[CHNOSZ-commits] r587 - 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 Jul 27 02:52:38 CEST 2020
Author: jedick
Date: 2020-07-27 02:52:35 +0200 (Mon, 27 Jul 2020)
New Revision: 587
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/CHECKLIST
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
pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
OBIGT: Add As-bearing species from Perfetti et al., 2008
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-26 14:54:53 UTC (rev 586)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-27 00:52:35 UTC (rev 587)
@@ -1,6 +1,6 @@
-Date: 2020-07-26
+Date: 2020-07-27
Package: CHNOSZ
-Version: 1.3.6-60
+Version: 1.3.6-61
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/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2020-07-26 14:54:53 UTC (rev 586)
+++ pkg/CHNOSZ/inst/CHECKLIST 2020-07-27 00:52:35 UTC (rev 587)
@@ -38,7 +38,7 @@
- Rebuild extdata/adds/OBIGT_check.csv after all data updates:
(not used elsewhere in CHNOSZ, but helpful to see which
- species data have self inconsistencies):
+ species entries have self inconsistencies):
co <- check.OBIGT()
write.csv(co, "OBIGT_check.csv", row.names=FALSE, na="")
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2020-07-26 14:54:53 UTC (rev 586)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-07-27 00:52:35 UTC (rev 587)
@@ -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 1.3.6-59 (2020-07-26)}{
+\section{Changes in CHNOSZ version 1.3.6-61 (2020-07-27)}{
\subsection{MAJOR CHANGES}{
\itemize{
@@ -18,13 +18,13 @@
\strong{methane} now applies exclusively to the gas; the formula
\strong{CH4} without a state continues to represent the aqueous species.
This behavior is consistent with inorganic gases but differs from most
- organic substances, where the English name refers to the aqueous species.
- This change was made because in the past there was no way to use
- \code{info()} or \code{subcrt()} with a single character argument to
- identify gaseous methane, which is common in geochemistry. (Note that
- \code{info("CH4", "gas")} can still be used.) A hack to revert to the old
- behavior, where \strong{methane} refers primarily to the aqueous species,
- is \code{mod.OBIGT(info("CH4"), name = "methane")}.
+ organic substances, where the name refers to the aqueous species. This
+ change was made because in the past there was no way to use \code{info()}
+ or \code{subcrt()} with a single character argument to identify gaseous
+ methane, which is common in geochemistry. (Note that \code{info("CH4",
+ "gas")} can still be used.) A hack to revert to the old behavior, where
+ \strong{methane} refers primarily to the aqueous species, is
+ \code{mod.OBIGT(info("CH4"), name = "methane")}.
\item The all-uppercase acronym \strong{OBIGT} is used everywhere it
appears in file, function, and object names. In particular, the
@@ -64,12 +64,13 @@
\item Add a \strong{stable} argument to \code{mosaic()} to use previously
calculated stabilities of species (e.g. minerals) for the changing basis
- species. This allows \code{mosaic()} calculations to be linked in series,
- for instance to sequentially add metals (Fe, then Cu) to a diagram.
+ species. This allows \code{mosaic()} calculations to be linked in series
+ (or "stacked"), for instance to sequentially add metals (Fe, then Cu) to
+ a diagram.
\item Add vignette \strong{multi-metal.Rmd} for examples that use these
- new features to make diagrams for minerals with multiple metals
- (specifically Fe and Cu).
+ new features to make diagrams for systems with multiple metals
+ (specifically Fe-V and Fe-Cu).
}
}
@@ -77,33 +78,36 @@
\subsection{CHANGES TO OBIGT DATABASE}{
\itemize{
- \item Update species parameters for the 2019 Deep Earth Water (DEW)
- model.
+ \item Update species parameters for the 2019 version of the Deep Earth
+ Water (DEW) model (\href{https://doi.org/10.1016/j.gca.2019.03.027}{Huang
+ and Sverjensky, 2019}).
- \item \samp{OBIGT/SUPCRT92.csv}: Change lowercase to uppercase "A"
+ \item \samp{inorganic_aq.csv}, \samp{inorganic_aq.csv}: Add arsenopyrite,
+ loellingite, westerveldite, and aqueous As(OH)\s{3} and AsO(OH)\s{3} from
+ \href{https://doi.org/10.1016/j.gca.2007.11.017}{Perfetti et al., 2008}.
+
+ \item Add GHS for almandine, dickite, fluorphlogopite, glaucophane,
+ grunerite, larnite, pyrope (\samp{SUPCRT92.csv}) and bromellite
+ (\samp{inorganic_cr.csv}) from
+ \href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway, 1995}.
+
+ \item \samp{inorganic_cr.csv}: Correct formulas for number of \H2O in
+ some As-bearing minerals.
+
+ \item \samp{SUPCRT92.csv}: Change lowercase to uppercase "A"
(Angstrom) in names of minerals with suffixes indicating interlayer
spacing (amesite, clinochlore, cronstedtite, daphnite).
- \item \samp{OBIGT/inorganic_aq.csv}: Update arsenopyrite with data from
- Naumov et al., 1974 (via Unitherm).
