diff --git a/DESCRIPTION b/DESCRIPTION index 9cff1ca..3a7af9b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ -Date: 2024-04-17 +Date: 2024-05-15 Package: CHNOSZ -Version: 2.1.0-10 +Version: 2.1.0-11 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors@R: c( person("Jeffrey", "Dick", , "j3ffdick@gmail.com", role = c("aut", "cre"), diff --git a/R/util.data.R b/R/util.data.R index 2c5fb30..c101e75 100644 --- a/R/util.data.R +++ b/R/util.data.R @@ -297,7 +297,7 @@ check.OBIGT <- function() { DG[!isHKF] <- DG.cgl } # Put it all together - out <- data.frame(table = what, ispecies = 1:ntot, name = tdata$name, state = tdata$state, E_units = tdata$E_units, DCp = DCp, DV = DV, DG = DG) + out <- data.frame(table = what, name = tdata$name, state = tdata$state, E_units = tdata$E_units, DCp = DCp, DV = DV, DG = DG) return(out) } # Check default database (OBIGT) diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 23ea9bf..672b3ac 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 2.1.0-10 (2024-04-17)}{ +\section{Changes in CHNOSZ version 2.1.0-11 (2024-05-15)}{ \itemize{ @@ -30,6 +30,12 @@ \item \code{check.EOS()} now uses values of Born coefficients \emph{X} and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending on the \code{model} defined in OBIGT (HKF or DEW, respectively). + \item Add aqueous uranyl complexes from \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)} and related U-bearing minerals from \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}. + + \item Except for HUO\s{4}\S{-}, aqueous uranium species from \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} have been moved to \file{SLOP98.csv}. + + \item Remove \code{ispecies} from output of \code{check.OBIGT()} to avoid superfluous diffs. + } } diff --git a/inst/extdata/OBIGT/SLOP98.csv b/inst/extdata/OBIGT/SLOP98.csv index a3fe4ed..8fc6490 100644 --- a/inst/extdata/OBIGT/SLOP98.csv +++ b/inst/extdata/OBIGT/SLOP98.csv @@ -10,7 +10,9 @@ Pd+2,Pd+2,Pd+2,aq,SS98a.3,NA,1992-04-09,HKF,cal,42200,42540,-21.1,-5.7,-19.4,-0. Pt+2,Pt+2,Pt+2,aq,SS98a.3,NA,1992-04-09,HKF,cal,61600,60900,-23.6,-7,-21.7,-0.6648,-9.3985,9.4293,-2.3904,16.8028,-4.4624,1.6005,2 PdSO4,Pd(SO4),Pd(SO4),aq,SS98a.3,NA,1992-04-14,HKF,cal,-139000,-173450,-0.9,-20.1,4,2.3022,-2.1585,6.5951,-2.6897,-5.8662,-7.1207,-0.03,0 PdO,PdO,PdO,aq,SS98a.3,NA,1992-04-14,HKF,cal,-11500,-24320,-9.5,-4.7,-16.3,-0.4755,-8.9398,9.256,-2.4093,3.1356,-3.9919,-0.03,0 +PdOH+,Pd(OH)+,Pd(OH)+,aq,SS98a.3,NA,1995-07-13,HKF,cal,-13130,-24120,-3.4,12.8,-13.5,0.1226,-7.4741,8.6697,-2.4699,19.2537,-0.4271,0.6063,1 Pd(SO4)2-2,Pd(SO4)2-2,Pd(SO4)2-2,aq,SS98a.3,NA,1995-04-14,HKF,cal,-319640,-388900,19.2,-34.4,27.4,6.502,8.0916,2.5759,-3.1134,12.9271,-10.0418,2.9221,-2 +Pd(SO4)3-4,Pd(SO4)3-4,Pd(SO4)3-4,aq,SS98a.3,NA,1994-07-28,HKF,cal,-499900,-603950,39.4,-48.2,50.8,10.7074,18.3646,-1.4712,-3.5381,32.1909,-12.8528,5.891,-4 PtCl+,PtCl+,PtCl+,aq,SS98a.3,NA,1995-04-14,HKF,cal,18380,10030,-7,21.7,1.1,2.3363,-2.0793,6.5718,-2.6929,22.821,0.6543,0.6557,1 