[CHNOSZ-commits] r893 - in pkg/CHNOSZ: . R inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat May 10 05:23:45 CEST 2025
Author: jedick
Date: 2025-05-10 05:23:45 +0200 (Sat, 10 May 2025)
New Revision: 893
Removed:
pkg/CHNOSZ/vignettes/equilibrium.Rmd
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/vignettes/multi-metal.Rmd
pkg/CHNOSZ/vignettes/postprocess.sh
Log:
Remove equilibrium.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-05-09 14:17:58 UTC (rev 892)
+++ pkg/CHNOSZ/DESCRIPTION 2025-05-10 03:23:45 UTC (rev 893)
@@ -1,6 +1,6 @@
-Date: 2025-05-09
+Date: 2025-05-10
Package: CHNOSZ
-Version: 2.1.0-64
+Version: 2.1.0-65
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2025-05-09 14:17:58 UTC (rev 892)
+++ pkg/CHNOSZ/R/diagram.R 2025-05-10 03:23:45 UTC (rev 893)
@@ -211,9 +211,9 @@
# Some additional steps for affinity values, but not for equilibrated activities
if(eout.is.aout) {
for(i in 1:length(pv)) {
- # TODO: The equilibrium.Rmd vignette shows predominance diagrams using
- # 'normalize' and 'as.residue' settings that are consistent with equilibrate(),
- # but what is the derivation of these equations?
+ # NOTE: CHNOSZ_equilibrium.Rmd in JMDplots shows predominance diagrams using
+ # 'normalize' and 'as.residue' settings that are consistent with equilibrate()
+ # TODO: what is the derivation of these equations?
if(normalize) pv[[i]] <- (pv[[i]] + eout$species$logact[i] / n.balance[i]) - log10(n.balance[i])
else if(as.residue) pv[[i]] <- pv[[i]] + eout$species$logact[i] / n.balance[i]
}
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2025-05-09 14:17:58 UTC (rev 892)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2025-05-10 03:23:45 UTC (rev 893)
@@ -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 2.1.0-57 (2025-04-28)}{
+\section{Changes in CHNOSZ version 2.1.0-65 (2025-05-10)}{
\subsection{OBIGT DEFAULT DATA}{
\itemize{
@@ -113,6 +113,10 @@
(2023)} and optional data for Au species from IGEM RAS, including
polynuclear Au\s{2}S\s{2}\S{-2}.
+ \item Move \file{equilibrium.Rmd} from CHNOSZ to
+ \file{CHNOSZ_equilibrium.Rmd} in the [JMDplots
+ package](https://github.com/jedick/JMDplots).
+
}
}
Deleted: pkg/CHNOSZ/vignettes/equilibrium.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rmd 2025-05-09 14:17:58 UTC (rev 892)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rmd 2025-05-10 03:23:45 UTC (rev 893)
@@ -1,494 +0,0 @@
----
-title: "Equilibrium in CHNOSZ"
-author: "Jeffrey M. Dick"
-output:
- html_vignette:
- mathjax: null
-vignette: >
- %\VignetteIndexEntry{Equilibrium in CHNOSZ}
- %\VignetteEngine{knitr::rmarkdown}
- %\VignetteEncoding{UTF-8}
-bibliography: vig.bib
-csl: elementa.csl
-link-citations: true
----
-<style>
-/* https://gomakethings.com/how-to-break-an-image-out-of-its-parent-container-with-css/ */
- at media (min-width: 700px) {
- .full-width {
- left: 50%;
- margin-left: -50vw;
- margin-right: -50vw;
- max-width: 100vw;
- position: relative;
- right: 50%;
- width: 100vw;
- }
-}
- at media (min-width: 1020px) {
- .full-width {
- left: 50vw; /* fallback if needed */
- left: calc(50vw - 160px);
- width: 1000px;
- position: relative;
- background-color: #9ecff7;
- padding:10px;
- }
-}
-/* Zero margin around pre blocks (looks more like R console output) */
-pre {
- margin-top: 0;
- margin-bottom: 0;
-}
-</style>
-<script>
-function ToggleDiv(ID) {
- var D = document.getElementById("D-" + ID);
- var B = document.getElementById("B-" + ID);
- if (D.style.display === "none") {
- // open the div and change button text
- D.style.display = "block";
- B.innerText = "Hide code";
- } else {
- // close the div and change button text
- D.style.display = "none";
- B.innerText = "Show code";
- }
-}
-</script>
-
-```{r setup, include=FALSE}
-## Use pngquant to optimize PNG images
-library(knitr)
-knit_hooks$set(pngquant = hook_pngquant)
-pngquant <- "--speed=1 --quality=0-25"
-if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
-
-# Set dpi 20231129
-knitr::opts_chunk$set(
- dpi = if(nzchar(Sys.getenv("CHNOSZ_BUILD_LARGE_VIGNETTES"))) 100 else 72
-)
-```
-
-```{r CHNOSZ_reset, include=FALSE}
-library(CHNOSZ)
-reset()
-```
-
-This vignette was compiled on `r Sys.Date()` with CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
-
-Scope of this document:
-
-- This document defines the concepts underlying equilibrium calculations with the `equilibrate()` function in CHNOSZ.
