[CHNOSZ-commits] r865 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/misc inst/extdata/thermo vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Jan 5 12:12:31 CET 2025 

Author: jedick
Date: 2025-01-05 12:12:30 +0100 (Sun, 05 Jan 2025)
New Revision: 865

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
   pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv
   pkg/CHNOSZ/inst/extdata/thermo/refs.csv
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
OBIGT: Add Sn+2, Th+4, and Sn chloride complexes from Liu et al. (2023)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2024-12-29 11:54:41 UTC (rev 864)
+++ pkg/CHNOSZ/DESCRIPTION	2025-01-05 11:12:30 UTC (rev 865)
@@ -1,6 +1,6 @@
 Date: 2024-12-29
 Package: CHNOSZ
-Version: 2.1.0-36
+Version: 2.1.0-37
 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	2024-12-29 11:54:41 UTC (rev 864)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-01-05 11:12:30 UTC (rev 865)
@@ -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 2.1.0-36 (2024-12-29)}{
+\section{Changes in CHNOSZ version 2.1.0-37 (2025-01-05)}{
 
   \subsection{OBIGT DEFAULT DATA}{
     \itemize{
@@ -36,6 +36,9 @@
       \item Add tantalum species from
       \href{https://doi.org/10.1016/j.gca.2024.10.019}{Hu et al. (2024)}.
 
+      \item Add Sn\S{+2}, Th\S{+4}, and Sn chloride complexes from
+      \href{https://doi.org/10.1016/j.gsf.2023.101624}{Liu et al. (2023)}.
+
       \item Move americium complexes from \file{SLOP98.csv} back to
       \file{inorganic_aq.csv} (entropy of the element Am has been available for
       checking GHS self-consistency since version 1.4.0).
@@ -56,8 +59,8 @@
     \itemize{
 
       \item Make new directory \file{OBIGT/testing} to hold optional data files
-      for testing, including \file{SiO2.csv} and \file{GEMSFIT.csv} in addition
-      to those listed below.
+      for testing, including \file{SiO2.csv} (renamed from \file{AS04.csv}) and
+      \file{GEMSFIT.csv} in addition to those listed below.
 
       \item Add \file{testing/IGEM.csv}: Au and Cu complexes and
       SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS.

