[CHNOSZ-commits] r686 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 1 12:55:31 CET 2022
Author: jedick
Date: 2022-02-01 12:55:31 +0100 (Tue, 01 Feb 2022)
New Revision: 686
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Add OBIGT/GEMSFIT.csv
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/DESCRIPTION 2022-02-01 11:55:31 UTC (rev 686)
@@ -1,6 +1,6 @@
Date: 2022-02-01
Package: CHNOSZ
-Version: 1.4.1-12
+Version: 1.4.1-13
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 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-02-01 11:55:31 UTC (rev 686)
@@ -10,7 +10,7 @@
\newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
\newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
-\section{Changes in CHNOSZ version 1.4.1-11 (2022-01-30)}{
+\section{Changes in CHNOSZ version 1.4.1-13 (2022-02-01)}{
\subsection{OBIGT DATABASE}{
\itemize{
@@ -26,6 +26,8 @@
\item Add H\s{2}WO\s{4}(aq) and Cp coefficients of scheelite (CaWO\s{4})
from \href{https://doi.org/10.1016/j.chemgeo.2021.120488}{Liu et al.
(2021)}.
+
+ \item Add aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl from \href{https://doi.org/10.1016/j.gca.2016.04.026}{Miron et al. (2016)} and \href{https://doi.org/10.2475/07.2017.01}{Miron et al. (2017)}.
}
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv 2022-02-01 11:55:31 UTC (rev 686)
@@ -17,9 +17,9 @@
"bG,NaCl",extended_term_parameter,Z0,aq,OH90,DEW19,2020-06-30,cal,175,NA,22,12.72,1.83,0.3006,-2.0255,-2.9092,2.0302,-1.5,5.33,-0.368,0
BO(OH),BO(OH)(0),BO(OH),aq,SH88,SHA14.2,2017-09-26,cal,-174854,-188505,24,3.76,20.49,5.54,1.38,3.1,-2.84,25,-10,0.1,0
BO2-,BO2(-),BO2-,aq,SH88,SHA14.4,2017-09-26,cal,-162240,-184600,-8.9,-9,-16.02,-0.855,-2.596,3.7,-2.6717,17.102,-4.8679,1.7595,-1
-Ca(HCO3)+,Ca(HCO3)(+),Ca(HCO3)+,aq,HS19,DEW19.1,2020-06-30,cal,-273830,-294350,26,51,30,7.4225,2.7838,2.5039,-2.8941,37.511,7.3541,0.158,1
-Ca(HCOO)+,Ca(HCOO)+,Ca(HCOO)+,aq,HS19,DEW19.1,2020-06-30,cal,-217930,-232236,11,68,17.5,5.1038,0.5762,4.355,-2.8028,49.5668,10.817,0.3851,1
-Ca(HSiO3)+,Ca(HSiO3)+,Ca(HSiO3)+,aq,HS19,DEW19.1,2020-06-30,cal,-376299,-397525,16.8,72,36,8.6546,3.9569,1.5203,-2.9426,51.1018,11.6318,0.2973,1
+CaHCO3+,Ca(HCO3)(+),Ca(HCO3)+,aq,HS19,DEW19.1,2020-06-30,cal,-273830,-294350,26,51,30,7.4225,2.7838,2.5039,-2.8941,37.511,7.3541,0.158,1
+CaHCOO+,Ca(HCOO)+,Ca(HCOO)+,aq,HS19,DEW19.1,2020-06-30,cal,-217930,-232236,11,68,17.5,5.1038,0.5762,4.355,-2.8028,49.5668,10.817,0.3851,1
+CaHSiO3+,Ca(HSiO3)+,Ca(HSiO3)+,aq,HS19,DEW19.1,2020-06-30,cal,-376299,-397525,16.8,72,36,8.6546,3.9569,1.5203,-2.9426,51.1018,11.6318,0.2973,1
CaOH+,Ca(OH)(+),Ca(OH)+,aq,SSWS97,DEW17.3,2017-09-26,cal,-171300,-179600,6.7,1.4,1.9,2.1051,-2.2789,6.749,-2.6848,11.1292,-2.7494,0.4496,1
Ca+2,Ca+2,Ca+2,aq,FDM+14,DEW19.5,2020-06-30,cal,-132120,-129800,-13.5,-7.51,-18.45,-0.245,-7.252,5,-2.48,9,-2.52,1.2366,2
CaCl+,CaCl(+),CaCl+,aq,SSH97,DEW17.5,2017-09-26,cal,-163100,-168607,4.5,17.5,11.3,3.9392,-0.5326,5.2847,-2.757,20.7297,0.5302,0.4675,1
@@ -53,8 +53,8 @@