-- Some illustrative examples of equilibrium calculations are provided, using proteins as a case study.
-- The main use case for `equilibriate()` is to calculate and visualize distributions of aqueous species subject to the limitations below.
-- A different function, `solubility()`, can be used to obtain the distributions of aqueous species in equilibrium with one or more minerals.
-- Many types of relative stablity diagrams (e.g. mineral and aqueous species predominance diagrams) can be made using the *maximum affinity method* (basis - species - [affinity|mosaic] - diagram) and do not require either of the `equilibrate()` or `solubility()` functions.
-
-Limitations:
-
-- CHNOSZ is not a general-purpose speciation code.
-- The types of equilibrium calculations it can handle are restricted to systems described as *balanced on an element*.
- - For example, we can predict the distribution of aqueous Au complexes with given activities of chloride, hydroxide, and sulfide.
- - But we can not at the same time predict the formation of species without Au (such as NaCl(aq)), which would be required for a complete equilibrium model.
-- Protein length can be used as the balancing constraint instead of an element.
-
-## Concepts
-
-System
-: Chemical system defined by formed species (referred to simply as species) and basis species, which are analogous to thermodynamic components.
-The possible species are any that are available in the [OBIGT thermodynamic database](OBIGT.html).
-
- Species
- : Selection of possible chemical species for which you want to calculate relative stabilities.
-
- Basis species
- : Any minimal set of possible species that can be used to balance the formation reactions of the species.
- Additionally, in CHNOSZ the number of basis species must be equal to the number of elements.
-
-Formation reaction
-: Chemical reaction giving the stoichiometry of basis species combined to make 1 mole of a species.
-
-Transformation reaction
-: Any combination of two formation reactions in opposite directions (1 mole of a species reacts to form 1 mole of another species).
-
-Balancing coefficients
-: (*n*~balance~) For a system that is balanced on one of the basis species,
-the number of moles of that basis species in the formation reaction of each of the species.
-The number can be positive or negative but not zero.
-Can also represent a virtual quantity, such as 1 (balance on moles of species) or number of amino acids in a protein sequence (balance on protein length).
-
-Speciation diagram
-: Diagram showing the equilibrium activities of species as a function of one variable.
-
-Predominance diagram
-: Diagram variables showing fields for species with highest equilibrium activity as a function of two variables.
-Also known as an equal activity diagram for aqueous species or stability diagram for minerals.
-
-Chemical affinity
-: Negative of the differential of Gibbs energy of a system with respect to reaction progress.
-For a given reaction, chemical affinity is the negative of Gibbs energy of reaction: *A* = 2.303*RT*log(*K*/*Q*),
-where *K* is the equilibrium constant and *Q* is the activity quotient of species in the reaction
-(log here denotes base-10 logarithms, i.e. `log10` in R).
-
-Maximum affinity method
-: Approach used to construct predominance diagrams not by finding the highest activity at equilibrium but by finding the highest affinity at a **reference activity**.
-The reference activities are user-defined equal activities of species (e.g. unit activity for minerals and 10^-3^ for aqueous species).
-
-Equilibration method
-: Calculations of the activities of species in equilibrium.
-
- Metastable equilibrium
- : The condition that the affinities of all *transformation* reactions are zero.
- Implemented with the `equilibrate()` function in CHNOSZ, which is used below.
