[CHNOSZ-commits] r608 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 4 23:50:22 CEST 2020
Author: jedick
Date: 2020-10-04 23:50:21 +0200 (Sun, 04 Oct 2020)
New Revision: 608
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Add metal carbonate and bicarbonate complexes from St Clair et al., 2019
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-09-18 04:20:07 UTC (rev 607)
+++ pkg/CHNOSZ/DESCRIPTION 2020-10-04 21:50:21 UTC (rev 608)
@@ -1,6 +1,6 @@
-Date: 2020-09-18
+Date: 2020-10-05
Package: CHNOSZ
-Version: 1.3.6-81
+Version: 1.3.6-82
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 2020-09-18 04:20:07 UTC (rev 607)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-10-04 21:50:21 UTC (rev 608)
@@ -9,7 +9,7 @@
\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 1.3.6-81 (2020-09-18)}{
+\section{Changes in CHNOSZ version 1.3.6-82 (2020-10-05)}{
\subsection{MAJOR CHANGES}{
\itemize{
@@ -94,6 +94,11 @@
\item \samp{inorganic_aq.csv}: Add Co-chloride species from
\href{https://doi.org/10.1016/j.gca.2010.12.002}{Liu et al., 2018}.
+ \item \samp{inorganic_aq.csv}: Add metal carbonate and bicarbonate
+ complexes and FeSO\s{4} from
+ \href{https://doi.org/10.1021/acsearthspacechem.9b00016}{St Clair et al.,
+ 2019}.
+
\item \samp{inorganic_cr.csv}: Add manganese and Mn oxides (manganosite,
pyrolusite, bixbyite, and hausmannite) from
\href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway,
@@ -286,6 +291,8 @@
\item TODO: replace CoCl2-4 example in anintro.Rmd with different species
(CoCl2-4 has been added to OBIGT).
+ \item TODO: add wustite from Robie and Hemingway (1995).
+
}
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2020-09-18 04:20:07 UTC (rev 607)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2020-10-04 21:50:21 UTC (rev 608)
@@ -839,3 +839,31 @@
CoCl2(oct),NA,CoCl2,aq,LBT+11,NA,2020-09-18,cal,-75781.9,-93044.7,2.62,1.11,25.06,5.1814,4.8721,3.4447,-2.9805,6.1805,-2.8194,-0.038,0
CoCl2(tet),NA,CoCl2,aq,LBT+11,NA,2020-09-18,cal,-73419.7,-96173.2,-15.7962,139.332,25.06,5.1814,4.8721,3.4448,-2.9805,90.315,25.336,-0.038,0
CoCl4-2,NA,CoCl4-2,aq,LBT+11,NA,2020-09-18,cal,-134150,-171558,19.55,72.09,27.74,6.5467,8.2069,2.013,-3.1183,76.3357,11.6389,2.9159,-2
+FeCO3,NA,FeCO3,aq,SPD+19,NA,2020-10-05,cal,-155442,-183875,-13.97,-30,NA,NA,NA,NA,NA,-11.7653,-9.1456,-0.038,0
+MnCO3,NA,MnCO3,aq,SPD+19,NA,2020-10-05,cal,-187703,-213178,-2.93,-26.2,NA,NA,NA,NA,NA,-9.5383,-8.3715,-0.038,0
+ZnCO3,NA,ZnCO3,aq,SPD+19,NA,2020-10-05,cal,-167872,-197642,-15.06,-27.43,NA,NA,NA,NA,NA,-10.2592,-8.6221,-0.038,0
+CuCO3,NA,CuCO3,aq,SPD+19,NA,2020-10-05,cal,-119725,-147820,-11.42,-27.8,NA,NA,NA,NA,NA,-10.476,-8.6975,-0.038,0
+CdCO3,NA,CdCO3,aq,SPD+19,NA,2020-10-05,cal,-150754,-178085,-4.39,-25.6,NA,NA,NA,NA,NA,-9.1867,-8.2493,-0.038,0