+ \item Remove bracketed suffixes in references (e.g. [S92] was used to
+ indicate that the data first appeared in \acronym{SUPCRT92}).
- \item \samp{OBIGT/inorganic_cr.csv}: Correct syntax for number of \H2O in
- formulas of some As-bearing minerals.
-
- \item Install bibtex file (\samp{docs/OBIGT.bib}) for use in the
- \pkg{logKcalc} package (\url{https://github.com/jedick/logKcalc}).
-
\item Use uncompressed data files (i.e. \samp{.csv}, not \samp{.csv.xz})
and rename \samp{DEW_aq.csv} to \samp{DEW.csv}.
- \item Remove old data file suffixes in references (e.g. [S92] was used to
- indicate that the data first appeared in \acronym{SUPCRT92}).
+ \item The package is now installed with the bibtex file for the OBIGT
+ database (\samp{docs/OBIGT.bib}), which is used by the \pkg{logKcalc}
+ package (\url{https://github.com/jedick/logKcalc}).
- \item Add GHS for almandine, dickite, fluorphlogopite, glaucophane,
- grunerite, larnite, pyrope (\samp{SUPCRT92.csv}) and bromellite
- (\samp{inorganic_cr.csv}) from
- \href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway, 1995}.
-
}
}
@@ -114,22 +118,19 @@
comproportionation, after
\href{https://doi.org/10.1111/1462-2920.14982}{Amend et al., 2020}.
- \item Convert \samp{equilibrium.Rnw} to \samp{equilibrium.Rmd} and revise
- and simplify content.
+ \item Revise and simplify \samp{anintro.Rmd} and \samp{equilibrium.Rmd}
+ (converted from \samp{equilibrium.Rnw}).
\item Revise \samp{OBIGT.Rmd} to reduce the size of the HTML file and
make deep linking to individual sections work.
- \item Remove vignette \samp{hotspring.Rnw}, demo \samp{bison.R}, and
- associated data files \samp{DS11.csv} and \samp{DS13.csv}. The plots are
- now in the \samp{bison.Rmd} vignette in the \pkg{JMDplots} package
- (\url{https://github.com/jedick/JMDplots}). Also move the demo
- \samp{bugstab.R} and supporting data files to \pkg{JMDplots}.
-
\item Add \samp{viglink} Rd macro so HTML versions of Rd files can link
to vignettes.
- \item \samp{anintro.Rmd} has been made considerably shorter.
+ \item Remove vignette \samp{hotspring.Rnw} and demos \samp{bison.R} and
+ \samp{bugstab.R}. The material is now in the \samp{bison.Rmd} vignette
+ and \samp{bugstab.R} demo in the \pkg{JMDplots} package
+ (\url{https://github.com/jedick/JMDplots}).
}
}
@@ -138,31 +139,33 @@
\itemize{
\item Change default resolution in \code{affinity()} from 128 to 256.
+ This greatly improves the appearance of diagrams made with the default
+ settings.
+ \item \code{which.pmax()} was rewritten to speed up identification of
+ predominant species, and the drawing of field boundaries in \code{diagram()}
+ was made more efficient. The latter change has prompted the removal of
+ the \samp{lty.aq} and \samp{lty.cr} arguments from \code{diagram()}.
+
\item Add a \strong{bottom} argument to \code{ratlab()} to allow changing
the ion in the denominator to something other than \Hplus.
- \item The \strong{srt} argument in \code{diagram()} now can be used to
+ \item The \strong{srt} argument in \code{diagram()} can now be used to
rotate field labels, not only line labels. This and other arguments
- (\strong{cex}, \strong{col}, \strong{font}, \strong{family},
- \strong{bold}, \strong{italic}) now can have length > 1 to apply
- different settings to each species.
+ (\strong{cex}, \strong{col}, \strong{col.names}, \strong{font},
+ \strong{family}, \strong{bold}, \strong{italic}) can have length > 1 to
+ apply different settings to each species.
\item Add a \strong{min.area} argument to \code{diagram()} to specify the
minimum area of fields that should be labeled. This is useful for
- removing labels from small fields on very crowded diagrams.
+ removing labels from small fields on crowded diagrams.
- \item The list returned by diagram \code{diagram()} now includes a
- \code{predominant.values} component, which has the affinities of the
+ \item The list returned by \code{diagram()} now includes a
+ \strong{predominant.values} component, which has the affinities of the
predominant species at each grid point. This can be used as shown in the
\code{multi-metal.Rmd} vignette to compute the Pourbaix energy
(Δ\emph{G}\s{pbx}) for a metastable material.
- \item \code{which.pmax()} was rewritten to speed up identification of
- stable species, and \code{diagram()} was made more efficient in drawing
- field boundaries. The latter change has prompted the removal of the
- \samp{lty.aq} and \samp{lty.cr} arguments from \code{diagram()}.
-
}
}
@@ -169,17 +172,17 @@
\subsection{OTHER CHANGES}{
\itemize{
- \item \code{subcrt()}: change \strong{action.unbalanced} argument to
+ \item \code{subcrt()}: replace \samp{action.unbalanced} argument with
\strong{autobalance}, which now provides the ability to prevent
autobalancing.
