[CHNOSZ-commits] r836 - in pkg/CHNOSZ: . demo vignettes

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2024-04-09 03:14:36 +0200 (Tue, 09 Apr 2024)
New Revision: 836

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/solubility.R
   pkg/CHNOSZ/vignettes/FAQ.Rmd
Log:
Update FAQ.Rmd


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2024-04-01 06:32:16 UTC (rev 835)
+++ pkg/CHNOSZ/DESCRIPTION	2024-04-09 01:14:36 UTC (rev 836)
@@ -1,6 +1,6 @@
-Date: 2024-04-01
+Date: 2024-04-09
 Package: CHNOSZ
-Version: 2.1.0-8
+Version: 2.1.0-9
 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/demo/solubility.R
===================================================================
--- pkg/CHNOSZ/demo/solubility.R	2024-04-01 06:32:16 UTC (rev 835)
+++ pkg/CHNOSZ/demo/solubility.R	2024-04-09 01:14:36 UTC (rev 836)
@@ -51,7 +51,7 @@
 basis(c("CO2", "Ca+2", "H2O", "O2", "H+"))
 species("calcite")
 iaq <- info(c("CO2", "HCO3-", "CO3-2"))
-# Change this to dissociate = 2 to reproduce straight lines in Fig. 4A of Manning et al., 2013
+# Optional: use dissociate = 2 to get straight lines like Fig. 4A of Manning et al., 2013
 s <- solubility(iaq, pH = c(pH, res), T = T1, IS = IS, dissociate = TRUE)
 diagram(s, ylim = c(-10, 4), type = "loga.balance", lwd = 4, col = "green2")
 diagram(s, add = TRUE, dy = 1)

Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd	2024-04-01 06:32:16 UTC (rev 835)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd	2024-04-09 01:14:36 UTC (rev 836)
@@ -831,7 +831,7 @@
 
 ## 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.
+The reason they are curved has to do with mass balance of elements in aqueous solution.
 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
@@ -840,9 +840,9 @@
 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.
+However, this is inconsistent with a *constant sum* constraint of activities that is sometimes 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 *constant activity* constraint is compatible with the *constant sum* constraint only well inside the predominance 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.
@@ -937,7 +937,7 @@
 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}
+```{r Fe-S-O-C, message = FALSE, results = "hide", fig.width = 5, fig.height = 5, out.width = "60%", 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)