[CHNOSZ-commits] r852 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Nov 30 09:23:48 CET 2024 

Author: jedick
Date: 2024-11-30 09:23:48 +0100 (Sat, 30 Nov 2024)
New Revision: 852

Added:
   pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/vignettes/OBIGT.Rmd
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
OBIGT: Add IGEM24.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2024-11-30 04:33:27 UTC (rev 851)
+++ pkg/CHNOSZ/DESCRIPTION	2024-11-30 08:23:48 UTC (rev 852)
@@ -1,6 +1,6 @@
 Date: 2024-11-30
 Package: CHNOSZ
-Version: 2.1.0-24
+Version: 2.1.0-25
 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/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2024-11-30 04:33:27 UTC (rev 851)
+++ pkg/CHNOSZ/R/util.data.R	2024-11-30 08:23:48 UTC (rev 852)
@@ -271,6 +271,7 @@
     else if(what == "AS04") tdata <- read.csv(system.file("extdata/OBIGT/AS04.csv", package = "CHNOSZ"), as.is = TRUE)
     else if(what == "AD") tdata <- read.csv(system.file("extdata/OBIGT/AD.csv", package = "CHNOSZ"), as.is = TRUE)
     else if(what == "GEMSFIT") tdata <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package = "CHNOSZ"), as.is = TRUE)
+    else if(what == "IGEM24") tdata <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE)
     ntot <- nrow(tdata)
     # Where to keep the results
     DCp <- DV <- DG <- rep(NA, ntot)
@@ -308,6 +309,7 @@
   out <- rbind(out, checkfun("SUPCRT92"))
   out <- rbind(out, checkfun("AS04"))
   out <- rbind(out, checkfun("GEMSFIT"))
+  out <- rbind(out, checkfun("IGEM24"))
   # Set differences within a tolerance to NA
   out$DCp[abs(out$DCp) < 1] <- NA
   out$DV[abs(out$DV) < 1] <- NA
@@ -390,8 +392,10 @@
   AD <- cbind(source = "AD", dat)
   dat <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package = "CHNOSZ"), as.is = TRUE)
   GEMSFIT <- cbind(source = "GEMSFIT", dat)
+  dat <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE)
+  IGEM24 <- cbind(source = "IGEM24", dat)
   # Put it all together
-  out <- rbind(OBIGT, SUPCRT92, SLOP98, AS04, AD, DEW, GEMSFIT)
+  out <- rbind(OBIGT, SUPCRT92, SLOP98, AS04, AD, DEW, GEMSFIT, IGEM24)
   # Quote columns 2 (name) and 3 (abbrv) because they have commas for some entries
   if(!is.null(file)) write.csv(out, file, row.names = FALSE, quote = c(2, 3))
   else(return(out))

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2024-11-30 04:33:27 UTC (rev 851)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2024-11-30 08:23:48 UTC (rev 852)
@@ -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 2.1.0-22 (2024-11-28)}{
+\section{Changes in CHNOSZ version 2.1.0-25 (2024-11-30)}{
 
     \itemize{
 
@@ -61,6 +61,10 @@
       \item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes,
       and add solubility contours for Fe and Au.
 
+      \item Add \file{OBIGT/IGEM24.csv} with updated data for Au and Cu
+      complexes and SO\s{4}\S{-2}-bearing species from
+      researchers at IGEM RAS.
+
     }
 
