[CHNOSZ-commits] r924 - 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
Mon Jun 9 08:55:31 CEST 2025 

Author: jedick
Date: 2025-06-09 08:55:31 +0200 (Mon, 09 Jun 2025)
New Revision: 924

Modified:
   pkg/CHNOSZ/DESCRIPTION
   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/FAQ.Rmd
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Add more U-bearing minerals from Grenthe et al. (2020)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2025-06-07 06:45:23 UTC (rev 923)
+++ pkg/CHNOSZ/DESCRIPTION	2025-06-09 06:55:31 UTC (rev 924)
@@ -1,6 +1,6 @@
-Date: 2025-06-07
+Date: 2025-06-09
 Package: CHNOSZ
-Version: 2.1.0-95
+Version: 2.1.0-96
 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	2025-06-07 06:45:23 UTC (rev 923)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-06-09 06:55:31 UTC (rev 924)
@@ -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 2.1.0-95 (2025-06-07)}{
+\section{Changes in CHNOSZ version 2.1.0-96 (2025-06-09)}{
 
   \subsection{OBIGT DATABASE FORMAT}{
     \itemize{
@@ -53,12 +53,10 @@
       \href{https://doi.org/10.1016/j.gca.2024.12.019}{Laskar et al. (2024)}.
 
       \item Add aqueous uranyl complexes from
-      \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}
-      and related U-bearing minerals from
-      \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}. Move
-      aqueous uranium species from
-      \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock, Sassani and Betz
-        (1997)} (except for HUO\s{4}\S{-}) to optional data.
+      \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}.
+      Move aqueous uranium species from
+      \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock, Sassani and
+        Betz (1997)} (except for HUO\s{4}\S{-}) to optional data.
 
       \item Add alkylamines, benzylamines, and aminiums from
       \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}.
@@ -67,6 +65,12 @@
       Th\S{+4} from \href{https://doi.org/10.1016/j.gsf.2023.101624}{Liu et al.
         (2023)}.
 
+      \item Add uranium, uraninite (UO\s{2}), beta-UO\s{2.25}, UO\s{2.25},
+      alpha-UO\s{2.3333}, beta-UO\s{2.3333}, UO\s{2.6667}, gamma-UO\s{3},
+      rutherfordine (UO\s{2}CO\s{3}), beta-UO\s{2}(OH)\s{2}, and
+      Na\s{2}U\s{2}O\s{7} from
+      \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}.
+
       \item Add Fe-bearing serpentinization-relevant minerals (ferrous
       hydroxide, ferrotremolite, greenalite, minnesotaite, Mg-cronstedtite, and
       hisingerite) from \href{https://doi.org/10.2475/03.2020.01}{Leong and

