.electrolyte, "."))
this.SHE.data <-
subset(this.SHE.data, electrolyte == fallback.electrolyte)
} else {
# else the user did change the electrolyte arg, use the user's value
subset.SHE.data <-
subset.SHE.data[which(subset.SHE.data$electrolyte == electrolyte), ]
# print only for debugging - disable before production!
print(subset.SHE.data)
# stop if the resulting dataframe contains no rows
if (dim(subset.SHE.data)[1] == 0) {
stop("Your choice of electrolyte does not match any data!")
}
this.SHE.data <-
subset(this.SHE.data, electrolyte == dfargs$electrolyte[p])
# but stop if the resulting dataframe contains no rows
if (dim(this.SHE.data)[1] == 0) stop("Your choice of electrolyte does not match any data!")
}
} else {
# data only contains one electrolyte
# just check that it matches whatever the user supplied, if not,
# issue a warning (but don't abort, typically the user did not set it
# because they don't care and want whatever is in the data)
if (any(subset.SHE.data$electrolyte != electrolyte)) {
warning(paste0("The requested electrolyte: ",
ifelse(any(electrolyte == ""),
"<none specified>",
electrolyte),
" was not found for E = ", df$potential[p], " V vs ", df$scale[p], ".\n",
"My data only lists one electrolyte for that scale - return value calculated on that basis."))
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == unique(subset.SHE.data$electrolyte))
# dataset contains only one unique electrolyte
# again, check if electrolyte in arg matches the one in dataset
# if it does, great, if it does not, print a message and use it anyway
if (unique(this.SHE.data$electrolyte) == dfargs$electrolyte[p]) {
this.SHE.data <-
subset(this.SHE.data, electrolyte == dfargs$electrolyte[p])
} else {
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == electrolyte)
# whatever electrolyte the user supplied does not match what's left in the datasubset
# but at this point the user is probably better served by returning the electrolyte we have
# along with an informative message (that's the only reason for the if-else below)
electrolytes.in.subset <-
unique(subset(as.SHE.data, electrode == dfargs$scale[p])$electrolyte)
if (dfargs$electrolyte[p] == "") {
message(
paste0('Electrolyte "" (empty string) not in dataset for E(',
dfargs$scale[p], '). ',
'These electrolytes are: ',
paste(electrolytes.in.subset, collapse = ', or '), '.',
"I'll assume you want ", fallback.electrolyte, ".")
)
} else {
message(paste0("Electrolyte ", dfargs$electrolyte[p], " not in dataset for E(",
dfargs$scale[p], "). ",
"These electrolytes are: ",
paste(electrolytes.in.subset, collapse = ", or "), ".",
"I'll assume you want ", fallback.electrolyte, ".")
)
}
}
}
# temperature
# either happens to match a temperature in the dataset, or we interpolate
# (under the assumption that potential varies linearly with temperature)
if (!any(subset.SHE.data$temp == df$temperature[p])) {
if (!any(this.SHE.data$temp == dfargs$temperature[p])) {
# sought temperature was not available in dataset, check that it falls inside
# note: important to use less/more-than-or-equal in case data only contains one value
if ((df$temperature[p] <= max(subset.SHE.data$temp)) &&
(df$temperature[p] >= min(subset.SHE.data$temp))) {
if ((dfargs$temperature[p] <= max(this.SHE.data$temp)) && (dfargs$temperature[p] >= min(this.SHE.data$temp))) {
# within dataset range, do linear interpolation
lm.subset <- stats::lm(SHE ~ temp, data = subset.SHE.data)
lm.subset <- stats::lm(SHE ~ temp, data = this.SHE.data)
