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OBIGT: Add Sn+2, Th+4, and Sn chloride complexes from Liu et al. (2023)
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git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@865 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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jedick committed Jan 5, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Date: 2024-12-29
Package: CHNOSZ
Version: 2.1.0-36
Version: 2.1.0-37
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors@R: c(
person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),
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9 changes: 6 additions & 3 deletions inst/NEWS.Rd
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\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{&Delta;<I>G</I>&deg;}}{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{
Expand All @@ -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).
Expand All @@ -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.
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8 changes: 6 additions & 2 deletions inst/extdata/OBIGT/inorganic_aq.csv
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Expand Up @@ -431,7 +431,6 @@ Mn+2,Mn+2,Mn+2,aq,SSWS97,NA,1997-11-07,HKF,cal,-55100,-52900,-16.2,-4.1,-17.1,-0
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
Expand All @@ -442,7 +441,6 @@ CN-,CN-,CN-,aq,SSWS97,NA,1997-11-11,HKF,cal,41200,36000,22.5,-17.7,23.9,5.4714,5
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
Expand Down Expand Up @@ -914,3 +912,9 @@ UO2(CO3)2-2,UO2(CO3)2-2,UO2(CO3)2-2,aq,MBA+24,NA,2024-04-23,HKF,cal,-502825,-564
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
4 changes: 3 additions & 1 deletion inst/extdata/misc/OBIGT_check.csv
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Expand Up @@ -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,
Expand Down Expand Up @@ -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,
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2 changes: 2 additions & 0 deletions inst/extdata/thermo/refs.csv
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Expand Up @@ -92,6 +92,7 @@ SSWS97.2,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61,
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
Expand Down Expand Up @@ -304,6 +305,7 @@ LXW21.1,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","scheelite
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
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12 changes: 12 additions & 0 deletions vignettes/OBIGT.bib
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Expand Up @@ -1825,6 +1825,18 @@ @Book{PMW87
url = {https://www.worldcat.org/oclc/16131757},
}

@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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