 }

Added: pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv	2024-11-30 08:23:48 UTC (rev 852)
@@ -0,0 +1,17 @@
+name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+KHSO4,NA,KHSO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-246551,NA,52.892,43.67,36.82,6.8032,8.8337,2.278,-3.1442,31.8025,5.8381,0,0
+KSO4-,NA,KSO4-,aq,TAT+24,NA,2024-11-30,HKF,cal,-246636,NA,60.893,-136.37,30.4,6.8612,6.0072,3.3889,-3.0273,-63.7366,-30.8131,1.0996,-1
+H2SO4,NA,H2SO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-178211,NA,28.058,67.18,83.42,13.1225,24.5891,-3.9144,-3.7955,45.8348,10.5047,0,0
+AuHS,NA,AuHS,aq,TAT+24,NA,2024-11-30,HKF,cal,8208,NA,38.583,26.25,45.73,8.0227,11.8073,1.1093,-3.2671,-49.3817,37.2185,0,0
+AuHS(H2S)3,NA,AuHS(H2S)3,aq,TAT+24,NA,2024-11-30,HKF,cal,-13146,NA,174.161,111.89,145.3,21.6476,45.0745,-11.966,-4.6424,-48.4088,78.8834,0,0
+Au(HS)2-,NA,Au(HS)2-,aq,TAT+24,NA,2024-11-30,HKF,cal,3532,NA,71.791,-30.47,67.97,11.5845,20.504,-2.3089,-3.6266,1.6472,-8.8534,1.5338,-1
+Au2S2-2,NA,Au2S2-2,aq,TAT+24,NA,2024-11-30,HKF,cal,28054,NA,78.65,-119.3,83.58,14.2429,26.9949,-4.86,-3.895,-35.3863,-27.3368,3.079,-2
+AuOH,NA,AuOH,aq,TAZ24,NA,2024-11-30,HKF,cal,-25947,NA,33.492,18.03,46.58,8.1395,12.0926,0.9972,-3.2789,1.6058,8.0824,0,0
+AuCl,NA,AuCl,aq,TAZ24,NA,2024-11-30,HKF,cal,-1900,NA,52.2,-71.9,50.8,8.7165,13.5013,0.4435,-3.3371,-35.9711,-17.6806,0,0
+AuCl2-,NA,AuCl2-,aq,TAZ24,NA,2024-11-30,HKF,cal,-36572,NA,43.5,9.5,68.52,11.4087,20.0747,-2.1401,-3.6089,16.8432,-0.463,0.7031,-1
+CuHS,NA,CuHS,aq,TTA+23,NA,2024-11-30,HKF,cal,-2969,NA,59.1,-67.713,44.85,7.9477,11.6243,1.1812,-3.2596,-32.4272,-16.8275,0.1197,0
+Cu(HS)2-,NA,Cu(HS)-2,aq,TTA+23,NA,2024-11-30,HKF,cal,-5665,NA,56.647,7.274,79.573,13.0153,23.9975,-3.6819,-3.7711,18.2332,-1.1267,0.9517,-1
+CuCl,NA,CuCl,aq,TTA+23,NA,2024-11-30,HKF,cal,-23360,NA,61.777,-101.336,26.967,5.4552,5.5383,3.5732,-3.008,-52.5985,-23.9839,0,0
+CuCl2-,NA,CuCl2-,aq,TTA+23,NA,2024-11-30,HKF,cal,-58026,NA,53.111,-19.991,32.604,6.6297,8.406,2.4461,-3.1265,4.1186,-7.1067,1.0612,-1
+Cu+,NA,Cu+,aq,AZ23,NA,2024-11-30,HKF,cal,11945,NA,9.7,13.66,-7.99,0.9243,-5.5244,7.9213,-2.5506,37.8578,-8.925,0.6653,1
+CuO-,NA,CuO-,aq,AZ23,NA,2024-11-30,HKF,cal,-19574,NA,-2.45,-12.69,-13.11,0.3673,-6.8845,8.4559,-2.4944,-55.4517,25.7204,1.0433,-1

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2024-11-30 04:33:27 UTC (rev 851)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2024-11-30 08:23:48 UTC (rev 852)
@@ -291,6 +291,10 @@
 HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93",carrollite,https://doi.org/10.3749/2300028
 NEA20,"Grenthe et al.",2020,"Second Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium","rutherfordine, beta-UO<sub>2</sub>(OH)<sub>2</sub>, and Na<sub>2</sub>U<sub>2</sub>O<sub>7</sub>",https://doi.org/10.1787/bf86a907-en
 NEA20.1,"Grenthe et al.",2020,"Second Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium",UO<sub>3</sub>,https://doi.org/10.1787/bf86a907-en
+AZ23,"N. N. Akinfiev and A. V. Zotov",2023,"Geol. Ore Deposits 65, 1-10","Cu<sup>+</sup> and CuO<sup>-</sup>",https://doi.org/10.1134/S1075701523010026
+TTA+23,"N. D. Trofimov, B. R. Tagirov et al.",2023,"Chem. Geol. 625, 121413","Cu hydrosulfide and chloride complexes",https://doi.org/10.1016/j.chemgeo.2023.121413
 MBA+24,"A. Migdisov, E. Bastrakov et al.",2024,"Geochim. Cosmochim. Acta","uranyl-carbonate, -chloride, -sulfate, and -hydroxide complexes",https://doi.org/10.1016/j.gca.2024.04.023
 RSS+24,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","alkylamines, benzylamines, and aminiums",https://doi.org/10.1016/j.gca.2024.03.013
 RSS+24.1,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","corrected V for tripropylaminium",https://doi.org/10.1016/j.gca.2024.03.013
+TAT+24,"B. R. Tagirov, N. N. Akinfiev et al.",2024,"Geochim. Cosmochim. Acta","Au-(hydro)sulfide species and SO<sub>4</sub><sup>-2</sup>-bearing species",https://doi.org/10.1016/j.gca.2024.08.022
+TAZ24,"B. R. Tagirov, N. N. Akinfiev and A. V. Zotov",2024,"Geol. Ore Deposits 66, 581--597","Au hydroxide and chloride complexes",https://doi.org/10.1134/S1075701524600403

Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd	2024-11-30 04:33:27 UTC (rev 851)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd	2024-11-30 08:23:48 UTC (rev 852)
@@ -73,6 +73,7 @@
   OpenDiv("optional-AS04");
   OpenDiv("optional-DEW");
   OpenDiv("optional-GEMSFIT");
+  OpenDiv("optional-IGEM24");
   // change the footer message
   document.getElementById("footer").style.display = "none";
   document.getElementById("all-open").style.display = "block";
@@ -93,6 +94,7 @@
   CloseDiv("optional-AS04");
   CloseDiv("optional-DEW");
   CloseDiv("optional-GEMSFIT");
+  CloseDiv("optional-IGEM24");
   // change the footer message
   document.getElementById("footer").style.display = "block";
   document.getElementById("all-open").style.display = "none";
@@ -204,7 +206,7 @@
 ### Aqueous Species <button id="B-aqueous-H2O" onclick='ToggleDiv("aqueous-H2O")'>H2O</button> <button id="B-aqueous-inorganic" onclick='ToggleDiv("aqueous-inorganic")'>Inorganic</button> <button id="B-aqueous-organic" onclick='ToggleDiv("aqueous-organic")'>Organic</button>
 ### Solids <button id="B-solid-inorganic" onclick='ToggleDiv("solid-inorganic")'>Inorganic</button> <button id="B-solid-organic" onclick='ToggleDiv("solid-organic")'>Organic</button> <button id="B-solid-Berman" onclick='ToggleDiv("solid-Berman")'>Berman</button>
 ### Gases <button id="B-gas-inorganic" onclick='ToggleDiv("gas-inorganic")'>Inorganic</button> <button id="B-gas-organic" onclick='ToggleDiv("gas-organic")'>Organic</button>    Liquids <button id="B-liquid-organic" onclick='ToggleDiv("liquid-organic")'>Organic</button>
-### Optional Data <button id="B-optional-SUPCRT92" onclick='ToggleDiv("optional-SUPCRT92")'>SUPCRT92</button> <button id="B-optional-SLOP98" onclick='ToggleDiv("optional-SLOP98")'>SLOP98</button> <button id="B-optional-AD" onclick='ToggleDiv("optional-AD")'>AD</button> <button id="B-optional-AS04" onclick='ToggleDiv("optional-AS04")'>AS04</button> <button id="B-optional-DEW" onclick='ToggleDiv("optional-DEW")'>DEW</button> <button id="B-optional-GEMSFIT" onclick='ToggleDiv("optional-GEMSFIT")'>GEMSFIT</button>
+### Optional Data <button id="B-optional-SUPCRT92" onclick='ToggleDiv("optional-SUPCRT92")'>SUPCRT92</button> <button id="B-optional-SLOP98" onclick='ToggleDiv("optional-SLOP98")'>SLOP98</button> <button id="B-optional-AD" onclick='ToggleDiv("optional-AD")'>AD</button> <button id="B-optional-AS04" onclick='ToggleDiv("optional-AS04")'>AS04</button> <button id="B-optional-DEW" onclick='ToggleDiv("optional-DEW")'>DEW</button> <button id="B-optional-GEMSFIT" onclick='ToggleDiv("optional-GEMSFIT")'>GEMSFIT</button> <button id="B-optional-IGEM24" onclick='ToggleDiv("optional-IGEM24")'>IGEM24</button>
 
