diff --git a/DESCRIPTION b/DESCRIPTION index 5b8c604..e65615f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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@R: c( person("Jeffrey", "Dick", , "j3ffdick@gmail.com", role = c("aut", "cre"), diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 789ff99..41ad3ba 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -15,7 +15,7 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{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. diff --git a/inst/extdata/OBIGT/inorganic_aq.csv b/inst/extdata/OBIGT/inorganic_aq.csv index 7a3ce18..6dc463f 100644 --- a/inst/extdata/OBIGT/inorganic_aq.csv +++ b/inst/extdata/OBIGT/inorganic_aq.csv @@ -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 @@ -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 @@ -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 diff --git a/inst/extdata/misc/OBIGT_check.csv b/inst/extdata/misc/OBIGT_check.csv index be13d75..8f5d3bb 100644 --- a/inst/extdata/misc/OBIGT_check.csv +++ b/inst/extdata/misc/OBIGT_check.csv @@ -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, diff --git a/inst/extdata/thermo/refs.csv b/inst/extdata/thermo/refs.csv index 24a7e2e..c73f596 100644 --- a/inst/extdata/thermo/refs.csv +++ b/inst/extdata/thermo/refs.csv @@ -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+3 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+2 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+2 and Th+4 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)2- and Ag(HS)2-",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",HSiO3-,https://doi.org/10.1016/S0016-7037(97)00009-4 @@ -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+ and CuO-",https://doi.org/10.1134/S1075701523010026 +LYX23,"X. Liu, P. Yu and C. Xiao",2023,"Geosci. Front. 14, 101624","Sn+2, Th+4, 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)2-MgCl2-H2O phases",https://doi.org/10.1016/j.apgeochem.2024.106032 diff --git a/inst/extdata/thermo/stoich.csv.xz b/inst/extdata/thermo/stoich.csv.xz index 67bf76d..0006aa6 100644 Binary files a/inst/extdata/thermo/stoich.csv.xz and b/inst/extdata/thermo/stoich.csv.xz differ diff --git a/vignettes/OBIGT.bib b/vignettes/OBIGT.bib index 3a654b8..7daf644 100644 --- a/vignettes/OBIGT.bib +++ b/vignettes/OBIGT.bib @@ -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},