- \item Setting the water model with \code{water()} now updates the
- literature references in \code{thermo()$OBIGT}.
+ \item Setting the water model with \code{water()} updates the literature
+ references in \code{thermo()$OBIGT}.
- \item \code{thermo.refs()} now shows CHNOSZ version and date.
+ \item \code{thermo.refs()} shows CHNOSZ version and date.
- \item \code{subcrt()} and \code{affinity()} use degree symbol in messages
- (\strong{°C}).
+ \item \code{subcrt()} and \code{affinity()} use degree symbol
+ (\strong{°C}) in messages.
\item Change \code{thermo$...} to \code{thermo()$...} in messages and
comments.
@@ -191,8 +194,9 @@
package-anchored link(s) in documentation object} in \command{R CMD
check}.
- \item Remove \code{wjd()} and demo and supporting data file
- \samp{DLEN67.csv}.
+ \item Remove \code{wjd()} (implementation of Gibbs energy minimization
+ method from \href{https://doi.org/10.1063/1.1744264}{White et al., 1958})
+ and demo \code{wjd.R} and supporting data file.
\item Convert this NEWS file to Rd format.
@@ -208,8 +212,6 @@
\item TODO: refresh extdata/supcrt/compare.R
- \item TODO: get arsenopyrite from Perfetti et al., 2008
-
\item TODO: make separate directories for default and optional data files
\item TODO: diagram(): make error or warning for NA values of affinity
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2020-07-26 14:54:53 UTC (rev 586)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2020-07-27 00:52:35 UTC (rev 587)
@@ -836,3 +836,5 @@
PtCl3-,NA,PtCl3-,aq,TBB15,NA,10.Oct.18,cal,-58216,-80732,29.95,187.4,41.6,7.8523,11.3912,1.2727,-3.2499,126.7713,35.1357,1.1679,-1
PtCl4-2,NA,PtCl4-2,aq,TBB15,NA,10.Oct.18,cal,-91665,-125004,35.9,-47.5,73.28,12.7049,23.2396,-3.3844,-3.7397,3.166,-12.7168,2.6993,-2
S3-,NA,S3-,aq,PD15,NA,02.Aug.18,cal,13160,10840,28.6,62.3,37.7,2.5,19.9,9.2,-3.6,50.2,9.6,0.8,-1
+As(OH)3,NA,As(OH)3,aq,PPB+08.1,NA,27.Jul.20,J,-639800,-737300,212.4,85,47.5,45.2,16.1,43.7,-18,186.2,-47.7,0.52,0
+AsO(OH)3,NA,AsO(OH)3,aq,PPB+08.1,NA,27.Jul.20,J,-766300,-898600,198.3,105,53,48.1,11.7,54.4,-12.6,198.7,-42.1,1,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2020-07-26 14:54:53 UTC (rev 586)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2020-07-27 00:52:35 UTC (rev 587)
@@ -134,4 +134,6 @@
dawsonite,NA,NaAlCO3(OH)2,cr,ZZL+16.3,RH95.2,16.Apr.19,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,BK73,22.Jan.19,J,-1538361,-1645150,126.4,NA,47.05,134.6,20.7,-24.4,0,0,0,0,1000
ferberite,NA,FeWO4,cr,WS00,Pol90,10.Sep.19,J,-1085200,NA,131.8,115.73,40.38,68.87,188.3,0,0,-9.08,0,0,1000
-arsenopyrite,NA,FeAsS,cr,NRK74,SB99,16.Jun.20,J,-109621,NA,108.4,NA,26.42,62.886,40.58,-1.423,0,0,0,0,NA
+arsenopyrite,NA,FeAsS,cr,PPB+08,NA,27.Jul.20,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,27.Jul.20,J,-80230,-85770,80.1,70.83,27.44,76.69,3.1,-6.03,0,0,0,0,1300
+westerveldite,NA,FeAs,cr,PPB+08,NA,27.Jul.20,J,-43360,-43510,62.5,50.36,16.64,27.95,46.5,7.6,0,0,0,0,1250
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-07-26 14:54:53 UTC (rev 586)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-07-27 00:52:35 UTC (rev 587)
@@ -5,7 +5,6 @@
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
-NRK74,"G. B. Naumov, B. N. Ryzhenko and I. L. Khodakovskii",1974,"Handbook of Thermodynamic Data, U. S. Geological Survey, Water Resources Division",arsenopyrite,https://trove.nla.gov.au/work/22192707
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
HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",https://www.worldcat.org/oclc/13594862
@@ -115,7 +114,6 @@
MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253",actinides,http://rimg.geoscienceworld.org/content/38/1/221
PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5
PSK99.1,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","Al(Mal)<sup>+</sup> and Al(Oxal)<sup>+</sup>",https://doi.org/10.1016/S0016-7037(99)00146-5
-SB99,"Yu. Shvarov and E. Bastrakov",1999,"HCh: A software package for geochemical equilibrium modelling. User's Guide","data from HCh Unitherm database",http://pid.geoscience.gov.au/dataset/ga/25473
SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",https://doi.org/10.2138/rmg.2000.40.9
TDDZ00,"B. R. Tagirov et al.",2000,"Chem. Geol. 162, 193-219",FeCl<sup>+2</sup>,https://doi.org/10.2138/rmg.2000.40.9
WS00,"S. A. Wood and I. M. Samson",2000,"Econ. Geol. 95, 143-182","scheelite and ferberite; GHS and V of scheelite and V of ferberite are from @RHF78.",https://doi.org/10.2113/gsecongeo.95.1.143
@@ -169,7 +167,9 @@
SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high-temperature HKF parameters from @AP01",http://geopig.asu.edu/?q=tools
ZW07,"S. P. Ziemer and E. M. Woolley",2007,"J. Chem. Thermodynamics 39, 645-666",glutamate,https://doi.org/10.1016/j.jct.2006.08.008
Ric08,"L. Richard",2008,"personal communication",alkenes,
-GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805 - 6815","kieserite, starkeyite, hexahydrite, and epsomite",https://doi.org/10.1016/j.gca.2009.08.005
+PPB+08,"E. Perfetti et al.",2008,"Geochim. Cosmochim. Acta 72, 713-731","arsenopyrite, loellingite, and westerveldite",https://doi.org/10.1016/j.gca.2007.11.017
+PPB+08.1,"E. Perfetti et al.",2008,"Geochim. Cosmochim. Acta 72, 713-731","As(OH)<sub>3</sub> and AsO(OH)<sub>3</sub>",https://doi.org/10.1016/j.gca.2007.11.017
+GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805-6815","kieserite, starkeyite, hexahydrite, and epsomite",https://doi.org/10.1016/j.gca.2009.08.005
HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695",kerogens,https://doi.org/10.1016/j.gca.2008.03.004
LRB09,"K. H. Lemke, R. J. Rosenbauer and D. K. Bird",2009,"Astrobiology 9, 141-146","diglycine and diketopiperazine",https://doi.org/10.1089/ast.2008.0166
AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-07-26 14:54:53 UTC (rev 586)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-07-27 00:52:35 UTC (rev 587)
@@ -111,162 +111,162 @@
"OBIGT",806,"CuHS","aq","cal",7.35,-16.2,
"OBIGT",814,"ZnO2-2","aq","cal",,-1.17,
"OBIGT",840,"S3-","aq","cal",,,661
-"OBIGT",841,"CH4","aq","cal",-2.61,,
-"OBIGT",846,"hexane","aq","cal",1.43,3.21,
-"OBIGT",849,"ethylene","aq","cal",6.12,-3.82,
-"OBIGT",873,"propanol","aq","cal",-1.89,,
-"OBIGT",920,"La(Ac)2+","aq","cal",,,-779
-"OBIGT",923,"Sm(Ac)+2","aq","cal",,,-660
-"OBIGT",924,"Sm(Ac)2+","aq","cal",,,-621
-"OBIGT",937,"Ca(Ac)2","aq","cal",,,-1006
-"OBIGT",953,"La(Ac)3","aq","cal",,,-564
-"OBIGT",973,"Ce(Ac)+2","aq","cal",,,797
-"OBIGT",974,"Ce(Ac)2+","aq","cal",,,567
-"OBIGT",1002,"urea","aq","cal",-23.26,23.32,
-"OBIGT",1015,"propanoic acid","aq","cal",1.42,,
-"OBIGT",1034,"pimelic acid","aq","cal",,,-19931
-"OBIGT",1038,"formate","aq","cal",1.96,,
-"OBIGT",1040,"propanoate","aq","cal",1.68,,
-"OBIGT",1047,"n-decanoate","aq","cal",-1.93,,
-"OBIGT",1063,"oxalate-2","aq","cal",-3.19,,
-"OBIGT",1104,"Fe(For)+","aq","cal",,,587
-"OBIGT",1105,"Fe(For)2","aq","cal",,,639