# interpolated temperature, calculated based on linear regression
# (more accurate than simple linear interpolation with approx())
pot.interp <-
lm.subset$coefficients[2] * df$temperature[p] + lm.subset$coefficients[1]
lm.subset$coefficients[2] * dfargs$temperature[p] + lm.subset$coefficients[1]
### CALC POTENTIAL vs SHE
df$SHE[p] <-
ifelse(df$vacuum[p],
pot.interp - df$potential[p],
pot.interp + df$potential[p])
dfargs$SHE[p] <-
ifelse(dfargs$scale[p] == "AVS",
pot.interp - dfargs$potential[p],
pot.interp + dfargs$potential[p])
}
} else {
# requested temperature does exist in dataset
### CALC POTENTIAL vs SHE
df$SHE[p] <-
ifelse(df$vacuum[p],
subset(subset.SHE.data, temp == df$temperature[p])$SHE - df$potential[p],
subset(subset.SHE.data, temp == df$temperature[p])$SHE + df$potential[p])
dfargs$SHE[p] <-
ifelse(dfargs$scale[p] == "AVS",
subset(this.SHE.data, temp == dfargs$temperature[p])$SHE - dfargs$potential[p],
subset(this.SHE.data, temp == dfargs$temperature[p])$SHE + dfargs$potential[p])
}
}
return(df$SHE)
return(dfargs$SHE)
}
@ -509,27 +525,29 @@ from.SHE <- function(potential,
temperature = 25,
as.SHE.data = potentials.as.SHE()) {
# make this work for arbitrary-length vectors of potential and scale
# make sure potential and scale args have the same length
# if the supplied temperature does not exist in the data, this function will attempt to interpolate
# note that concentration has to match, no interpolation is attempted for conc
# potential and scale vectors supplied by user could have arbitrary length
# just make sure potential and scale args have the same length (or length(scale) == 1)
if (length(potential) == 0 | length(scale) == 0) {
stop("Arguments potential or scale cannot be empty!")
stop("Potential or scale arguments cannot be empty!")
} else if (length(potential) != length(scale)) {
# stop, unless length(scale) == 1 where we will assume it should be recycled
if (length(scale) == 1) {
message("Argument <scale> has unit length. Recycling it to match length of <potential>. ")
message("Arg <scale> has unit length. We'll recycle it to match length of <potential>.")
scale <- rep(scale, length(potential))
} else {
stop(paste0("Correspondence between the supplied potentials and scales could not be worked out.\n",
"Please make sure the number of elements in each match, or make <scale> unit length."))
stop("Length of <potential> and <scale> must be equal OR <scale> may be unit length.")
}
}
arglength <- length(potential)
# make the args concentration, temperature and electrolyte this same length,
# unless the user supplied them (only necessary for > 1)
# unless the user supplied them (only necessary for length > 1)
if (arglength > 1) {
# handle two cases:
# 1. user did not touch concentration, temperature or electrolyte args.
# 1. user did not touch concentration, temperature and electrolyte args.
# Assume they forgot and reset their length and print a message
# 2. user did change concentration or temperature or electrolyte, but still failed to
# ensure length equal to arglength. In this case, abort.
@ -538,7 +556,7 @@ from.SHE <- function(potential,
identical(temperature, formals(from.SHE)$temperature) &
identical(electrolyte, formals(from.SHE)$electrolyte)) {
# case 1
message(paste0("Default concentration (", formals(from.SHE)$concentration, "), temperature (", formals(from.SHE)$temperature, "C) used for all supplied potential and scale values."))
message(paste0("The default concentration (", formals(from.SHE)$concentration, ") and temperature (", formals(from.SHE)$temperature, "C) will be assumed for all your potential/scale values."))
