[CHNOSZ-commits] r682 - 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
Mon Sep 27 03:53:11 CEST 2021
Author: jedick
Date: 2021-09-27 03:53:11 +0200 (Mon, 27 Sep 2021)
New Revision: 682
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.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 H2WO4 and Cp of scheelite (CaWO4) from Liu et al., 2021
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-09-27 00:17:09 UTC (rev 681)
+++ pkg/CHNOSZ/DESCRIPTION 2021-09-27 01:53:11 UTC (rev 682)
@@ -1,6 +1,6 @@
Date: 2021-09-27
Package: CHNOSZ
-Version: 1.4.1-8
+Version: 1.4.1-9
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 2021-09-27 00:17:09 UTC (rev 681)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2021-09-27 01:53:11 UTC (rev 682)
@@ -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 1.4.1-7 (2021-07-09)}{
+\section{Changes in CHNOSZ version 1.4.1-9 (2021-09-27)}{
\subsection{OBIGT DATABASE}{
\itemize{
@@ -21,6 +21,10 @@
acids). This file is now available in the JMDplots package.
\item Fix formula of CaCl2 in DEW.csv. Thanks to Grayson Boyer.
+
+ \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)}.
}
}
@@ -28,8 +32,7 @@
\subsection{OTHER CHANGES}{
\itemize{
- \item \strong{multi-metal.Rmd} now has a link to the paper published in
- *Applied Computing & Geosciences*
+ \item \strong{multi-metal.Rmd} now has a link to the associated paper
(\href{https://doi.org/10.1016/j.acags.2021.100059}{Dick, 2021}).
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2021-09-27 00:17:09 UTC (rev 681)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2021-09-27 01:53:11 UTC (rev 682)
@@ -879,3 +879,4 @@
TaOF3,NA,TaOF3,aq,AKK+20,NA,2021-03-20,cal,-353531,-365642,66.51,-11.173,-118.44,-14.654,-40.226,14.7116,-1.1161,-5.405,-5.0203,-0.5386,0
HNbO3F-,NA,HNbO3F-,aq,AKK+20,NA,2021-03-20,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,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,cal,-232653,-276736.39,-10.757,125.839,-114.547,-13.9096,-41.7437,22.1569,-1.0533,79.916,22.5989,0,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2021-09-27 00:17:09 UTC (rev 681)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2021-09-27 01:53:11 UTC (rev 682)
@@ -132,7 +132,7 @@
boehmite,NA,AlO(OH),cr,HRA91,ZZL+16.2,2017-10-17,J,-918400,-996400,37.19,54.24,19.535,169.4,-17.2,2.9131,-1955.6,0,0,0,NA
gibbsite,NA,Al(OH)3,cr,RHF78.3,ZZL+16.2,2017-10-17,J,-1154889,-1293128,68.44,91.7,NA,92.8,189.438,1.3387,-1034.3,0,0,0,NA
dawsonite,NA,NaAlCO3(OH)2,cr,ZZL+16.3,RH95.2,2019-04-16,J,-1782300,-1939100,137.7,142.6,59.3,34.41,334.7,7.464,0,0,0,0,NA
-scheelite,NA,CaWO4,cr,WS00,BK73,2019-01-22,J,-1538361,-1645150,126.4,NA,47.05,134.6,20.7,-24.4,0,0,0,0,1000
+scheelite,NA,CaWO4,cr,WS00,LXW21.1,2021-09-27,J,-1538361,-1645150,126.4,113.32,47.05,232.15,-42.9,1.6,-1912.3,2.75,0,0,1000
ferberite,NA,FeWO4,cr,WS00,Pol90,2019-09-10,J,-1085200,NA,131.8,115.73,40.38,68.87,188.3,0,0,-9.08,0,0,1000
arsenopyrite,NA,FeAsS,cr,PPB+08,NA,2020-07-27,J,-136450,-144360,68.5,68.44,26.27,75.51,4.78,-7.543,0,0,0,0,900