+PbCO3,NA,PbCO3,aq,SPD+19,NA,2020-10-05,cal,-140701,-161150,21.81,-34.8,NA,NA,NA,NA,NA,-14.5784,-10.1234,-0.038,0
+CoCO3,NA,CoCO3,aq,SPD+19,NA,2020-10-05,cal,-145208,-174468,-16.03,-29.9,NA,NA,NA,NA,NA,-11.7067,-9.1252,-0.038,0
+NiCO3,NA,NiCO3,aq,SPD+19,NA,2020-10-05,cal,-143681,-174283,-20.64,-33.8,NA,NA,NA,NA,NA,-13.9924,-9.9197,-0.038,0
+Fe(CO3)2-2,NA,Fe(CO3)2-2,aq,SPD+19,NA,2020-10-05,cal,-283939,-354507,-33.02,-56.1,NA,NA,NA,NA,NA,7.4869,-14.4622,3.712,-2
+Zn(CO3)2-2,NA,Zn(CO3)2-2,aq,SPD+19,NA,2020-10-05,cal,-294950,-366798,-34.11,-53.53,NA,NA,NA,NA,NA,9.1454,-13.9387,3.7286,-2
+Cu(CO3)2-2,NA,Cu(CO3)2-2,aq,SPD+19,NA,2020-10-05,cal,-250760,-321123,-30.47,-53.9,NA,NA,NA,NA,NA,8.4209,-14.014,3.6735,-2
+Pb(CO3)2-2,NA,Pb(CO3)2-2,aq,SPD+19,NA,2020-10-05,cal,-271913,-336371,2.76,-60.9,NA,NA,NA,NA,NA,-0.3186,-15.4399,3.1701,-2
+NaCO3-,NA,NaCO3-,aq,SPD+19,NA,2020-10-05,cal,-189567,-223464,-10.94,-8.82,NA,NA,NA,NA,NA,-12.4895,-4.8318,-1.4638,-1
+KCO3-,NA,KCO3-,aq,SPD+19,NA,2020-10-05,cal,-194807,-221063,17.89,-16.12,NA,NA,NA,NA,NA,-20.7896,-6.3182,-1.9005,-1
+LiCO3-,NA,LiCO3-,aq,SPD+19,NA,2020-10-05,cal,-197222,-239041,-42.81,-3.9,NA,NA,NA,NA,NA,-5.1587,-3.829,-0.9812,-1
+RbCO3-,NA,RbCO3-,aq,SPD+19,NA,2020-10-05,cal,-195096,-218275,31.05,-21.1,NA,NA,NA,NA,NA,-25.5442,-7.3327,-2.0998,-1
+NH4CO3-,NA,NH4CO3-,aq,SPD+19,NA,2020-10-05,cal,-146442,-191478,24.74,-2.36,NA,NA,NA,NA,NA,-13.681,-3.5153,-2.0042,-1
+FeHCO3+,NA,FeHCO3+,aq,SPD+19,NA,2020-10-05,cal,-164158,-184997,11.5,55.02,NA,NA,NA,NA,NA,41.887,8.1736,0.377,1
+MnHCO3+,NA,MnHCO3+,aq,SPD+19,NA,2020-10-05,cal,-197142,-214597,23.97,63.57,NA,NA,NA,NA,NA,45.1584,9.9153,0.1882,1
+ZnHCO3+,NA,ZnHCO3+,aq,SPD+19,NA,2020-10-05,cal,-177692,-199910,10.27,60.81,NA,NA,NA,NA,NA,45.4479,9.3515,0.3957,1
+CuHCO3+,NA,CuHCO3+,aq,SPD+19,NA,2020-10-05,cal,-127117,-147520,14.38,59.97,NA,NA,NA,NA,NA,44.3866,9.1819,0.3334,1
+CdHCO3+,NA,CdHCO3+,aq,SPD+19,NA,2020-10-05,cal,-161571,-180938,22.33,64.92,NA,NA,NA,NA,NA,46.179,10.1903,0.2131,1
+PbHCO3+,NA,PbHCO3+,aq,SPD+19,NA,2020-10-05,cal,-148530,-160004,51.92,44.22,NA,NA,NA,NA,NA,29.9188,5.9737,-0.235,1
+CoHCO3+,NA,CoHCO3+,aq,SPD+19,NA,2020-10-05,cal,-156284,-178030,9.17,55.25,NA,NA,NA,NA,NA,42.3438,8.2195,0.4123,1
+NiHCO3+,NA,NiHCO3+,aq,SPD+19,NA,2020-10-05,cal,-154211,-176473,7.33,46.47,NA,NA,NA,NA,NA,37.4577,6.432,0.4401,1
+NaHCO3,NA,NaHCO3,aq,SPD+19,NA,2020-10-05,cal,-203093,-222193,38.69,47.88,NA,NA,NA,NA,NA,33.9093,6.7192,-0.0347,0
+KHCO3,NA,KHCO3,aq,SPD+19,NA,2020-10-05,cal,-207437,-223501,52.08,31.95,NA,NA,NA,NA,NA,22.7051,3.4743,-0.2375,0
+FeSO4,NA,FeSO4,aq,SPD+19,NA,2020-10-05,cal,-203784,-238961,-5.8,-28.4,NA,NA,NA,NA,NA,-10.8255,-8.819,-0.038,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-09-18 04:20:07 UTC (rev 607)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-10-04 21:50:21 UTC (rev 608)