-"OBIGT",1177,"Mg(But)2","aq","cal",,,-3347811
-"OBIGT",1206,"Yb(But)+2","aq","cal",,,665
-"OBIGT",1225,"Fe(Pent)2","aq","cal",,,532
-"OBIGT",1310,"Ba(HCO3)+","aq","cal",,,-5800
-"OBIGT",1330,"Li(Mal)-","aq","cal",,-3.22,
-"OBIGT",1334,"Pb(Mal)","aq","cal",,1.16,
-"OBIGT",1338,"Pb(Succ)","aq","cal",,1.49,
-"OBIGT",1339,"Na(Oxal)-","aq","cal",,-3.14,
-"OBIGT",1340,"K(Oxal)-","aq","cal",,-2.75,
-"OBIGT",1341,"Fe(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1343,"Na(Mal)-","aq","cal",,-3.11,17018
-"OBIGT",1344,"K(Mal)-","aq","cal",,-2.63,17013
-"OBIGT",1346,"La(Mal)+","aq","cal",,-1.92,
-"OBIGT",1347,"Gd(Mal)+","aq","cal",,-1.73,
-"OBIGT",1348,"Lu(Mal)+","aq","cal",,-2.25,
-"OBIGT",1349,"Yb(Mal)+","aq","cal",,-2.05,
-"OBIGT",1350,"Th(Mal)+2","aq","cal",-1.29,-4.79,
-"OBIGT",1352,"Ce(Mal)+","aq","cal",,-1.75,
-"OBIGT",1353,"Nd(Mal)+","aq","cal",4.52,,
-"OBIGT",1354,"Sm(Mal)+","aq","cal",,-1.77,
-"OBIGT",1355,"Pr(Mal)+","aq","cal",,-1.75,
-"OBIGT",1356,"Eu(Mal)+","aq","cal",,-1.87,
-"OBIGT",1357,"Tb(Mal)+","aq","cal",,-1.92,
-"OBIGT",1358,"Dy(Mal)+","aq","cal",,-1.89,
-"OBIGT",1359,"Tm(Mal)+","aq","cal",,-2.08,
-"OBIGT",1360,"Ho(Mal)+","aq","cal",,-2.08,
-"OBIGT",1361,"Er(Mal)+","aq","cal",,-2.11,
-"OBIGT",1362,"Sc(Mal)+","aq","cal",,-1.97,
-"OBIGT",1363,"Fe(Mal)+","aq","cal",,-1.97,
-"OBIGT",1364,"Na(Succ)-","aq","cal",,-2.82,
-"OBIGT",1365,"K(Succ)-","aq","cal",,-2.39,
-"OBIGT",1371,"Th(Succ)+2","aq","cal",-1.21,-4.47,
-"OBIGT",1376,"NH4(Oxal)-","aq","cal",,-2.62,
-"OBIGT",1381,"Yb(Oxal)+","aq","cal",,-2.02,
-"OBIGT",1382,"Ce(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1383,"Nd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1384,"Eu(Oxal)+","aq","cal",,-1.89,
-"OBIGT",1385,"Gd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1386,"Ru(Oxal)+","aq","cal",,-2.41,
-"OBIGT",1387,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1388,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
-"OBIGT",1389,"U(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1391,"Y(Oxal)+","aq","cal",,-2.11,
-"OBIGT",1396,"La(Oxal)+","aq","cal",,-1.87,
-"OBIGT",1397,"Tb(Oxal)+","aq","cal",,-1.92,
-"OBIGT",1398,"Er(Oxal)+","aq","cal",,-2.05,
-"OBIGT",1399,"Lu(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1400,"Cr(Oxal)+","aq","cal",,-2.58,
-"OBIGT",1401,"Ga(Oxal)+","aq","cal",,-2.66,
-"OBIGT",1402,"Sc(Oxal)+","aq","cal",,-2.13,
-"OBIGT",1403,"In(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1404,"Sm(Oxal)+","aq","cal",,-1.84,
-"OBIGT",1405,"Cs(Mal)-","aq","cal",,-2.39,
-"OBIGT",1406,"NH4(Mal)-","aq","cal",,-2.54,
-"OBIGT",1411,"In(Mal)+","aq","cal",,-2.11,
-"OBIGT",1412,"Y(Mal)+","aq","cal",,-2.02,29999
-"OBIGT",1420,"La(Succ)+","aq","cal",,-1.52,
-"OBIGT",1421,"NH4(Succ)-","aq","cal",,-2.26,
-"OBIGT",1423,"Fe(Succ)+","aq","cal",,-1.92,
-"OBIGT",1424,"Sc(Succ)+","aq","cal",,-1.77,
-"OBIGT",1426,"Sm(Succ)+","aq","cal",,-1.48,
-"OBIGT",1427,"Er(Succ)+","aq","cal",,-1.68,
-"OBIGT",1428,"U(Succ)+2","aq","cal",-1.15,-4.27,
-"OBIGT",1432,"La(Glut)+","aq","cal",,-1.23,
-"OBIGT",1433,"Y(Glut)+","aq","cal",,-1.46,
-"OBIGT",1434,"Sc(Glut)+","aq","cal",,-1.5,
-"OBIGT",1435,"Th(Glut)+2","aq","cal",-1.09,-4.05,
-"OBIGT",1438,"Fe(Glut)+","aq","cal",,-1.05,
-"OBIGT",1439,"Sm(Glut)+","aq","cal",,-1.2,
-"OBIGT",1441,"Er(Glut)+","aq","cal",,-1.4,-4673
-"OBIGT",1443,"Ba(Adip)","aq","cal",,1.19,
-"OBIGT",1450,"Pb(Adip)","aq","cal",,1.25,
-"OBIGT",1451,"Sc(Adip)+","aq","cal",,-1.22,
-"OBIGT",1453,"Th(Adip)+2","aq","cal",-1.02,-3.76,