loellingite,NA,FeAs2,cr,PPB+08,NA,2020-07-27,J,-80230,-85770,80.1,70.83,27.44,76.69,3.1,-6.03,0,0,0,0,1300
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2021-09-27 00:17:09 UTC (rev 681)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2021-09-27 01:53:11 UTC (rev 682)
@@ -4,7 +4,6 @@
Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https://www.worldcat.org/oclc/693388901
Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,https://www.worldcat.org/oclc/14154245
PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",https://www.worldcat.org/oclc/14154292
-BK73,"I. Barin and O. Knacke",1973,"Thermochemical Properties of Inorganic Substances","scheelite Cp",https://www.worldcat.org/oclc/695258
BKK77,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","willemite Cp",https://www.worldcat.org/oclc/695258
HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals and phase transitions",https://www.worldcat.org/oclc/13594862
HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","litharge S, V, and Cp parameters",https://www.worldcat.org/oclc/13594862
@@ -276,3 +275,5 @@
AKK+20,"N. N. Akinfiev et al.",2020,"Geochim. Cosmochim. Acta 280, 102-115","Nb and Ta species",https://doi.org/10.1016/j.gca.2020.04.009
LX20,"Liu and Xiao",2020,"Ore Geol. Rev. 117, 103289","huebnerite Cp",https://doi.org/10.1016/j.oregeorev.2019.103289
MP20,"Materials Project",2020,"mp-1513: Co9S8","Co-pentlandite V calculated from density of Co<sub>9</sub>S<sub>8</sub> from Materials Project",https://doi.org/10.17188/1191033
+LXW21,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","H2WO4",https://doi.org/10.1016/j.chemgeo.2021.120488
+LXW21.1,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","scheelite Cp",https://doi.org/10.1016/j.chemgeo.2021.120488
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2021-09-27 00:17:09 UTC (rev 681)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2021-09-27 01:53:11 UTC (rev 682)
@@ -127,169 +127,168 @@
"OBIGT",877,"NbO3-","aq","cal",-1.51,,
"OBIGT",879,"TaO3-","aq","cal",-1.61,,
"OBIGT",883,"HTaO3F-","aq","cal",-1.15,-1.91,
-"OBIGT",888,"hexane","aq","cal",1.43,3.21,
-"OBIGT",891,"ethylene","aq","cal",6.12,-3.82,
-"OBIGT",915,"propanol","aq","cal",-1.89,,
-"OBIGT",962,"La(Ac)2+","aq","cal",,,-779
-"OBIGT",965,"Sm(Ac)+2","aq","cal",,,-660
-"OBIGT",966,"Sm(Ac)2+","aq","cal",,,-621
-"OBIGT",979,"Ca(Ac)2","aq","cal",,,-1006
-"OBIGT",995,"La(Ac)3","aq","cal",,,-564
-"OBIGT",1015,"Ce(Ac)+2","aq","cal",,,797
-"OBIGT",1016,"Ce(Ac)2+","aq","cal",,,567
-"OBIGT",1044,"urea","aq","cal",-23.26,23.32,
-"OBIGT",1057,"propanoic acid","aq","cal",1.42,,
-"OBIGT",1080,"formate","aq","cal",1.96,,
-"OBIGT",1082,"propanoate","aq","cal",1.68,,
-"OBIGT",1089,"n-decanoate","aq","cal",-1.93,,
-"OBIGT",1105,"oxalate-2","aq","cal",-3.19,,
-"OBIGT",1146,"Fe(For)+","aq","cal",,,587
-"OBIGT",1147,"Fe(For)2","aq","cal",,,639
-"OBIGT",1219,"Mg(But)2","aq","cal",,,-3347811
-"OBIGT",1248,"Yb(But)+2","aq","cal",,,665
