[CHNOSZ-commits] r913 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/thermo vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Jun 1 07:26:10 CEST 2025 

Author: jedick
Date: 2025-06-01 07:26:09 +0200 (Sun, 01 Jun 2025)
New Revision: 913

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/CHECKLIST
   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/OBIGT.bib
Log:
Add beta-Nb2O5 (Naumov et al., 1974) and beta-Ta2O5 (Jacob et al., 2009)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2025-06-01 03:29:57 UTC (rev 912)
+++ pkg/CHNOSZ/DESCRIPTION	2025-06-01 05:26:09 UTC (rev 913)
@@ -1,6 +1,6 @@
 Date: 2025-06-01
 Package: CHNOSZ
-Version: 2.1.0-84
+Version: 2.1.0-85
 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/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2025-06-01 03:29:57 UTC (rev 912)
+++ pkg/CHNOSZ/inst/CHECKLIST	2025-06-01 05:26:09 UTC (rev 913)
@@ -27,17 +27,19 @@
 
 - Rebuild extdata/thermo/stoich.csv.xz after all data updates
   (used in retrieve() to search the databse by element):
-  formula <- thermo()$OBIGT$formula
-  stoich <- i2A(formula)
-  write.csv(stoich, "stoich.csv")
-  system("xz -f stoich.csv")
 
+formula <- thermo()$OBIGT$formula
+stoich <- i2A(formula)
+write.csv(stoich, "stoich.csv")
+system("xz -f stoich.csv")
+
 - Rebuild extdata/misc/OBIGT_check.csv after all data updates:
   (not used elsewhere in CHNOSZ, but helpful to see which
   species entries have self inconsistencies):
-  co <- check.OBIGT()
-  write.csv(co, "OBIGT_check.csv", row.names = FALSE, na = "")
 
+co <- check.OBIGT()
+write.csv(co, "OBIGT_check.csv", row.names = FALSE, na = "")
+
 ***************
 R compatibility
 ***************

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2025-06-01 03:29:57 UTC (rev 912)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-06-01 05:26:09 UTC (rev 913)
@@ -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 2.1.0-84 (2025-06-01)}{
+\section{Changes in CHNOSZ version 2.1.0-85 (2025-06-01)}{
 
   \subsection{OBIGT DATABASE FORMAT}{
     \itemize{
@@ -68,6 +68,9 @@
       from \href{https://doi.org/10.1016/0016-7037(95)00314-P}{Haas et al.
         (1995)} to optional data.
 
+      \item Add beta-Ta\s{2}O\s{5} from
+      \href{https://doi.org/10.1016/j.jct.2008.12.006}{Jacob et al. (2009)}.
+
       \item Add chromite (FeCr\s{2}O\s{4}) and cassiterite (SnO\s{2}) from
       \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}. Move
       cassiterite from
@@ -74,9 +77,13 @@
       \href{https://doi.org/10.2113/gsecongeo.80.5.1365}{Jackson and Helgeson
         (1985)} to optional data.
 
+      \item Add beta-Nb\s{2}O\s{5} from
+      \href{https://www.worldcat.org/oclc/8139446}{Naumov et al. (1974)}. A PDF
+      of this book is available from the
+      \href{https://ntrl.ntis.gov/NTRL/}{National Technical Reports Library}.
+
       \item Move americium complexes from optional to default data. Entropy of
-      the element Am has been available for checking GHS self-consistency since
-      CHNOSZ 1.4.0.
+      the element Am has been listed in \file{element.csv} since CHNOSZ 1.4.0.
 
       \item Fix sign of \emph{c} parameter for nesquehonite. Thanks to James
       Leong and Grayson Boyer.

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2025-06-01 03:29:57 UTC (rev 912)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2025-06-01 05:26:09 UTC (rev 913)
@@ -231,3 +231,5 @@
 YbPO4,YbPO4,YbPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1817000,-1929400,133.9,NA,41.11,247.56,-0.02291,256022.1,-2463.215,6.87E-06,0,0,1273
 LuPO4,LuPO4,LuPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1840600,-1955400,117.2,NA,41.9,268.28,-0.04472,570634.2,-2803.989,1.1187E-05,0,0,1273
 YPO4,YPO4,YPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1872400,-1987700,108.8,NA,44.57,134.06,0.01833,-3490000,-52.4841,4.24E-07,0,0,1273
+beta-Ta2O5,Ta2O5,Ta2O5,cr,JSW09,AKK+20.1,2025-06-01,CGL_Ttr,J,-1904040,-2038033,146.389,135.279,54.021,142.29,0.05545,-1975090,0,-1.48944E-05,0,0,1593
+beta-Nb2O5,Nb2O5,Nb2O5,cr,NRK74,AKK+20.1,2025-06-01,CGL_Ttr,cal,-421600,-453500,32.8,31.57,59.47,36.9,0.00512,-610000,0,0,0,0,1785

Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-01 03:29:57 UTC (rev 912)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-01 05:26:09 UTC (rev 913)
@@ -4,7 +4,7 @@
 Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https://www.worldcat.org/oclc/693388901
 Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,https://www.worldcat.org/oclc/14154245
 PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",https://www.worldcat.org/oclc/14154292
-NRK74,"Naumov, G. B., Ryzhenko, B. N., & Khodakovsky, I. L.",1974,"Handbook of Thermodynamic Data (U.S. Geol. Surv.)",GeS<sub>2</sub>,https://www.worldcat.org/oclc/8139446
+NRK74,"Naumov, G. B., Ryzhenko, B. N., & Khodakovsky, I. L.",1974,"Handbook of Thermodynamic Data (U.S. Geol. Surv.)","GeS<sub>2</sub> and beta-Nb<sub>2</sub>O<sub>5</sub>",https://www.worldcat.org/oclc/8139446
 RH72,"R. A. Robie and B. S. Hemingway",1972,"Am. Mineral. 57, 1768-1781","nesquehonite Cp",https://pubs.geoscienceworld.org/msa/ammin/article-pdf/57/11-12/1768/4256711/am-1972-1768.pdf
 BKK77,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","willemite Cp",https://www.worldcat.org/oclc/695258
 BKK77.1,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","Ga<sub>2</sub>S<sub>3</sub> and In<sub>2</sub>(SO<sub>4</sub>)<sub>3</sub>",https://www.worldcat.org/oclc/695258
@@ -187,6 +187,7 @@
 HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695","kerogens (C128, C292, C406, C415, C515) and pyrobitumen (C<sub>54</sub>H<sub>42</sub>)",https://doi.org/10.1016/j.gca.2008.03.004
 LRB09,"K. H. Lemke, R. J. Rosenbauer and D. K. Bird",2009,"Astrobiology 9, 141-146","diglycine and diketopiperazine",https://doi.org/10.1089/ast.2008.0166
 MWW09,"A. A. Migdisov, A. E. Williams-Jones and T. Wagner",2009,"Geochim. Cosmochim. Acta 73, 7087-7109","REE F<sup>-</sup> and Cl<sup>-</sup> complexes",https://doi.org/10.1016/j.gca.2009.08.023
+JSW09,"K. T. Jacob et al.",2009,"J. Chem. Thermodynamics 41, 748-753",beta-Ta<sub>2</sub>O<sub>5</sub>,https://doi.org/10.1016/j.jct.2008.12.006
 BZA10,"E. F. Bazarkina, A. V. Zotov and N. N. Akinfiev",2010,"Geol. Ore Deposits 52, 167-178","Cd chloride complexes",https://doi.org/10.1134/S1075701510020054
 AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010
 AML10.1,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","Np- and Am-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010
@@ -306,6 +307,7 @@
 LA19,"D. E. LaRowe and J. P. Amend",2019,"Geomicrobiol. J. 36, 492-505","dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid",https://doi.org/10.1080/01490451.2019.1573278
 SPD+19,"B. St Clair et al.",2019,"ACS Earth Space Chem 3, 905-921","metal carbonate and bicarbonate complexes and FeSO<sub>4</sub>",https://doi.org/10.1021/acsearthspacechem.9b00016
 AKK+20,"N. N. Akinfiev et al.",2020,"Geochim. Cosmochim. Acta 280, 102-115","Nb and Ta species",https://doi.org/10.1016/j.gca.2020.04.009
+AKK+20.1,"N. N. Akinfiev et al.",2020,"Geochim. Cosmochim. Acta 280, 102-115","V of beta-Nb<sub>2</sub>O<sub>5</sub> and beta-Ta<sub>2</sub>O<sub>5</sub>",https://doi.org/10.1016/j.gca.2020.04.009
 LX20,"Liu and Xiao",2020,"Ore Geol. Rev. 117, 103289","huebnerite Cp",https://doi.org/10.1016/j.oregeorev.2019.103289
 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

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

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-01 03:29:57 UTC (rev 912)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-01 05:26:09 UTC (rev 913)
@@ -2120,3 +2120,14 @@
   volume    = {123},
   doi       = {10.1016/j.gca.2013.07.031},
 }
+
+ at Article{JSW09,
+  author    = {K. T. Jacob and Chander Shekhar and Y. Waseda},
+  journal   = {The Journal of Chemical Thermodynamics},
+  title     = {An update on the thermodynamics of {T}a\textsubscript{2}{O}\textsubscript{5}},
+  year      = {2009},
+  number    = {6},
+  pages     = {748--753},
+  volume    = {41},
+  doi       = {10.1016/j.jct.2008.12.006},
+}

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