[CHNOSZ-commits] r835 - in pkg/CHNOSZ: . inst inst/tinytest vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 1 08:32:17 CEST 2024
Author: jedick
Date: 2024-04-01 08:32:16 +0200 (Mon, 01 Apr 2024)
New Revision: 835
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/tinytest/test-add.protein.R
pkg/CHNOSZ/vignettes/FAQ.Rmd
pkg/CHNOSZ/vignettes/mklinks.sh
pkg/CHNOSZ/vignettes/multi-metal.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
Add FAQ: Why are mineral stability boundaries curved on mosaic diagrams?
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2024-03-22 03:29:19 UTC (rev 834)
+++ pkg/CHNOSZ/DESCRIPTION 2024-04-01 06:32:16 UTC (rev 835)
@@ -1,6 +1,6 @@
-Date: 2024-03-22
+Date: 2024-04-01
Package: CHNOSZ
-Version: 2.1.0-7
+Version: 2.1.0-8
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
@@ -9,7 +9,7 @@
Author: Jeffrey Dick [aut, cre] (0000-0002-0687-5890)
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Depends: R (>= 3.1.0)
-Suggests: tinytest, knitr, rmarkdown, tufte, canprot
+Suggests: tinytest, knitr, rmarkdown, tufte, canprot (>= 2.0.0)
Imports: grDevices, graphics, stats, utils
Description: An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2024-03-22 03:29:19 UTC (rev 834)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2024-04-01 06:32:16 UTC (rev 835)
@@ -15,7 +15,7 @@
\newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
\newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{Δ<I>G</I>°}}{ΔG°}}}
-\section{Changes in CHNOSZ version 2.1.0-5 (2024-03-16)}{
+\section{Changes in CHNOSZ version 2.1.0-8 (2024-04-01)}{
\itemize{
@@ -25,6 +25,8 @@
\item Remove \code{add.alpha()}. Now \code{grDevices::adjustcolor()} is
used in \code{stack_mosaic()} to add transparency.
+
+ \item Add FAQ question: Why are mineral stability boundaries curved on mosaic diagrams?
}
Modified: pkg/CHNOSZ/inst/tinytest/test-add.protein.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-add.protein.R 2024-03-22 03:29:19 UTC (rev 834)
+++ pkg/CHNOSZ/inst/tinytest/test-add.protein.R 2024-04-01 06:32:16 UTC (rev 835)
@@ -32,13 +32,9 @@
expect_equal(V, lprop$V, tolerance = 1e-4, info = info)
expect_equal(formula, lprop$formula, info = info)
-info <- "read_fasta() identifies sequences correctly and gives amino acid compositions in the correct format"
+info <- "add.protein() works with output of canprot::read_fasta()"
ffile <- system.file("extdata/protein/rubisco.fasta", package = "CHNOSZ")
-aa <- canprot::read_fasta(ffile)
-expect_equal(aa[1, ], canprot::read_fasta(ffile, 1), info = info)
-# Use unlist here so that different row names are not compared
aa8 <- canprot::read_fasta(ffile, 1:8)
-expect_equal(unlist(aa[1:8, ]), unlist(aa8), info = info)
expect_message(ip1 <- add.protein(aa8), "added 8 new protein\\(s\\)", info = info)
expect_message(ip2 <- add.protein(aa8), "replaced 8 existing protein\\(s\\)", info = info)
# add.protein should return the correct indices for existing proteins
Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd 2024-03-22 03:29:19 UTC (rev 834)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd 2024-04-01 06:32:16 UTC (rev 835)
@@ -829,4 +829,129 @@
*Added on 2023-11-28.*
+## Why are mineral stability boundaries curved on mosaic diagrams?
+
+The reason they are curved has to do with mass balance of elements in different aqueous species.
+For example, take two reactions between pyrite (FeS~2~) and pyrrhotite (FeS), one with H~2~S and the other with HS^-^:
+
+1. FeS~2~ + H~2~O = FeS + 0.5 O~2~ + H~2~S
+2. FeS~2~ + H~2~O = FeS + 0.5 O~2~ + HS^-^ + H^+^
+
+If a pH 4 solution at 150 °C has 0.001 mol/kg H~2~S, then raising the pH to 8 would give 0.001 mol/kg of HS^-^ and essentially no H~2~S.