-
- Stable equilibrium
- : The condition that the affinities of all *formation* reactions are zero.
- Implemented with the `solubility()` function in CHNOSZ, which is not described here.
-
-## Example 1: Amino acids
-
-In this sytem the basis species are CO~2~, H~2~O, NH~3~, H~2~S, and O~2~ and the formed species are 20 amino acids.
-
-```{r AAsetup, results = "hide", message = FALSE}
-library(CHNOSZ)
-reset()
-basis("CHNOS")
-species(aminoacids(""))
-```
-
-These functions are used for the different diagrams in the figure.
-
-```{r AAfunctions}
-aaA <- function() {
- a <- affinity(O2 = c(-90, -70), H2O = c(-20, 10))
- diagram(a, balance = 1, names = aa)
-}
-
-aaB <- function() {
- a <- affinity(O2 = c(-90, -70), H2O = c(-20, 10))
- e <- equilibrate(a, balance = 1)
- diagram(e, names = aa)
-}
-
-aaC <- function() {
- a <- affinity(O2 = c(-71, -66), H2O = c(-8, 4))
- diagram(a, balance = "CO2", names = aa)
-}
-
-aaD <- function() {
- a <- affinity(O2 = c(-71, -66), H2O = c(-8, 4))
- e <- equilibrate(a, balance = "CO2")
- diagram(e, names = aa)
-}
-
-aaE <- function() {
- basis("O2", -66)
- a <- affinity(H2O = c(-8, 4))
- e <- equilibrate(a, balance = "CO2")
- diagram(e, ylim = c(-5, -1), names = aa)
-}
-
-aaF <- function() {
- species(1:20, -7)
- a <- affinity(H2O = c(-8, 4))
- e <- equilibrate(a, balance = "CO2")
- diagram(e, ylim = c(-8, -4), names = aa)
-}
-```
-
-The labels used for the diagrams are the one-letter abbreviations for the amino acids.
-
-```{r AAabbrv}
-aa <- aminoacids()
-aa
-```
-
-Press the button to show all of the code for making the figure.
-
-<button id="B-AAplot" onclick="ToggleDiv('AAplot')">Show code</button>
-<div id="D-AAplot" style="display: none">
-```{r AAplot, eval = FALSE}
-showtime <- function(st) {
- # Plot time in lower-right of figure region
- f <- usrfig()
- par(xpd=TRUE)
- if(st[3] > 2) col <- "red" else col <- "black"
- text(f$x[2], f$y[1], paste(round(st[3], 1), "s\n"), adj=1, col=col)
- par(xpd=FALSE)
-}
-
-layout(t(matrix(c(1:7, 11, 8:10, 12), nrow=4)), widths=c(1, 4, 4, 4), heights=c(0.7, 4, 4))
-
-## Row 0 (column titles)
-opar <- par(mar=c(0, 0, 0, 0))
-plot.new()
-plot.new()
-text(0.58, 0.5, "maximum affinity", cex=1.4)
-plot.new()
-text(0.58, 0.5, "equilibration", cex=1.4)
-plot.new()
-text(0.58, 0.5, "equilibration", cex=1.4)
-par(opar)
-
-## Row 1 (balance = 1)
-opar <- par(mar=c(0, 0, 0, 0))
-plot.new()
-text(0.5, 0.5, "balance = 1", srt=90, cex=1.4)
-par(opar)
-# Figure A
-st <- system.time(dA <- aaA())
-showtime(st)
-title(main="loga(species) = -3", cex.main=1)
-label.figure("A", yfrac=0.92, xfrac=0.1, font = 2)
-# Figure B
-st <- system.time(dB <- aaB())
-showtime(st)
-title(main=paste("loga(total species) =", round(dB$loga.balance[1], 2)), cex.main=1)
-label.figure("C", yfrac=0.92, xfrac=0.1, font = 2)
-
-## Row 2 (balance = nCO2)
-opar <- par(mar=c(0, 0, 0, 0))
-plot.new()
-text(0.5, 0.5, 'balance = "CO2"', srt=90, cex=1.4)
-par(opar)
-# Figure C
-st <- system.time(dC <- aaC())
-showtime(st)
-title(main="loga(species) = -3", cex.main=1)
-label.figure("B", yfrac=0.92, xfrac=0.1, font = 2)
-# Figure D
-st <- system.time(dD <- aaD())