-"OBIGT",1267,"Fe(Pent)2","aq","cal",,,532
-"OBIGT",1352,"Ba(HCO3)+","aq","cal",,,-5800
-"OBIGT",1372,"Li(Mal)-","aq","cal",,-3.22,
-"OBIGT",1376,"Pb(Mal)","aq","cal",,1.16,
-"OBIGT",1380,"Pb(Succ)","aq","cal",,1.49,
-"OBIGT",1381,"Na(Oxal)-","aq","cal",,-3.14,
-"OBIGT",1382,"K(Oxal)-","aq","cal",,-2.75,
-"OBIGT",1383,"Fe(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1385,"Na(Mal)-","aq","cal",,-3.11,17018
-"OBIGT",1386,"K(Mal)-","aq","cal",,-2.63,17013
-"OBIGT",1388,"La(Mal)+","aq","cal",,-1.92,
-"OBIGT",1389,"Gd(Mal)+","aq","cal",,-1.73,
-"OBIGT",1390,"Lu(Mal)+","aq","cal",,-2.25,
-"OBIGT",1391,"Yb(Mal)+","aq","cal",,-2.05,
-"OBIGT",1392,"Th(Mal)+2","aq","cal",-1.29,-4.79,
-"OBIGT",1394,"Ce(Mal)+","aq","cal",,-1.75,
-"OBIGT",1395,"Nd(Mal)+","aq","cal",4.52,,
-"OBIGT",1396,"Sm(Mal)+","aq","cal",,-1.77,
-"OBIGT",1397,"Pr(Mal)+","aq","cal",,-1.75,
-"OBIGT",1398,"Eu(Mal)+","aq","cal",,-1.87,
-"OBIGT",1399,"Tb(Mal)+","aq","cal",,-1.92,
-"OBIGT",1400,"Dy(Mal)+","aq","cal",,-1.89,
-"OBIGT",1401,"Tm(Mal)+","aq","cal",,-2.08,
-"OBIGT",1402,"Ho(Mal)+","aq","cal",,-2.08,
-"OBIGT",1403,"Er(Mal)+","aq","cal",,-2.11,
-"OBIGT",1404,"Sc(Mal)+","aq","cal",,-1.97,
-"OBIGT",1405,"Fe(Mal)+","aq","cal",,-1.97,
-"OBIGT",1406,"Na(Succ)-","aq","cal",,-2.82,
-"OBIGT",1407,"K(Succ)-","aq","cal",,-2.39,
-"OBIGT",1413,"Th(Succ)+2","aq","cal",-1.21,-4.47,
-"OBIGT",1418,"NH4(Oxal)-","aq","cal",,-2.62,
-"OBIGT",1423,"Yb(Oxal)+","aq","cal",,-2.02,
-"OBIGT",1424,"Ce(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1425,"Nd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1426,"Eu(Oxal)+","aq","cal",,-1.89,
-"OBIGT",1427,"Gd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1428,"Ru(Oxal)+","aq","cal",,-2.41,
-"OBIGT",1429,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1430,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
-"OBIGT",1431,"U(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1433,"Y(Oxal)+","aq","cal",,-2.11,
-"OBIGT",1438,"La(Oxal)+","aq","cal",,-1.87,
-"OBIGT",1439,"Tb(Oxal)+","aq","cal",,-1.92,
-"OBIGT",1440,"Er(Oxal)+","aq","cal",,-2.05,
-"OBIGT",1441,"Lu(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1442,"Cr(Oxal)+","aq","cal",,-2.58,
-"OBIGT",1443,"Ga(Oxal)+","aq","cal",,-2.66,
-"OBIGT",1444,"Sc(Oxal)+","aq","cal",,-2.13,
-"OBIGT",1445,"In(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1446,"Sm(Oxal)+","aq","cal",,-1.84,
-"OBIGT",1447,"Cs(Mal)-","aq","cal",,-2.39,
-"OBIGT",1448,"NH4(Mal)-","aq","cal",,-2.54,
-"OBIGT",1453,"In(Mal)+","aq","cal",,-2.11,
-"OBIGT",1454,"Y(Mal)+","aq","cal",,-2.02,29999
-"OBIGT",1462,"La(Succ)+","aq","cal",,-1.52,
-"OBIGT",1463,"NH4(Succ)-","aq","cal",,-2.26,
-"OBIGT",1465,"Fe(Succ)+","aq","cal",,-1.92,
-"OBIGT",1466,"Sc(Succ)+","aq","cal",,-1.77,
-"OBIGT",1468,"Sm(Succ)+","aq","cal",,-1.48,
-"OBIGT",1469,"Er(Succ)+","aq","cal",,-1.68,
-"OBIGT",1470,"U(Succ)+2","aq","cal",-1.15,-4.27,
-"OBIGT",1474,"La(Glut)+","aq","cal",,-1.23,
-"OBIGT",1475,"Y(Glut)+","aq","cal",,-1.46,
-"OBIGT",1476,"Sc(Glut)+","aq","cal",,-1.5,