Eu+3,Eu(+3),Eu+3,aq,SSWS97,DEW17.2,2017-09-26,cal,-137300,-144700,-53,-36.6,-41.3,-8.1578,-2.214,13.8765,-2.6875,6.0547,-10.49,2.3161,3
Fe(Ac)+,Fe(CH3COO)(+),Fe(CH3COO)+,aq,SSWS97,DEW17.6,2017-09-26,cal,-111900,-139060,-1.5,81.2,25.2,6.6906,2.087,3.0882,-2.8653,59.0576,13.5058,0.5756,1
Fe(Ac)2,Fe(CH3COO)2(0),Fe(CH3COO)2,aq,SSWS97,DEW17.6,2017-09-26,cal,-201800,-259100,11.53,184.2,66.9,14.4948,9.5174,-3.1421,-3.1724,113.7691,34.4869,-0.038,0
-Fe(HCOO)+,Fe(HCOO)+,Fe(HCOO)+,aq,HS19,DEW19.1,2020-06-30,cal,-111800,-112263,59,30,27,6.6001,2.0008,3.1604,-2.8617,20.5995,3.0764,-0.3418,1
-Fe(HSiO3)+,Fe(HSiO3)+,Fe(HSiO3)+,aq,HS19,DEW19.1,2020-06-30,cal,-277500,-298539,14,77,38.2,9.1022,4.383,1.163,-2.9602,54.4228,12.6503,0.3397,1
+FeHCOO+,Fe(HCOO)+,Fe(HCOO)+,aq,HS19,DEW19.1,2020-06-30,cal,-111800,-112263,59,30,27,6.6001,2.0008,3.1604,-2.8617,20.5995,3.0764,-0.3418,1
+FeHSiO3+,Fe(HSiO3)+,Fe(HSiO3)+,aq,HS19,DEW19.1,2020-06-30,cal,-277500,-298539,14,77,38.2,9.1022,4.383,1.163,-2.9602,54.4228,12.6503,0.3397,1
FeOH+,FeOH(+),FeOH+,aq,SSWS97,DEW17.13,2017-09-26,cal,-65850,NA,-10,15,2,2.2461,-2.1446,6.6364,-2.6903,21.4354,0.0209,0.7031,1
Fe+2,Fe(+2),Fe+2,aq,SSWS97,DEW19.6,2020-07-11,cal,-21870,NA,-25.3,-7.9,-22.2,-1.0416,-9.0072,9.6653,-2.4066,14.9634,-4.6439,1.4574,2
Fe+3,Fe(+3),Fe+3,aq,SSWS97,DEW17.2,2017-09-26,cal,-4120,-11850,-66.3,-18.6,-37,-6.3271,-3.5568,12.7493,-2.632,19.0461,-6.8234,2.5812,3
@@ -122,8 +122,8 @@
Lu+3,Lu(+3),Lu+3,aq,SSWS97,DEW17.1,2017-09-26,cal,-159400,-167900,-63.1,-32.8,-45,-9.398,-1.3044,14.6401,-2.7251,9.5649,-9.716,2.4554,3
CH4,CH4,CH4,aq,PS01,DEW17.3,2017-09-26,cal,-8234,-21010,20.99,57.69,36,8.32,3.64,1.79,-2.93,40.9,6.45,-0.4,0
methanol,METHANOL,CH3OH,aq,PS01,DEW17.01,2017-09-26,cal,-42050,-58870,31.6,37.73,38.69,8.4,4.1,-0.24,-1.43,34.4,0.96,-0.15,0
-Mg(HCO3)+,Mg(HCO3)(+),Mg(HCO3)+,aq,SBS14,DEW17.26,2017-09-26,cal,-250280,-275750,-5,59,25.9,6.8514,2.2401,2.9598,-2.8716,46.5246,8.9837,0.6274,1
-Mg(HSiO3)+,Mg(HSiO3)(+),Mg(HSiO3)+,aq,SSWS97,DEW17.4,2017-09-26,cal,-353025,-385700,-23.78,37.82,2.5,2.4433,-1.9569,6.4789,-2.6981,36.7319,4.6693,0.9118,1
+MgHCO3+,Mg(HCO3)(+),Mg(HCO3)+,aq,SBS14,DEW17.26,2017-09-26,cal,-250280,-275750,-5,59,25.9,6.8514,2.2401,2.9598,-2.8716,46.5246,8.9837,0.6274,1
+MgHSiO3+,Mg(HSiO3)(+),Mg(HSiO3)+,aq,SSWS97,DEW17.4,2017-09-26,cal,-353025,-385700,-23.78,37.82,2.5,2.4433,-1.9569,6.4789,-2.6981,36.7319,4.6693,0.9118,1
MgCl+,MgCl(+),MgCl+,aq,SSWS97,DEW17.6,2017-09-26,cal,-139700,-150933,-19,25,1.25,3.21,-4.92,6.27,-2.58,28.6,2.058,0.8449,1
MgCO3,MgCO3(0),MgCO3,aq,SSWS97,DEW17.27,2017-09-26,cal,-238760,-270570,-24,-24.8,17.9,5.1407,0.6113,4.3256,-2.8043,-5.6039,-8.0864,0.3,0
MgO,MgO,MgO,aq,HS19,DEW19.1,2020-06-30,cal,-137500,-139804,24.6,-24.5,6.2,2.8684,-1.5521,6.1396,-2.7148,-5.4281,-8.0252,0.3,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2022-02-01 11:55:31 UTC (rev 686)
@@ -421,8 +421,8 @@
PbF2,PbF2,PbF2,aq,SSH97,NA,1997-10-09,cal,-145056,-162783,4.48,18.32,-4.85,1.0888,-5.1199,7.7554,-2.5673,16.5543,0.6976,-0.038,0
