[CHNOSZ-commits] r885 - in pkg/CHNOSZ: . demo inst inst/extdata/OBIGT inst/extdata/thermo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 28 07:09:16 CEST 2025
Author: jedick
Date: 2025-04-28 07:09:15 +0200 (Mon, 28 Apr 2025)
New Revision: 885
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/comproportionation.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
pkg/CHNOSZ/inst/extdata/thermo/refs.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
OBIGT: Add aluminum from Robie and Hemingway (1995)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-04-23 11:17:59 UTC (rev 884)
+++ pkg/CHNOSZ/DESCRIPTION 2025-04-28 05:09:15 UTC (rev 885)
@@ -1,6 +1,6 @@
-Date: 2025-04-23
+Date: 2025-04-28
Package: CHNOSZ
-Version: 2.1.0-56
+Version: 2.1.0-57
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/comproportionation.R
===================================================================
--- pkg/CHNOSZ/demo/comproportionation.R 2025-04-23 11:17:59 UTC (rev 884)
+++ pkg/CHNOSZ/demo/comproportionation.R 2025-04-28 05:09:15 UTC (rev 885)
@@ -18,13 +18,17 @@
m <- mosaic(bases, T = c(0, 100), pH = c(0, 7))
a <- m$A.species
-# Get plot values
+# Get grid values for variables
T <- a$vals[[1]]
pH <- a$vals[[2]]
# The affinity as a function of T (rows) and pH (columns)
A <- a$values[[1]]
-# Convert dimensionless affinity (A/2.303RT) to delta G (kJ / mol)
+# Get values of Kelvin along the temperature scale
TK <- convert(T, "K")
+## NOTE: If T was in the columns of A, we would need to transpose to get T into the rows of A
+## (i.e., the first indexed dimension), then transpose again to get back to the original dimensions
+#G.J <- t(convert(t(A), "G", T = TK))
+# Since T is in the rows of A (first indexed dimension), no transposition is needed here
G.J <- convert(A, "G", T = TK)
G.kJ <- G.J / 1000
# Multiply by 4
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2025-04-23 11:17:59 UTC (rev 884)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2025-04-28 05:09:15 UTC (rev 885)
@@ -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 2.1.0-56 (2025-04-23)}{
+\section{Changes in CHNOSZ version 2.1.0-57 (2025-04-28)}{
\subsection{OBIGT DEFAULT DATA}{
\itemize{
@@ -340,9 +340,9 @@
\item Merge \file{biotic_aq.csv} into \file{organic_aq.csv}.
- \item \samp{OBIGT/inorganic_cr.csv}: Add cobalt monoxide (CoO), guite
- (Co\s{3}O\s{4}), and zinc from \href{https://doi.org/10.3133/b2131}{Robie
- and Hemingway (1995)}.
+ \item \samp{OBIGT/inorganic_cr.csv}: Add aluminum (Al), cobalt monoxide
+ (CoO), guite (Co\s{3}O\s{4}), and zinc from
+ \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}.
\item \samp{OBIGT/inorganic_cr.csv}: Modify linnaeite (Co\s{3}S\s{4}) to
use 25 \degC parameters from \href{https://doi.org/10.3133/b2131}{Robie
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2025-04-23 11:17:59 UTC (rev 884)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2025-04-28 05:09:15 UTC (rev 885)
@@ -161,3 +161,4 @@
chromite,Chr,FeCr2O4,cr,RH95,NA,2024-05-23,CGL,J,-1344500,-1445500,146,133.58,44.01,301.8,-0.04157,487700,-2803,1.147E-05,0,0,1800
cerianite,Cei,CeO2,cr,RH95,NA,2024-05-23,CGL,J,-1024600,-1088700,62.3,61.63,23.85,80.29,0.005699,-729400,-209.9,0,0,0,1800
cassiterite,Cst,SnO2,cr,RH95,NA,2025-01-17,CGL_Ttr,J,-515800,-577600,49.02,53.22,21.55,76.04,0.007364,-2224000,0,0,0,0,1903
+aluminum,Al,Al,cr,RH95,NA,2025-04-28,CGL_Ttr,J,0,0,28.3,24.21,9.999,41.32,-0.01988,-126500,-181.6,1.93E-05,0,0,933.5
Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-04-23 11:17:59 UTC (rev 884)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-04-28 05:09:15 UTC (rev 885)
@@ -64,7 +64,7 @@
HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P
PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255
PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964
-RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bixbyite, cassiterite, cattierite, cerianite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, zinc",https://doi.org/10.3133/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","aluminum, bixbyite, cassiterite, cattierite, cerianite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, zinc",https://doi.org/10.3133/b2131
RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://doi.org/10.3133/b2131
RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://doi.org/10.3133/b2131
RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, halloysite, pyrope: GHS and Cp at 25 °C",https://doi.org/10.3133/b2131
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2025-04-23 11:17:59 UTC (rev 884)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2025-04-28 05:09:15 UTC (rev 885)
@@ -508,6 +508,10 @@
Let's put together #8-10 to make a set of diagrams for a single metal.
The example here uses Fe; try changing it to Cu, Zn, Pb, Au, or something else!
+CHNOSZ emits warning messages about being above the Cp limits for various iron oxyhydroxides.
+If you see warning messages like this, it's a good idea not to ignore them; instead, consider whether you might be pushing extrapolations of the Cp equation too far.
+For the present calculation, the warnings are probably harmless because the set of stable minerals on the diagram (pyrite, pyrrhotite, magnetite, and hematite) is consistent with many previous publications.
+
```{r solubility, echo=FALSE, fig.cap="Mineral stability diagram; aqueous species predominance diagram; composite diagram with one solubility contour; diagram with multiple solubility contours in units of log *m*", fig.margin=FALSE, fig.fullwidth=TRUE, fig.width=16, fig.height=3, cache=TRUE}
par(mfrow = c(1, 4))
@@ -546,8 +550,8 @@
bases <- c("H2S", "HS-", "HSO4-", "SO4-2")
# Git minerals and aqueous species
-icr <- retrieve(metal, c("Cl", "S", "O"), state = "cr")
-iaq <- retrieve(metal, c("Cl", "S", "O"), state = "aq")
+icr <- retrieve(metal, c("Cl", "S", "O", "H"), state = "cr")
+iaq <- retrieve(metal, c("Cl", "S", "O", "H"), state = "aq")
# Make diagram for minerals
species(icr)
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