[CHNOSZ-commits] r920 - 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
Thu Jun 5 10:35:14 CEST 2025 

Author: jedick
Date: 2025-06-05 10:35:13 +0200 (Thu, 05 Jun 2025)
New Revision: 920

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv
   pkg/CHNOSZ/inst/extdata/thermo/refs.csv
   pkg/CHNOSZ/vignettes/OBIGT.Rmd
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Cite Denbigh (1981) for the hydrogen ion convention


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2025-06-05 06:55:16 UTC (rev 919)
+++ pkg/CHNOSZ/DESCRIPTION	2025-06-05 08:35:13 UTC (rev 920)
@@ -1,6 +1,6 @@
 Date: 2025-06-05
 Package: CHNOSZ
-Version: 2.1.0-91
+Version: 2.1.0-92
 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	2025-06-05 06:55:16 UTC (rev 919)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-06-05 08:35:13 UTC (rev 920)
@@ -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 2.1.0-91 (2025-06-05)}{
+\section{Changes in CHNOSZ version 2.1.0-92 (2025-06-05)}{
 
   \subsection{OBIGT DATABASE FORMAT}{
     \itemize{
@@ -104,8 +104,13 @@
       \item Move americium complexes from optional to default data. Entropy of
       the element Am has been listed in \file{element.csv} since CHNOSZ 1.4.0.
 
-      \item Corrected Δ\emph{H}°\s{f} by -7335 cal/mol to maintain GHS
-      consistency for In\s{+3} and derived species. This is in addition to the
+      \item Cite \href{https://doi.org/10.1017/CBO9781139167604}{Denbigh
+        (1981)} for the hydrogen ion convention.
+
+      \item Due to an apparent typo in
+      \href{https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf}{Wagman et al. (1982)},
+      Δ\emph{H}°\s{f} for In\s{+3} and derived species was corrected by -7335
+      cal/mol to maintain GHS consistency. This is in addition to the
       correction for S° previously noted by
       \href{https://doi.org/10.1016/0016-7037(88)90181-0}{Shock and Helgeson
         (1988)}.

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv	2025-06-05 06:55:16 UTC (rev 919)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv	2025-06-05 08:35:13 UTC (rev 920)
@@ -1,4 +1,4 @@
 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
-water,NA,H2O,liq,HGK84,JOH92,2006-10-25,H2O,cal,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-e-,NA,(Z-1),aq,electron,NA,2006-10-28,HKF,cal,0,0,15.6166,0,0,0,0,0,0,0,0,0,0
-H+,H+,H+,aq,proton,NA,1997-11-06,HKF,cal,0,0,0,0,0,0,0,0,0,0,0,0,0
+water,NA,H2O,liq,JOH92,HGK84,2006-10-25,H2O,cal,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+e-,NA,(Z-1),aq,OBIGT06,NA,2006-10-28,HKF,cal,0,0,15.6166,0,0,0,0,0,0,0,0,0,0
+H+,H+,H+,aq,Den81,NA,1997-11-06,HKF,cal,0,0,0,0,0,0,0,0,0,0,0,0,0

Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-05 06:55:16 UTC (rev 919)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-05 08:35:13 UTC (rev 920)
@@ -16,12 +16,13 @@
 RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://doi.org/10.3133/b1452
 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
 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
 WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","Mn(OH)<sub>2</sub> (amorphous) and MgSO<sub>4</sub>",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
 BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,https://doi.org/10.1016/0016-7037(83)90066-2
-HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",H<sub>2</sub>O,https://www.worldcat.org/oclc/858456124
+HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",thermodynamic properties of H<sub>2</sub>O outside of the critical region,https://www.worldcat.org/oclc/858456124
 Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845
 JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365
 PMW87,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","cattierite, linnaeite, and Co-pentlandite",https://www.worldcat.org/oclc/16131757
@@ -49,7 +50,7 @@
 SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
 SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
 JUN92,"C. de Capitani",1992,"JUN92.bs database supplied with Theriak/Domino software","data as listed in `JUN92.bs` data file",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html
-JOH92,"J. W. Johnson and E. H. Oelkers and H. C. Helgeson",1992,"Comp. Geosci. 18, 899-947",H<sub>2</sub>O,https://doi.org/10.1016/0098-3004(92)90029-Q
+JOH92,"J. W. Johnson and E. H. Oelkers and H. C. Helgeson",1992,"Comp. Geosci. 18, 899-947","thermodynamic and electrostatic properties of H<sub>2</sub>O calculated using HO92D.f source file from SUPCRT92 modified for use in CHNOSZ",https://doi.org/10.1016/0098-3004(92)90029-Q
 Joh92,"J. W. Johnson",1992,"Personal calculation","steam: "Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."",
 SPRONS92.1,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
 SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
@@ -108,7 +109,6 @@
 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
 DRT98,"I. I. Diakonov et al.",1998,"Chem. Geol. 151, 327-347","REE hydroxides",https://doi.org/10.1016/S0009-2541(98)00088-6
-proton,OBIGT,1997,"Hydrogen-ion convention","""The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature"" [@JOH92]",https://chnosz.net
 HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6
 HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6
 PS98,"G. S. Pokrovski and J. Schott",1998,"Geochim. Cosmochim. Acta 62, 1631-1642","GeO<sub>2</sub> (hex) and (tetr) (augite)",https://doi.org/10.1016/S0016-7037(98)00081-7
@@ -160,7 +160,7 @@
 SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",https://doi.org/10.1016/j.gca.2003.06.001
 VPV05,"O. Vidal, T. Parra and P. Viellard",2005,"Am. Mineral. 90, 347-358",Fe-amesite,https://doi.org/10.2138/am.2005.1554
 ZZX+05,"Y. Zhu et al.",2005,"J. Hazard. Mater. A120, 37-44","barium arsenate and barium hydrogen arsenate: G",https://doi.org/10.1016/j.jhazmat.2004.12.025
-electron,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",https://chnosz.net
+OBIGT06,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","non-zero entropy of the electron based on the hydrogen ion convention",https://chnosz.net
 ARHB06,"C. Akilan et al.",2006,"ChemPhysChem 7, 2319-2330",MgSO<sub>4</sub>,https://doi.org/10.1002/cphc.200600342
 AVZP06,"N. N. Akinfiev et al.",2006,"Geochem. Int. 44, 867-878",AgCl<sub>3</sub><sup>-2</sup>,https://doi.org/10.1134/S0016702906090035
 BL06,"A. V. Bandura and S. N. Lvov",2006,"J. Phys. Chem. Ref. Data 35, 15-30",OH<sup>-</sup>,https://doi.org/10.1063/1.1928231

Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd	2025-06-05 06:55:16 UTC (rev 919)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd	2025-06-05 08:35:13 UTC (rev 920)
@@ -257,7 +257,7 @@
 
 By convention, the standard Gibbs energy of formation, entropy, and heat capacity of the aqueous proton (H<sup>+</sup>) are 0 at all *T* and *P* ([e.g. Cox et al., 1989](https://www.worldcat.org/oclc/18559968)).
 The formation reaction of the proton can be expressed as &frac12;H<sub>2,(*g*)</sub> + Z = H<sup>+</sup>, where Z is the "element" of positive charge.
-Because the conventional standard Gibbs energy of this reaction is 0 at all *T*, the standard entropy of the reaction is also constrained to be zero (cf. Puigdomenech et al., 1997).
+Because the conventional standard Gibbs energy of this reaction is 0 at all *T*, the standard entropy of the reaction is also constrained to be zero (cf. Denbigh, 1981; Puigdomenech et al., 1997).
 Therefore, the "element" of positive charge (Z) has zero thermodynamic properties except for an entropy, *S*°<sub>*T*<sub>r</sub></sub>, that is negative one-half that of H<sub>2,(*g*)</sub>.
 The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by *e*<sup>-</sup> = -Z, is opposite that of Z.
 

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-05 06:55:16 UTC (rev 919)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-05 08:35:13 UTC (rev 920)
@@ -1362,6 +1362,16 @@
   doi       = {10.1127/0935-1221/2010/0022-2021},
 }
 
+ at Book{Den81,
+  author    = {Denbigh, Kenneth},
+  publisher = {Cambridge University Press},
+  title     = {The Principles of Chemical Equilibrium},
+  year      = {1981},
+  address   = {Cambridge},
+  edition   = {4th},
+  doi       = {10.1017/CBO9781139167604},
+}
+
 @Article{AKAE19,
   author    = {M.R. Azadi and A. Karrech and M. Attar and M. Elchalakani},
   journal   = {Fluid Phase Equilibria},
@@ -1638,22 +1648,12 @@
   url         = {https://thermoddem.brgm.fr/page/brgm-reports},
 }
 
- at TechReport{electron,
-  author      = {OBIGT},
-  institution = {OBIGT database in CHNOSZ},
-  title       = {Non-zero entropy of the electron based on the hydrogen-ion convention},
-  year        = {2006},
-  note        = {Because the standard thermodynamic properties of the formation reaction of H+ (0.5H2(g) = H+ + e-) are defined to be zero, the standard entropy of e- is half that of H2(g).},
+ at TechReport{OBIGT06,
+  author    = {{OBIGT database in CHNOSZ}},
+  title     = {The standard entropy of \emph{e}\textsuperscript{-} is assigned to be half that of {H}\textsubscript{2}(g) as implied by the hydrogen ion convention},
+  year      = {2006},
 }
 
- at TechReport{proton,
-  author      = {OBIGT},
-  institution = {OBIGT database in CHNOSZ},
-  title       = {Hydrogen-ion convention},
-  year        = {1997},
-  note        = {"The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature" [@JOH92]},
-}
-
 
 
 @Article{ARHB06,
@@ -2141,10 +2141,9 @@
 }
 
 @TechReport{OBIGT25,
-  author    = {OBIGT},
-  title     = {Corrected {Δ\emph{H}}°\textsubscript{f} by -7335 cal/mol to maintain {GHS} consistency for {In}\textsuperscript{+3} and derived species},
+  author    = {{OBIGT database in CHNOSZ}},
+  title     = {Corrected {Δ\emph{H}}°\textsubscript{\emph{f}} by -7335 cal/mol to maintain {GHS} consistency for {In}\textsuperscript{+3} and derived species},
   year      = {2025},
-  school    = {OBIGT database in CHNOSZ},
 }
 
 @Article{Shv08,

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