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2025-06-07 06:45:23 UTC (rev 923)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2025-06-09 06:55:31 UTC (rev 924)
@@ -68,7 +68,6 @@
 romarchite,Sn-Ox,SnO,cr,JH85,NA,1978-05-05,CGL,cal,-61459,-68340,13.66,NA,20.895,9.55,0.0035,0,0,0,0,0,1237
 tin,Sn,Sn,cr,JH85,NA,1985-08-00,CGL,cal,0,0,12.24,NA,16.289,4.42,0.0063,0,0,0,0,0,505.06
 tin,Sn,Sn,cr2,JH85,OBIGT.1,1985-08-00,CGL,cal,679.802,1607.605,15.3519,NA,16.289,7.3,0,0,0,0,0,0,3000
-uraninite,UO2,UO2,cr,SSB97.1,RH95.7,1994-09-08,CGL_Ttr,cal,-246610,-259320,18.4,NA,24.638,15.0033,0.007586,-183867,0,0,0,0,3151
 ruthenium,Ru,Ru,cr,SS98a.1,NA,1992-04-14,CGL,cal,0,0,6.82,5.76,8.175,5,0.001696,22300,0,0,0,0,1400
 rhodium,Rh,Rh,cr,SS98a.1,NA,1992-04-14,CGL,cal,0,0,7.53,5.92,8.281,5.73,0.001895,-33300,0,0,0,0,1800
 palladium,Pd,Pd,cr,SS98a.1,NA,1992-04-14,CGL,cal,0,0,9.04,6.06,8.861,5.73,0.001418,-8500,0,0,0,0,1800
@@ -155,9 +154,9 @@
 cattierite,"cobalt disulfide",CoS2,cr,WV22,PMW87,2024-02-05,CGL,J,-147365,-153140,74.793,68.26,25.52,65.82,0.0303,-587000,0,0,0,0,1223
 carrollite,Cli,Cu0.92Co2.07S4,cr,HDR+24,NA,2024-02-05,CGL,J,-331140,-344460,176.33,158.48,63.91,197.951,-0.0298,-2687000,0,0,0,0,377
 carrollite,Cli,Cu0.92Co2.07S4,cr2,HDR+24,NA,2024-02-05,CGL_Ttr,J,-331157,-345026,174.49,NA,63.91,234.11,-0.18038,0,0,0,0,0,650
-rutherfordine,Rfd,UO2CO3,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-1564701,-1691302,144.2,120.1,0,122.8563,0.04468312,-2706665,0,0,0,0,1273
-beta-UO2(OH)2,Sho,UO2(OH)2,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-1398683,-1533800,138,141,0,41.8,0.2,3530000,0,0,0,0,1273
-Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-3011454,-3203800,275.9,227.3,0,262.83,0.014653,-3549000,0,0,0,0,1273
+rutherfordine,Rfd,UO2CO3,cr,NEA20,Hem82,2023-08-07,CGL_Ttr,J,-1564701,-1691302,144.2,120.1,57.69,122.8563,0.04468312,-2706665,0,0,0,0,700
+beta-UO2(OH)2,Sho,UO2(OH)2,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-1398683,-1533800,138,141,52.29,41.8,0.2,3530000,0,0,0,0,473
+Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-3011454,-3203800,275.9,227.3,52.5,262.83,0.014653,-3549000,0,0,0,0,540
 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
 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
@@ -264,3 +263,11 @@
 minnesotaite,Mns,Fe3Si4O10(OH)2,cr,LS20,NA,2025-06-06,CGL,cal,-1070060,-1153380,83.5,88.5,148,88.31,0.04261,-1115000,0,0,0,0,1000
 Mg-cronstedtite,Cro-Mg,(Mg2Fe)(FeSi)O5(OH)4,cr,LS20,NA,2025-06-06,CGL,cal,-789000,-865180,60.8,71.8,108,77.03,0.04052,-1540000,0,0,0,0,1000
 hisingerite,Hsg,Fe2Si2O5(OH)4,cr,LS20,NA,2025-06-06,CGL,cal,-703430,-777330,57.3,63.4,105,68.77,0.04498,-1669000,0,0,0,0,1000
+uranium,uranium,U,cr,NEA20,NA,2023-08-07,CGL,J,0,0,50.2,27.66,12.49,26.92,-0.002502,-76986,0,2.6556E-05,0,NA,941
+uraninite,Urn,UO2,cr,NEA20,NA,2023-08-07,CGL,J,-1031833,-1085000,77.03,63.6,24.618,66.7437,0.0431393,-1168630,0,-3.564E-05,1.1655E-08,3,3000
+beta-UO2.25,beta-UO2.25,UO2.25,cr,NEA20,NA,2023-08-07,CGL,J,-1069083,-1127400,85.4,NA,NA,79.089,0.01365,-1038000,0,0,NA,NA,600
+UO2.25,UO2.25,UO2.25,cr,NEA20,NA,2024-07-02,CGL,J,-1069125,-1128000,83.53,73.34,25.08,1487.6,-6.9737,-17860000,0,0.009736,NA,NA,348
+alpha-UO2.3333,alpha-UO2.3333,UO2.3333,cr,NEA20,NA,2024-07-02,CGL,J,NA,NA,82.17,71.42,23.977,64.149,0.04914,-672000,0,0,NA,NA,347
+beta-UO2.3333,beta-UO2.3333,UO2.3333,cr,NEA20,NA,2024-07-02,CGL,J,-1079572,-1141000,83.51,71.84,23.877,64.338,0.04979,-655000,0,0,NA,NA,346
+UO2.6667,UO2.67,UO2.6667,cr,NEA20,NA,2024-07-02,CGL,J,-1123157,-1191600,94.18,79.31,33.44,93.089,0.00916,-1437200,0,0,NA,NA,2000
+gamma-UO3,gamma-UO3,UO3,cr,NEA20,NA,2024-07-02,CGL,J,-1145739,-1223800,96.11,81.67,35.56,88.103,0.01664,-1012800,0,0,NA,NA,850

Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-07 06:45:23 UTC (rev 923)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-09 06:55:31 UTC (rev 924)
@@ -17,6 +17,7 @@
 RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://doi.org/10.3133/b1452
 RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://doi.org/10.3133/b1452
 Den81,"K. Denbigh",1981,"The Principles of Chemical Equilibrium","hydrogen ion convention",https://doi.org/10.1017/CBO9781139167604
+Hem82,"B. S. Hemingway",1982,"U. S. Geological Survey Open-File Report 82-619","Cp values of rutherfordine used to obtain parameters of Maier-Kelley equation",https://doi.org/10.3133/ofr82619
 Pan82,"L. B. Pankratz",1987,"Thermodynamic Properties of Elements and Oxides (U.S. Bureau of Mines Bull. 672)","gallium, Ga<sub>2</sub>O<sub>3</sub>, indium, In<sub>2</sub>O<sub>3</sub>",https://catalog.hathitrust.org/Record/102119912
 PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
 WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
@@ -104,7 +105,6 @@
 SSH97.5,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","NaHSiO<sub>3</sub>, CaHSiO<sub>3</sub><sup>+</sup>, and MgHSiO<sub>3</sub><sup>+</sup>",https://doi.org/10.1016/S0016-7037(97)00009-4
 SSH97.6,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","In fluoride complex",https://doi.org/10.1016/S0016-7037(97)00009-4
 SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",https://doi.org/10.1016/S0016-7037(97)00240-8
-SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,https://doi.org/10.1016/S0016-7037(97)00240-8
 TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",https://doi.org/10.1016/S1251-8050(97)83981-X
 TZA97,"B. R. Tagirov, A. V. Zotov and N. N. Akinfiev",2007,"Geochim. Cosmochim. Acta 61, 4267-4280","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00274-3
 ST97,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylammonium chloride HKF parameters",https://doi.org/10.1023/A:1022977006327
@@ -311,7 +311,7 @@
 AKK+20.2,"N. N. Akinfiev et al.",2020,"Geochim. Cosmochim. Acta 280, 102-115","V of beta-Nb<sub>2</sub>O<sub>5</sub>",https://doi.org/10.1016/j.gca.2020.04.009
 LS20,"J. A. M. Leong and E. L. Shock",2020,"Am. J. Sci. 320, 185-235","Fe-bearing serpentinization-relevant minerals",https://doi.org/10.2475/03.2020.01
 LX20,"X. Liu and C. 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,"Grenthe et al.",2020,"Second Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium","uranium, uraninite (UO<sub>2</sub>), beta-UO<sub>2.25</sub>, UO<sub>2.25</sub>, alpha-UO<sub>2.3333</sub>, beta-UO<sub>2.3333</sub>, UO<sub>2.6667</sub>, gamma-UO<sub>3</sub>, rutherfordine (UO</sub>2</sub>CO<sub>3</sub>), 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
 LXW21,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488",H<sub>2</sub>WO<sub>4</sub>,https://doi.org/10.1016/j.chemgeo.2021.120488
 LXW21.1,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","scheelite Cp",https://doi.org/10.1016/j.chemgeo.2021.120488

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

Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd	2025-06-07 06:45:23 UTC (rev 923)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd	2025-06-09 06:55:31 UTC (rev 924)
@@ -228,7 +228,7 @@
 SUPCRT is an abbreviation for supercritical [@JOH92], but `subcrt()` is just a different name and is not limited to subcritical conditions.
 
 I would like to acknowledge Jan Amend for the suggestion to use a different function name than SUPCRT
-and for possibly being the first person to try to pronounce CHNOSZ while looking at the program's output.
+and for being possibly the first person to try to pronounce CHNOSZ while looking at the program's output.
 That interaction at the 2007 Goldschmidt conference led me to use CHNOSZ as the name for the package.
 
 *Added on 2025-06-05.*

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-07 06:45:23 UTC (rev 923)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-09 06:55:31 UTC (rev 924)
@@ -1957,6 +1957,16 @@
   doi       = {10.1016/j.apgeochem.2024.106032},
 }
 
+ at TechReport{Hem82,
+  author      = {Hemingway, B. S.},
+  institution = {U.S. Geological Survey},
+  title       = {Thermodynamic properties of selected uranium compounds and aqueous species at 298.15 {K} and 1 bar and at higher temperatures; preliminary models for the origin of coffinite deposits},
+  year        = {1982},
+  number      = {82-619},
+  type        = {Open-File Report},
+  doi         = {10.3133/ofr82619},
+}
+
 @Article{RH72,
   author    = {Robie, Richard A. and Hemingway, Bruce S.},
   journal   = {American Mineralogist},

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