 <!-- Normal or "all open" footer message --> 
 
@@ -324,6 +326,7 @@
 **NOTE:** Other minerals from SUPCRT92, including native elements, sulfides, halides, sulfates, and selected carbonates and oxides that do not duplicate those in the Berman dataset, are still present in the default database (**inorganic_cr.csv**).
 
 ```{r optreflist, results="asis", echo=FALSE}
+optused <- c(optused, filerefs(csvfile))
 ```
 </div>
 
@@ -373,7 +376,6 @@
 Most of the comments below were transcribed from the DEW spreadsheet. (Comments in parentheses were added by JMD.)
 
 ```{r optreflist, results="asis", echo=FALSE}
-optused <- c(optused, filerefs(csvfile))
 ```
 </div>
 
@@ -386,6 +388,15 @@
 ```
 </div>
 
+<div id="D-optional-IGEM24" style="display: none">
+## <a id="optional-IGEM24" class="anchor"></a> `r setfile("IGEM24.csv")`
+Data updates from researchers at the Institute of Geology of Ore Deposits, Petrography, Mineralogy, and Geochemistry, Russian Academy of Sciences (IGEM RAS).
+Use `add.OBIGT("IGEM24")` to load the data.
+
+```{r optreflist, results="asis", echo=FALSE}
+```
+</div>
+
 <hr>
 
 <b>Total count of species</b>: References were found for `r length(used)` of `r nrow(thermo()$OBIGT)` species in the default OBIGT database and `r length(optused)` optional species.

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2024-11-30 04:33:27 UTC (rev 851)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2024-11-30 08:23:48 UTC (rev 852)
@@ -1788,6 +1788,16 @@
   url       = {https://www.worldcat.org/oclc/16131757},
 }
 
+ at Article{TTA+23,
+  author    = {Nikolay D. Trofimov and Boris R. Tagirov and Nikolay N. Akinfiev and Vladimir L. Reukov and Maximilian S. Nickolsky and Irina Yu. Nikolaeva and Maria E. Tarnopolskaya and Andrey A. Afanasyev},
+  journal   = {Chemical Geology},
+  title     = {Chalcocite {Cu\textsubscript{2}S} solubility in aqueous sulfide and chloride fluids. Thermodynamic properties of copper({I}) aqueous species and copper transport in hydrothermal systems},
+  year      = {2023},
+  pages     = {121413},
+  volume    = {625},
+  doi       = {10.1016/j.chemgeo.2023.121413},
+}
+
 @Book{NEA20,
   author    = {I. Grenthe and X. Gaona and A. Plyasunov and L. Rao and W. Runde and B. Grambow},
   publisher = {OECD and Nuclear Energy Agency},
@@ -1835,3 +1845,33 @@
   pages     = {1768--1781},
   volume    = {57},
 }
+
+ at Article{TAZ24,
+  author    = {Tagirov, B. R. and Akinfiev, N. N. and Zotov, A. V.},
+  journal   = {Geology of Ore Deposits},
+  title     = {Gold({I}) complexation in chloride hydrothermal fluids},
+  year      = {2024},
+  number    = {5},
+  pages     = {581--597},
+  volume    = {66},
+  doi       = {10.1134/S1075701524600403},
+}
+
+ at Article{TAT+24,
+  author    = {Boris R. Tagirov and Nikolay N. Akinfiev and Mariia E. Tarnopolskaia and Irina Yu. Nikolaeva and Irina Yu. Zlivko and Valentina A. Volchenkova and Luydmila A. Koroleva and Alexander V. Zotov},
+  journal   = {Geochimica et Cosmochimica Acta},
+  title     = {Gold in sulfide fluids revisited},
+  year      = {2024},
+  doi       = {10.1016/j.gca.2024.08.022},
+}
+
+ at Article{AZ23,
+  author    = {Akinfiev, N. N. and Zotov, A. V.},
+  journal   = {Geology of Ore Deposits},
+  title     = {Copper in hydrothermal systems: a thermodynamic description of hydroxocomplexes},
+  year      = {2023},
+  number    = {1},
+  pages     = {1--10},
+  volume    = {65},
+  doi       = {10.1134/S1075701523010026},
+}

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