@@ -275,4 +275,5 @@
DEW19.6,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(Fe<sup>+2</sup>: HKF a<sub>1</sub>-a<sub>4</sub> parameters taken from @HS19, which are different from 2019 DEW spreadsheet)",http://www.dewcommunity.org
HS19,"F. Huang and D. A. Sverjensky",2019,"Geochim. Cosmochim. Acta 254, 192-230","ions and metal complexes",https://doi.org/10.1016/j.gca.2019.03.027
LA19,"D. E. LaRowe and J. P. Amend",2019,"Geomicrobiol. J. 36, 492-505","dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid",https://doi.org/10.1080/01490451.2019.1573278
+SPD+19,"B. St Clair et al.",2019,"ACS Earth Space Chem 3, 905-921","Metal carbonate and bicarbonate complexes and FeSO<sub>4</sub>",https://doi.org/10.1021/acsearthspacechem.9b00016
LX20,"Liu and Xiao",2020,"Ore Geol. Rev. 117, 103289","huebnerite Cp",https://doi.org/10.1016/j.oregeorev.2019.103289
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-09-18 04:20:07 UTC (rev 607)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-10-04 21:50:21 UTC (rev 608)
@@ -113,162 +113,166 @@
"OBIGT",837,"S3-","aq","cal",,,661
"OBIGT",842,"CoCl2(tet)","aq","cal",2.81,,
"OBIGT",843,"CoCl4-2","aq","cal",1.33,-1.19,
-"OBIGT",844,"CH4","aq","cal",-2.61,,
-"OBIGT",849,"hexane","aq","cal",1.43,3.21,
-"OBIGT",852,"ethylene","aq","cal",6.12,-3.82,
-"OBIGT",876,"propanol","aq","cal",-1.89,,
-"OBIGT",923,"La(Ac)2+","aq","cal",,,-779
-"OBIGT",926,"Sm(Ac)+2","aq","cal",,,-660
-"OBIGT",927,"Sm(Ac)2+","aq","cal",,,-621
-"OBIGT",940,"Ca(Ac)2","aq","cal",,,-1006
-"OBIGT",956,"La(Ac)3","aq","cal",,,-564
-"OBIGT",976,"Ce(Ac)+2","aq","cal",,,797
-"OBIGT",977,"Ce(Ac)2+","aq","cal",,,567
-"OBIGT",1005,"urea","aq","cal",-23.26,23.32,
-"OBIGT",1018,"propanoic acid","aq","cal",1.42,,
-"OBIGT",1037,"pimelic acid","aq","cal",,,-19931
-"OBIGT",1041,"formate","aq","cal",1.96,,
-"OBIGT",1043,"propanoate","aq","cal",1.68,,
-"OBIGT",1050,"n-decanoate","aq","cal",-1.93,,
-"OBIGT",1066,"oxalate-2","aq","cal",-3.19,,
-"OBIGT",1107,"Fe(For)+","aq","cal",,,587
-"OBIGT",1108,"Fe(For)2","aq","cal",,,639
-"OBIGT",1180,"Mg(But)2","aq","cal",,,-3347811
-"OBIGT",1209,"Yb(But)+2","aq","cal",,,665
-"OBIGT",1228,"Fe(Pent)2","aq","cal",,,532
-"OBIGT",1313,"Ba(HCO3)+","aq","cal",,,-5800
-"OBIGT",1333,"Li(Mal)-","aq","cal",,-3.22,
-"OBIGT",1337,"Pb(Mal)","aq","cal",,1.16,
-"OBIGT",1341,"Pb(Succ)","aq","cal",,1.49,
-"OBIGT",1342,"Na(Oxal)-","aq","cal",,-3.14,
-"OBIGT",1343,"K(Oxal)-","aq","cal",,-2.75,
-"OBIGT",1344,"Fe(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1346,"Na(Mal)-","aq","cal",,-3.11,17018
-"OBIGT",1347,"K(Mal)-","aq","cal",,-2.63,17013
-"OBIGT",1349,"La(Mal)+","aq","cal",,-1.92,
-"OBIGT",1350,"Gd(Mal)+","aq","cal",,-1.73,
-"OBIGT",1351,"Lu(Mal)+","aq","cal",,-2.25,
-"OBIGT",1352,"Yb(Mal)+","aq","cal",,-2.05,