-"OBIGT",1454,"U(Adip)+2","aq","cal",-1,-3.71,
-"OBIGT",1456,"Li(Oxal)-","aq","cal",,-3.3,
-"OBIGT",1460,"Li(Succ)-","aq","cal",,-2.94,
-"OBIGT",1462,"Na(Glut)-","aq","cal",,-2.34,
-"OBIGT",1463,"K(Glut)-","aq","cal",,-2.05,
-"OBIGT",1464,"Li(Glut)-","aq","cal",,-2.66,
-"OBIGT",1469,"Na(Adip)-","aq","cal",,-2.05,
-"OBIGT",1470,"K(Adip)-","aq","cal",,-1.76,
-"OBIGT",1471,"Li(Adip)-","aq","cal",,-2.38,
-"OBIGT",1477,"cyclohexane","aq","cal",9.35,6.64,
-"OBIGT",1478,"Ar","aq","cal",-1.24,-8.59,
-"OBIGT",1479,"benzene","aq","cal",,-1.14,
-"OBIGT",1480,"CO2","aq","cal",-4.94,,
-"OBIGT",1481,"Xe","aq","cal",2.8,,
-"OBIGT",1489,"ethanethiol","aq","cal",,,753
-"OBIGT",1491,"n-butanethiol","aq","cal",2.19,,
-"OBIGT",1513,"methyldiethanolamine","aq","cal",1.61,,
-"OBIGT",1516,"dimethylamine","aq","J",-8.05,,
-"OBIGT",1530,"cysteinate","aq","cal",-1,,
-"OBIGT",1556,"glucose","aq","cal",1.11,,
-"OBIGT",1584,"guanine","aq","cal",-4.26,,
-"OBIGT",1628,"dHUMP-","aq","cal",-3.13,,
-"OBIGT",1725,"MgADP-","aq","cal",-1.01,,
-"OBIGT",1736,"HNicMP(ox)","aq","cal",,9.4,
-"OBIGT",1744,"ribose-5-phosphate","aq","cal",,7.48,
-"OBIGT",1746,"ribose-5-phosphate-2","aq","cal",1.53,,
-"OBIGT",1747,"H4NADP(red)","aq","cal",1.73,,
-"OBIGT",1748,"H3NADP(red)-","aq","cal",2.41,,
-"OBIGT",1749,"H2NADP(red)-2","aq","cal",1.28,,
-"OBIGT",1750,"HNADP(red)-3","aq","cal",2.09,,
-"OBIGT",1751,"NADP(red)-4","aq","cal",1.09,,
-"OBIGT",1753,"H3NADP(ox)","aq","cal",1.05,,
-"OBIGT",1824,"diglycine+","aq","cal",-177.69,,
-"OBIGT",1825,"diglycine-","aq","cal",-49.22,,565
-"OBIGT",1826,"triglycine+","aq","cal",,1.75,
-"OBIGT",1827,"triglycine-","aq","cal",,1.78,
-"OBIGT",1886,"hydromagnesite","cr","cal",,,-2569
-"OBIGT",1964,"jarosite","cr","cal",,,20697
-"OBIGT",1965,"natrojarosite","cr","cal",,,17554
-"OBIGT",1973,"realgar,alpha","cr","J",,,768
-"OBIGT",1974,"realgar,beta","cr","J",,,989
-"OBIGT",1975,"orpiment","cr","J",,,-1036
-"OBIGT",1983,"dawsonite","cr","J",,,19466
-"OBIGT",1985,"ferberite","cr","J",1.21,,
-"OBIGT",2005,"octadecane","cr","cal",-2.63,,
-"OBIGT",2006,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2007,"eicosane","cr","cal",-2.79,,
-"OBIGT",2008,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2009,"docosane","cr","cal",-2.63,,
-"OBIGT",2010,"tricosane","cr","cal",-5.22,,
-"OBIGT",2011,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2012,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2013,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2014,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2066,"carbazole","cr","cal",-43.39,,
-"OBIGT",2107,"triphenylene","cr","cal",,,541
-"OBIGT",2420,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2578,"ethylene","gas","cal",-4.59,,
-"OBIGT",2588,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2898,"nonacontane","liq","cal",,,635
-"OBIGT",2905,"2-methyloctane","liq","cal",10,,
-"OBIGT",3318,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",843,"CH4","aq","cal",-2.61,,
+"OBIGT",848,"hexane","aq","cal",1.43,3.21,
+"OBIGT",851,"ethylene","aq","cal",6.12,-3.82,
+"OBIGT",875,"propanol","aq","cal",-1.89,,
+"OBIGT",922,"La(Ac)2+","aq","cal",,,-779
+"OBIGT",925,"Sm(Ac)+2","aq","cal",,,-660
+"OBIGT",926,"Sm(Ac)2+","aq","cal",,,-621
+"OBIGT",939,"Ca(Ac)2","aq","cal",,,-1006
+"OBIGT",955,"La(Ac)3","aq","cal",,,-564
+"OBIGT",975,"Ce(Ac)+2","aq","cal",,,797
+"OBIGT",976,"Ce(Ac)2+","aq","cal",,,567
+"OBIGT",1004,"urea","aq","cal",-23.26,23.32,