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv	2024-12-29 11:54:41 UTC (rev 864)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv	2025-01-05 11:12:30 UTC (rev 865)
@@ -431,7 +431,6 @@
 Co+2,Co+2,Co+2,aq,SSWS97,SH88.1,1997-11-07,HKF,cal,-13000,-13900,-27,-7.8,-25.5,-1.2252,-8.9356,5.3191,-2.4095,15.2013,-4.6234,1.4769,2
 Cr+3,Cr+3,Cr+3,aq,SSWS97,NA,1997-11-07,HKF,cal,-49300,-60000,-77,-22.9,-40,-2.7824,-14.5709,11.4661,-2.1765,17.9914,-7.6992,2.7403,3
 UO2+2,UO2+2,UO2+2,aq,SSWS97,NA,1997-11-07,HKF,cal,-227680,-243550,-23.5,10.2,5.73,3.0256,-4.1084,15.3326,-2.6091,21.07,0.43,1.4099,2
-Th+4,Th+4,Th+4,aq,SSWS97,NA,1997-11-07,HKF,cal,-168500,-183800,-101,-0.2,-53.4,-4.2886,-18.25,12.9154,-2.0244,40.2222,-3.0752,3.7093,4
 Fr+,Fr+,Fr+,aq,SSWS97,NA,1997-11-11,HKF,cal,-70500,-62500,35.1,-6.5,21.5,4.7139,3.7284,4.2849,-2.933,2.5442,-4.3586,0.0203,1
 Be+2,Be+2,Be+2,aq,SSWS97,NA,1997-11-11,HKF,cal,-90550,-91500,-32.1,-5.8,-20.9,-0.5718,-9.1742,9.3462,-2.3996,17.0245,-4.216,1.5475,2
 Ra+2,Ra+2,Ra+2,aq,SSWS97,NA,1997-11-11,HKF,cal,-134200,-126100,12.9,-14.3,-12.3,0.374,-6.8598,8.4279,-2.4953,5.7496,-5.9474,0.8644,2
@@ -442,7 +441,6 @@
 OCN-,OCN-,OCN-,aq,SSWS97,NA,1997-11-11,HKF,cal,-23280,-34900,25.5,-15.8,26.12,5.7591,6.2815,3.279,-3.0386,8.3509,-6.253,1.2422,-1
 SCN-,SCN-,SCN-,aq,SSWS97,NA,1997-11-11,HKF,cal,22160,18270,34.5,-9.6,35.7,7.0244,9.3687,2.0708,-3.1662,10.7414,-4.99,1.1073,-1
 SeCN-,SeCN-,SeCN-,aq,SSWS97,NA,1997-11-11,HKF,cal,19500,18530,46.6,-2.7,49.68,8.8752,13.8922,0.2829,-3.3532,13.0877,-3.5845,0.923,-1
-Sn+2,Sn+2,Sn+2,aq,SSWS97,NA,1997-11-11,HKF,cal,-6570,-2100,-4,-15.5,-15.6,0.0094,-7.7516,8.781,-2.4584,7.416,-6.1919,1.1216,2
 HNO2,HNO2,HNO2,aq,SSWS97,NA,1997-11-11,HKF,cal,-12100,-28500,32.4,6.7,30.7,5.9151,6.659,3.1378,-3.0542,8.705,-1.6697,-0.1507,0
 HNO3,HNO3,HNO3,aq,SSWS97,NA,1997-11-11,HKF,cal,-24730,-45410,42.7,18,40.2,7.1623,9.7063,1.9367,-3.1802,13.8907,0.632,-0.3066,0
 N2O2-2,N2O2-2,N2O2-2,aq,SSWS97,NA,1997-11-11,HKF,cal,33200,-2590,6.6,-59.3,3.6,3.3102,0.2986,5.638,-2.7912,0.1067,-15.1139,3.1145,-2
@@ -914,3 +912,9 @@
 UO2(CO3)3-4,UO2(CO3)3-4,UO2(CO3)3-4,aq,MBA+24,NA,2024-04-23,HKF,cal,-635898,-741562,-6.14,-48.3,-4.53,3.3318,0.3538,5.6111,-2.7936,-59.7866,34.9856,6.4701,-4
 Ta(OH)3F3-,Ta(OH)3F3-,Ta(OH)3F3-,aq,HET+24,NA,2024-12-26,HKF,cal,-464794,NA,49.87,102.537,60.003,8.517,72.6759,-126.173,-6.85,94.3167,6.6323,0.5706,-1
 TaF7-2,TaF7-2,TaF7-2,aq,HET+24,NA,2024-12-26,HKF,cal,-585453,NA,46.13,-57.1404,60.309,4.4045,-109.973,371.972,0.8805,268.318,-150.173,3.3215,-2
+Sn+4,Sn+4,Sn+4,aq,LYX23,NA,2025-01-05,HKF,cal,600,-18083.8,-112.9,-56.12,-61.76,-5.3731,-20.9004,13.9648,-1.915,9.0585,-14.4665,3.884,4
+Th+4,Th+4,Th+4,aq,LYX23,SSWS97.6,2025-01-05,HKF,cal,-168500,-183800,-101,-53.54,-60.6,-5.2739,-20.6582,13.8696,-1.925,8.9637,-13.9401,3.7093,4
+Sn+2,Sn+2,Sn+2,aq,LYX23,SSWS97.6,2025-01-05,HKF,cal,-6570,-2100,-4,-11.14,-15.5584,0.0142,-7.7466,8.7948,-2.4588,9.9465,-5.3042,1.119,2
+SnCl+,SnCl+,SnCl+,aq,LYX23,NA,2025-01-05,HKF,cal,-39962,-41670,17.5442,8.7913,9.2717,3.1277,-0.1446,5.8069,-2.773,13.8796,-1.2438,0.278,1
+SnCl2,SnCl2,SnCl2,aq,LYX23,NA,2025-01-05,HKF,cal,-72232,-81852,32.2825,13.9082,37.0637,6.8239,8.8804,2.2598,-3.1461,13.9676,-0.2015,-0.038,0
+SnCl3-,SnCl3-,SnCl3-,aq,LYX23,NA,2025-01-05,HKF,cal,-103547,-121668,45.0481,4.2091,68.0292,11.3814,20.0081,-2.1139,-3.6061,17.0106,-2.1772,0.9093,-1