-showtime(st)
-title(main=paste("loga(total CO2) =", round(dD$loga.balance[1], 2)), cex.main=1)
-label.figure("D", yfrac=0.92, xfrac=0.1, font = 2)
-
-## Right column (speciation at different total activity of CO2)
-par(xpd=NA)
-lines(c(-66, -64.5), c(4, 9), lty=2)
-lines(c(-66, -64.5), c(-8, -8.5), lty=2)
-par(xpd=FALSE)
-# Figure E
-st <- system.time(dE <- aaE())
-showtime(st)
-title(main=paste("loga(total CO2) =", round(dE$loga.balance[1], 2)), cex.main=1)
-label.figure("E", yfrac=0.92, xfrac=0.1, font = 2)
-# Figure F
-st <- system.time(dF <- aaF())
-showtime(st)
-title(main=paste("loga(total CO2) =", round(dF$loga.balance[1], 2)), cex.main=1)
-label.figure("F", yfrac=0.92, xfrac=0.1, font = 2)
-```
-</div>
-
-```{r AAplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant}
-```
-
-Diagrams **A** and **B** use the *maximum affinity method*, where the reference
-activities of species are set to a single value. Diagrams **C** and **D** use
-the *equilibration method*, where the activities of species change across the
-diagram and the lines are drawn at equal activity. Other comments on the
-figure:
-
-* The equal-activity lines in Diagrams **A** and **C** are the same. That is,
- with the setting `balance = 1`, the conditions for equal activity of two
- species do not depend on the actual value of that activity.
-
-* Diagrams **B** and **D** are different. Because balance ≠ 1 (in this case,
- the reactions are balanced on CO~2~), the conditions for equal activity of
- species depend on the actual value of that activity. In particular, with the
- equilibration method, the lines are curved due to the distribution of more
- than two species.
-
-* Diagrams **E** and **F** both use the equilibration method to calculate
- activities of species as a function of log*a*H~2~O at log*f*O~2~ = -66.
- Diagram **F** shows the default setting, where *a*CO~2~ is taken from the sum
- of initial activities of species (each 10^-3^). The positions of equal
- activities (where the lines cross) are the same as in Diagram **D** at
- log*f*O~2~ = -66.
-
-* Diagram **F** is drawn for a lower total activity of *a*CO~2~. Not only are
- the activities of all amino acids decreased, but glycine starts to become
- predominant at some conditions. This is because, compared to other amino
- acids, it is smaller and has a lower coefficient on CO~2~ in its formation
- reaction.
-
-## Example 2: Proteins
-
-In this sytem the basis species are CO~2~, H~2~O, NH~3~, H~2~S, O~2~, and H^+^ and the
-formed species are 6 proteins from the set of archaeal and bacterial surface
-layer proteins considered by @Dic08.
-
-The inclusion of charge in the basis species (with H^+^) allows ionization of
-proteins to be calculated [@DLH06].
-
-```{r PRsetup, results = "hide", message = FALSE}
-basis("CHNOS+")
-organisms <- c("METJA", "HALJP", "METVO", "ACEKI", "GEOSE", "BACLI")
-proteins <- c(rep("CSG", 3), rep("SLAP", 3))
-species(proteins, organisms)
-```
-
-Here are the lengths of the proteins.
-
-```{r PRlength}
-protein.length(species()$name)
-```
-
-These functions are used for the different diagrams in the figure.