+"OBIGT",1017,"propanoic acid","aq","cal",1.42,,
+"OBIGT",1036,"pimelic acid","aq","cal",,,-19931
+"OBIGT",1040,"formate","aq","cal",1.96,,
+"OBIGT",1042,"propanoate","aq","cal",1.68,,
+"OBIGT",1049,"n-decanoate","aq","cal",-1.93,,
+"OBIGT",1065,"oxalate-2","aq","cal",-3.19,,
+"OBIGT",1106,"Fe(For)+","aq","cal",,,587
+"OBIGT",1107,"Fe(For)2","aq","cal",,,639
+"OBIGT",1179,"Mg(But)2","aq","cal",,,-3347811
+"OBIGT",1208,"Yb(But)+2","aq","cal",,,665
+"OBIGT",1227,"Fe(Pent)2","aq","cal",,,532
+"OBIGT",1312,"Ba(HCO3)+","aq","cal",,,-5800
+"OBIGT",1332,"Li(Mal)-","aq","cal",,-3.22,
+"OBIGT",1336,"Pb(Mal)","aq","cal",,1.16,
+"OBIGT",1340,"Pb(Succ)","aq","cal",,1.49,
+"OBIGT",1341,"Na(Oxal)-","aq","cal",,-3.14,
+"OBIGT",1342,"K(Oxal)-","aq","cal",,-2.75,
+"OBIGT",1343,"Fe(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1345,"Na(Mal)-","aq","cal",,-3.11,17018
+"OBIGT",1346,"K(Mal)-","aq","cal",,-2.63,17013
+"OBIGT",1348,"La(Mal)+","aq","cal",,-1.92,
+"OBIGT",1349,"Gd(Mal)+","aq","cal",,-1.73,
+"OBIGT",1350,"Lu(Mal)+","aq","cal",,-2.25,
+"OBIGT",1351,"Yb(Mal)+","aq","cal",,-2.05,
+"OBIGT",1352,"Th(Mal)+2","aq","cal",-1.29,-4.79,
+"OBIGT",1354,"Ce(Mal)+","aq","cal",,-1.75,
+"OBIGT",1355,"Nd(Mal)+","aq","cal",4.52,,
+"OBIGT",1356,"Sm(Mal)+","aq","cal",,-1.77,
+"OBIGT",1357,"Pr(Mal)+","aq","cal",,-1.75,
+"OBIGT",1358,"Eu(Mal)+","aq","cal",,-1.87,
+"OBIGT",1359,"Tb(Mal)+","aq","cal",,-1.92,
+"OBIGT",1360,"Dy(Mal)+","aq","cal",,-1.89,
+"OBIGT",1361,"Tm(Mal)+","aq","cal",,-2.08,
+"OBIGT",1362,"Ho(Mal)+","aq","cal",,-2.08,
+"OBIGT",1363,"Er(Mal)+","aq","cal",,-2.11,
+"OBIGT",1364,"Sc(Mal)+","aq","cal",,-1.97,
+"OBIGT",1365,"Fe(Mal)+","aq","cal",,-1.97,
+"OBIGT",1366,"Na(Succ)-","aq","cal",,-2.82,
+"OBIGT",1367,"K(Succ)-","aq","cal",,-2.39,
+"OBIGT",1373,"Th(Succ)+2","aq","cal",-1.21,-4.47,
+"OBIGT",1378,"NH4(Oxal)-","aq","cal",,-2.62,
+"OBIGT",1383,"Yb(Oxal)+","aq","cal",,-2.02,
+"OBIGT",1384,"Ce(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1385,"Nd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1386,"Eu(Oxal)+","aq","cal",,-1.89,
+"OBIGT",1387,"Gd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1388,"Ru(Oxal)+","aq","cal",,-2.41,
+"OBIGT",1389,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1390,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
+"OBIGT",1391,"U(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1393,"Y(Oxal)+","aq","cal",,-2.11,
+"OBIGT",1398,"La(Oxal)+","aq","cal",,-1.87,
+"OBIGT",1399,"Tb(Oxal)+","aq","cal",,-1.92,
+"OBIGT",1400,"Er(Oxal)+","aq","cal",,-2.05,
+"OBIGT",1401,"Lu(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1402,"Cr(Oxal)+","aq","cal",,-2.58,
+"OBIGT",1403,"Ga(Oxal)+","aq","cal",,-2.66,
+"OBIGT",1404,"Sc(Oxal)+","aq","cal",,-2.13,
+"OBIGT",1405,"In(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1406,"Sm(Oxal)+","aq","cal",,-1.84,
+"OBIGT",1407,"Cs(Mal)-","aq","cal",,-2.39,
+"OBIGT",1408,"NH4(Mal)-","aq","cal",,-2.54,
+"OBIGT",1413,"In(Mal)+","aq","cal",,-2.11,
+"OBIGT",1414,"Y(Mal)+","aq","cal",,-2.02,29999
+"OBIGT",1422,"La(Succ)+","aq","cal",,-1.52,
+"OBIGT",1423,"NH4(Succ)-","aq","cal",,-2.26,
+"OBIGT",1425,"Fe(Succ)+","aq","cal",,-1.92,
+"OBIGT",1426,"Sc(Succ)+","aq","cal",,-1.77,
+"OBIGT",1428,"Sm(Succ)+","aq","cal",,-1.48,
+"OBIGT",1429,"Er(Succ)+","aq","cal",,-1.68,
+"OBIGT",1430,"U(Succ)+2","aq","cal",-1.15,-4.27,
+"OBIGT",1434,"La(Glut)+","aq","cal",,-1.23,
+"OBIGT",1435,"Y(Glut)+","aq","cal",,-1.46,
+"OBIGT",1436,"Sc(Glut)+","aq","cal",,-1.5,