-"OBIGT",1477,"Th(Glut)+2","aq","cal",-1.09,-4.05,
-"OBIGT",1480,"Fe(Glut)+","aq","cal",,-1.05,
-"OBIGT",1481,"Sm(Glut)+","aq","cal",,-1.2,
-"OBIGT",1483,"Er(Glut)+","aq","cal",,-1.4,-4673
-"OBIGT",1485,"Ba(Adip)","aq","cal",,1.19,
-"OBIGT",1492,"Pb(Adip)","aq","cal",,1.25,
-"OBIGT",1493,"Sc(Adip)+","aq","cal",,-1.22,
-"OBIGT",1495,"Th(Adip)+2","aq","cal",-1.02,-3.76,
-"OBIGT",1496,"U(Adip)+2","aq","cal",-1,-3.71,
-"OBIGT",1498,"Li(Oxal)-","aq","cal",,-3.3,
-"OBIGT",1502,"Li(Succ)-","aq","cal",,-2.94,
-"OBIGT",1504,"Na(Glut)-","aq","cal",,-2.34,
-"OBIGT",1505,"K(Glut)-","aq","cal",,-2.05,
-"OBIGT",1506,"Li(Glut)-","aq","cal",,-2.66,
-"OBIGT",1511,"Na(Adip)-","aq","cal",,-2.05,
-"OBIGT",1512,"K(Adip)-","aq","cal",,-1.76,
-"OBIGT",1513,"Li(Adip)-","aq","cal",,-2.38,
-"OBIGT",1519,"cyclohexane","aq","cal",9.35,6.64,
-"OBIGT",1520,"benzene","aq","cal",,-1.14,
-"OBIGT",1528,"ethanethiol","aq","cal",,,753
-"OBIGT",1530,"n-butanethiol","aq","cal",2.19,,
-"OBIGT",1552,"methyldiethanolamine","aq","cal",1.61,,
-"OBIGT",1555,"dimethylamine","aq","J",-8.05,,
-"OBIGT",1562,"oleate","aq","J",,,39179
-"OBIGT",1563,"palmitoleate","aq","J",,,-242150
-"OBIGT",1567,"heptose","aq","J",,,-75027
-"OBIGT",1571,"N-acetylmuramic acid","aq","J",,,-38589
-"OBIGT",1572,"ethanolamine","aq","J",,,4598
-"OBIGT",1584,"cysteinate","aq","cal",-1,,
-"OBIGT",1610,"glucose","aq","cal",1.11,,
-"OBIGT",1638,"guanine","aq","cal",-4.26,,
-"OBIGT",1682,"dHUMP-","aq","cal",-3.13,,
-"OBIGT",1779,"MgADP-","aq","cal",-1.01,,
-"OBIGT",1790,"HNicMP(ox)","aq","cal",,9.4,
-"OBIGT",1798,"ribose-5-phosphate","aq","cal",,7.48,
-"OBIGT",1800,"ribose-5-phosphate-2","aq","cal",1.53,,
-"OBIGT",1801,"H4NADP(red)","aq","cal",1.73,,
-"OBIGT",1802,"H3NADP(red)-","aq","cal",2.41,,
-"OBIGT",1803,"H2NADP(red)-2","aq","cal",1.28,,
-"OBIGT",1804,"HNADP(red)-3","aq","cal",2.09,,
-"OBIGT",1805,"NADP(red)-4","aq","cal",1.09,,
-"OBIGT",1807,"H3NADP(ox)","aq","cal",1.05,,
-"OBIGT",1878,"diglycine+","aq","cal",-177.69,,
-"OBIGT",1879,"diglycine-","aq","cal",-49.22,,565
-"OBIGT",1880,"triglycine+","aq","cal",,1.75,
-"OBIGT",1881,"triglycine-","aq","cal",,1.78,
-"OBIGT",1941,"hydromagnesite","cr","cal",,,-2569
-"OBIGT",2018,"jarosite","cr","cal",,,20697
-"OBIGT",2019,"natrojarosite","cr","cal",,,17554
-"OBIGT",2027,"realgar,alpha","cr","J",,,768
-"OBIGT",2028,"realgar,beta","cr","J",,,989
-"OBIGT",2029,"orpiment","cr","J",,,-1036
-"OBIGT",2037,"dawsonite","cr","J",,,19466
-"OBIGT",2039,"ferberite","cr","J",1.21,,
-"OBIGT",2052,"Co-pentlandite","cr","cal",,,-3630
-"OBIGT",2055,"willemite","cr","J",-1.47,,
-"OBIGT",2074,"octadecane","cr","cal",-2.63,,
-"OBIGT",2075,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2076,"eicosane","cr","cal",-2.79,,
-"OBIGT",2077,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2078,"docosane","cr","cal",-2.63,,
-"OBIGT",2079,"tricosane","cr","cal",-5.22,,
-"OBIGT",2080,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2081,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2082,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2083,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2135,"carbazole","cr","cal",-43.39,,