Pb(HS)2,Pb(HS)2,Pb(HS)2,aq,SSH97,NA,1997-10-09,cal,-20058,-22851,52.56,38.71,41.88,7.4825,10.4917,1.6193,-3.2127,28.5025,4.8505,-0.038,0
Pb(HS)3-,Pb(HS)3-,Pb(HS)3-,aq,SSH97,NA,1997-10-09,cal,-18971,-28704,68.08,47.8,75.8,12.3397,22.3518,-3.0422,-3.703,39.6902,6.7025,0.598,-1
-Mg(HSiO3)+,Mg(HSiO3)+,Mg(HSiO3)+,aq,SSH97,NA,1997-10-09,cal,-353025,-385700,-23.78,37.82,-10.57,0.6289,-6.2428,8.1967,-2.5209,36.7882,4.6702,0.9177,1
-Ca(HSiO3)+,Ca(HSiO3)+,Ca(HSiO3)+,aq,SSH97,NA,1997-10-09,cal,-376299,-403109,-1.99,32.87,-6.56,1.0647,-5.1787,7.7785,-2.5649,30.8048,3.6619,0.5831,1
+MgHSiO3+,Mg(HSiO3)+,Mg(HSiO3)+,aq,SSH97,NA,1997-10-09,cal,-353025,-385700,-23.78,37.82,-10.57,0.6289,-6.2428,8.1967,-2.5209,36.7882,4.6702,0.9177,1
+CaHSiO3+,Ca(HSiO3)+,Ca(HSiO3)+,aq,SSH97,NA,1997-10-09,cal,-376299,-403109,-1.99,32.87,-6.56,1.0647,-5.1787,7.7785,-2.5649,30.8048,3.6619,0.5831,1
CuCl3-2,CuCl3-2,CuCl3-2,aq,SSH97,NA,1997-10-02,cal,-89963,-118524,23.28,53.72,76.86,13.2482,24.57,-3.914,-3.7947,63.9808,7.9089,2.8579,-2
CuCl+,CuCl+,CuCl+,aq,SSH97,NA,1997-10-02,cal,-16250,-23847,-6.51,29.39,-1.72,1.748,-3.5103,7.1228,-2.6338,29.356,2.953,0.6472,1
CuCl2,CuCl2,CuCl2,aq,SSH97,NA,1997-10-02,cal,-46142,-64160,0.78,54.22,24.32,5.0806,4.627,3.9244,-2.9702,37.5948,8.0108,-0.038,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2022-02-01 11:55:31 UTC (rev 686)
@@ -467,12 +467,12 @@
Eu(Lac)2,NA,Eu(CH3CH2OCO2)2,aq,SK95,NA,1993-08-30,cal,-376425,-451723,77.437,338,135.1,20.2419,41.6449,-10.6207,-4.5005,203.9641,65.8108,-0.03,0
Li(Glyc),NA,LiCH3OCO2,aq,SK95,NA,1993-08-30,cal,-190953,-221668,27,NA,NA,8.2991,12.4812,0.8472,-3.2949,57.0031,14.7309,-0.03,0
Lu(Lac)+2,NA,LuCH3CH2OCO2+2,aq,SK95,NA,1993-08-30,cal,-287182,-338081,-34.08,NA,NA,4.3587,2.8618,4.6243,-2.8972,85.9749,19.6485,1.579,2
-Ba(HCO3)+,NA,Ba(HCO3)+,aq,SK95,SLOP98.8,1992-11-00,cal,-275700,-294350,46.83,NA,NA,7.882,11.464,1.244,-3.253,26.273,4.46,-0.158,1
-Ca(HCO3)+,NA,Ca(HCO3)+,aq,SK95,SLOP98.8,1991-01-00,cal,-273830,-294350,16,NA,NA,3.706,1.267,5.252,-2.831,41.722,8.336,0.308,1
+BaHCO3+,NA,Ba(HCO3)+,aq,SK95,SLOP98.8,1992-11-00,cal,-275700,-294350,46.83,NA,NA,7.882,11.464,1.244,-3.253,26.273,4.46,-0.158,1
+CaHCO3+,NA,Ca(HCO3)+,aq,SK95,SLOP98.8,1991-01-00,cal,-273830,-294350,16,NA,NA,3.706,1.267,5.252,-2.831,41.722,8.336,0.308,1
La(Lac)+2,NA,LaCH3CH2OCO2+2,aq,SK95,SLOP98.8,1993-08-30,cal,-291087,-337701,-18.338,NA,NA,5.2529,5.0431,3.7711,-2.9874,76.8931,17.2652,1.3375,2
Li(Lac),NA,LiCH3CH2OCO2,aq,SK95,SLOP98.8,1993-08-30,cal,-192736,-232028,30.798,NA,NA,10.5433,17.9646,-1.316,-3.5216,78.9753,22.3678,-0.03,0
-Mg(HCO3)+,NA,Mg(HCO3)+,aq,SK95,SLOP98.8,1991-01-00,cal,-250200,-275750,-3,NA,NA,3.271,0.206,5.669,-2.788,47.284,9.34,0.599,1
-Sr(HCO3)+,NA,Sr(HCO3)+,aq,SK95,SLOP98.8,1992-11-00,cal,-276720,-291688,38,NA,NA,3.694,1.237,5.264,-2.83,35.345,7.181,-0.023,1
+MgHCO3+,NA,Mg(HCO3)+,aq,SK95,SLOP98.8,1991-01-00,cal,-250200,-275750,-3,NA,NA,3.271,0.206,5.669,-2.788,47.284,9.34,0.599,1
+SrHCO3+,NA,Sr(HCO3)+,aq,SK95,SLOP98.8,1992-11-00,cal,-276720,-291688,38,NA,NA,3.694,1.237,5.264,-2.83,35.345,7.181,-0.023,1