+"OBIGT",1437,"Th(Glut)+2","aq","cal",-1.09,-4.05,
+"OBIGT",1440,"Fe(Glut)+","aq","cal",,-1.05,
+"OBIGT",1441,"Sm(Glut)+","aq","cal",,-1.2,
+"OBIGT",1443,"Er(Glut)+","aq","cal",,-1.4,-4673
+"OBIGT",1445,"Ba(Adip)","aq","cal",,1.19,
+"OBIGT",1452,"Pb(Adip)","aq","cal",,1.25,
+"OBIGT",1453,"Sc(Adip)+","aq","cal",,-1.22,
+"OBIGT",1455,"Th(Adip)+2","aq","cal",-1.02,-3.76,
+"OBIGT",1456,"U(Adip)+2","aq","cal",-1,-3.71,
+"OBIGT",1458,"Li(Oxal)-","aq","cal",,-3.3,
+"OBIGT",1462,"Li(Succ)-","aq","cal",,-2.94,
+"OBIGT",1464,"Na(Glut)-","aq","cal",,-2.34,
+"OBIGT",1465,"K(Glut)-","aq","cal",,-2.05,
+"OBIGT",1466,"Li(Glut)-","aq","cal",,-2.66,
+"OBIGT",1471,"Na(Adip)-","aq","cal",,-2.05,
+"OBIGT",1472,"K(Adip)-","aq","cal",,-1.76,
+"OBIGT",1473,"Li(Adip)-","aq","cal",,-2.38,
+"OBIGT",1479,"cyclohexane","aq","cal",9.35,6.64,
+"OBIGT",1480,"Ar","aq","cal",-1.24,-8.59,
+"OBIGT",1481,"benzene","aq","cal",,-1.14,
+"OBIGT",1482,"CO2","aq","cal",-4.94,,
+"OBIGT",1483,"Xe","aq","cal",2.8,,
+"OBIGT",1491,"ethanethiol","aq","cal",,,753
+"OBIGT",1493,"n-butanethiol","aq","cal",2.19,,
+"OBIGT",1515,"methyldiethanolamine","aq","cal",1.61,,
+"OBIGT",1518,"dimethylamine","aq","J",-8.05,,
+"OBIGT",1532,"cysteinate","aq","cal",-1,,
+"OBIGT",1558,"glucose","aq","cal",1.11,,
+"OBIGT",1586,"guanine","aq","cal",-4.26,,
+"OBIGT",1630,"dHUMP-","aq","cal",-3.13,,
+"OBIGT",1727,"MgADP-","aq","cal",-1.01,,
+"OBIGT",1738,"HNicMP(ox)","aq","cal",,9.4,
+"OBIGT",1746,"ribose-5-phosphate","aq","cal",,7.48,
+"OBIGT",1748,"ribose-5-phosphate-2","aq","cal",1.53,,
+"OBIGT",1749,"H4NADP(red)","aq","cal",1.73,,
+"OBIGT",1750,"H3NADP(red)-","aq","cal",2.41,,
+"OBIGT",1751,"H2NADP(red)-2","aq","cal",1.28,,
+"OBIGT",1752,"HNADP(red)-3","aq","cal",2.09,,
+"OBIGT",1753,"NADP(red)-4","aq","cal",1.09,,
+"OBIGT",1755,"H3NADP(ox)","aq","cal",1.05,,
+"OBIGT",1826,"diglycine+","aq","cal",-177.69,,
+"OBIGT",1827,"diglycine-","aq","cal",-49.22,,565
+"OBIGT",1828,"triglycine+","aq","cal",,1.75,
+"OBIGT",1829,"triglycine-","aq","cal",,1.78,
+"OBIGT",1888,"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",2009,"octadecane","cr","cal",-2.63,,
+"OBIGT",2010,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2011,"eicosane","cr","cal",-2.79,,
+"OBIGT",2012,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2013,"docosane","cr","cal",-2.63,,
+"OBIGT",2014,"tricosane","cr","cal",-5.22,,
+"OBIGT",2015,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2016,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2017,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2018,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2070,"carbazole","cr","cal",-43.39,,
+"OBIGT",2111,"triphenylene","cr","cal",,,541
+"OBIGT",2424,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2582,"ethylene","gas","cal",-4.59,,
+"OBIGT",2592,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2902,"nonacontane","liq","cal",,,635
+"OBIGT",2909,"2-methyloctane","liq","cal",10,,
+"OBIGT",3322,"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
@@ -287,7 +287,7 @@
"DEW",115,"KOH","aq","cal",,,-71448
"DEW",124,"Mg(HCO3)+","aq","cal",,,686
"DEW",129,"MgOH+","aq","cal",,,11274
-"DEW",130,"Mg(SiO2)(HCO3)+","aq","cal",,,-39713
+"DEW",130,"Mg(SiO2)(HCO3)+","aq","cal",,,1491
"DEW",131,"MgSO4","aq","cal",,,-3852
"DEW",136,"MnSO4","aq","cal",,,1203
"DEW",143,"NaHCO3","aq","cal",,,4657
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 587
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