-"OBIGT",2176,"triphenylene","cr","cal",,,541
-"OBIGT",2489,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2647,"ethylene","gas","cal",-4.59,,
-"OBIGT",2657,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2967,"nonacontane","liq","cal",,,635
-"OBIGT",2974,"2-methyloctane","liq","cal",10,,
-"OBIGT",3387,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",889,"hexane","aq","cal",1.43,3.21,
+"OBIGT",892,"ethylene","aq","cal",6.12,-3.82,
+"OBIGT",916,"propanol","aq","cal",-1.89,,
+"OBIGT",963,"La(Ac)2+","aq","cal",,,-779
+"OBIGT",966,"Sm(Ac)+2","aq","cal",,,-660
+"OBIGT",967,"Sm(Ac)2+","aq","cal",,,-621
+"OBIGT",980,"Ca(Ac)2","aq","cal",,,-1006
+"OBIGT",996,"La(Ac)3","aq","cal",,,-564
+"OBIGT",1016,"Ce(Ac)+2","aq","cal",,,797
+"OBIGT",1017,"Ce(Ac)2+","aq","cal",,,567
+"OBIGT",1045,"urea","aq","cal",-23.26,23.32,
+"OBIGT",1058,"propanoic acid","aq","cal",1.42,,
+"OBIGT",1081,"formate","aq","cal",1.96,,
+"OBIGT",1083,"propanoate","aq","cal",1.68,,
+"OBIGT",1090,"n-decanoate","aq","cal",-1.93,,
+"OBIGT",1106,"oxalate-2","aq","cal",-3.19,,
+"OBIGT",1147,"Fe(For)+","aq","cal",,,587
+"OBIGT",1148,"Fe(For)2","aq","cal",,,639
+"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",1373,"Li(Mal)-","aq","cal",,-3.22,
+"OBIGT",1377,"Pb(Mal)","aq","cal",,1.16,
+"OBIGT",1381,"Pb(Succ)","aq","cal",,1.49,
+"OBIGT",1382,"Na(Oxal)-","aq","cal",,-3.14,
+"OBIGT",1383,"K(Oxal)-","aq","cal",,-2.75,
+"OBIGT",1384,"Fe(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1386,"Na(Mal)-","aq","cal",,-3.11,17018
+"OBIGT",1387,"K(Mal)-","aq","cal",,-2.63,17013
+"OBIGT",1389,"La(Mal)+","aq","cal",,-1.92,
+"OBIGT",1390,"Gd(Mal)+","aq","cal",,-1.73,
+"OBIGT",1391,"Lu(Mal)+","aq","cal",,-2.25,
+"OBIGT",1392,"Yb(Mal)+","aq","cal",,-2.05,
+"OBIGT",1393,"Th(Mal)+2","aq","cal",-1.29,-4.79,
+"OBIGT",1395,"Ce(Mal)+","aq","cal",,-1.75,
+"OBIGT",1396,"Nd(Mal)+","aq","cal",4.52,,
+"OBIGT",1397,"Sm(Mal)+","aq","cal",,-1.77,
+"OBIGT",1398,"Pr(Mal)+","aq","cal",,-1.75,
+"OBIGT",1399,"Eu(Mal)+","aq","cal",,-1.87,
+"OBIGT",1400,"Tb(Mal)+","aq","cal",,-1.92,
+"OBIGT",1401,"Dy(Mal)+","aq","cal",,-1.89,
+"OBIGT",1402,"Tm(Mal)+","aq","cal",,-2.08,
+"OBIGT",1403,"Ho(Mal)+","aq","cal",,-2.08,
+"OBIGT",1404,"Er(Mal)+","aq","cal",,-2.11,
+"OBIGT",1405,"Sc(Mal)+","aq","cal",,-1.97,
+"OBIGT",1406,"Fe(Mal)+","aq","cal",,-1.97,
+"OBIGT",1407,"Na(Succ)-","aq","cal",,-2.82,
+"OBIGT",1408,"K(Succ)-","aq","cal",,-2.39,
+"OBIGT",1414,"Th(Succ)+2","aq","cal",-1.21,-4.47,
+"OBIGT",1419,"NH4(Oxal)-","aq","cal",,-2.62,
+"OBIGT",1424,"Yb(Oxal)+","aq","cal",,-2.02,
+"OBIGT",1425,"Ce(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1426,"Nd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1427,"Eu(Oxal)+","aq","cal",,-1.89,
+"OBIGT",1428,"Gd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1429,"Ru(Oxal)+","aq","cal",,-2.41,