concentration <- rep(concentration, arglength)
temperature <- rep(temperature, arglength)
electrolyte <- rep(electrolyte, arglength)
@ -551,147 +569,154 @@ from.SHE <- function(potential,
## we can now safely assume that length(<args>) == arglength
# place args into a single dataframe
# this way, we can correlate columns to each other by row
df <-
dfargs <-
data.frame(potential = potential, # vs SHE
scale = common::RefCanonicalName(scale), # target scale
electrolyte = electrolyte,
concentration = concentration,
temperature = temperature,
stringsAsFactors = FALSE)
# # add column to keep track of vacuum scale
# df$vacuum <- as.logical(FALSE)
# # add column to hold calc potential vs target scale
# df$targetscale <- as.numeric(NA)
## Special considerations
# SHE scale independent of concentration, per definition
if (any(df$scale == common::RefCanonicalName("SHE"))) {
df$concentration[which(df$scale == common::RefCanonicalName("SHE"))] <- ""
df$electrolyte[which(df$scale == common::RefCanonicalName("SHE"))] <- ""
## From here on, ONLY access the arguments via this dataframe
## That is, use dfargs$electrolyte, NOT electrolyte (and so on)
# SHE scale special considerations
# 1. concentration is constant for SHE
if (any(dfargs$scale == common::RefCanonicalName("SHE"))) {
dfargs$concentration[which(dfargs$scale == common::RefCanonicalName("SHE"))] <- ""
dfargs$electrolyte[which(dfargs$scale == common::RefCanonicalName("SHE"))] <- ""
}
# AVS scale: concentration is meaningless (no electrolyte)
if (any(df$scale == common::RefCanonicalName("AVS"))) {
df$concentration[which(df$scale == common::RefCanonicalName("AVS"))] <- ""
df$electrolyte[which(df$scale == common::RefCanonicalName("AVS"))] <- ""
# AVS scale special considerations
# 1. concentration is meaningless for AVS
if (any(dfargs$scale == common::RefCanonicalName("AVS"))) {
# concentration is meaningless for AVS (no electrolyte) so for those rows, we'll reset it
dfargs$concentration[which(dfargs$scale == common::RefCanonicalName("AVS"))] <- ""
dfargs$electrolyte[which(dfargs$scale == common::RefCanonicalName("AVS"))] <- ""
}
for (p in 1:dim(df)[1]) {
# First, subset against electrode scale. If as.SHE.data only contains one row
# for this electrode scale we are DONE. If not, proceed to subset against concentration
subset.scale <- subset(as.SHE.data, electrode == df$scale[p])
if (dim(subset.scale)[1] > 1) {
# now just work our way through dfargs, line-by-line to determine potential as SHE
# all necessary conditions should be recorded right here in dfargs
for (p in 1:dim(dfargs)[1]) {
## WE ARE NOW WORKING ROW-BY-ROW THROUGH THE SUPPLIED ARGUMENTS IN dfargs
# Step-wise matching:
# + first, we subset against electrode scale. If dataset only has one row, done. Else,
# + we subset against either conc.string or conc.num. Stop if zero rows in dataset (error), otherwise proceed.
# Our "dataset" is the literature data supplied via the argument as.SHE.data
this.data.scale <- subset(as.SHE.data, electrode == dfargs$scale[p])
# subset.scale <- subset(as.SHE.data, electrode == dfargs$scale[p])
if (dim(this.data.scale)[1] > 1) {
# continue matching, now against conc.string or conc.num
if (is.character(df$concentration[p])) {
subset.concentration <-
subset(subset.scale, conc.string == df$concentration[p])
if (is.character(dfargs$concentration[p])) {
this.data.concentration <-
subset(this.data.scale, conc.string == dfargs$concentration[p])
} else {
subset.concentration <-
subset(subset.scale, conc.num == df$concentration[p])
this.data.concentration <-
subset(this.data.scale, conc.num == dfargs$concentration[p])
}
# stop if the resulting dataframe after matching contains no rows
if (dim(subset.concentration)[1] == 0) {
stop("Sorry, it seems we failed to find any matching entries in potentials.as.SHE().")
