[CHNOSZ-commits] r922 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/thermo vignettes

Fri Jun 6 05:14:10 CEST 2025

Author: jedick
Date: 2025-06-06 05:14:09 +0200 (Fri, 06 Jun 2025)
New Revision: 922

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/OBIGT.bib
Log:
OBIGT: Add Fe-bearing serpentinization-relevant minerals from Leong and Shock (2020)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2025-06-05 21:56:45 UTC (rev 921)
+++ pkg/CHNOSZ/DESCRIPTION	2025-06-06 03:14:09 UTC (rev 922)
@@ -1,6 +1,6 @@
 Date: 2025-06-06
 Package: CHNOSZ
-Version: 2.1.0-93
+Version: 2.1.0-94
 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 21:56:45 UTC (rev 921)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-06-06 03:14:09 UTC (rev 922)
@@ -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 2.1.0-92 (2025-06-05)}{
+\section{Changes in CHNOSZ version 2.1.0-94 (2025-06-06)}{
 
   \subsection{OBIGT DATABASE FORMAT}{
     \itemize{
@@ -67,6 +67,11 @@
       Th\S{+4} from \href{https://doi.org/10.1016/j.gsf.2023.101624}{Liu et al.
         (2023)}.
 
+      \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
+        Shock (2020)}.
+
       \item Add REE minerals from the compilation of
       \href{https://doi.org/10.1016/j.chemgeo.2016.06.005}{Migdisov et al.
         (2016)} with modifications.

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2025-06-05 21:56:45 UTC (rev 921)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2025-06-06 03:14:09 UTC (rev 922)
@@ -258,3 +258,9 @@
 Co(OH)2,Co(OH)2,Co(OH)2,cr,SB99,Shv08,2021-07-07,CGL,J,-455661,NA,84,,24.74,96.912,0.014076,-987500,0,0,0,0,1500
 CoSO4,CoSO4,CoSO4,cr,NRK74,NA,2021-07-07,CGL,cal,-187310,-212560,28.1,24.67,360,30.1,0.00992,0,0,0,0,0,1200
 spherocobaltite,Scbt,CoCO3,cr,BKK77,NA,2021-07-07,CGL,cal,NA,-170000,21.18,19.936,28.22,22,0.0093,-430000,0,0,0,0,800
+"ferrous hydroxide",OH-Fe,Fe(OH)2,cr,LS20,NA,2025-06-06,CGL,cal,-117730,-137340,21,21.3,26,26.06,0.00435,-538000,0,0,0,0,1000
+ferrotremolite,Tr-Fe,Ca2Fe5Si8O22(OH)2,cr,LS20,NA,2025-06-06,CGL,cal,-2349100,-2511300,163.5,169.2,283,197.93,0.05895,-4117000,0,0,0,0,1000
+greenalite,Gre,Fe3Si2O5(OH)4,cr,LS20,NA,2025-06-06,CGL,cal,-716530,-787810,72.6,74.1,115,81.65,0.0326,-1539000,0,0,0,0,1000
+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

Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-05 21:56:45 UTC (rev 921)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-06-06 03:14:09 UTC (rev 922)
@@ -309,7 +309,8 @@
 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-Ta<sub>2</sub>O<sub>5</sub>",https://doi.org/10.1016/j.gca.2020.04.009
 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
-LX20,"Liu and Xiao",2020,"Ore Geol. Rev. 117, 103289","huebnerite Cp",https://doi.org/10.1016/j.oregeorev.2019.103289
+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
 NEA20.1,"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

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

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-05 21:56:45 UTC (rev 921)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2025-06-06 03:14:09 UTC (rev 922)
@@ -662,7 +662,7 @@
 @Article{RH98,
   author    = {Richard, Laurent and Helgeson, Harold C.},
   journal   = {Geochimica et Cosmochimica Acta},
-  title     = {{C}alculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest},
+  title     = {Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest},
   year      = {1998},
   number    = {23-24},
   pages     = {3591--3636},
@@ -1626,6 +1626,17 @@
   doi       = {10.1016/j.oregeorev.2019.103289},
 }
 
+ at Article{LS20,
+  author    = {Leong, James Andrew M. and Shock, Everett L.},
+  journal   = {American Journal of Science},
+  title     = {Thermodynamic constraints on the geochemistry of low-temperature, continental, serpentinization-generated fluids},
+  year      = {2020},
+  number    = {3},
+  pages     = {185--235},
+  volume    = {320},
+  doi       = {10.2475/03.2020.01},
+}
+
 @Book{NRK74,
   author    = {Naumov, Georgii Borisovich and Ryzhenko, Boris Nikolaevich and Khodakovsky, Igor L'vovich},
   editor    = {Ivan Barnes and Velma Speltz},