+"OBIGT",1430,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1431,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
+"OBIGT",1432,"U(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1434,"Y(Oxal)+","aq","cal",,-2.11,
+"OBIGT",1439,"La(Oxal)+","aq","cal",,-1.87,
+"OBIGT",1440,"Tb(Oxal)+","aq","cal",,-1.92,
+"OBIGT",1441,"Er(Oxal)+","aq","cal",,-2.05,
+"OBIGT",1442,"Lu(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1443,"Cr(Oxal)+","aq","cal",,-2.58,
+"OBIGT",1444,"Ga(Oxal)+","aq","cal",,-2.66,
+"OBIGT",1445,"Sc(Oxal)+","aq","cal",,-2.13,
+"OBIGT",1446,"In(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1447,"Sm(Oxal)+","aq","cal",,-1.84,
+"OBIGT",1448,"Cs(Mal)-","aq","cal",,-2.39,
+"OBIGT",1449,"NH4(Mal)-","aq","cal",,-2.54,
+"OBIGT",1454,"In(Mal)+","aq","cal",,-2.11,
+"OBIGT",1455,"Y(Mal)+","aq","cal",,-2.02,29999
+"OBIGT",1463,"La(Succ)+","aq","cal",,-1.52,
+"OBIGT",1464,"NH4(Succ)-","aq","cal",,-2.26,
+"OBIGT",1466,"Fe(Succ)+","aq","cal",,-1.92,
+"OBIGT",1467,"Sc(Succ)+","aq","cal",,-1.77,
+"OBIGT",1469,"Sm(Succ)+","aq","cal",,-1.48,
+"OBIGT",1470,"Er(Succ)+","aq","cal",,-1.68,
+"OBIGT",1471,"U(Succ)+2","aq","cal",-1.15,-4.27,
+"OBIGT",1475,"La(Glut)+","aq","cal",,-1.23,
+"OBIGT",1476,"Y(Glut)+","aq","cal",,-1.46,
+"OBIGT",1477,"Sc(Glut)+","aq","cal",,-1.5,
+"OBIGT",1478,"Th(Glut)+2","aq","cal",-1.09,-4.05,
+"OBIGT",1481,"Fe(Glut)+","aq","cal",,-1.05,
+"OBIGT",1482,"Sm(Glut)+","aq","cal",,-1.2,
+"OBIGT",1484,"Er(Glut)+","aq","cal",,-1.4,-4673
+"OBIGT",1486,"Ba(Adip)","aq","cal",,1.19,
+"OBIGT",1493,"Pb(Adip)","aq","cal",,1.25,
+"OBIGT",1494,"Sc(Adip)+","aq","cal",,-1.22,
+"OBIGT",1496,"Th(Adip)+2","aq","cal",-1.02,-3.76,
+"OBIGT",1497,"U(Adip)+2","aq","cal",-1,-3.71,
+"OBIGT",1499,"Li(Oxal)-","aq","cal",,-3.3,
+"OBIGT",1503,"Li(Succ)-","aq","cal",,-2.94,
+"OBIGT",1505,"Na(Glut)-","aq","cal",,-2.34,
+"OBIGT",1506,"K(Glut)-","aq","cal",,-2.05,
+"OBIGT",1507,"Li(Glut)-","aq","cal",,-2.66,
+"OBIGT",1512,"Na(Adip)-","aq","cal",,-2.05,
+"OBIGT",1513,"K(Adip)-","aq","cal",,-1.76,
+"OBIGT",1514,"Li(Adip)-","aq","cal",,-2.38,
+"OBIGT",1520,"cyclohexane","aq","cal",9.35,6.64,
+"OBIGT",1521,"benzene","aq","cal",,-1.14,
+"OBIGT",1529,"ethanethiol","aq","cal",,,753
+"OBIGT",1531,"n-butanethiol","aq","cal",2.19,,
+"OBIGT",1553,"methyldiethanolamine","aq","cal",1.61,,
+"OBIGT",1556,"dimethylamine","aq","J",-8.05,,
+"OBIGT",1563,"oleate","aq","J",,,39179
+"OBIGT",1564,"palmitoleate","aq","J",,,-242150
+"OBIGT",1568,"heptose","aq","J",,,-75027
+"OBIGT",1572,"N-acetylmuramic acid","aq","J",,,-38589
+"OBIGT",1573,"ethanolamine","aq","J",,,4598
+"OBIGT",1585,"cysteinate","aq","cal",-1,,
+"OBIGT",1611,"glucose","aq","cal",1.11,,
+"OBIGT",1639,"guanine","aq","cal",-4.26,,
+"OBIGT",1683,"dHUMP-","aq","cal",-3.13,,
+"OBIGT",1780,"MgADP-","aq","cal",-1.01,,
+"OBIGT",1791,"HNicMP(ox)","aq","cal",,9.4,
+"OBIGT",1799,"ribose-5-phosphate","aq","cal",,7.48,
+"OBIGT",1801,"ribose-5-phosphate-2","aq","cal",1.53,,
+"OBIGT",1802,"H4NADP(red)","aq","cal",1.73,,
+"OBIGT",1803,"H3NADP(red)-","aq","cal",2.41,,
