diff --git a/DESCRIPTION b/DESCRIPTION index fdc7250..36f9f9e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ -Date: 2025-01-08 +Date: 2025-01-17 Package: CHNOSZ -Version: 2.1.0-39 +Version: 2.1.0-40 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 a40c727..9658474 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 2.1.0-39 (2025-01-08)}{ +\section{Changes in CHNOSZ version 2.1.0-40 (2025-01-17)}{ \subsection{OBIGT DEFAULT DATA}{ \itemize{ @@ -36,15 +36,16 @@ \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 Add Sn chloride complexes and updated parameters for Sn\S{+2}, + Th\S{+4} 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). - \item \file{inorganic_cr.csv}: Add cerianite (CeO\s{2}) and - chromite (FeCr\s{2}O\s{4}) from + \item \file{inorganic_cr.csv}: Add cerianite (CeO\s{2}), chromite + (FeCr\s{2}O\s{4}), and cassiterite (SnO\s{2}) from \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}. \item Restore steam (H\s{2}O,g) in \file{inorganic_gas.csv}. @@ -83,10 +84,11 @@ \subsection{OTHER CHANGES}{ \itemize{ - \item \code{OBIGT} now lists \samp{CGL_Ttr} in \code{model} for species - whose \code{T} value denotes a phase stability limit (as opposed to a Cp - equation limit). This replaces the (overloaded) use of signed values of - \code{T}. + \item \code{OBIGT} now uses \samp{CGL_Ttr} as the \code{model} for + species whose \code{T} value denotes a phase stability limit above which + \code{subcrt()} returns NA values (in contrast to \samp{CGL}, for which + the value of \code{T} is a Cp equation limit that only produces a + warning). This replaces the use of signed values of \code{T}. \item \code{check.EOS()} now uses values of Born coefficients \emph{X} and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending diff --git a/inst/extdata/OBIGT/SLOP98.csv b/inst/extdata/OBIGT/SLOP98.csv index aa9a1a3..a7f38e6 100644 --- a/inst/extdata/OBIGT/SLOP98.csv +++ b/inst/extdata/OBIGT/SLOP98.csv @@ -148,3 +148,5 @@ PdCl2,PdCl2,PdCl2,aq,SS98a.3,NA,2015-08-16,HKF,cal,-34080,-51390,4.2,37.8,32.4,6 PdCl3-,PdCl3-,PdCl3-,aq,SS98a.3,NA,2015-08-16,HKF,cal,-68390,-98890,2.5,44.6,62.9,10.9057,18.8497,-1.6645,-3.5581,46.9452,6.0491,1.5895,-1 PdCl4-2,PdCl4-2,PdCl4-2,aq,SS98a.3,NA,2015-08-16,HKF,cal,-102130,-149470,-11.7,41.4,96.8,16.1552,31.6662,-6.698,-4.088,61.6845,5.4024,3.3914,-2 CoCl+,CoCl+,CoCl+,aq,SSH97,NA,2007-10-16,HKF,cal,-45157,-53965,-11.27,17.02,-1.5,1.8028,-3.3766,7.0702,-2.6394,22.7656,0.4323,0.7191,1 +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 +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 diff --git a/inst/extdata/OBIGT/SUPCRT92.csv b/inst/extdata/OBIGT/SUPCRT92.csv index cbc8bfc..870f4df 100644 --- a/inst/extdata/OBIGT/SUPCRT92.csv +++ b/inst/extdata/OBIGT/SUPCRT92.csv @@ -31,6 +31,7 @@ brucite,Brc,Mg(OH)2,cr,HDNB78,NA,1978-05-05,CGL,cal,-199646,-221390,15.09,NA,24. Ca-Al-pyroxene,Ca-Al-Px,CaAl(AlSi)O6,cr,HDNB78,SPRONS92.2,1990-03-15,CGL,cal,-742067,-783793,35,NA,63.5,54.13,0.00642,-1490000,0,0,0,0,1400 Ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr,HDNB78,NA,1978-05-05,CGL,cal,NA,NA,166.6,NA,265,145.82,0.05267,-1913000,0,0,0,0,848 Ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr2,HDNB78,OBIGT.1,1978-05-05,CGL,cal,-3.895,NA,165.3767,NA,265,149.01,0.04641,-1643000,0,0,0,0,1000 +cassiterite,Cst,SnO2,cr,JH85,RH95.7,1978-05-05,CGL_Ttr,cal,-124260,-138800,12.5,NA,21.55,17.246,0.0028026,-490010,0,0,0,0,1903 calcite,Cal,CaCO3,cr,HDNB78,PB82,1990-03-09,CGL,cal,-269880,-288552,22.15,NA,36.934,24.98,0.00524,-620000,0,0,0,0,1200 celadonite,Cln,K(MgAl)Si4O10(OH)2,cr,HDNB78,NA,1978-05-05,CGL,cal,NA,NA,74.9,NA,157.1,80.25,0.0253,-1854000,0,0,0,0,1000 chabazite,Cbz,Ca(Al2Si4)O12*6H2O,cr,HDNB78,NA,1978-05-05,CGL,cal,NA,NA,152.9,NA,247.76,146,0.04447,-1643000,0,0,0,0,1000 diff --git a/inst/extdata/OBIGT/inorganic_aq.csv