demo/NaCl.R

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

# CHNOSZ/demo/NaCl.R
## NaCl dissocation logK f(T,P)
## after Shock et al., 1992, Fig. 1
## (Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) 
##  Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: 
##  Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 degrees C and 5 kbar. 
##  J. Chem. Soc. Faraday Trans. 88, 803-826. https://doi.org/10.1039/FT9928800803 )
library(CHNOSZ)

## Uncomment these lines to make the plot with the g-function disabled
#mod.OBIGT("Cl-", z=0)
#mod.OBIGT("Na+", z=0)

# Start a new plot and show the experimental logK
thermo.plot.new(xlim=c(0, 1000), ylim=c(-5.5, 1),
  xlab=axis.label("T"), ylab=axis.label("logK"))
expt <- read.csv(system.file("extdata/misc/SOJSH.csv", 
  package="CHNOSZ"), as.is=TRUE)
points(expt$T,expt$logK, pch=expt$pch)

# We'll be at 9 distinct pressure conditions, including Psat
# Psat is repeated to show "not considered" region
# (T >= 355 degC; Fig. 6 of Shock et al., 1992)
P <- c(list("Psat", "Psat"), as.list(seq(500, 4000, by=500)))
# For each of those what's the range of temperature
T <- list()
T[[1]] <- seq(0, 354, 1)
T[[2]] <- seq(354, 370, 1)
T[[3]] <- seq(265, 465, 1)
T[[4]] <- seq(285, 760, 1)
T[[5]] <- seq(395, 920, 1)
T[[6]] <- T[[7]] <- T[[8]] <- T[[9]] <- T[[10]] <- seq(400, 1000, 1)

# Calculate and plot the logK
species <- c("NaCl", "Na+", "Cl-")
coeffs <- c(-1, 1, 1)
logK <- numeric()
for(i in 1:length(T)) {
  s <- suppressWarnings(subcrt(species, coeffs, T=T[[i]], P=P[[i]]))
  if(i==2) lty <- 3 else lty <- 1
  lines(s$out$T, s$out$logK, lty=lty)
  # keep the calculated values for each experimental condition (excluding Psat)
  iexpt <- which(P[[i]]==expt$P)
  Texpt <- expt$T[iexpt]
  if(i > 2) logK <- c(logK, splinefun(s$out$T, s$out$logK)(Texpt))
}

# Add title, labels, and legends
title(describe.reaction(s$reaction, states = 1))
text(150, -0.1, quote(italic(P)[sat]), cex=1.2)
text(462, -4, "500 bar")
text(620, -4.3, "1000 bar")
text(796, -4.3, "1500 bar")
text(813, -1.4, "4000 bar")
legend("bottomleft",pch=unique(expt$pch),
  legend=c(unique(expt$source),tail(expt$source,1)), bty="n")
#mtitle(c(describe.reaction(s$reaction), expression(italic(P)[sat]~"and 500-4000 bar")))
l1 <- quote("Revised HKF model with " * italic(g) * " function (Shock et al., 1992)")
l2 <- "Non-recommended region (Shock et al., 1992, Fig. 6)"
legend("topright", as.expression(c(l1, l2)), lty=c(1, 3), bty="n")

# Test for average divergence (excluding Psat)
expt <- expt[!expt$P %in% "Psat", ]
stopifnot(mean(abs(logK - expt$logK)) < 0.09)