-"OBIGT",1353,"Th(Mal)+2","aq","cal",-1.29,-4.79,
-"OBIGT",1355,"Ce(Mal)+","aq","cal",,-1.75,
-"OBIGT",1356,"Nd(Mal)+","aq","cal",4.52,,
-"OBIGT",1357,"Sm(Mal)+","aq","cal",,-1.77,
-"OBIGT",1358,"Pr(Mal)+","aq","cal",,-1.75,
-"OBIGT",1359,"Eu(Mal)+","aq","cal",,-1.87,
-"OBIGT",1360,"Tb(Mal)+","aq","cal",,-1.92,
-"OBIGT",1361,"Dy(Mal)+","aq","cal",,-1.89,
-"OBIGT",1362,"Tm(Mal)+","aq","cal",,-2.08,
-"OBIGT",1363,"Ho(Mal)+","aq","cal",,-2.08,
-"OBIGT",1364,"Er(Mal)+","aq","cal",,-2.11,
-"OBIGT",1365,"Sc(Mal)+","aq","cal",,-1.97,
-"OBIGT",1366,"Fe(Mal)+","aq","cal",,-1.97,
-"OBIGT",1367,"Na(Succ)-","aq","cal",,-2.82,
-"OBIGT",1368,"K(Succ)-","aq","cal",,-2.39,
-"OBIGT",1374,"Th(Succ)+2","aq","cal",-1.21,-4.47,
-"OBIGT",1379,"NH4(Oxal)-","aq","cal",,-2.62,
-"OBIGT",1384,"Yb(Oxal)+","aq","cal",,-2.02,
-"OBIGT",1385,"Ce(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1386,"Nd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1387,"Eu(Oxal)+","aq","cal",,-1.89,
-"OBIGT",1388,"Gd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1389,"Ru(Oxal)+","aq","cal",,-2.41,
-"OBIGT",1390,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1391,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
-"OBIGT",1392,"U(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1394,"Y(Oxal)+","aq","cal",,-2.11,
-"OBIGT",1399,"La(Oxal)+","aq","cal",,-1.87,
-"OBIGT",1400,"Tb(Oxal)+","aq","cal",,-1.92,
-"OBIGT",1401,"Er(Oxal)+","aq","cal",,-2.05,
-"OBIGT",1402,"Lu(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1403,"Cr(Oxal)+","aq","cal",,-2.58,
-"OBIGT",1404,"Ga(Oxal)+","aq","cal",,-2.66,
-"OBIGT",1405,"Sc(Oxal)+","aq","cal",,-2.13,
-"OBIGT",1406,"In(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1407,"Sm(Oxal)+","aq","cal",,-1.84,
-"OBIGT",1408,"Cs(Mal)-","aq","cal",,-2.39,
-"OBIGT",1409,"NH4(Mal)-","aq","cal",,-2.54,
-"OBIGT",1414,"In(Mal)+","aq","cal",,-2.11,
-"OBIGT",1415,"Y(Mal)+","aq","cal",,-2.02,29999
-"OBIGT",1423,"La(Succ)+","aq","cal",,-1.52,
-"OBIGT",1424,"NH4(Succ)-","aq","cal",,-2.26,
-"OBIGT",1426,"Fe(Succ)+","aq","cal",,-1.92,
-"OBIGT",1427,"Sc(Succ)+","aq","cal",,-1.77,
-"OBIGT",1429,"Sm(Succ)+","aq","cal",,-1.48,
-"OBIGT",1430,"Er(Succ)+","aq","cal",,-1.68,
-"OBIGT",1431,"U(Succ)+2","aq","cal",-1.15,-4.27,
-"OBIGT",1435,"La(Glut)+","aq","cal",,-1.23,
-"OBIGT",1436,"Y(Glut)+","aq","cal",,-1.46,
-"OBIGT",1437,"Sc(Glut)+","aq","cal",,-1.5,
-"OBIGT",1438,"Th(Glut)+2","aq","cal",-1.09,-4.05,
-"OBIGT",1441,"Fe(Glut)+","aq","cal",,-1.05,
-"OBIGT",1442,"Sm(Glut)+","aq","cal",,-1.2,
-"OBIGT",1444,"Er(Glut)+","aq","cal",,-1.4,-4673
-"OBIGT",1446,"Ba(Adip)","aq","cal",,1.19,
-"OBIGT",1453,"Pb(Adip)","aq","cal",,1.25,
-"OBIGT",1454,"Sc(Adip)+","aq","cal",,-1.22,
-"OBIGT",1456,"Th(Adip)+2","aq","cal",-1.02,-3.76,