+For the remainder of this discussion we will assume that mol/kg is equivalent to activity (i.e., that activity cofficients are unity).
+If we use the same value (0.001) for H~2~S and HS^-^ in reactions 1 and 2 (the *constant activity* constraint), then we will get straight lines on a `r logfO2`–pH diagram.
+There is nothing inherently wrong with this, but it is inconsistent with a *constant sum* constraint of activities that is often attributed to these diagrams.
+
+The *constant activity* constraint is compatible with the *constant sum* constraint only well inside the predomince field of a given aqueous species.
+The equivalence breaks down near the transitions between aqueous species.
+For instance, if the total activity of S is 0.001, then at the p*K*~a~ of H~2~S (about 6.5 at 150 °C), the activities of H~2~S and HS^-^ are equal to each other and by mass balance are both 0.0005.
+The position of the stability boundary should be calculated with these activities to satisfy the *constant sum* constraint.
+
+The following code defines functions to calculate `r logfO2` for these two reactions.
+
+<button id="B-PyPo_logfO2" onclick="ToggleDiv('PyPo_logfO2')">Show code</button>
+<div id="D-PyPo_logfO2" style="display: none">
+```{r PyPo_logfO2, message = FALSE, results = "hide"}
+# Constants
+a_S <- 0.001
+T <- 150
+
+# Get the pKa of H2S (note the minus sign!)
+pKa_H2S <- - subcrt(c("H2S", "HS-", "H+"), c(-1, 1, 1), T = T)$out$logK
+
+# Reaction 1 between pyrite and pyrrhotite with H2S
+basis(c("pyrite", "H2S", "oxygen", "H2O", "H+"))
+PyPo_H2S <- subcrt("pyrrhotite", 1, T = T)
+
+# Reaction 1 law of mass action (LMA)
+# logf_O2 = 2 logK_1 - 2 loga_H2S
+logf_O2_1 <- function(loga_H2S) 2 * PyPo_H2S$out$logK - 2 * loga_H2S
+
+# Reaction 2 between pyrite and pyrrhotite with HS-
+basis(c("pyrite", "HS-", "oxygen", "H2O", "H+"))
+PyPo_HS <- subcrt("pyrrhotite", 1, T = T)
+
+# Reaction 2 LMA
+# logf_O2 = 2 pH + 2 logK_2 - 2 loga_HS-
+logf_O2_2 <- function(pH, loga_HS) 2 * pH + 2 * PyPo_HS$out$logK - 2 * loga_HS
+
+# The logf_O2 for each reaction is the same at the pKa of H2S
+stopifnot(all.equal(logf_O2_1(log10(a_S)), logf_O2_2(pKa_H2S, log10(a_S))))
+stopifnot(all.equal(logf_O2_1(log10(a_S / 2)), logf_O2_2(pKa_H2S, log10(a_S / 2))))
+```
+</div>
+
+At 150 °C and the p*K*~a~ of H~2~S, we get `r logfO2` = `r round(logf_O2_1(log10(0.001)), 2)` for *a*<sub>H~2~S</sub> = *a*<sub>HS^-^</sub> = 0.001 but `r logfO2` = `r round(logf_O2_1(log10(0.0005)), 2)` for *a*<sub>H~2~S</sub> + *a*<sub>HS^-^</sub> = 0.001.
+In other words, the *constant activity* and *constant sum* constraints produce different results; the former yields two straight lines while the latter yields a curve.
+This is shown graphically in the plots below.
