[CHNOSZ-commits] r732 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Jun 21 02:10:00 CEST 2022 

Author: jedick
Date: 2022-06-21 02:10:00 +0200 (Tue, 21 Jun 2022)
New Revision: 732

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/man/stack_mosaic.Rd
   pkg/CHNOSZ/vignettes/OBIGT.Rmd
Log:
Add cobalt monoxide and guite from Robie and Hemingway (1995)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2022-06-20 09:04:39 UTC (rev 731)
+++ pkg/CHNOSZ/DESCRIPTION	2022-06-21 00:10:00 UTC (rev 732)
@@ -1,6 +1,6 @@
-Date: 2022-06-20
+Date: 2022-06-21
 Package: CHNOSZ
-Version: 1.9.9-24
+Version: 1.9.9-25
 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/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2022-06-20 09:04:39 UTC (rev 731)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2022-06-21 00:10:00 UTC (rev 732)
@@ -10,7 +10,7 @@
 \newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
 \newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
 
-\section{Changes in CHNOSZ version 1.9.9-24 (2022-06-20)}{
+\section{Changes in CHNOSZ version 1.9.9-25 (2022-06-21)}{
 
   \subsection{MAJOR CHANGE}{
     \itemize{
@@ -41,6 +41,10 @@
 
       \item Merge \file{biotic_aq.csv} into \file{organic_aq.csv}.
 
+      \item \samp{OBIGT/inorganic_cr.csv}: Add cobalt monoxide (CoO) and guite
+      (Co\s{3}O\s{4}) from \href{https://doi.org/10.3133/b2131}{Robie and
+        Hemingway (1995)}.
+
     }
   }
 
@@ -119,7 +123,7 @@
       removed before drawing boundaries for the second species, and so on,
       species for which different-colored or -styled lines are desired should
       be placed at the top of the species list. This change makes possible one
-      less call to \code{diagram()} in the Mosaic Stacking sections in
+      less call to \code{diagram()} in Mosaic Stacking 1 and 2 in
       \strong{multi-metal.Rmd}, and now the entire chalcopyrite field in Mosaic
       Stacking 2 is bounded by a thick orange line, instead of just the border
       shared with bornite.

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2022-06-20 09:04:39 UTC (rev 731)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2022-06-21 00:10:00 UTC (rev 732)
@@ -150,3 +150,5 @@
 cobalt,NA,Co,cr,RH95,NA,2020-10-06,J,0,0,30.04,24.81,6.67,0,41.844,-1.5646,268.75,-1.6498,0,0,700
 wustite,NA,Fe0.947O,cr,RH95,NA,2020-11-10,J,-244900,-266300,56.6,48.13,12.04,-19.3,30.17,-25.33,1501,0,0,0,1652
 willemite,NA,Zn2SiO4,cr,RH95,BKK77,2021-03-22,J,-1523100,-1636700,131.4,123.3,52.42,144.892,36.945,-30.292,0,0,0,0,1785
+guite,NA,Co3O4,cr,RH95,NA,2022-06-21,J,-802200,-918800,109.3,123.39,39.77,131.6,66.02,-24.8,0,0,0,0,1000
+"cobalt monoxide",NA,CoO,cr,RH95,NA,2022-06-21,J,-214100,-237900,52.8,43.34,11.64,-30.47,29.46,-41.66,1932,0,0,0,1000

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2022-06-20 09:04:39 UTC (rev 731)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2022-06-21 00:10:00 UTC (rev 732)
@@ -58,7 +58,7 @@
 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","gypsum, manganese, manganosite, pyrolusite, bixbyite, hausmannite, heubnerite, cattierite, cobalt, wustite, and willemite",https://doi.org/10.3133/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum, manganese, manganosite, pyrolusite, bixbyite, hausmannite, huebnerite, cattierite, cobalt, cobalt monoxide, guite, wustite, and willemite",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/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2022-06-20 09:04:39 UTC (rev 731)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2022-06-21 00:10:00 UTC (rev 732)
@@ -267,24 +267,24 @@
 "OBIGT",2040,"ferberite","cr","J",1.21,,
 "OBIGT",2053,"Co-pentlandite","cr","cal",,,-3630
 "OBIGT",2056,"willemite","cr","J",-1.47,,
-"OBIGT",2075,"octadecane","cr","cal",-2.63,,
-"OBIGT",2076,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2077,"eicosane","cr","cal",-2.79,,
-"OBIGT",2078,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2079,"docosane","cr","cal",-2.63,,
-"OBIGT",2080,"tricosane","cr","cal",-5.22,,
-"OBIGT",2081,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2082,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2083,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2084,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2136,"carbazole","cr","cal",-43.39,,
-"OBIGT",2177,"triphenylene","cr","cal",,,541
-"OBIGT",2490,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2649,"ethylene","gas","cal",-4.59,,
-"OBIGT",2659,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2969,"nonacontane","liq","cal",,,635
-"OBIGT",2976,"2-methyloctane","liq","cal",10,,
-"OBIGT",3389,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",2077,"octadecane","cr","cal",-2.63,,
+"OBIGT",2078,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2079,"eicosane","cr","cal",-2.79,,
+"OBIGT",2080,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2081,"docosane","cr","cal",-2.63,,
+"OBIGT",2082,"tricosane","cr","cal",-5.22,,
+"OBIGT",2083,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2084,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2085,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2086,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2138,"carbazole","cr","cal",-43.39,,
+"OBIGT",2179,"triphenylene","cr","cal",,,541
+"OBIGT",2492,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2651,"ethylene","gas","cal",-4.59,,
+"OBIGT",2661,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2971,"nonacontane","liq","cal",,,635
+"OBIGT",2978,"2-methyloctane","liq","cal",10,,
+"OBIGT",3391,"5,6-dithiadecane","liq","cal",2,,
 "DEW",8,"AlO2(SiO2)-","aq","cal",,,-897
 "DEW",17,"BO(OH)","aq","cal",,,-1111
 "DEW",19,"CaHCO3+","aq","cal",,,-2971

Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)

Modified: pkg/CHNOSZ/man/stack_mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/stack_mosaic.Rd	2022-06-20 09:04:39 UTC (rev 731)
+++ pkg/CHNOSZ/man/stack_mosaic.Rd	2022-06-21 00:10:00 UTC (rev 732)
@@ -71,7 +71,7 @@
 basis(c("pyrite", "Cu", "Cl-", "H2S", "H2O", "oxygen", "H+"))
 basis("H2S", -2)
 # Calculate solution composition for 1 mol/kg NaCl
-NaCl <- NaCl(T = T, P = P, m_tot=1)
+NaCl <- NaCl(T = T, P = P, m_tot = 1)
 basis("Cl-", log10(NaCl$m_Cl))
 
 # Define arguments for stack_mosaic: Speciate aqueous sulfur

Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd	2022-06-20 09:04:39 UTC (rev 731)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd	2022-06-21 00:10:00 UTC (rev 732)
@@ -377,6 +377,7 @@
 <div id="D-optional-GEMSFIT" style="display: none">
 ## <a id="optional-GEMSFIT" class="anchor"></a> `r setfile("GEMSFIT.csv")`
 [Miron et al. (2016)](https://doi.org/10.1016/j.gca.2016.04.026) and [Miron et al. (2017)](https://doi.org/10.2475/07.2017.01) described an internally consistent thermodynamic dataset for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl that was obtained by using the [GEMSFIT](https://doi.org/10.1016/j.apgeochem.2014.10.013) package.
+Use `add.OBIGT("GEMSFIT")` to load the data.
 
 ```{r optreflist, results="asis", echo=FALSE}
 ```

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