-"OBIGT",1457,"U(Adip)+2","aq","cal",-1,-3.71,
-"OBIGT",1459,"Li(Oxal)-","aq","cal",,-3.3,
-"OBIGT",1463,"Li(Succ)-","aq","cal",,-2.94,
-"OBIGT",1465,"Na(Glut)-","aq","cal",,-2.34,
-"OBIGT",1466,"K(Glut)-","aq","cal",,-2.05,
-"OBIGT",1467,"Li(Glut)-","aq","cal",,-2.66,
-"OBIGT",1472,"Na(Adip)-","aq","cal",,-2.05,
-"OBIGT",1473,"K(Adip)-","aq","cal",,-1.76,
-"OBIGT",1474,"Li(Adip)-","aq","cal",,-2.38,
-"OBIGT",1480,"cyclohexane","aq","cal",9.35,6.64,
-"OBIGT",1481,"Ar","aq","cal",-1.24,-8.59,
-"OBIGT",1482,"benzene","aq","cal",,-1.14,
-"OBIGT",1483,"CO2","aq","cal",-4.94,,
-"OBIGT",1484,"Xe","aq","cal",2.8,,
-"OBIGT",1492,"ethanethiol","aq","cal",,,753
-"OBIGT",1494,"n-butanethiol","aq","cal",2.19,,
-"OBIGT",1516,"methyldiethanolamine","aq","cal",1.61,,
-"OBIGT",1519,"dimethylamine","aq","J",-8.05,,
-"OBIGT",1533,"cysteinate","aq","cal",-1,,
-"OBIGT",1559,"glucose","aq","cal",1.11,,
-"OBIGT",1587,"guanine","aq","cal",-4.26,,
-"OBIGT",1631,"dHUMP-","aq","cal",-3.13,,
-"OBIGT",1728,"MgADP-","aq","cal",-1.01,,
-"OBIGT",1739,"HNicMP(ox)","aq","cal",,9.4,
-"OBIGT",1747,"ribose-5-phosphate","aq","cal",,7.48,
-"OBIGT",1749,"ribose-5-phosphate-2","aq","cal",1.53,,
-"OBIGT",1750,"H4NADP(red)","aq","cal",1.73,,
-"OBIGT",1751,"H3NADP(red)-","aq","cal",2.41,,
-"OBIGT",1752,"H2NADP(red)-2","aq","cal",1.28,,
-"OBIGT",1753,"HNADP(red)-3","aq","cal",2.09,,
-"OBIGT",1754,"NADP(red)-4","aq","cal",1.09,,
-"OBIGT",1756,"H3NADP(ox)","aq","cal",1.05,,
-"OBIGT",1827,"diglycine+","aq","cal",-177.69,,
-"OBIGT",1828,"diglycine-","aq","cal",-49.22,,565
-"OBIGT",1829,"triglycine+","aq","cal",,1.75,
-"OBIGT",1830,"triglycine-","aq","cal",,1.78,
-"OBIGT",1889,"hydromagnesite","cr","cal",,,-2569
-"OBIGT",1966,"jarosite","cr","cal",,,20697
-"OBIGT",1967,"natrojarosite","cr","cal",,,17554
-"OBIGT",1975,"realgar,alpha","cr","J",,,768
-"OBIGT",1976,"realgar,beta","cr","J",,,989
-"OBIGT",1977,"orpiment","cr","J",,,-1036
-"OBIGT",1985,"dawsonite","cr","J",,,19466
-"OBIGT",1987,"ferberite","cr","J",1.21,,
-"OBIGT",2016,"octadecane","cr","cal",-2.63,,
-"OBIGT",2017,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2018,"eicosane","cr","cal",-2.79,,
-"OBIGT",2019,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2020,"docosane","cr","cal",-2.63,,
-"OBIGT",2021,"tricosane","cr","cal",-5.22,,
-"OBIGT",2022,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2023,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2024,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2025,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2077,"carbazole","cr","cal",-43.39,,
-"OBIGT",2118,"triphenylene","cr","cal",,,541
-"OBIGT",2431,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2589,"ethylene","gas","cal",-4.59,,
-"OBIGT",2599,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2909,"nonacontane","liq","cal",,,635