phenol,PHOL,C6H5OH,aq,DSM+97,NA,1997-11-20,cal,-12215,-36320,45.5,74.2,86.17,13.4599,23.7816,-0.7952,-3.762,67.7515,2.37,-0.2857,0
o-cresol,o-CRESOL,C6H4OHCH3,aq,DSM+97,NA,1996-02-22,cal,-12725,-45081,50.4,102.8,100.4,15.4181,28.2184,-1.8079,-3.9454,89.9089,5.1956,-0.2532,0
m-cresol,m-CRESOL,C6H4OHCH3,aq,DSM+97,NA,1996-02-22,cal,-13890,-45560,52.7,101.3,100.4,15.4233,28.2298,-1.8101,-3.9459,88.8505,5.0474,-0.238,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2022-02-01 11:55:31 UTC (rev 686)
@@ -28,6 +28,7 @@
SH88.1,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","values of GHS",https://doi.org/10.1016/0016-7037(88)90181-0
SH88.2,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",H<sub>2</sub>AsO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
SH88.3,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",Ag<sup>+</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
+SH88.4,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",Ca<sup>+2</sup> and Mg<sup>+2</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4
SHS89.1,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","aqueous SiO<sub>2</sub>",https://doi.org/10.1016/0016-7037(89)90341-4
Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344",annite,http://ammin.geoscienceworld.org/content/75/3-4/328
@@ -87,6 +88,7 @@
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
SSH97.3,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au-, Ag-, Cu- and Zn-chloride complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
SSH97.4,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Zn-acetate complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
+SSH97.5,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412",CaHSiO<sub>3</sub><sup>+</sup> and MgHSiO<sub>3</sub><sup>+</sup>,https://doi.org/10.1016/S0016-7037(97)00009-4
SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",https://doi.org/10.1016/S0016-7037(97)00240-8
SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,https://doi.org/10.1016/S0016-7037(97)00240-8
TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",https://doi.org/10.1016/S1251-8050(97)83981-X
@@ -207,6 +209,7 @@
TBB15,"B. R. Tagirov et al.",2015,"Geochem. Int. 53, 327-340","Pt<sup>+2</sup> and complexes",https://doi.org/10.1134/S0016702915040084
CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid cycle metabolites",https://doi.org/10.1016/j.gca.2016.08.028
CS16.1,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid species HKF a<sub>1</sub>--a<sub>4</sub> parameters",https://doi.org/10.1016/j.gca.2016.08.028
+MWKH16,"G. D. Miron et al.",2016,"Geochim. Cosmochim. Acta 187, 41-78","aqueous species in the system Na-K-Al-Si-O-H-Cl",https://doi.org/10.1016/j.gca.2016.04.026
ZZL+16,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","data listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
ZZL+16.1,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","As(α): V listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