+
+<button id="B-PyPo_plot" onclick="ToggleDiv('PyPo_plot')">Show code</button>
+<div id="D-PyPo_plot" style="display: none">
+```{r PyPo_plot, eval = FALSE}
+par(mfrow = c(1, 2))
+
+# Let's draw this out
+thermo.plot.new(c(2, 10), c(-56, -46), xlab = "pH", ylab = axis.label("O2"))
+lines(c(2, pKa_H2S), c(logf_O2_1(log10(a_S)), logf_O2_1(log10(a_S))), col = 2)
+lines(c(pKa_H2S, 10), c(logf_O2_2(pKa_H2S, log10(a_S)), logf_O2_2(10, log10(a_S))), col = 4)
+abline(v = pKa_H2S, lty = 2, col = 8)
+text(6, -46.5, expr.species("H2S"), adj = c(0.5, 1))
+text(7, -46.5, expr.species("HS-"), adj = c(0.5, 1))
+text(4, -54, "pyrite")
+text(4, -55.5, "pyrrhotite")
+points(pKa_H2S, logf_O2_1(log10(a_S)), pch = 0)
+points(pKa_H2S, logf_O2_1(log10(a_S / 2)), pch = 19)
+legend("bottomright", c("Yes", "No"), pch = c(19, 0), title = as.expression(quote(sum(S) == "constant")), bty = "n")
+legend("topleft", legend = lT(T), bty = "n")
+title(quote("Straight lines for" ~ italic(a)[H[2]*S] ~ "=" ~ italic(a)[HS^"-"] == "0.001"), font.main = 1)
+
+# Do it with mosaic()
+basis(c("pyrite", "H2S", "oxygen", "H2O", "H+"))
+# This sets the activity of H2S, which is used for total S when mosaic is called with blend = TRUE
+basis("H2S", -3)
+# This defines the basis species to swap through
+bases <- c("H2S", "HS-")
+species(c("pyrite", "pyrrhotite"))
+m <- mosaic(bases, pH = c(2, 10, 500), O2 = c(-56, -46, 500), T = T)
+diagram(m$A.species, dx = c(-1, -3), dy = c(-3, -1.5), col = 6)
+abline(v = pKa_H2S, lty = 2, col = 8)
+text(6, -46.5, expr.species("H2S"), adj = c(0.5, 1))
+text(7, -46.5, expr.species("HS-"), adj = c(0.5, 1))
+points(pKa_H2S, logf_O2_1(log10(a_S)), pch = 0)
+points(pKa_H2S, logf_O2_1(log10(a_S / 2)), pch = 19)
+legend("bottomright", c("Yes", "No"), pch = c(19, 0), title = as.expression(quote(sum(S) == "constant")), bty = "n")
+legend("topleft", legend = lT(T), bty = "n")
+title(quote("Curved line for" ~ italic(a)[H[2]*S] + italic(a)[HS^"-"] == "0.001"), font.main = 1)
+```
+</div>
+
+```{r PyPo_plot, echo = FALSE, message = FALSE, results = "hide", fig.width = 9, fig.height = 4.5, out.width = "100%", fig.align = "center", pngquant = pngquant, cache = TRUE}
+```
+
+The plot on the left is made "by hand" (using equilibrium constants calculated with `subcrt()`)
+while the plot on the right is made with the `mosaic()` and `diagram()` functions.
+The gray area is where water is unstable and is automatically added by `diagram()`.
+If you'd like to make a plot without curved lines (i.e., for *constant activity* instead of *constant sum*), then set `blend = FALSE` in `mosaic()`.
+
+There are relatively few published `r logfO2`–pH diagrams with curved mineral stability lines.
+An example of one is in Figure 5 of @CBLM00.
+The code below makes a diagram for the minerals shown in that figure:
+
+```{r Fe-S-O-C, message = FALSE, results = "hide", fig.width = 5, fig.height = 5, fig.align = "center", pngquant = pngquant, cache = TRUE}
+basis(c("FeO", "SO4-2", "CO3-2", "H2O", "H+", "oxygen"))
+basis("SO4-2", -3)
+basis("CO3-2", -0.6)
+species(c("hematite", "pyrite", "pyrrhotite", "magnetite", "siderite"))
+bases <- list( c("SO4-2", "HSO4-", "HS-", "H2S"), c("CO3-2", "HCO3-", "CO2") )
+m <- mosaic(bases, pH = c(0, 14, 500), O2 = c(-57, -35, 500), T = 150, IS = 0.77)
+d <- diagram(m$A.species, fill = "terrain", dx = c(0, 0, 0, 0, 0.3))
+water.lines(d)
+```
+
+This result suggests two improvements to Fig. 5A in @CBLM00.
+First, the triangular area above the water stability limit should be labeled as part of the siderite field (which is interrupted by the pyrite wedge), not as pyrrhotite.
+Second, the boundary between pyrite and magnetite has one kink, not two.