-
-```{r PRfunctions}
-prA <- function() {
- a <- affinity(O2 = c(-90, -70), H2O = c(-20, 0))
- diagram(a, balance = "length", names = organisms)
-}
-
-prB <- function() {
- a <- affinity(O2 = c(-90, -70))
- e <- equilibrate(a, balance = "length")
- ylab <- quote(log~italic(a)~protein)
- diagram(e, names = organisms, ylim = c(-5, -1), ylab = ylab)
-}
-
-prC <- function() {
- a <- affinity(O2 = c(-90, -70), H2O = c(-20, 0))
- diagram(a, normalize = TRUE, names = organisms)
-}
-
-prD <- function() {
- a <- affinity(O2 = c(-90, -70))
- e <- equilibrate(a, normalize = TRUE)
- ylab <- quote(log~italic(a)~protein)
- diagram(e, names = organisms, ylim = c(-5, -1), ylab = ylab)
-}
-
-prE <- function() {
- a <- affinity(O2 = c(-90, -70), H2O = c(-20, 0))
- diagram(a, as.residue = TRUE, names = organisms)
-}
-
-prF <- function() {
- a <- affinity(O2 = c(-90, -70))
- e <- equilibrate(a, as.residue = TRUE, loga.balance = 0)
- ylab <- quote(log~italic(a)~residue)
- diagram(e, names = organisms, ylim = c(-3, 1), ylab = ylab)
-}
-```
-
-<button id="B-PRplot" onclick="ToggleDiv('PRplot')">Show code</button>
-<div id="D-PRplot" style="display: none">
-```{r PRplot, eval = FALSE}
-```
-</div>
-
-```{r PRplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant}
-layout(t(matrix(1:12, nrow=4)), widths=c(1, 4, 4, 4), heights=c(0.7, 4, 4))
-
-## Row 0 (column titles)
-opar <- par(mar=c(0, 0, 0, 0))
-plot.new()
-plot.new()
-text(0.58, 0.5, 'balance = "length"', cex=1.4)
-plot.new()
-text(0.58, 0.5, "normalize = TRUE\n(balance = 1)", cex=1.4)
-plot.new()
-text(0.58, 0.5, "as.residue = TRUE\n(balance = 1)", cex=1.4)
-par(opar)
-
-## Row 1 (maximum affinity 2D)
-opar <- par(mar=c(0, 0, 0, 0))
-plot.new()
-text(0.5, 0.5, "maximum affinity", srt=90, cex=1.4)
-par(opar)
-# Figure A (balance = "length")
-st <- system.time(dA <- prA())
-showtime(st)
-label.figure("A", yfrac=0.9, xfrac=0.1, font = 2)
-# Figure C (normalize = TRUE)
-st <- system.time(dC <- prC())
-showtime(st)
-label.figure("C", yfrac=0.9, xfrac=0.1, font = 2)
-# Figure E (as.residue = TRUE)
-st <- system.time(dE <- prE())
-showtime(st)
-label.figure("E", yfrac=0.9, xfrac=0.1, font = 2)
-
-## Row 2 (equilibrate 1D)
-opar <- par(mar=c(0, 0, 0, 0))
-plot.new()
-text(0.5, 0.5, "equilibration", srt=90, cex=1.4)
-par(opar)
-# Figure B (balance = "length")
-st <- system.time(prB())
-showtime(st)
-label.figure("B", yfrac=0.9, xfrac=0.1, font = 2)
-# Figure D (normalize = TRUE)
-st <- system.time(prD())
-showtime(st)
-label.figure("D", yfrac=0.9, xfrac=0.1, font = 2)
-# Figure F (as.residue = TRUE)
-st <- system.time(prF())
-showtime(st)
-label.figure("F", yfrac=0.9, xfrac=0.1, font = 2)
-```
-
-Diagrams **A**, **C**, and **E** are predominance (equal-activity) diagrams
-made with different balancing constraints. Diagrams **B**, **D**, and **F**
-show a cross-section of the same system at log*a*H~2~O = 0.
-
-* In Diagrams **A** and **B**, the reactions are balanced on protein length.
- The drastic transitions between proteins in **B** result from the large
- balancing coefficients, which become exponents on activities in the
- expression for the activity quotient (*Q*).
-
-* In Diagrams **C** and **D**, the chemical formulas of the proteins are
- *normalized*, or divided by the protein length, before the equilibration or
- maximum affinity calculation. However, the final diagram is not drawn for
- activities of these "residue equivalents", but for rescaled activities of
- whole proteins. Because of the rescaling, the fields of the shorter METJA and
- METVO proteins grow at the expense of the longer BACLI protein.
-
-* Diagrams **E** and **F** are like the normalization calculation, except that
- the final diagram is drawn for the residue equivalents and not the whole
- proteins. The predominance diagram is the same as that for non-normalized
- reactions (**A**), but the equilibrium activities of residues are higher than
- those of the proteins.
-
-## Example 3: Normalization
-
-Here is another figure showing the effects of normalization.