if (dim(this.data.concentration)[1] == 0) {
stop(paste0("Failed to find any matching entries in dataset for ",
paste(dfargs[p, ], collapse = " ", sep = "")))
}
# Note: it's ok at this point if the resulting df contains more than one row as
# Note: it's ok at this point if the resulting dataset contains more than one row as
# more matching will be done below
# If we haven't had reason to stop(), we should be good
# just housekeeping: rename the variable so we don't have to edit code below
subset.SHE.data <- subset.concentration
this.SHE.data <- this.data.concentration
} else {
# just housekeeping again
subset.SHE.data <- subset.scale
this.SHE.data <- this.data.scale
}
# use KCl(aq) as default to avoid aborting
# (good assumption at this point, as we always have KCl for the cases
# where an electrode system has more than one electrolyte)
default.electrolyte <- "KCl(aq)"
# If this subset contains more than one unique electrolyte (e.g., NaCl and KCl)
# the user MUST have made a choice (in the "electrolyte" argument) that results
# in a single electrolyte remaining, or else we will warn and abort
if (length(unique(subset.SHE.data$electrolyte)) > 1) {
# data (in subset.SHE.data) contains more than one electrolyte
# if user did not change electrolyte arg value, use default and issue warning
if (identical(electrolyte, formals(as.SHE)$electrolyte)) {
warning(paste0("You did not specify an electrolyte, but more than one ",
"is available for E = ", df$potential[p], " V vs ", df$scale[p], ".\n",
"We'll use the default electrolyte: ", default.electrolyte))
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == default.electrolyte)
## Electrolyte
# == We would like to transparently handle the following scenario:
# || if the user did not specify electrolyte solution (which we can check by using formals())
# || but the dataset (after subsetting against scale and concentration above) still contains
# || more than one electrolyte
# >> Approach: we'll specify a "fallback" electrolyte, KCl (usually that's what the user wants)
# >> and inform/warn about it
# KCl is a good assumption, as we always have KCl for the cases where
# an electrode system has more than one electrolyte
fallback.electrolyte <- "KCl(aq)"
if (length(unique(this.SHE.data$electrolyte)) > 1) {
if (formals(as.SHE)$electrolyte == "") {
warning(paste0("More than one electrolyte ",
"available for E(", dfargs$scale[p], ") in dataset. ",
"I'll assume you want ", fallback.electrolyte, "."))
this.SHE.data <-
subset(this.SHE.data, electrolyte == fallback.electrolyte)
} else {
# else the user did change the electrolyte arg, use the user's value
subset.SHE.data <-
subset.SHE.data[which(subset.SHE.data$electrolyte == electrolyte), ]
# print only for debugging - disable before production!
print(subset.SHE.data)
# stop if the resulting dataframe contains no rows
if (dim(subset.SHE.data)[1] == 0) {
stop("Your choice of electrolyte does not match any data!")
}
this.SHE.data <-
subset(this.SHE.data, electrolyte == dfargs$electrolyte[p])
# but stop if the resulting dataframe contains no rows
if (dim(this.SHE.data)[1] == 0) stop("Your choice of electrolyte does not match any data!")
}
} else {
# data only contains one electrolyte
# just check that it matches whatever the user supplied, if not,
# issue a warning (but don't abort, typically the user did not set it
# because they don't care and want whatever is in the data)
if (any(subset.SHE.data$electrolyte != electrolyte)) {
warning(paste0("The requested electrolyte: ",
ifelse(any(electrolyte == ""),
"<none specified>",
electrolyte),
" was not found for E = ", df$potential[p], " V vs ", df$scale[p], ".\n",
"My data only lists one electrolyte for that scale - return value calculated on that basis."))
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == unique(subset.SHE.data$electrolyte))
# dataset contains only one unique electrolyte
# again, check if electrolyte in arg matches the one in dataset
# if it does, great, if it does not, print a message and use it anyway
if (unique(this.SHE.data$electrolyte) == dfargs$electrolyte[p]) {
this.SHE.data <-
subset(this.SHE.data, electrolyte == dfargs$electrolyte[p])
} else {
subset.SHE.data <-
subset(subset.SHE.data, electrolyte == electrolyte)
# whatever electrolyte the user supplied does not match what's left in the datasubset
# but at this point the user is probably better served by returning the electrolyte we have
# along with an informative message (that's the only reason for the if-else below)
electrolytes.in.subset <-
unique(subset(as.SHE.data, electrode == dfargs$scale[p])$electrolyte)
if (dfargs$electrolyte[p] == "") {
message(
paste0('Electrolyte "" (empty string) not in dataset for E(',
dfargs$scale[p], '). ',
'These electrolytes are: ',
paste(electrolytes.in.subset, collapse = ', or '), '.',
"I'll assume you want ", fallback.electrolyte, ".")
