[CHNOSZ-commits] r855 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Dec 23 11:30:11 CET 2024 

Author: jedick
Date: 2024-12-23 11:30:11 +0100 (Mon, 23 Dec 2024)
New Revision: 855

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Add Mg(OH)2-MgCl2-H2O phases from Knight et al. (2024)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2024-12-23 09:49:41 UTC (rev 854)
+++ pkg/CHNOSZ/DESCRIPTION	2024-12-23 10:30:11 UTC (rev 855)
@@ -1,6 +1,6 @@
 Date: 2024-12-23
 Package: CHNOSZ
-Version: 2.1.0-27
+Version: 2.1.0-28
 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	2024-12-23 09:49:41 UTC (rev 854)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2024-12-23 10:30:11 UTC (rev 855)
@@ -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 2.1.0-26 (2024-12-01)}{
+\section{Changes in CHNOSZ version 2.1.0-28 (2024-12-23)}{
 
     \itemize{
 
@@ -87,6 +87,10 @@
       example of the new formatting is log \emph{f}O\s{2}). Similar formatting
       for other expressions has been used in the vignettes.
 
+      \item OBIGT: Add Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
+      \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
+        (2024)}.
+
     }
 
 }

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv	2024-12-23 09:49:41 UTC (rev 854)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv	2024-12-23 10:30:11 UTC (rev 855)
@@ -8,7 +8,6 @@
 anorthite,An,Al2CaSi2O8,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 anthophyllite,Ath,Mg7Si8O24H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 antigorite,Atg,Mg48Si34O99H62O48,cr,Ber88,BDat17.1,2017-10-09,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-brucite,Brc,MgO2H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 Ca-Al-pyroxene,CTs,CaAl2SiO6,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 calcite,Cal,CaCO3,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 chrysotile,Ctl,Mg3Si2O9H4,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2024-12-23 09:49:41 UTC (rev 854)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2024-12-23 10:30:11 UTC (rev 855)
@@ -160,3 +160,10 @@
 Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL,J,-3011454,-3203800,275.9,227.3,0,262.83,0.014653,-3549000,0,0,0,0,1273
 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
 cerianite,Cei,CeO2,cr,RH95,NA,2024-05-23,CGL,J,-1024600,-1088700,62.3,61.63,23.85,80.29,0.005699,-729400,-209.9,0,0,0,-1800
+brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000
+bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000
+"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000
+"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000
+"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000
+"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000
+"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2024-12-23 09:49:41 UTC (rev 854)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2024-12-23 10:30:11 UTC (rev 855)
@@ -67,6 +67,7 @@
 RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://doi.org/10.3133/b2131
 RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (melting temperature and G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
 RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","phase stability limit",https://doi.org/10.3133/b2131
+RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","brucite V",https://doi.org/10.3133/b2131
 SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
 Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
 DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,https://doi.org/10.1016/0016-7037(95)00403-3
@@ -285,16 +286,18 @@
 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
 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
 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
 WV22,"A. E. Williams-Jones and O. V. Vasyukova",2022,"Econ. Geol. 117, 513-528","parameters listed here",https://doi.org/10.5382/econgeo.4895
-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
+HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93",carrollite,https://doi.org/10.3749/2300028
+KBJ24,"A. W. Knight, C. R. Bryan and C. F. Jové-Colón",2024,"Appl. Geochem. 169, 106032","Mg(OH)<sub>2</sub>-MgCl<sub>2</sub>-H<sub>2</sub>O phases",https://doi.org/10.1016/j.apgeochem.2024.106032
 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/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2024-12-23 09:49:41 UTC (rev 854)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2024-12-23 10:30:11 UTC (rev 855)
@@ -310,6 +310,7 @@
 "OBIGT","ferberite","cr","J",1.21,,
 "OBIGT","willemite","cr","J",-1.47,,
 "OBIGT","rutherfordine","cr","J",-14.37,,
+"OBIGT","2-1-4 phase","cr","J",-4.39,,
 "OBIGT","octadecane","cr","cal",-2.63,,
 "OBIGT","nonadecane","cr","cal",-13.32,,
 "OBIGT","eicosane","cr","cal",-2.79,,

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

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2024-12-23 09:49:41 UTC (rev 854)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2024-12-23 10:30:11 UTC (rev 855)
@@ -1837,6 +1837,16 @@
   doi       = {10.1016/j.gca.2024.04.023},
 }
 
+ at Article{KBJ24,
+  author    = {Andrew W. Knight and Charles R. Bryan and Carlos F. Jové-Colón},
+  journal   = {Applied Geochemistry},
+  title     = {Development of a consistent geochemical model of the {Mg(OH)\textsubscript{2}}–{MgCl\textsubscript{2}}–{H\textsubscript{2}O} system from 25º{C} to 120º{C}},
+  year      = {2024},
+  pages     = {106032},
+  volume    = {169},
+  doi       = {10.1016/j.apgeochem.2024.106032},
+}
+
 @Article{RH72,
   author    = {Robie, Richard A. and Hemingway, Bruce S.},
   journal   = {American Mineralogist},

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