-"OBIGT",2916,"2-methyloctane","liq","cal",10,,
-"OBIGT",3329,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",852,"Fe(CO3)2-2","aq","cal",,,-4792
+"OBIGT",853,"Zn(CO3)2-2","aq","cal",,,-4724
+"OBIGT",854,"Cu(CO3)2-2","aq","cal",,,-4929
+"OBIGT",855,"Pb(CO3)2-2","aq","cal",,,-6676
+"OBIGT",872,"CH4","aq","cal",-2.61,,
+"OBIGT",877,"hexane","aq","cal",1.43,3.21,
+"OBIGT",880,"ethylene","aq","cal",6.12,-3.82,
+"OBIGT",904,"propanol","aq","cal",-1.89,,
+"OBIGT",951,"La(Ac)2+","aq","cal",,,-779
+"OBIGT",954,"Sm(Ac)+2","aq","cal",,,-660
+"OBIGT",955,"Sm(Ac)2+","aq","cal",,,-621
+"OBIGT",968,"Ca(Ac)2","aq","cal",,,-1006
+"OBIGT",984,"La(Ac)3","aq","cal",,,-564
+"OBIGT",1004,"Ce(Ac)+2","aq","cal",,,797
+"OBIGT",1005,"Ce(Ac)2+","aq","cal",,,567
+"OBIGT",1033,"urea","aq","cal",-23.26,23.32,
+"OBIGT",1046,"propanoic acid","aq","cal",1.42,,
+"OBIGT",1065,"pimelic acid","aq","cal",,,-19931
+"OBIGT",1069,"formate","aq","cal",1.96,,
+"OBIGT",1071,"propanoate","aq","cal",1.68,,
+"OBIGT",1078,"n-decanoate","aq","cal",-1.93,,
+"OBIGT",1094,"oxalate-2","aq","cal",-3.19,,
+"OBIGT",1135,"Fe(For)+","aq","cal",,,587
+"OBIGT",1136,"Fe(For)2","aq","cal",,,639
+"OBIGT",1208,"Mg(But)2","aq","cal",,,-3347811
+"OBIGT",1237,"Yb(But)+2","aq","cal",,,665
+"OBIGT",1256,"Fe(Pent)2","aq","cal",,,532
+"OBIGT",1341,"Ba(HCO3)+","aq","cal",,,-5800
+"OBIGT",1361,"Li(Mal)-","aq","cal",,-3.22,
+"OBIGT",1365,"Pb(Mal)","aq","cal",,1.16,
+"OBIGT",1369,"Pb(Succ)","aq","cal",,1.49,
+"OBIGT",1370,"Na(Oxal)-","aq","cal",,-3.14,
+"OBIGT",1371,"K(Oxal)-","aq","cal",,-2.75,
+"OBIGT",1372,"Fe(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1374,"Na(Mal)-","aq","cal",,-3.11,17018
+"OBIGT",1375,"K(Mal)-","aq","cal",,-2.63,17013
+"OBIGT",1377,"La(Mal)+","aq","cal",,-1.92,
+"OBIGT",1378,"Gd(Mal)+","aq","cal",,-1.73,
+"OBIGT",1379,"Lu(Mal)+","aq","cal",,-2.25,
+"OBIGT",1380,"Yb(Mal)+","aq","cal",,-2.05,
+"OBIGT",1381,"Th(Mal)+2","aq","cal",-1.29,-4.79,
+"OBIGT",1383,"Ce(Mal)+","aq","cal",,-1.75,
+"OBIGT",1384,"Nd(Mal)+","aq","cal",4.52,,
+"OBIGT",1385,"Sm(Mal)+","aq","cal",,-1.77,
+"OBIGT",1386,"Pr(Mal)+","aq","cal",,-1.75,
+"OBIGT",1387,"Eu(Mal)+","aq","cal",,-1.87,
+"OBIGT",1388,"Tb(Mal)+","aq","cal",,-1.92,
+"OBIGT",1389,"Dy(Mal)+","aq","cal",,-1.89,
+"OBIGT",1390,"Tm(Mal)+","aq","cal",,-2.08,
+"OBIGT",1391,"Ho(Mal)+","aq","cal",,-2.08,
+"OBIGT",1392,"Er(Mal)+","aq","cal",,-2.11,
+"OBIGT",1393,"Sc(Mal)+","aq","cal",,-1.97,
+"OBIGT",1394,"Fe(Mal)+","aq","cal",,-1.97,
+"OBIGT",1395,"Na(Succ)-","aq","cal",,-2.82,
+"OBIGT",1396,"K(Succ)-","aq","cal",,-2.39,
+"OBIGT",1402,"Th(Succ)+2","aq","cal",-1.21,-4.47,
+"OBIGT",1407,"NH4(Oxal)-","aq","cal",,-2.62,
+"OBIGT",1412,"Yb(Oxal)+","aq","cal",,-2.02,