b/inst/extdata/OBIGT/inorganic_aq.csv index 6dc463f..6b3bd27 100644 --- a/inst/extdata/OBIGT/inorganic_aq.csv +++ b/inst/extdata/OBIGT/inorganic_aq.csv @@ -916,5 +916,5 @@ Sn+4,Sn+4,Sn+4,aq,LYX23,NA,2025-01-05,HKF,cal,600,-18083.8,-112.9,-56.12,-61.76, 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 +SnCl2,SnCl2,SnCl2,aq,LYX23,NA,2025-01-05,HKF,cal,-72232,-81852,33.2825,13.9082,37.0637,6.8239,8.8804,2.2598,-3.1461,13.9676,-0.2015,-0.038,0 +SnCl3-,SnCl3-,SnCl3-,aq,LYX23,NA,2025-01-05,HKF,cal,-103547,-121668,47.0481,4.2091,68.0292,11.3814,20.0081,-2.1139,-3.6061,17.0106,-2.1772,0.9093,-1 diff --git a/inst/extdata/OBIGT/inorganic_cr.csv b/inst/extdata/OBIGT/inorganic_cr.csv index 7adfb4d..da6bb7b 100644 --- a/inst/extdata/OBIGT/inorganic_cr.csv +++ b/inst/extdata/OBIGT/inorganic_cr.csv @@ -64,7 +64,6 @@ sylvite,Sy,KCl,cr,HDNB78,NA,1978-05-05,CGL_Ttr,cal,-97735,-104370,19.73,NA,37.52 tenorite,Tn,CuO,cr,HDNB78,NA,1978-05-05,CGL,cal,-30568,-37200,10.18,NA,12.22,11.53,0.00188,-176000,0,0,0,0,1600 wurtzite,Wur,ZnS,cr,HDNB78,NA,1978-05-05,CGL,cal,-44810,-45850,14.064,NA,23.846,11.82,0.00116,-104000,0,0,0,0,1300 berndtite,Brn,SnS2,cr,JH85,NA,1978-05-05,CGL,cal,-34750,-36700,20.9,NA,40.96,15.51,0.0042,0,0,0,0,0,1000 -cassiterite,Cst,SnO2,cr,JH85,RH95.7,1978-05-05,CGL_Ttr,cal,-124260,-138800,12.5,NA,21.55,17.246,0.0028026,-490010,0,0,0,0,1903 romarchite,Sn-Ox,SnO,cr,JH85,NA,1978-05-05,CGL,cal,-61459,-68340,13.66,NA,20.895,9.55,0.0035,0,0,0,0,0,1237 tin,Sn,Sn,cr,JH85,NA,1985-08-00,CGL,cal,0,0,12.24,NA,16.289,4.42,0.0063,0,0,0,0,0,505.06 tin,Sn,Sn,cr2,JH85,OBIGT.1,1985-08-00,CGL,cal,679.802,1607.605,15.3519,NA,16.289,7.3,0,0,0,0,0,0,3000 @@ -160,3 +159,4 @@ beta-UO2(OH)2,Sho,UO2(OH)2,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-1398683,-1533800,13 Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL_Ttr,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 +cassiterite,Cst,SnO2,cr,RH95,NA,2025-01-17,CGL_Ttr,J,-515800,-577600,49.02,53.22,21.55,76.04,0.007364,-2224000,0,0,0,0,1903 diff --git a/inst/extdata/misc/OBIGT_check.csv b/inst/extdata/misc/OBIGT_check.csv index 8f5d3bb..df6a6bb 100644 --- a/inst/extdata/misc/OBIGT_check.csv +++ b/inst/extdata/misc/OBIGT_check.csv @@ -135,7 +135,6 @@ "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, @@ -392,6 +391,7 @@ "SLOP98","MnAsO4-","aq","cal",-1.45,, "SLOP98","AmCrO4+2","aq","cal",,,-4654 "SLOP98","PdCl4-2","aq","cal",,-1.05, +"SLOP98","Th+4","aq","cal",,-1.14, "SUPCRT92","almandine","cr","cal",4.43,, "SUPCRT92","antigorite","cr","cal",,,812 "SUPCRT92","clinochlore,7A","cr","cal",,,666 diff --git a/inst/extdata/thermo/refs.csv b/inst/extdata/thermo/refs.csv index c73f596..e80d8bf 100644 --- a/inst/extdata/thermo/refs.csv +++ b/inst/extdata/thermo/refs.csv @@ -64,7 +64,7 @@ OC95,"P. A. G. O'Hare and L. A. Curtiss",1995,"J. Chem. Thermodynamics 27, 643-6 HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255 PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964 -RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bixbyite, cattierite, cerianite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, zinc",https://doi.org/10.3133/b2131 +RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bixbyite, cassiterite, cattierite, cerianite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, zinc",https://doi.org/10.3133/b2131 RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://doi.org/10.3133/b2131 RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://doi.org/10.3133/b2131 RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, halloysite, pyrope: GHS and Cp at 25 °C",https://doi.org/10.3133/b2131 diff --git a/inst/extdata/thermo/stoich.csv.xz b/inst/extdata/thermo/stoich.csv.xz index 0006aa6..573d25f 100644 Binary files a/inst/extdata/thermo/stoich.csv.xz and b/inst/extdata/thermo/stoich.csv.xz differ