ZZL+16.2,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","Cp parameters listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
@@ -261,6 +264,8 @@
DEW17.40,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","urea: Revised Feb. 2015 by Dimitri: c<sub>1</sub>, c<sub>2</sub>, and omega from PS01 based on Stokes (1967) data; V from Cabani et al. (1981) with a<sub>1</sub>-a<sub>4</sub> predicted.",http://www.dewcommunity.org
DEW17.101,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","formate and lactate: revised with new predicted a<sub>1</sub> for ions",https://doi.org/10.1016/0016-7037(90)90429-O
BDat17.1,"D. A. Sverjensky et al.",2017,"berman.dat file in SUPCRT92b.zip on the DEW website","antigorite: "Oct. 21, 2016: Revised volume coefficients consistent with @HDR06 and @YIY+14 "",http://www.dewcommunity.org/resources.html
+MWKL17,"G. D. Miron et al.",2017,"Am. J. Sci. 317, 755-806","aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl",https://doi.org/10.2475/07.2017.01
+MWKL17.1,"G. D. Miron et al.",2017,"Am. J. Sci. 317, 755-806","ΔG°<sub>f</sub> values",https://doi.org/10.2475/07.2017.01
AKAE19,"M. R. Azadi et al.",2019,"Fluid Phase Equilib. 480, 25-40","metal-glycinate complexes",https://doi.org/10.1016/j.fluid.2018.10.002
DEW19,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(values listed in DEW spreadsheet)",http://www.dewcommunity.org
DEW19.1,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(values from @HS19 listed in DEW spreadsheet)",http://www.dewcommunity.org
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2022-02-01 11:55:31 UTC (rev 686)
@@ -148,7 +148,7 @@
"OBIGT",1220,"Mg(But)2","aq","cal",,,-3347811
"OBIGT",1249,"Yb(But)+2","aq","cal",,,665
"OBIGT",1268,"Fe(Pent)2","aq","cal",,,532
-"OBIGT",1353,"Ba(HCO3)+","aq","cal",,,-5800
+"OBIGT",1353,"BaHCO3+","aq","cal",,,-5800
"OBIGT",1373,"Li(Mal)-","aq","cal",,-3.22,
"OBIGT",1377,"Pb(Mal)","aq","cal",,1.16,
"OBIGT",1381,"Pb(Succ)","aq","cal",,1.49,
@@ -287,12 +287,12 @@
"OBIGT",3388,"5,6-dithiadecane","liq","cal",2,,
"DEW",8,"AlO2(SiO2)-","aq","cal",,,-897
"DEW",17,"BO(OH)","aq","cal",,,-1111
-"DEW",19,"Ca(HCO3)+","aq","cal",,,-2971
+"DEW",19,"CaHCO3+","aq","cal",,,-2971
"DEW",24,"CaCl+","aq","cal",,,-593
"DEW",26,"CaCO3","aq","cal",,,661
"DEW",31,"Ce+4","aq","cal",,-1.13,
"DEW",37,"CO3-2","aq","cal",,-1.41,
-"DEW",55,"Fe(HCOO)+","aq","cal",,,-1082
+"DEW",55,"FeHCOO+","aq","cal",,,-1082
"DEW",61,"FeCl+2","aq","cal",,,-4165
"DEW",63,"FeCl2+","aq","cal",,,-8614
"DEW",64,"FeCl3","aq","cal",,,-14671
@@ -302,7 +302,7 @@
"DEW",102,"HPO4-2","aq","cal",,-1.02,
"DEW",112,"In+3","aq","cal",,,7335
"DEW",115,"KOH","aq","cal",,,-71448
-"DEW",124,"Mg(HCO3)+","aq","cal",,,686
+"DEW",124,"MgHCO3+","aq","cal",,,686
"DEW",129,"MgOH+","aq","cal",,,11274
"DEW",130,"Mg(SiO2)(HCO3)+","aq","cal",,,1491
"DEW",131,"MgSO4","aq","cal",,,-3852
Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-02-01 11:55:31 UTC (rev 686)
@@ -67,11 +67,12 @@
OpenDiv("gas-inorganic");
OpenDiv("gas-organic");
OpenDiv("liquid-organic");
- OpenDiv("optional-DEW");