+"OBIGT",1413,"Ce(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1414,"Nd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1415,"Eu(Oxal)+","aq","cal",,-1.89,
+"OBIGT",1416,"Gd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1417,"Ru(Oxal)+","aq","cal",,-2.41,
+"OBIGT",1418,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1419,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
+"OBIGT",1420,"U(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1422,"Y(Oxal)+","aq","cal",,-2.11,
+"OBIGT",1427,"La(Oxal)+","aq","cal",,-1.87,
+"OBIGT",1428,"Tb(Oxal)+","aq","cal",,-1.92,
+"OBIGT",1429,"Er(Oxal)+","aq","cal",,-2.05,
+"OBIGT",1430,"Lu(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1431,"Cr(Oxal)+","aq","cal",,-2.58,
+"OBIGT",1432,"Ga(Oxal)+","aq","cal",,-2.66,
+"OBIGT",1433,"Sc(Oxal)+","aq","cal",,-2.13,
+"OBIGT",1434,"In(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1435,"Sm(Oxal)+","aq","cal",,-1.84,
+"OBIGT",1436,"Cs(Mal)-","aq","cal",,-2.39,
+"OBIGT",1437,"NH4(Mal)-","aq","cal",,-2.54,
+"OBIGT",1442,"In(Mal)+","aq","cal",,-2.11,
+"OBIGT",1443,"Y(Mal)+","aq","cal",,-2.02,29999
+"OBIGT",1451,"La(Succ)+","aq","cal",,-1.52,
+"OBIGT",1452,"NH4(Succ)-","aq","cal",,-2.26,
+"OBIGT",1454,"Fe(Succ)+","aq","cal",,-1.92,
+"OBIGT",1455,"Sc(Succ)+","aq","cal",,-1.77,
+"OBIGT",1457,"Sm(Succ)+","aq","cal",,-1.48,
+"OBIGT",1458,"Er(Succ)+","aq","cal",,-1.68,
+"OBIGT",1459,"U(Succ)+2","aq","cal",-1.15,-4.27,
+"OBIGT",1463,"La(Glut)+","aq","cal",,-1.23,
+"OBIGT",1464,"Y(Glut)+","aq","cal",,-1.46,
+"OBIGT",1465,"Sc(Glut)+","aq","cal",,-1.5,
+"OBIGT",1466,"Th(Glut)+2","aq","cal",-1.09,-4.05,
+"OBIGT",1469,"Fe(Glut)+","aq","cal",,-1.05,
+"OBIGT",1470,"Sm(Glut)+","aq","cal",,-1.2,
+"OBIGT",1472,"Er(Glut)+","aq","cal",,-1.4,-4673
+"OBIGT",1474,"Ba(Adip)","aq","cal",,1.19,
+"OBIGT",1481,"Pb(Adip)","aq","cal",,1.25,
+"OBIGT",1482,"Sc(Adip)+","aq","cal",,-1.22,
+"OBIGT",1484,"Th(Adip)+2","aq","cal",-1.02,-3.76,
+"OBIGT",1485,"U(Adip)+2","aq","cal",-1,-3.71,
+"OBIGT",1487,"Li(Oxal)-","aq","cal",,-3.3,
+"OBIGT",1491,"Li(Succ)-","aq","cal",,-2.94,
+"OBIGT",1493,"Na(Glut)-","aq","cal",,-2.34,
+"OBIGT",1494,"K(Glut)-","aq","cal",,-2.05,
+"OBIGT",1495,"Li(Glut)-","aq","cal",,-2.66,
+"OBIGT",1500,"Na(Adip)-","aq","cal",,-2.05,
+"OBIGT",1501,"K(Adip)-","aq","cal",,-1.76,
+"OBIGT",1502,"Li(Adip)-","aq","cal",,-2.38,
+"OBIGT",1508,"cyclohexane","aq","cal",9.35,6.64,
+"OBIGT",1509,"Ar","aq","cal",-1.24,-8.59,
+"OBIGT",1510,"benzene","aq","cal",,-1.14,
+"OBIGT",1511,"CO2","aq","cal",-4.94,,
+"OBIGT",1512,"Xe","aq","cal",2.8,,
+"OBIGT",1520,"ethanethiol","aq","cal",,,753
+"OBIGT",1522,"n-butanethiol","aq","cal",2.19,,
+"OBIGT",1544,"methyldiethanolamine","aq","cal",1.61,,
+"OBIGT",1547,"dimethylamine","aq","J",-8.05,,
+"OBIGT",1561,"cysteinate","aq","cal",-1,,
+"OBIGT",1587,"glucose","aq","cal",1.11,,
+"OBIGT",1615,"guanine","aq","cal",-4.26,,