Modified: pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv	2024-12-29 11:54:41 UTC (rev 864)
+++ pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv	2025-01-05 11:12:30 UTC (rev 865)
@@ -43,7 +43,6 @@
 "OBIGT","WO4-2","aq","cal",,,19984
 "OBIGT","PO4-3","aq","cal",,-1.72,
 "OBIGT","UO2+2","aq","cal",-1.1,,
-"OBIGT","Th+4","aq","cal",,-1.14,
 "OBIGT","In+3","aq","cal",,,7335
 "OBIGT","P2O7-4","aq","cal",,-2.11,
 "OBIGT","HP2O7-3","aq","cal",,-1.42,
@@ -134,6 +133,9 @@
 "OBIGT","HTaO3F-","aq","cal",-1.15,-1.91,
 "OBIGT","UO2(CO3)3-4","aq","cal",,-1.98,
 "OBIGT","TaF7-2","aq","cal",-9.97,-4.13,
+"OBIGT","Sn+4","aq","cal",,-1.18,
+"OBIGT","Th+4","aq","cal",,-1.13,
+"OBIGT","SnCl3-","aq","cal",,,596
 "OBIGT","CH4","aq","cal",-2.61,,
 "OBIGT","hexane","aq","cal",1.43,3.21,
 "OBIGT","ethylene","aq","cal",6.12,-3.82,

Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2024-12-29 11:54:41 UTC (rev 864)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv	2025-01-05 11:12:30 UTC (rev 865)
@@ -92,6 +92,7 @@
 SSWS97.3,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","arsenate and arsenite species",https://doi.org/10.1016/S0016-7037(96)00339-0
 SSWS97.4,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Al<sup>+3</sup> and Al-hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0
 SSWS97.5,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Zn<sup>+2</sup> and Zn-hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0
+SSWS97.6,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Sn<sup>+2</sup> and Th<sup>+4</sup> GHS",https://doi.org/10.1016/S0016-7037(96)00339-0
 SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
 SSH97.1,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au(HS)<sub>2</sub><sup>-</sup> and Ag(HS)<sub>2</sub><sup>-</sup>",https://doi.org/10.1016/S0016-7037(97)00009-4
 SSH97.2,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412",HSiO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/S0016-7037(97)00009-4
@@ -304,6 +305,7 @@
 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
 BS23,"G. Boyer and E. Shock",2023,"The Complicator (prototype)","In (indium) complexes",https://doi.org/10.5281/zenodo.8206644
 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
+LYX23,"X. Liu, P. Yu and C. Xiao",2023,"Geosci. Front. 14, 101624","Sn<sup>+2</sup>, Th<sup>+4</sup>, and Sn chloride complexes",https://doi.org/10.1016/j.gsf.2023.101624
 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

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

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2024-12-29 11:54:41 UTC (rev 864)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2025-01-05 11:12:30 UTC (rev 865)
@@ -1825,6 +1825,18 @@
   url       = {https://www.worldcat.org/oclc/16131757},
 }
 
+ at Article{LYX23,
+  author    = {Xiangchong Liu and Pingping Yu and Changhao Xiao},
+  journal   = {Geoscience Frontiers},
+  title     = {Tin transport and cassiterite precipitation from hydrothermal fluids},
+  year      = {2023},
+  number    = {6},
+  pages     = {101624},
+  volume    = {14},
+  doi       = {10.1016/j.gsf.2023.101624},
+  issn      = {1674-9871},
+}
+
 @Article{TTA+23,
   author    = {Nikolay D. Trofimov and Boris R. Tagirov and Nikolay N. Akinfiev and Vladimir L. Reukov and Maximilian S. Nickolsky and Irina Yu. Nikolaeva and Maria E. Tarnopolskaya and Andrey A. Afanasyev},
   journal   = {Chemical Geology},

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