OpenDiv("optional-SUPCRT92");
OpenDiv("optional-SLOP98");
+ OpenDiv("optional-AkDi");
OpenDiv("optional-AS04");
- OpenDiv("optional-AkDi");
+ OpenDiv("optional-DEW");
+ OpenDiv("optional-GEMSFIT");
// change the footer message
document.getElementById("footer").style.display = "none";
document.getElementById("all-open").style.display = "block";
@@ -87,11 +88,12 @@
CloseDiv("gas-inorganic");
CloseDiv("gas-organic");
CloseDiv("liquid-organic");
- CloseDiv("optional-DEW");
CloseDiv("optional-SUPCRT92");
CloseDiv("optional-SLOP98");
+ CloseDiv("optional-AkDi");
CloseDiv("optional-AS04");
- CloseDiv("optional-AkDi");
+ CloseDiv("optional-DEW");
+ CloseDiv("optional-GEMSFIT");
// change the footer message
document.getElementById("footer").style.display = "block";
document.getElementById("all-open").style.display = "none";
@@ -203,7 +205,7 @@
### Aqueous Species <button id="B-aqueous-H2O" onclick='ToggleDiv("aqueous-H2O")'>H2O</button> <button id="B-aqueous-inorganic" onclick='ToggleDiv("aqueous-inorganic")'>Inorganic</button> <button id="B-aqueous-organic" onclick='ToggleDiv("aqueous-organic")'>Organic</button> <button id="B-aqueous-biotic" onclick='ToggleDiv("aqueous-biotic")'>Biotic</button>
### Solids <button id="B-solid-inorganic" onclick='ToggleDiv("solid-inorganic")'>Inorganic</button> <button id="B-solid-berman" onclick='ToggleDiv("solid-berman")'>Berman</button> <button id="B-solid-organic" onclick='ToggleDiv("solid-organic")'>Organic</button>
### Gases <button id="B-gas-inorganic" onclick='ToggleDiv("gas-inorganic")'>Inorganic</button> <button id="B-gas-organic" onclick='ToggleDiv("gas-organic")'>Organic</button> Liquids <button id="B-liquid-organic" onclick='ToggleDiv("liquid-organic")'>Organic</button>
-### Optional Data <button id="B-optional-DEW" onclick='ToggleDiv("optional-DEW")'>DEW</button> <button id="B-optional-SUPCRT92" onclick='ToggleDiv("optional-SUPCRT92")'>SUPCRT92</button> <button id="B-optional-SLOP98" onclick='ToggleDiv("optional-SLOP98")'>SLOP98</button> <button id="B-optional-AS04" onclick='ToggleDiv("optional-AS04")'>AS04</button> <button id="B-optional-AkDi" onclick='ToggleDiv("optional-AkDi")'>AkDi</button>
+### Optional Data <button id="B-optional-SUPCRT92" onclick='ToggleDiv("optional-SUPCRT92")'>SUPCRT92</button> <button id="B-optional-SLOP98" onclick='ToggleDiv("optional-SLOP98")'>SLOP98</button> <button id="B-optional-AkDi" onclick='ToggleDiv("optional-AkDi")'>AkDi</button> <button id="B-optional-AS04" onclick='ToggleDiv("optional-AS04")'>AS04</button> <button id="B-optional-DEW" onclick='ToggleDiv("optional-DEW")'>DEW</button> <button id="B-optional-GEMSFIT" onclick='ToggleDiv("optional-GEMSFIT")'>GEMSFIT</button>
<!-- normal or "all open" footer message -->
@@ -320,23 +322,6 @@
<!-- Optional species divs -->
-<div id="D-optional-DEW" style="display: none">
-## <a id="optional-DEW" class="anchor"></a> `r setfile("DEW.csv")`
-The [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model extends the applicability of the revised HKF equations of state to 60 kbar.