-This is like Figure 5 of @Dic08, extended to more extreme conditions.
-If you wish to reproduce the diagram from the 2008 paper more closely, uncomment the `add.OBIGT()` command.
-
-```{r ProteinSpeciation, results = "hide", message = FALSE, fig.width = 8, fig.height = 5.5, out.width = "100%", pngquant = pngquant}
-organisms <- c("METSC", "METJA", "METFE", "METVO", "METBU",
- "HALJP", "ACEKI", "GEOSE", "BACLI", "AERSA")
-proteins <- c(rep("CSG", 6), rep("SLAP", 4))
-# Use red for Methano* genera
-col <- c(rep(2, 5), rep(1, 5))
-basis("CHNOS+")
-species(proteins, organisms)
-a <- affinity(O2 = c(-100, -65))
-layout(matrix(1:2), heights = c(1, 2))
-e <- equilibrate(a)
-diagram(e, ylim = c(-2.8, -1.6), names = organisms, col = col)
-water.lines(e, col = 4)
-title(main="Equilibrium activities of proteins, normalize = FALSE")
-e <- equilibrate(a, normalize = TRUE)
-diagram(e, ylim = c(-4, -2), names = organisms, col = col)
-water.lines(e, col = 4)
-title(main = "Equilibrium activities of proteins, normalize = TRUE")
-```
-
-Although it is below the stability limit of H~2~O (vertical dashed line), there
-is an interesting convergence of the metastable equilibrium activities of some
-proteins at low log *f*O~2~.
-
-## Document history
-
-* 2009-11-29 Initial version with CSG example, titled "Calculating relative abundances of proteins"
-* 2012-09-30 Renamed to "Equilibrium in CHNOSZ"; remove activity comparisons and add maximum affinity method.
-* 2015-11-08 Move previous material to Appendix and add sections on concepts, organization, examples, and applications; use knitr vignette engine.
-* 2020-07-10 Simplify to concepts and examples (amino acids, proteins, normalization); convert document from LaTeX (Rnw) to R Markdown (Rmd).
-
-## References
Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2025-05-09 14:17:58 UTC (rev 892)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2025-05-10 03:23:45 UTC (rev 893)
@@ -113,7 +113,7 @@
cat("```")
```
-Basic diagrams in CHNOSZ are made for reactions that are *balanced on an element* (see [Equilibrium in CHNOSZ](equilibrium.html)) and therefore represent minerals or aqueous species that all have one element, often a metal, in common.
+Basic diagrams in CHNOSZ are made for reactions that are *balanced on an element* and therefore represent minerals or aqueous species that all have one element, often a metal, in common.
The package documentation has many examples of diagrams for a single metal appearing in different minerals or complexed with different ligands, but a common request is to make diagrams for multiple metals.
This vignette describes some methods for constructing diagrams for multi-metal minerals and other multi-element systems.
The methods are **mashing**, **mixing**, **mosaic stacking**, and **secondary balancing**.
Modified: pkg/CHNOSZ/vignettes/postprocess.sh
===================================================================
--- pkg/CHNOSZ/vignettes/postprocess.sh 2025-05-09 14:17:58 UTC (rev 892)
+++ pkg/CHNOSZ/vignettes/postprocess.sh 2025-05-10 03:23:45 UTC (rev 893)
@@ -74,11 +74,6 @@
sed -i 's/water(/<a href="..\/html\/water.html" style="color:\ green;">water<\/a>(/g' OBIGT.html
sed -i 's/demo(/<a href="..\/demo">demo<\/a>(/g' OBIGT.html
-# Add links to equilibrium.html 20200710
-sed -i 's/equilibrate()/<a href="..\/html\/equilibrate.html">equilibrate()<\/a>/g' equilibrium.html
-sed -i 's/solubility()/<a href="..\/html\/solubility.html">solubility()<\/a>/g' equilibrium.html
-sed -i 's/add.OBIGT()/<a href="..\/html\/add.OBIGT.html">add.OBIGT()<\/a>/g' equilibrium.html
-
# Add links to multi-metal.html 20200716
sed -i 's/affinity()/<a href="..\/html\/affinity.html">affinity()<\/a>/g' multi-metal.html
sed -i 's/mash()/<a href="..\/html\/mix.html">mash()<\/a>/g' multi-metal.html
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