+"OBIGT",1804,"H2NADP(red)-2","aq","cal",1.28,,
+"OBIGT",1805,"HNADP(red)-3","aq","cal",2.09,,
+"OBIGT",1806,"NADP(red)-4","aq","cal",1.09,,
+"OBIGT",1808,"H3NADP(ox)","aq","cal",1.05,,
+"OBIGT",1879,"diglycine+","aq","cal",-177.69,,
+"OBIGT",1880,"diglycine-","aq","cal",-49.22,,565
+"OBIGT",1881,"triglycine+","aq","cal",,1.75,
+"OBIGT",1882,"triglycine-","aq","cal",,1.78,
+"OBIGT",1942,"hydromagnesite","cr","cal",,,-2569
+"OBIGT",2019,"jarosite","cr","cal",,,20697
+"OBIGT",2020,"natrojarosite","cr","cal",,,17554
+"OBIGT",2028,"realgar,alpha","cr","J",,,768
+"OBIGT",2029,"realgar,beta","cr","J",,,989
+"OBIGT",2030,"orpiment","cr","J",,,-1036
+"OBIGT",2038,"dawsonite","cr","J",,,19466
+"OBIGT",2040,"ferberite","cr","J",1.21,,
+"OBIGT",2053,"Co-pentlandite","cr","cal",,,-3630
+"OBIGT",2056,"willemite","cr","J",-1.47,,
+"OBIGT",2075,"octadecane","cr","cal",-2.63,,
+"OBIGT",2076,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2077,"eicosane","cr","cal",-2.79,,
+"OBIGT",2078,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2079,"docosane","cr","cal",-2.63,,
+"OBIGT",2080,"tricosane","cr","cal",-5.22,,
+"OBIGT",2081,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2082,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2083,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2084,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2136,"carbazole","cr","cal",-43.39,,
+"OBIGT",2177,"triphenylene","cr","cal",,,541
+"OBIGT",2490,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2648,"ethylene","gas","cal",-4.59,,
+"OBIGT",2658,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2968,"nonacontane","liq","cal",,,635
+"OBIGT",2975,"2-methyloctane","liq","cal",10,,
+"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",24,"CaCl+","aq","cal",,,-593
-"DEW",25,"CaCl2","aq","cal",,,-7937
"DEW",26,"CaCO3","aq","cal",,,661
"DEW",31,"Ce+4","aq","cal",,-1.13,
"DEW",37,"CO3-2","aq","cal",,-1.41,
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2021-09-27 00:17:09 UTC (rev 681)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2021-09-27 01:53:11 UTC (rev 682)
@@ -118,17 +118,17 @@
}
@PhdThesis{Dic07,
- author = {Dick, Jeffrey Michael},
- title = {{C}alculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments},
- school = {University of California},
- year = {2007},
- type = {Ph.D. dissertation},
+ author = {Dick, Jeffrey Michael},
+ school = {University of California},
+ title = {{C}alculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments},
+ year = {2007},
+ type = {Ph.D. dissertation},
}
@Article{DEH+13,
author = {Dick, Jeffrey M. and Evans, Katy A. and Holman, Alex I. and Jaraula, Caroline M. B. and Grice, Kliti},
journal = {Geochimica et Cosmochimica Acta},
- title = {{E}stimation and application of the thermodynamic properties of aqueous phenanthrene and isomers of methylphenanthrene at high temperature},
+ title = {Estimation and application of the thermodynamic properties of aqueous phenanthrene and isomers of methylphenanthrene at high temperature},