-Accuracy of the thermodynamic calculations at these conditions is improved by revised correlations for the <i>a</i><sub>1</sub> HKF parameter, as described by [Sverjensky et al., 2014](https://doi.org/10.1016/j.gca.2013.12.019).
-The data here were taken from the May 2017 and January 2019 versions of the [DEW spreadsheet](http://www.dewcommunity.org/resources.html).
-The following species are present in the spreadsheet, but are not used here because the parameters are unchanged from the default database in CHNOSZ: B(OH)<sub>3</sub>, Br<sup>-</sup>, Ca<sup>+2</sup>, Cl<sup>-</sup>, Cs<sup>+</sup>, F<sup>-</sup>, H<sup>+</sup>, H<sub>2</sub>, He, I<sup>-</sup>, K<sup>+</sup>, Kr, Li<sup>+</sup>, Mg<sup>+2</sup>, Na<sup>+</sup>, Ne, O<sub>2</sub>, Rb<sup>+</sup>, Rn, SO<sub>4</sub><sup>-2</sup>.
-
-Besides using `add.OBIGT("DEW")` to load these data, you should also run `water("DEW")` to activate the DEW equations in CHNOSZ.
-See `demo(DEW)` for some examples.
-
-Most of the comments below were transcribed from the DEW spreadsheet. (Comments in parentheses were added by JMD.)
-
-```{r optreflist, results="asis", echo=FALSE}
-optused <- c(optused, filerefs(csvfile))
-```
-</div>
-
<div id="D-optional-SUPCRT92" style="display: none">
## <a id="optional-SUPCRT92" class="anchor"></a> `r setfile("SUPCRT92.csv")`
These minerals and aqueous species, taken from the SUPCRT92 database, were present in earlier versions of CHNOSZ but have since been superseded by @Ber88 (minerals) and @NA03 (H<sub>2</sub>AsO<sub>3</sub><sup>-</sup>).
@@ -362,6 +347,15 @@
```
</div>
+<div id="D-optional-AkDi" style="display: none">
+## <a id="optional-AkDi" class="anchor"></a> `r setfile("AkDi.csv")`
+This file has parameters for aqueous nonelectrolytes in the Akinfiev-Diamond model [@AD03].
+Use `add.OBIGT("AkDi")` to load the data; see `demo(AkDi)` for an example.
+
+```{r optreflist, results="asis", echo=FALSE}
+```
+</div>
+
<div id="D-optional-AS04" style="display: none">
## <a id="optional-AS04" class="anchor"></a> `r setfile("AS04.csv")`
This file has data for aqueous SiO<sub>2</sub> from @AS04 and a HSiO<sub>3</sub><sup>-</sup> modified to be consistent with the SiO<sub>2</sub> here.
@@ -372,15 +366,31 @@
```
</div>
-<div id="D-optional-AkDi" style="display: none">
-## <a id="optional-AkDi" class="anchor"></a> `r setfile("AkDi.csv")`
-This file has parameters for aqueous nonelectrolytes in the Akinfiev-Diamond model [@AD03].
-Use `add.OBIGT("AkDi")` to load the data; see `demo(AkDi)` for an example.
+<div id="D-optional-DEW" style="display: none">
+## <a id="optional-DEW" class="anchor"></a> `r setfile("DEW.csv")`
+The [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model extends the applicability of the revised HKF equations of state to 60 kbar.