)
} else {
message(paste0("Electrolyte ", dfargs$electrolyte[p], " not in dataset for E(",
dfargs$scale[p], "). ",
"These electrolytes are: ",
paste(electrolytes.in.subset, collapse = ", or "), ".",
"I'll assume you want ", fallback.electrolyte, ".")
)
}
}
}
# temperature
# either happens to match a temperature in the dataset, or we interpolate
# (under the assumption that potential varies linearly with temperature)
if (!any(subset.SHE.data$temp == df$temperature[p])) {
if (!any(this.SHE.data$temp == dfargs$temperature[p])) {
# sought temperature was not available in dataset, check that it falls inside
# note: important to use less/more-than-or-equal in case data only contains one value
if ((df$temperature[p] <= max(subset.SHE.data$temp)) &&
(df$temperature[p] >= min(subset.SHE.data$temp))) {
if ((dfargs$temperature[p] <= max(this.SHE.data$temp)) && (dfargs$temperature[p] >= min(this.SHE.data$temp))) {
# within dataset range, do linear interpolation
lm.subset <- stats::lm(SHE ~ temp, data = subset.SHE.data)
lm.subset <- stats::lm(SHE ~ temp, data = this.SHE.data)
# interpolated temperature, calculated based on linear regression
# (more accurate than simple linear interpolation with approx())
pot.interp <-
lm.subset$coefficients[2] * df$temperature[p] + lm.subset$coefficients[1]
# message("Calc potential using interp temperature")
lm.subset$coefficients[2] * dfargs$temperature[p] + lm.subset$coefficients[1]
### CALC POTENTIAL vs requested scale
if (df$scale[p] == common::RefCanonicalName("AVS")) {
# message("Target scale is AVS")
df$potentialvsscale[p] <-
pot.interp - df$potential[p]
} else {
# message("Target scale is not AVS")
df$potentialvsscale[p] <-
df$potential[p] - pot.interp
}
dfargs$potentialvsscale[p] <-
ifelse(dfargs$scale[p] == "AVS",
pot.interp - dfargs$potential[p],
dfargs$potential[p] - pot.interp)
}
} else {
# requested temperature does exist in dataset
### CALC POTENTIAL vs requested scale
# message("Calc potential using exact temperature match")
if (df$scale[p] == common::RefCanonicalName("AVS")) {
# message("Target scale is AVS")
df$potentialvsscale[p] <-
subset(subset.SHE.data, temp == df$temperature[p])$SHE - df$potential[p]
} else {
# message("Target scale is not AVS")
df$potentialvsscale[p] <-
df$potential[p] - subset(subset.SHE.data, temp == df$temperature[p])$SHE
}
dfargs$potentialvsscale[p] <-
ifelse(dfargs$scale[p] == "AVS",
subset(this.SHE.data, temp == dfargs$temperature[p])$SHE - dfargs$potential[p],
dfargs$potential[p] - subset(this.SHE.data, temp == dfargs$temperature[p])$SHE)
}
}
return(df$potentialvsscale)
return(dfargs$potentialvsscale)
}

6
README.md

@ -2,9 +2,3 @@
Includes common numerical functions, unit converters,
some LaTeX-specific functions, as well as reference data.
## Known bugs
`as.SHE()` and `from.SHE()` will fail to return any results if a vector of potentials is supplied along with a vector containing more than one reference scale (e.g., `as.SHE(potentials = c(0.24, 0.46, -0.15), scale = c("AgCl", "SCE", "AVS"))`).
This bug was first confirmed for vesion `0.0.0.9011`.

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