+"OBIGT",1659,"dHUMP-","aq","cal",-3.13,,
+"OBIGT",1756,"MgADP-","aq","cal",-1.01,,
+"OBIGT",1767,"HNicMP(ox)","aq","cal",,9.4,
+"OBIGT",1775,"ribose-5-phosphate","aq","cal",,7.48,
+"OBIGT",1777,"ribose-5-phosphate-2","aq","cal",1.53,,
+"OBIGT",1778,"H4NADP(red)","aq","cal",1.73,,
+"OBIGT",1779,"H3NADP(red)-","aq","cal",2.41,,
+"OBIGT",1780,"H2NADP(red)-2","aq","cal",1.28,,
+"OBIGT",1781,"HNADP(red)-3","aq","cal",2.09,,
+"OBIGT",1782,"NADP(red)-4","aq","cal",1.09,,
+"OBIGT",1784,"H3NADP(ox)","aq","cal",1.05,,
+"OBIGT",1855,"diglycine+","aq","cal",-177.69,,
+"OBIGT",1856,"diglycine-","aq","cal",-49.22,,565
+"OBIGT",1857,"triglycine+","aq","cal",,1.75,
+"OBIGT",1858,"triglycine-","aq","cal",,1.78,
+"OBIGT",1917,"hydromagnesite","cr","cal",,,-2569
+"OBIGT",1994,"jarosite","cr","cal",,,20697
+"OBIGT",1995,"natrojarosite","cr","cal",,,17554
+"OBIGT",2003,"realgar,alpha","cr","J",,,768
+"OBIGT",2004,"realgar,beta","cr","J",,,989
+"OBIGT",2005,"orpiment","cr","J",,,-1036
+"OBIGT",2013,"dawsonite","cr","J",,,19466
+"OBIGT",2015,"ferberite","cr","J",1.21,,
+"OBIGT",2044,"octadecane","cr","cal",-2.63,,
+"OBIGT",2045,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2046,"eicosane","cr","cal",-2.79,,
+"OBIGT",2047,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2048,"docosane","cr","cal",-2.63,,
+"OBIGT",2049,"tricosane","cr","cal",-5.22,,
+"OBIGT",2050,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2051,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2052,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2053,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2105,"carbazole","cr","cal",-43.39,,
+"OBIGT",2146,"triphenylene","cr","cal",,,541
+"OBIGT",2459,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2617,"ethylene","gas","cal",-4.59,,
+"OBIGT",2627,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2937,"nonacontane","liq","cal",,,635
+"OBIGT",2944,"2-methyloctane","liq","cal",10,,
+"OBIGT",3357,"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
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2020-09-18 04:20:07 UTC (rev 607)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2020-10-04 21:50:21 UTC (rev 608)
@@ -1462,6 +1462,17 @@
doi = {10.1111/j.1525-1314.1992.tb00109.x},
}
+ at Article{SPD+19,
+ author = {St Clair, Brian and Pottenger, Justin and Debes, Randall and Hanselmann, Kurt and Shock, Everett L.},
+ journal = {ACS Earth and Space Chemistry},
+ title = {{D}istinguishing biotic and abiotic iron oxidation at low temperatures},
+ year = {2019},
+ number = {6},
+ pages = {905--921},
+ volume = {3},
+ doi = {10.1021/acsearthspacechem.9b00016},
+}
+
@Article{LA19,
author = {Douglas E. LaRowe and Jan P. Amend},
journal = {Geomicrobiology Journal},
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