+Accuracy of the thermodynamic calculations at these conditions is improved by revised correlations for the <i>a</i><sub>1</sub> HKF parameter, as described by [Sverjensky et al. (2014)](https://doi.org/10.1016/j.gca.2013.12.019).
+The data here were taken from the May 2017 and January 2019 versions of the [DEW spreadsheet](http://www.dewcommunity.org/resources.html).
+The following species are present in the spreadsheet, but are not used here because the parameters are unchanged from the default database in CHNOSZ: B(OH)<sub>3</sub>, Br<sup>-</sup>, Ca<sup>+2</sup>, Cl<sup>-</sup>, Cs<sup>+</sup>, F<sup>-</sup>, H<sup>+</sup>, H<sub>2</sub>, He, I<sup>-</sup>, K<sup>+</sup>, Kr, Li<sup>+</sup>, Mg<sup>+2</sup>, Na<sup>+</sup>, Ne, O<sub>2</sub>, Rb<sup>+</sup>, Rn, SO<sub>4</sub><sup>-2</sup>.
+Besides using `add.OBIGT("DEW")` to load these data, you should also run `water("DEW")` to activate the DEW equations in CHNOSZ.
+See `demo(DEW)` for some examples.
+
+Most of the comments below were transcribed from the DEW spreadsheet. (Comments in parentheses were added by JMD.)
+
```{r optreflist, results="asis", echo=FALSE}
+optused <- c(optused, filerefs(csvfile))
```
</div>
+<div id="D-optional-GEMSFIT" style="display: none">
+## <a id="optional-GEMSFIT" class="anchor"></a> `r setfile("GEMSFIT.csv")`
+[Miron et al. (2016)](https://doi.org/10.1016/j.gca.2016.04.026) and [Miron et al. (2017)](https://doi.org/10.2475/07.2017.01) described an internally consistent thermodynamic dataset for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl that was obtained by using the [GEMSFIT](https://doi.org/10.1016/j.apgeochem.2014.10.013) package.
+
+```{r optreflist, results="asis", echo=FALSE}
+```
+</div>
+
<hr>
<b>Total count of species</b>: References were found for `r length(used)` of `r nrow(thermo()$OBIGT)` species in the default OBIGT database and `r length(optused)` optional species.
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2022-02-01 09:40:34 UTC (rev 685)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2022-02-01 11:55:31 UTC (rev 686)
@@ -289,7 +289,7 @@
@Article{Kit14,
author = {Kitadai, Norio},
- journal = {J. Mol. Evol.},
+ journal = {Journal of Molecular Evolution},
title = {{T}hermodynamic prediction of glycine polymerization as a function of temperature and p{H} consistent with experimentally obtained results},
year = {2014},
number = {3-4},
@@ -311,7 +311,7 @@
@Article{LD12,
author = {LaRowe, Douglas E. and Dick, Jeffrey M.},
- journal = {Geochim. Cosmochim. Acta},
+ journal = {Geochimica et Cosmochimica Acta},
title = {Calculation of the standard molal thermodynamic properties of crystalline peptides},
year = {2012},
pages = {70--91},
@@ -965,6 +965,16 @@
doi = {10.1016/S0016-7037(99)00276-8},
}
+ at Article{MWKH16,
+ author = {George D. Miron and Thomas Wagner and Dmitrii A. Kulik and Christoph A. Heinrich},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{I}nternally consistent thermodynamic data for aqueous species in the system {N}a--{K}--{A}l--{S}i--{O}--{H}--{C}l},
+ year = {2016},
+ pages = {41--78},
+ volume = {187},
+ doi = {10.1016/j.gca.2016.04.026},
+}
+
@Article{Ber88,
author = {Berman, R. G.},
journal = {Journal of Petrology},
@@ -1736,3 +1746,14 @@
volume = {584},
doi = {10.1016/j.chemgeo.2021.120488},
}
+
+ at Article{MWKL17,
+ author = {Miron, George D. and Wagner, Thomas and Kulik, Dmitrii A. and Lothenbach, Barbara},
+ journal = {American Journal of Science},
+ title = {An internally consistent thermodynamic dataset for aqueous species in the system {Ca-Mg-Na-K-Al-Si-O-H-C-Cl} to 800 °{C} and 5 kbar},
+ year = {2017},
+ number = {7},
+ pages = {755--806},
+ volume = {317},
+ doi = {10.2475/07.2017.01},
+}
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