+
+*Added on 2024-04-01.*
+
## References
Modified: pkg/CHNOSZ/vignettes/mklinks.sh
===================================================================
--- pkg/CHNOSZ/vignettes/mklinks.sh 2024-03-22 03:29:19 UTC (rev 834)
+++ pkg/CHNOSZ/vignettes/mklinks.sh 2024-04-01 06:32:16 UTC (rev 835)
@@ -146,3 +146,4 @@
sed -i 's/<code>check.GHS()<\/code>/<code><a href="..\/html\/util.data.html" style="color:\ green;">check.GHS()<\/a><\/code>/g' FAQ.html
sed -i 's/<code>affinity()<\/code>/<code><a href="..\/html\/affinity.html" style="color:\ green;">affinity()<\/a><\/code>/g' FAQ.html
sed -i 's/<code>diagram()<\/code>/<code><a href="..\/html\/diagram.html" style="color:\ green;">diagram()<\/a><\/code>/g' FAQ.html
+sed -i 's/<code>mosaic()<\/code>/<code><a href="..\/html\/mosaic.html" style="color:\ green;">mosaic()<\/a><\/code>/g' FAQ.html
Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2024-03-22 03:29:19 UTC (rev 834)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2024-04-01 06:32:16 UTC (rev 835)
@@ -500,7 +500,7 @@
species(c(FeCu.cr, Cu.cr))
mFeCu <- mosaic(list(S.aq, Fe.cr), pH = pH, O2 = O2,
T = T, stable = list(NULL, dFe$predominant))
-col <- c("#FF8C00", rep(2, 6))
+col <- c(rep("#FF8C00", 2), rep(2, 5))
lwd <- c(2, 1, 1, 1, 1, 1, 1)
dy = c(0, 0, 0, 0, 0, 1, 0)
diagram(mFeCu$A.species, add = TRUE, col = col, lwd = lwd, col.names = col, bold = TRUE, names = FeCu.abbrv, dy = dy)
@@ -516,7 +516,7 @@
Because the Fe-bearing minerals are the second group of changing basis species (`Fe.cr`), their stabilities are given in the second position of the `stable` list.
The result is used to plot the last layer of the diagram:
-4. Stability areas for Cu-bearing minerals (red text and lines; orange for chalcopyrite)
+4. Stability areas for Cu-bearing minerals (red text and lines; orange for chalcopyrite and bornite)
After that we add the legend and title.
@@ -610,10 +610,11 @@
dy[names == "CuCl2-"] <- 2
cex[names == "Bn"] <- 0.8
srt[names == "Bn"] <- 85
-# Highlight Ccp field
col.names <- col <- rep(2, nrow(mFeCu$A.species$species))
-col[1] <- "#FF8C00"
-col.names[1] <- "#FF8C00"
+# Highlight Ccp and Bn in orange
+col[1:2] <- "#FF8C00"
+col.names[1:2] <- "#FF8C00"
+# Thick line around Ccp field
lwd <- rep(1, nrow(mFeCu$A.species$species))
lwd[1] <- 2
diagram(mFeCu$A.species, add = TRUE, lwd = lwd, col = col, col.names = col.names, names = names, bold = bold, dx = dx, dy = dy, cex.names = cex, srt = srt)
@@ -1163,5 +1164,6 @@
* 2020-07-15 First version.
* 2021-03-01 Improve mineral abbreviations and placement of labels; use updated DFT energies from Materials Project; add Mosaic Stacking 2 (minerals and aqueous species); add *K*~eff~ calculation; add Δ*G*~pbx~ color scale.
+* 2024-03-25 Use orange for both chalcopyrite and bornite in Mosaic Stacking 1 and 2
## References
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2024-03-22 03:29:19 UTC (rev 834)
+++ pkg/CHNOSZ/vignettes/vig.bib 2024-04-01 06:32:16 UTC (rev 835)
@@ -1,4 +1,3 @@
-
@Book{Alb03,
author = {Alberty, Robert A.},
publisher = {Wiley-Interscience},
@@ -49,6 +48,18 @@
pages = {397},
}
+ at Article{CBLM00,
+ author = {Cooke, David R. and Bull, Stuart W. and Large, Ross R. and McGoldrick, Peter J.},
+ journal = {Economic Geology},
+ title = {The importance of oxidized brines for the formation of {A}ustralian {P}roterozoic stratiform sediment-hosted {P}b-{Z}n ({S}edex) deposits},
+ year = {2000},
+ month = jan,
+ number = {1},
+ pages = {1--17},
+ volume = {95},
+ doi = {10.2113/gsecongeo.95.1.1},
+}
+
@Article{Dic08,
author = {Dick, Jeffrey M.},
journal = {Geochemical Transactions},
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