PtCl2,PtCl2,PtCl2,aq,SS98a.3,NA,1995-04-14,HKF,cal,-22290,-41110,0.1,39.2,27.3,5.8026,6.3859,3.2424,-3.0429,24.6982,3.5025,-0.03,0 PtCl3-,PtCl3-,PtCl3-,aq,SS98a.3,NA,1995-04-14,HKF,cal,-57760,-90150,-3.1,45.6,57.4,10.4995,17.8547,-1.2658,-3.517,42.0877,4.0842,1.6759,-1 @@ -20,8 +22,23 @@ Pt(SO4)2-2,Pt(SO4)2-2,Pt(SO4)2-2,aq,SS98a.3,NA,1995-04-14,HKF,cal,-300670,-37108 Pt(SO4)3-4,Pt(SO4)3-4,Pt(SO4)3-4,aq,SS98a.3,NA,1995-04-14,HKF,cal,-480380,-588630,36.3,-50.2,49.3,10.5204,17.906,-1.2876,-3.5191,31.4399,-13.2501,5.9335,-4 PtOH+,Pt(OH)+,Pt(OH)+,aq,SS98a.3,NA,1992-04-14,HKF,cal,1560,-10700,-6.7,16.6,-15,-0.0659,-7.935,8.8518,-2.4509,21.9365,0.3468,0.6557,1 PtO,PtO,PtO,aq,SS98a.3,NA,1992-04-14,HKF,cal,-1130,-15300,-13,-0.7,-17.9,-0.6945,-9.4705,9.4567,-2.3874,5.4799,-3.1771,-0.03,0 -PdOH+,Pd(OH)+,Pd(OH)+,aq,SS98a.3,NA,1995-07-13,HKF,cal,-13130,-24120,-3.4,12.8,-13.5,0.1226,-7.4741,8.6697,-2.4699,19.2537,-0.4271,0.6063,1 -Pd(SO4)3-4,Pd(SO4)3-4,Pd(SO4)3-4,aq,SS98a.3,NA,1994-07-28,HKF,cal,-499900,-603950,39.4,-48.2,50.8,10.7074,18.3646,-1.4712,-3.5381,32.1909,-12.8528,5.891,-4 +UOH+2,U(OH)+2,U(OH)+2,aq,SSB97,NA,1994-05-18,HKF,cal,-161800,-167700,1.2,-38.6,5.1,2.8136,-0.9087,6.1004,-2.7413,-6.8963,-10.8973,1.0376,2 +UO+,UO+,UO+,aq,SSB97,NA,1994-05-18,HKF,cal,-152900,-153900,17.5,-80.8,7.7,2.9158,-0.6648,6.0168,-2.7514,-38.0715,-19.3305,0.2873,1 +HUO2,HUO2,HUO2,aq,SSB97,NA,1994-05-18,HKF,cal,-198000,-205100,52.9,-144.6,24.9,5.1622,4.8252,3.8489,-2.9784,-78.8543,-32.4895,-0.03,0 +UO2-,NA,UO2-,aq,SSB97,NA,2007-10-11,HKF,cal,-183700,-193600,43.3,-123.7,22.5,5.1728,4.8473,3.8491,-2.9793,-57.3622,-28.2322,0.9733,-1 +U(OH)+3,U(OH)+3,U(OH)+3,aq,SSB97,NA,1994-05-18,HKF,cal,-182600,-198400,-47.8,17.3,-2.8,2.1611,-2.5064,6.739,-2.6753,37.5484,0.4894,2.3058,3 +UO+2,UO+2,UO+2,aq,SSB97,NA,2007-10-16,HKF,cal,-180600,-192100,-33.4,-22.7,-0.4,2.2403,-2.3083,6.6513,-2.6835,7.3127,-7.6585,1.5684,2 +HUO2+,HUO2+,HUO2+,aq,SSB97,NA,1994-05-18,HKF,cal,-233200,-254800,-11.4,2,8.9,3.2291,0.1055,5.7039,-2.7833,14.0517,-2.6271,0.7287,1 +UO2,UO2,UO2,aq,SSB97,NA,1994-03-28,HKF,cal,-233800,-259700,-26,19.1,5.2,2.4664,-1.7587,6.4404,-2.7062,17.084,0.8561,-0.03,0 +HUO3-,HUO3-,HUO3-,aq,SSB97,NA,1994-05-18,HKF,cal,-274100,-321200,-41.3,70.2,4.8,3.1824,-0.0092,5.7491,-2.7785,68.04,11.2651,2.2503,-1 +UO2OH,UO2OH,UO2OH,aq,SSB97,NA,1994-05-18,HKF,cal,-261600,-295900,-13.9,24.8,14.5,3.739,1.3467,5.2242,-2.8346,20.4246,2.0172,-0.03,0 +UO3-,UO3-,UO3-,aq,SSB97,NA,1994-05-18,HKF,cal,-236600,-272600,-19.5,6.7,12.6,4.1388,2.3272,4.8294,-2.8751,27.8024,-1.6697,1.9223,-1 +UO2OH+,UO2OH+,UO2OH+,aq,SSB97,NA,1994-05-18,HKF,cal,-277250,-301550,4.1,4.3,20.7,4.764,3.8529,4.2318,-2.9382,13.224,-2.1586,0.4925,1 +UO3,UO3(AQ),UO3,aq,SSB97,NA,1994-05-18,HKF,cal,-270300,-299600,-12.9,-0.8,14.8,3.7801,1.4512,5.1736,-2.8389,5.4213,-3.1975,-0.03,0 +HUO4-,HUO4-,HUO4-,aq,SSB97,NA,1994-05-18,HKF,cal,-314800,-362900,-20.2,22.1,18.4,4.9364,4.2748,4.0637,-2.9556,36.9351,1.4672,1.9339,-1 +UO4-2,UO4-2,UO4-2,aq,SSB97,NA,1994-05-18,HKF,cal,-296000,-346200,-27.1,-44.4,15.4,5.0964,4.6606,3.9223,-2.9716,13.513,-12.0788,3.6219,-2 +HNbO3,HNbO3,HNbO3,aq,SSWS97,NA,1995-03-15,HKF,cal,-236800,-257950,31.1,31.4,30,5.711,6.1642,3.3252,-3.0337,20.2299,3.3616,-0.471,0 +NbO3-,NbO3-,NbO3-,aq,SSWS97,NA,1997-11-13,HKF,cal,-227100,-255300,3.2,-41.1,20.4,5.0915,4.6485,3.9273,-2.9711,-3.3376,-11.4066,1.5829,-1 HCl,HCl,HCl,aq,MS97.2,SLOP98.11,1996-07-30,HKF,cal,-30410,-42054,3.2,NA,NA,1.2547,-4.7177,7.6043,-2.584,16.7134,2.8727,-0.7,0 ZnCl+,ZnCl+,ZnCl+,aq,SSH97.3,NA,1997-09-16,HKF,cal,-66850,-66240,23,19.9,-1.28,1.6583,-3.7293,7.2088,-2.6248,19.6947,1.0191,0.2025,1 ZnCl2,ZnCl2,ZnCl2,aq,SSH97.3,NA,1997-09-16,HKF,cal,-98300,-109080,27.03,34.7,24.82,5.1486,4.7929,3.8592,-2.9771,26.1528,4.0338,-0.038,0 @@ -169,5 +186,3 @@ 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 -HNbO3,HNbO3,HNbO3,aq,SSWS97,NA,1995-03-15,HKF,cal,-236800,-257950,31.1,31.4,30,5.711,6.1642,3.3252,-3.0337,20.2299,3.3616,-0.471,0 -NbO3-,NbO3-,NbO3-,aq,SSWS97,NA,1997-11-13,HKF,cal,-227100,-255300,3.2,-41.1,20.4,5.0915,4.6485,3.9273,-2.9711,-3.3376,-11.4066,1.5829,-1 diff --git a/inst/extdata/OBIGT/inorganic_aq.csv b/inst/extdata/OBIGT/inorganic_aq.csv index 5b72ae7..2b257b4 100644 --- a/inst/extdata/OBIGT/inorganic_aq.csv +++ b/inst/extdata/OBIGT/inorganic_aq.csv @@ -321,21 +321,6 @@ LuCO3+,NA,LuCO3+,aq,HSS95,SLOP98.10,1998-06-02,HKF,cal,-296900,-335420,-57.7,-58 LuSO4+,NA,LuSO4+,aq,HSS95,NA,2007-10-11,HKF,cal,-342200,-380630,-26.6,-53.7,-6.2,1.2811,-4.6503,7.5708,-2.5867,-16.5465,-13.9936,0.957,1 MgSO4,MgSO4,MgSO4,aq,MS97,SLOP98.11,1994-11-28,HKF,cal,-289477,-327367,-13.5,NA,NA,1.9369,-3.0547,6.9554,-2.6526,-6.839,-7.4589,-0.03,0 NaSO4-,NaSO4-,NaSO4-,aq,MS97,SLOP98.11,1994-11-28,HKF,cal,-241476,-273733,25.46,NA,NA,6.4638,8.0045,2.597,-3.1098,14.4928,-4.1182,1.2422,-1 -UOH+2,U(OH)+2,U(OH)+2,aq,SSB97,NA,1994-05-18,HKF,cal,-161800,-167700,1.2,-38.6,5.1,2.8136,-0.9087,6.1004,-2.7413,-6.8963,-10.8973,1.0376,2 -UO+,UO+,UO+,aq,SSB97,NA,1994-05-18,HKF,cal,-152900,-153900,17.5,-80.8,7.7,2.9158,-0.6648,6.0168,-2.7514,-38.0715,-19.3305,0.2873,1 -HUO2,HUO2,HUO2,aq,SSB97,NA,1994-05-18,HKF,cal,-198000,-205100,52.9,-144.6,24.9,5.1622,4.8252,3.8489,-2.9784,-78.8543,-32.4895,-0.03,0 -UO2-,NA,UO2-,aq,SSB97,NA,2007-10-11,HKF,cal,-183700,-193600,43.3,-123.7,22.5,5.1728,4.8473,3.8491,-2.9793,-57.3622,-28.2322,0.9733,-1 -U(OH)+3,U(OH)+3,U(OH)+3,aq,SSB97,NA,1994-05-18,HKF,cal,-182600,-198400,-47.8,17.3,-2.8,2.1611,-2.5064,6.739,-2.6753,37.5484,0.4894,2.3058,3 -UO+2,UO+2,UO+2,aq,SSB97,NA,2007-10-16,HKF,cal,-180600,-192100,-33.4,-22.7,-0.4,2.2403,-2.3083,6.6513,-2.6835,7.3127,-7.6585,1.5684,2 -HUO2+,HUO2+,HUO2+,aq,SSB97,NA,1994-05-18,HKF,cal,-233200,-254800,-11.4,2,8.9,3.2291,0.1055,5.7039,-2.7833,14.0517,-2.6271,0.7287,1 -UO2,UO2,UO2,aq,SSB97,NA,1994-03-28,HKF,cal,-233800,-259700,-26,19.1,5.2,2.4664,-1.7587,6.4404,-2.7062,17.084,0.8561,-0.03,0 -HUO3-,HUO3-,HUO3-,aq,SSB97,NA,1994-05-18,HKF,cal,-274100,-321200,-41.3,70.2,4.8,3.1824,-0.0092,5.7491,-2.7785,68.04,11.2651,2.2503,-1 -UO2OH,UO2OH,UO2OH,aq,SSB97,NA,1994-05-18,HKF,cal,-261600,-295900,-13.9,24.8,14.5,3.739,1.3467,5.2242,-2.8346,20.4246,2.0172,-0.03,0 -UO3-,UO3-,UO3-,aq,SSB97,NA,1994-05-18,HKF,cal,-236600,-272600,-19.5,6.7,12.6,4.1388,2.3272,4.8294,-2.8751,27.8024,-1.6697,1.9223,-1 -UO2OH+,UO2OH+,UO2OH+,aq,SSB97,NA,1994-05-18,HKF,cal,-277250,-301550,4.1,4.3,20.7,4.764,3.8529,4.2318,-2.9382,13.224,-2.1586,0.4925,1 -UO3,UO3(AQ),UO3,aq,SSB97,NA,1994-05-18,HKF,cal,-270300,-299600,-12.9,-0.8,14.8,3.7801,1.4512,5.1736,-2.8389,5.4213,-3.1975,-0.03,0 -HUO4-,HUO4-,HUO4-,aq,SSB97,NA,1994-05-18,HKF,cal,-314800,-362900,-20.2,22.1,18.4,4.9364,4.2748,4.0637,-2.9556,36.9351,1.4672,1.9339,-1 -UO4-2,UO4-2,UO4-2,aq,SSB97,NA,1994-05-18,HKF,cal,-296000,-346200,-27.1,-44.4,15.4,5.0964,4.6606,3.9223,-2.9716,13.513,-12.0788,3.6219,-2 NaCl,NaCl,NaCl,aq,SSH97,NA,1997-09-16,HKF,cal,-92910,-96160,28,8.5,24,5.0364,4.5189,3.9669,-2.9658,10.798,-1.3031,-0.038,0 PbCl+,PbCl+,PbCl+,aq,SSH97,NA,1997-09-16,HKF,cal,-39050,-38630,28,4.9,8.53,2.9756,-0.513,5.9446,-2.7577,10.2182,-2.0364,0.1281,1 PbCl2,PbCl2,PbCl2,aq,SSH97,NA,1997-09-16,HKF,cal,-71200,-77700,47,2,35.74,6.6429,8.4416,2.4251,-3.1279,6.9886,-2.6272,-0.038,0 @@ -879,3 +864,13 @@ TaOF3,NA,TaOF3,aq,AKK+20,NA,2021-03-20,HKF,cal,-353531,-365642,66.51,-11.173,-11 HNbO3F-,NA,HNbO3F-,aq,AKK+20,NA,2021-03-20,HKF,cal,-297901,-318676,68.03,-104.73,75.003,12.2344,22.0907,-2.9325,-3.6922,-50.4591,-24.311,0.5913,-1 HTaO3F-,NA,HTaO3F-,aq,AKK+20,NA,2021-03-20,HKF,cal,-296835,-300079,128.05,-148.17,86.4,14.0434,25.5077,-4.6685,-3.8748,-69.9033,-33.2161,1.3079,-1 H2WO4,NA,H2WO4,aq,LXW21,NA,2021-09-27,HKF,cal,-232653,-276736.39,-10.757,125.839,-114.547,-13.9096,-41.7437,22.1569,-1.0533,79.916,22.5989,0,0 +UO2OH+,UO2OH+,UO2OH+,aq,MBA+24,NA,2024-04-23,HKF,cal,-277188,-300762,6.48,77.91,20.7,4.7507,3.8183,4.2494,-2.9369,56.0019,12.8361,0.4531,1 +UO3,UO3,UO3,aq,MBA+24,NEA20.1,2024-04-23,HKF,cal,-267659,-292369,2.67,-0.8,14.8,3.7774,1.4418,5.1834,-2.8386,5.3475,-3.1975,-0.038,0 +HUO4-,HUO4-,HUO4-,aq,SSB97,NA,1994-05-18,HKF,cal,-314800,-362900,-20.2,22.1,18.4,4.9364,4.2748,4.0637,-2.9556,36.9351,1.4672,1.9339,-1 +UO2Cl+,UO2Cl+,UO2Cl+,aq,MBA+24,NA,2024-04-23,HKF,cal,-259342,-283192,-7.92,53.65,33.12,6.5237,8.1473,2.5479,-3.1158,43.792,7.8937,0.6712,1 +UO2Cl2,UO2Cl2,UO2Cl2,aq,MBA+24,NA,2024-04-23,HKF,cal,-289862,-317554,21.47,6.28,63.63,10.4596,17.7573,-1.2292,-3.5131,9.4946,-1.7562,-0.038,0 +UO2SO4,UO2SO4,UO2SO4,aq,MBA+24,NA,2024-04-23,HKF,cal,-410182,-460211,-1.04,109.16,21.21,4.6545,3.5834,4.3417,-2.9271,69.7926,19.2018,-0.038,0 +UO2(SO4)2-2,UO2(SO4)2-2,UO2(SO4)2-2,aq,MBA+24,NA,2024-04-23,HKF,cal,-589461,-673514,21.8,67.87,36.69,7.7597,11.165,1.3618,-3.2406,72.4911,10.7898,2.8819,-2 +UO2CO3,UO2CO3,UO2CO3,aq,MBA+24,NA,2024-04-23,HKF,cal,-367270,-403994,12.78,-59.3,2.31,2.0683,-2.7313,6.8236,-2.6661,-0.8475,-28.9369,-0.038,0 +UO2(CO3)2-2,UO2(CO3)2-2,UO2(CO3)2-2,aq,MBA+24,NA,2024-04-23,HKF,cal,-502825,-564657,34.72,-28.8,-1.11,2.521,-1.626,6.3892,-2.7118,-42.4375,18.8896,2.6863,-2 +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 diff --git a/inst/extdata/OBIGT/inorganic_cr.csv b/inst/extdata/OBIGT/inorganic_cr.csv index 814cebc..a6bc4e5 100644 --- a/inst/extdata/OBIGT/inorganic_cr.csv +++ b/inst/extdata/OBIGT/inorganic_cr.csv @@ -155,3 +155,6 @@ linnaeite,"tricobalt tetrasulfide",Co3S4,cr,PMW87,WV22,2024-02-05,CGL,J,-346347, cattierite,"cobalt disulfide",CoS2,cr,PMW87,WV22,2024-02-05,CGL,J,-147365,-153140,74.793,68.26,25.52,65.82,0.0303,-587000,0,0,0,0,-1223 carrollite,NA,Cu0.92Co2.07S4,cr,HDR+24,NA,2024-02-05,CGL,J,-331140,-344460,176.33,158.48,63.91,197.951,-0.0298,-2687000,0,0,0,0,377 carrollite,NA,Cu0.92Co2.07S4,cr2,HDR+24,NA,2024-02-05,CGL,J,-331157,-345026,174.49,NA,63.91,234.11,-0.18038,0,0,0,0,0,650 +rutherfordine,Rfd,UO2CO3,cr,NEA20,NA,2023-08-07,CGL,J,-1564701,-1691302,144.2,120.1,0,122.8563,0.04468312,-2706665,0,0,0,0,1273 +beta-UO2(OH)2,Sho,UO2(OH)2,cr,NEA20,NA,2023-08-07,CGL,J,-1398683,-1533800,138,141,0,41.8,0.2,3530000,0,0,0,0,1273 +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 diff --git a/inst/extdata/OBIGT/refs.csv b/inst/extdata/OBIGT/refs.csv index bb44c19..a912106 100644 --- a/inst/extdata/OBIGT/refs.csv +++ b/inst/extdata/OBIGT/refs.csv @@ -288,3 +288,6 @@ LXW21,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","H22(OH)2, and Na2U2O7",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","UO3",https://doi.org/10.1787/bf86a907-en +MBA+24,"A. Migdisov, E. Bastrakov et al.",2024,"Geochim. Cosmochim. Acta 62","uranyl-carbonate, -chloride, -sulfate, and -hydroxide complexes",https://doi.org/10.1016/j.gca.2024.04.023 diff --git a/inst/extdata/adds/OBIGT_check.csv b/inst/extdata/adds/OBIGT_check.csv index 7a28f90..fefaae1 100644 --- a/inst/extdata/adds/OBIGT_check.csv +++ b/inst/extdata/adds/OBIGT_check.csv @@ -1,372 +1,374 @@ -"table","ispecies","name","state","E_units","DCp","DV","DG" -"OBIGT",14,"CO3-2","aq","cal",,-1.04, -"OBIGT",20,"HPO4-2","aq","cal",,-1.02, -"OBIGT",26,"S2O3-2","aq","cal",,,939 -"OBIGT",48,"BO2-","aq","cal",,-19.31, -"OBIGT",60,"Cu+2","aq","cal",3.62,, -"OBIGT",64,"NH3","aq","cal",2.75,, -"OBIGT",73,"SO2","aq","cal",11.1,, -"OBIGT",91,"LaSO4+","aq","cal",-6.02,, -"OBIGT",107,"CeNO3+2","aq","cal",,,874 -"OBIGT",134,"NdF2+","aq","cal",16.64,6.19, -"OBIGT",180,"EuF+","aq","cal",4.11,-19.19, -"OBIGT",181,"EuF2","aq","cal",9.75,-40.4, -"OBIGT",182,"EuF3-","aq","cal",17.18,-64.45, -"OBIGT",183,"EuF4-2","aq","cal",26.07,-91.02, 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+"OBIGT","La(Oxal)+","aq","cal",,-1.87, +"OBIGT","Tb(Oxal)+","aq","cal",,-1.92, +"OBIGT","Er(Oxal)+","aq","cal",,-2.05, +"OBIGT","Lu(Oxal)+","aq","cal",,-2.19, +"OBIGT","Cr(Oxal)+","aq","cal",,-2.58, +"OBIGT","Ga(Oxal)+","aq","cal",,-2.66, +"OBIGT","Sc(Oxal)+","aq","cal",,-2.13, +"OBIGT","In(Oxal)+","aq","cal",,-2.19, +"OBIGT","Sm(Oxal)+","aq","cal",,-1.84, +"OBIGT","Cs(Mal)-","aq","cal",,-2.39, +"OBIGT","NH4(Mal)-","aq","cal",,-2.54, +"OBIGT","In(Mal)+","aq","cal",,-2.11, +"OBIGT","Y(Mal)+","aq","cal",,-2.02,29999 +"OBIGT","La(Succ)+","aq","cal",,-1.52, +"OBIGT","NH4(Succ)-","aq","cal",,-2.26, +"OBIGT","Fe(Succ)+","aq","cal",,-1.92, +"OBIGT","Sc(Succ)+","aq","cal",,-1.77, +"OBIGT","Sm(Succ)+","aq","cal",,-1.48, +"OBIGT","Er(Succ)+","aq","cal",,-1.68, +"OBIGT","U(Succ)+2","aq","cal",-1.15,-4.27, +"OBIGT","La(Glut)+","aq","cal",,-1.23, +"OBIGT","Y(Glut)+","aq","cal",,-1.46, +"OBIGT","Sc(Glut)+","aq","cal",,-1.5, +"OBIGT","Th(Glut)+2","aq","cal",-1.09,-4.05, +"OBIGT","Fe(Glut)+","aq","cal",,-1.05, +"OBIGT","Sm(Glut)+","aq","cal",,-1.2, +"OBIGT","Er(Glut)+","aq","cal",,-1.4,-4673 +"OBIGT","Ba(Adip)","aq","cal",,1.19, +"OBIGT","Pb(Adip)","aq","cal",,1.25, +"OBIGT","Sc(Adip)+","aq","cal",,-1.22, +"OBIGT","Th(Adip)+2","aq","cal",-1.02,-3.76, +"OBIGT","U(Adip)+2","aq","cal",-1,-3.71, +"OBIGT","Li(Oxal)-","aq","cal",,-3.3, +"OBIGT","Li(Succ)-","aq","cal",,-2.94, +"OBIGT","Na(Glut)-","aq","cal",,-2.34, +"OBIGT","K(Glut)-","aq","cal",,-2.05, +"OBIGT","Li(Glut)-","aq","cal",,-2.66, +"OBIGT","Na(Adip)-","aq","cal",,-2.05, +"OBIGT","K(Adip)-","aq","cal",,-1.76, +"OBIGT","Li(Adip)-","aq","cal",,-2.38, +"OBIGT","cyclohexane","aq","cal",9.35,6.64, +"OBIGT","benzene","aq","cal",,-1.14, +"OBIGT","ethanethiol","aq","cal",,,753 +"OBIGT","n-butanethiol","aq","cal",2.19,, +"OBIGT","guanine","aq","cal",-4.26,, +"OBIGT","dHUMP-","aq","cal",-3.13,, +"OBIGT","MgADP-","aq","cal",-1.01,, +"OBIGT","HNicMP(ox)","aq","cal",,9.4, +"OBIGT","ribose-5-phosphate","aq","cal",,7.48, +"OBIGT","ribose-5-phosphate-2","aq","cal",1.53,, +"OBIGT","H4NADP(red)","aq","cal",1.73,, +"OBIGT","H3NADP(red)-","aq","cal",2.41,, +"OBIGT","H2NADP(red)-2","aq","cal",1.28,, +"OBIGT","HNADP(red)-3","aq","cal",2.09,, +"OBIGT","NADP(red)-4","aq","cal",1.09,, +"OBIGT","H3NADP(ox)","aq","cal",1.05,, +"OBIGT","cysteinate","aq","cal",-1,, +"OBIGT","glucose","aq","cal",1.11,, +"OBIGT","methyldiethanolamine","aq","cal",1.61,, +"OBIGT","diglycine+","aq","cal",-177.69,, +"OBIGT","diglycine-","aq","cal",-49.22,,565 +"OBIGT","triglycine+","aq","cal",,1.75, +"OBIGT","triglycine-","aq","cal",,1.78, +"OBIGT","dimethylamine","aq","J",-8.05,, +"OBIGT","oleate","aq","J",,,39179 +"OBIGT","palmitoleate","aq","J",,,-242150 +"OBIGT","heptose","aq","J",,,-75027 +"OBIGT","N-acetylmuramic acid","aq","J",,,-38589 +"OBIGT","ethanolamine","aq","J",,,4598 +"OBIGT","alaninate","aq","cal",1.89,, +"OBIGT","histidinate","aq","cal",2.52,, +"OBIGT","isoleucinate","aq","cal",1.61,, +"OBIGT","methionate","aq","cal",2.42,, +"OBIGT","prolinate","aq","cal",1.73,, +"OBIGT","serinate","aq","cal",2.92,, +"OBIGT","threonate","aq","cal",1.97,, +"OBIGT","tryptophanate","aq","cal",,,2998 +"OBIGT","valinate","aq","cal",2.06,, +"OBIGT","hydromagnesite","cr","cal",,,-2569 +"OBIGT","jarosite","cr","cal",,,20697 +"OBIGT","natrojarosite","cr","cal",,,17554 +"OBIGT","realgar,alpha","cr","J",,,768 +"OBIGT","realgar,beta","cr","J",,,989 +"OBIGT","orpiment","cr","J",,,-1036 +"OBIGT","dawsonite","cr","J",,,19466 +"OBIGT","ferberite","cr","J",1.21,, +"OBIGT","willemite","cr","J",-1.47,, +"OBIGT","rutherfordine","cr","J",-14.37,, +"OBIGT","octadecane","cr","cal",-2.63,, +"OBIGT","nonadecane","cr","cal",-13.32,, +"OBIGT","eicosane","cr","cal",-2.79,, +"OBIGT","heneicosane","cr","cal",-8.61,, +"OBIGT","docosane","cr","cal",-2.63,, +"OBIGT","tricosane","cr","cal",-5.22,, +"OBIGT","tetracosane","cr","cal",-2.02,, +"OBIGT","pentacosane","cr","cal",-2.93,, +"OBIGT","hexacosane","cr","cal",-1.29,, +"OBIGT","heptacosane","cr","cal",-1.23,, +"OBIGT","carbazole","cr","cal",-43.39,, +"OBIGT","triphenylene","cr","cal",,,541 +"OBIGT","deoxyadenosine","cr","cal",,,-2977 +"OBIGT","ethylene","gas","cal",-4.59,, +"OBIGT","3,5-dimethylphenol","gas","cal",,,628 +"OBIGT","nonacontane","liq","cal",,,635 +"OBIGT","2-methyloctane","liq","cal",10,, +"OBIGT","5,6-dithiadecane","liq","cal",2,, +"DEW","AlO2(SiO2)-","aq","cal",,,-897 +"DEW","BO(OH)","aq","cal",,,-1111 +"DEW","CaHCO3+","aq","cal",,,-2971 +"DEW","CaCl+","aq","cal",,,-593 +"DEW","CaCO3","aq","cal",,,661 +"DEW","Ce+4","aq","cal",,-1.13, +"DEW","CO3-2","aq","cal",,-1.41, +"DEW","FeHCOO+","aq","cal",,,-1082 +"DEW","FeCl+2","aq","cal",,,-4165 +"DEW","FeCl2+","aq","cal",,,-8614 +"DEW","FeCl3","aq","cal",,,-14671 +"DEW","FeCl4-","aq","cal",,,-21499 +"DEW","HCN","aq","cal",,,907 +"DEW","Hg2+2","aq","cal",,,9334 +"DEW","HPO4-2","aq","cal",,-1.02, +"DEW","In+3","aq","cal",,,7335 +"DEW","KOH","aq","cal",,,-71448 +"DEW","MgHCO3+","aq","cal",,,686 +"DEW","MgOH+","aq","cal",,,11274 +"DEW","Mg(SiO2)(HCO3)+","aq","cal",,,1491 +"DEW","MgSO4","aq","cal",,,-3852 +"DEW","MnSO4","aq","cal",,,1203 +"DEW","NaHCO3","aq","cal",,,4657 +"DEW","OH-","aq","cal",,,730 +"DEW","PO4-3","aq","cal",,-1.72, +"DEW","S2O3-2","aq","cal",,,939 +"DEW","S2O6-2","aq","cal",,,-607 +"DEW","S5O6-2","aq","cal",,,664 +"DEW","Si3O6","aq","cal",,,-21928 +"DEW","SO3-2","aq","cal",,-1.02, +"DEW","U+4","aq","cal",,-1.13, +"DEW","ZnCl3-","aq","cal",,,2264 +"SLOP98","Pd(SO4)3-4","aq","cal",,-1.8, +"SLOP98","PtCl+","aq","cal",-3.52,1.25, +"SLOP98","PtCl2","aq","cal",-7.11,2.29, +"SLOP98","PtCl3-","aq","cal",-10.48,1.78, +"SLOP98","PtCl4-2","aq","cal",-13.86,, +"SLOP98","Pt(SO4)3-4","aq","cal",,-1.79,-2915 +"SLOP98","UO4-2","aq","cal",,-1.11, +"SLOP98","HNbO3","aq","cal",,,-1244 +"SLOP98","ZnCl3-","aq","cal",,,2264 +"SLOP98","Zn(Ac)+","aq","cal",,,-4547 +"SLOP98","Zn(Ac)3-","aq","cal",,,-13968 +"SLOP98","AsO4-3","aq","cal",,-1.65, +"SLOP98","Al+3","aq","cal",1.74,, +"SLOP98","ZnO2-2","aq","cal",,-1.17, +"SLOP98","AmOH+2","aq","cal",,,11642 +"SLOP98","AmO+","aq","cal",,,11636 +"SLOP98","HAmO2","aq","cal",,,23273 +"SLOP98","AmCO3+","aq","cal",,,-9689 +"SLOP98","Am(CO3)2-","aq","cal",,,69826 +"SLOP98","AmSO4+","aq","cal",,,46571 +"SLOP98","Am(SO4)2-","aq","cal",,,93130 +"SLOP98","Al(Mal)+","aq","cal",,-2.19, +"SLOP98","Al(Oxal)+","aq","cal",,-2.62, +"SLOP98","PuO2(Oxal)","aq","cal",,,2913 +"SLOP98","Pu(Oxal)+2","aq","cal",-1.2,-4.44,-1743 +"SLOP98","PuO2(Succ)","aq","cal",,,2912 +"SLOP98","Am(Oxal)+","aq","cal",,-1.8,3036 +"SLOP98","Cm(Oxal)+","aq","cal",,-1.8,3834 +"SLOP98","Np(Oxal)+2","aq","cal",-1.27,-4.69,2753 +"SLOP98","NpO2(Oxal)","aq","cal",,-1.94,2729 +"SLOP98","NpO2(Succ)","aq","cal",,-3.16,2728 +"SLOP98","NpO2(Glut)","aq","cal",,,2728 +"SLOP98","MgAsO4-","aq","cal",1.3,, +"SLOP98","MnAsO4-","aq","cal",-1.45,, +"SLOP98","AmCrO4+2","aq","cal",,,-4654 +"SLOP98","PdCl4-2","aq","cal",,-1.05, +"SUPCRT92","almandine","cr","cal",4.43,, +"SUPCRT92","antigorite","cr","cal",,,812 +"SUPCRT92","clinochlore,7A","cr","cal",,,666 +"SUPCRT92","daphnite,14A","cr","cal",,,-836 +"SUPCRT92","ferrosilite","cr","cal",,,694 +"SUPCRT92","ferrosilite","cr2","cal",,,694 +"SUPCRT92","glaucophane","cr","cal",-2.57,, +"SUPCRT92","greenalite","cr","cal",,,142507 +"SUPCRT92","grunerite","cr","cal",9.72,, +"SUPCRT92","halloysite","cr","cal",-1.6,, diff --git a/inst/extdata/thermo/stoich.csv.xz b/inst/extdata/thermo/stoich.csv.xz index e0e9948..e00ddc3 100644 Binary files a/inst/extdata/thermo/stoich.csv.xz and b/inst/extdata/thermo/stoich.csv.xz differ diff --git a/man/util.data.Rd b/man/util.data.Rd index c92609a..80fcc28 100644 --- a/man/util.data.Rd +++ b/man/util.data.Rd @@ -59,9 +59,9 @@ The default tolerances are 1 J/K.mol or 1 cal/K.mol for Cp (depending on the \co These can be changed by setting \code{thermo()$opt$Cp.tol}, \code{thermo()$opt$V.tol}, and \code{thermo()$opt$G.tol}. \code{check.OBIGT} is a function to check self-consistency of each entry in the thermodynamic database, using \code{check.EOS} and \code{check.GHS}. -The output is a table listing only species that exceed at least one of the tolerance limits, giving the species index (rownumber in `thermo()$OBIGT`), species name and state, and DCp, DV and DG, for the calculated differences (only those above the tolerances are given). +The output is a table listing only species that exceed at least one of the tolerance limits, giving the species name and state, and DCp, DV and DG, for the calculated differences (only those above the tolerances are given). Values of DCp and DG are given in the units present in the data files. -This function is used to generate the file found at \code{extdata/thermo/OBIGT_check.csv}. +This function is used to generate the file found at \file{extdata/adds/OBIGT_check.csv}. \code{dumpdata} returns all of the available data, from both the default and optional data files, or writes it to a file if \code{file} is not NULL. The format is the same as \code{\link{thermo}$OBIGT}, except for a single prepended column named \samp{source}, giving the source of the data (\samp{OBIGT} refers to the default database, and \samp{DEW}, \samp{SLOP98}, and \samp{SUPCRT92} are the optional data files). diff --git a/vignettes/OBIGT.Rmd b/vignettes/OBIGT.Rmd index caa5763..fc6751d 100644 --- a/vignettes/OBIGT.Rmd +++ b/vignettes/OBIGT.Rmd @@ -330,7 +330,10 @@ Use `add.OBIGT("SUPCRT92")` to load the data.