[CHNOSZ-commits] r820 - in pkg/CHNOSZ: . vignettes

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

Author: jedick
Date: 2023-12-06 01:00:43 +0100 (Wed, 06 Dec 2023)
New Revision: 820

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/vignettes/FAQ.Rmd
   pkg/CHNOSZ/vignettes/vig.bib
Log:
Update FAQ about mineral pH buffers


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2023-12-04 11:27:43 UTC (rev 819)
+++ pkg/CHNOSZ/DESCRIPTION	2023-12-06 00:00:43 UTC (rev 820)
@@ -1,6 +1,6 @@
-Date: 2023-12-04
+Date: 2023-12-05
 Package: CHNOSZ
-Version: 2.0.0-39
+Version: 2.0.0-40
 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/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd	2023-12-04 11:27:43 UTC (rev 819)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd	2023-12-06 00:00:43 UTC (rev 820)
@@ -809,21 +809,19 @@
 ```
 
 The gray area, which is automatically drawn by `diagram()`, is below the reducing stability limit of water; that is, this area is where the equilibrium fugacity of `r H2` exceeds unity.
+NOTE: Although the muscovite–kaolinite (MC) buffer was mentioned by @HC14 in the context of "clay-rich but feldspar-free sediments", this example uses the feldspathic Ab–Kfs reaction for calculating `r Kplus` molality for both the KMQ and MC buffers.
+A more appropriate reaction to constrain the Na/K ratio with the MC buffer may be that between paragonite and muscovite [e.g., @Yar05].
 
 The diagram in Fig. 4 of @HC14 shows the buffer lines at somewhat higher pH values of ca. 5 and 6.
-There are several possible reasons for these differences:
-
-1. We used different thermodynamic data for the minerals;
-2. Activity coefficients either were not calculated or were calculated differently by @HC14 (however, removing `IS` from the code moves the lines to lower rather than higher pH); or
-3. We calculated `r Kplus` molality incorrectly for the MC buffer. Although @HC14 invoked the muscovite–kaolinite buffer for "clay-rich but feldspar-free sediments", we used the feldspathic Ab–Kfs reaction for calculating `r Kplus` molality [no alternative reaction was given by @HC14].
-
-Regarding only the first point, note that the parameters for these minerals in the default OBIGT database come from @Ber88 and @SHD91.
+Removing `IS` from the code moves the lines to lower rather than higher pH (*not shown -- try it yourself!*), so the calculation of activity coefficients does not explain the differences.
+One possible reason for these differences is the use of different thermodynamic data for the minerals.
+The parameters for these minerals in the default OBIGT database come from @Ber88 and @SHD91.
 ```{r KMQ_refs, message = FALSE}
 thermo.refs(species()$ispecies)
 ```
 
-If we use the thermodynamic parameters for minerals from @HDNB78, we get the lines shown in the second plot above, representing a larger stability field for muscovite.
-For most purposes, the default database (generating the smaller muscovite field in the first plot) should be used as it is consistent with revisions described by @SHD91.
+If we use the thermodynamic parameters for minerals from @HDNB78 [these do not include the revisions for aluminosilicates described by @SHD91], we get the lines shown in the second plot above, representing a larger stability field for muscovite.
+This moves the KMQ buffer closer to the value shown by @HC14, but the MC buffer further away, so this still doesn't explain why we get a different result.
 
 ```{r KMQ_diagram, eval = FALSE, echo = 11:15}
 ```

Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib	2023-12-04 11:27:43 UTC (rev 819)
+++ pkg/CHNOSZ/vignettes/vig.bib	2023-12-06 00:00:43 UTC (rev 820)
@@ -875,3 +875,14 @@
   volume    = {5},
   doi       = {10.1089/ast.2005.5.444},
 }
+
+ at Article{Yar05,
+  author    = {Yardley, Bruce W. D.},
+  journal   = {Economic Geology},
+  title     = {100th {A}nniversary {S}pecial {P}aper: {M}etal concentrations in crustal fluids and their relationship to ore formation},
+  year      = {2005},
+  number    = {4},
+  pages     = {613--632},
+  volume    = {100},
+  doi       = {10.2113/gsecongeo.100.4.613},
+}