year = {2013},
pages = {247--266},
volume = {122},
@@ -138,7 +138,7 @@
@Article{DLH06,
author = {Dick, Jeffrey M. and LaRowe, Douglas E. and Helgeson, Harold C.},
journal = {Biogeosciences},
- title = {{T}emperature, pressure, and electrochemical constraints on protein speciation: {G}roup additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins},
+ title = {Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins},
year = {2006},
number = {3},
pages = {311--336},
@@ -164,7 +164,6 @@
year = {1984},
address = {Washington, D. C.},
pages = {320},
- url = {https://www.worldcat.org/oclc/858456124},
}
@Article{HSS95,
@@ -231,6 +230,7 @@
volume = {281},
doi = {10.2475/ajs.281.10.1249},
size = {268 p.},
+ sourceid = {ISI:A1981MZ34200001},
}
@Article{HOKR98,
@@ -289,7 +289,7 @@
@Article{Kit14,
author = {Kitadai, Norio},
- journal = {Journal of Molecular Evolution},
+ journal = {J. Mol. Evol.},
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},
@@ -311,8 +311,8 @@
@Article{LD12,
author = {LaRowe, Douglas E. and Dick, Jeffrey M.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the standard molal thermodynamic properties of crystalline peptides},
+ journal = {Geochim. Cosmochim. Acta},
+ title = {Calculation of the standard molal thermodynamic properties of crystalline peptides},
year = {2012},
pages = {70--91},
volume = {80},
@@ -892,7 +892,7 @@
@Article{WEP+82,
author = {Wagman, Donald D. and Evans, William H. and Parker, Vivian B. and Schumm, Richard H. and Halow, Iva and Bailey, Sylvia M. and Churney, Kenneth L. and Nuttall, Ralph L.},
- journal = {Journal of Physical and Chemical Reference Data},
+ journal = {J. Phys. Chem. Ref. Data},
title = {{T}he {NBS} tables of chemical thermodynamic properties. {S}elected values for inorganic and {C}\textsubscript{1} and {C}\textsubscript{2} organic substances in {SI} units},
year = {1982},
number = {Suppl. 2},
@@ -1390,6 +1390,7 @@
journal = {Geochemistry International},
title = {{T}hermodynamic properties of platinum chloride complexes in aqueous solutions: {D}erivation of consistent parameters from literature data and experiments on {P}t$_\text{(cr)}$ solubility at 400--475°{C} and 1 kbar},
year = {2015},
+ month = {Apr},
number = {4},
pages = {327--340},
volume = {53},
@@ -1434,6 +1435,7 @@
journal = {American Mineralogist},
title = {{T}hermodynamic properties of the {T}schermak solid solution in {F}e-chlorite: {A}pplication to natural examples and possible role of oxidation},
year = {2005},
+ month = feb,
number = {2-3},
pages = {347--358},
volume = {90},
@@ -1724,3 +1726,13 @@
year = {2020},
doi = {10.17188/1191033},
}
+
+ at Article{LXW21,
+ author = {Xiangchong Liu and Changhao Xiao and Yong Wang},
+ journal = {Chemical Geology},
+ title = {The relative solubilities of wolframite and scheelite in hydrothermal fluids: Insights from thermodynamic modeling},
+ year = {2021},
+ pages = {120488},
+ volume = {584},
+ doi = {10.1016/j.chemgeo.2021.120488},
+}
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