[CHNOSZ-commits] r597 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo man man/macros
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 15 04:15:17 CEST 2020
Author: jedick
Date: 2020-08-15 04:15:16 +0200 (Sat, 15 Aug 2020)
New Revision: 597
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
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/man/macros/macros.Rd
pkg/CHNOSZ/man/thermo.Rd
Log:
OBIGT: Add Mn oxides from Robie and Hemingway, 1995
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-08-15 00:13:56 UTC (rev 596)
+++ pkg/CHNOSZ/DESCRIPTION 2020-08-15 02:15:16 UTC (rev 597)
@@ -1,6 +1,6 @@
-Date: 2020-08-11
+Date: 2020-08-15
Package: CHNOSZ
-Version: 1.3.6-70
+Version: 1.3.6-71
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 2020-08-15 00:13:56 UTC (rev 596)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-08-15 02:15:16 UTC (rev 597)
@@ -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 1.3.6-62 (2020-07-27)}{
+\section{Changes in CHNOSZ version 1.3.6-71 (2020-08-15)}{
\subsection{MAJOR CHANGES}{
\itemize{
@@ -87,6 +87,11 @@
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 \samp{inorganic_cr.csv}: Add Mn oxides (manganosite, pyrolusite,
+ bixbyite, and hausmannite) from
+ \href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway,
+ 1995}.
+
\item Add GHS for almandine, dickite, fluorphlogopite, glaucophane,
grunerite, larnite, pyrope (\samp{SUPCRT92.csv}) and bromellite
(\samp{inorganic_cr.csv}) from
@@ -246,6 +251,10 @@
\item TODO: get retrieve() into more examples/demos
+ \item TODO: convert dates in OBIGT to ISO 8601 format (2020-08-12).
+
+ \item TODO: get entropies for Am, Pu, Cm, Np.
+
}
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2020-08-15 00:13:56 UTC (rev 596)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2020-08-15 02:15:16 UTC (rev 597)
@@ -40,7 +40,6 @@
iron,Fe,Fe,cr3,RHF78.2,CHNOSZ.1,5.May.78,cal,1293.526,1865.343,8.438,NA,7.092,5.8,1.98,0,0,0,0,0,1673
iron,Fe,Fe,cr4,RHF78.2,CHNOSZ.1,5.May.78,cal,979.29,1252.891,7.438,NA,7.092,6.74,1.6,0,0,0,0,0,1812
malachite,Mal,Cu2(OH)2(CO3),cr,HDNB78,NA,5.May.78,cal,-214204,-251900,44.5,NA,54.86,27.76,43.78,-1.34,0,0,0,0,780
-manganosite,Mng,MnO,cr,HDNB78,WEP+82.1,5.May.78,cal,-86735,-92070,14.27,NA,13.221,11.11,1.94,-0.88,0,0,0,0,1800
metacinnabar,Met-Cin,HgS,cr,HDNB78,NA,5.May.78,cal,-10437,-11800,21.2,NA,30.169,10.52,3.63,0,0,0,0,0,1000
nesquehonite,Nsh,MgCO3*3H2O,cr,HDNB78,NA,5.May.78,cal,-412035,-472576,46.76,NA,74.79,-1574.804,3899.173,-417.325,0,0,0,0,306.5
nesquehonite,Nsh,MgCO3*3H2O,cr2,HDNB78,CHNOSZ.1,5.May.78,cal,-412132.322,-479914.417,22.4732,NA,74.79,25.246,91.289,-4.222,0,0,0,0,340
@@ -115,7 +114,7 @@
jarosite,NA,KFe3(SO4)2(OH)6,cr,SAJ00,NA,13.Apr.09,cal,-791061.2,-887930.2,92.949,NA,NA,147.44,23.599,-47.706,0,0,0,0,NA
natrojarosite,NA,NaFe3(SO4)2(OH)6,cr,SAJ00,NA,13.Apr.09,cal,-778370,-877892,91.396,NA,NA,147.321,21.8,-48.7,0,0,0,0,NA
melanterite,NA,FeSO4*7H2O,cr,PK95,NA,13.Apr.09,cal,-599366.6,-720028.7,97.801,NA,NA,0,0,0,0,0,0,0,NA
-gypsum,NA,CaSO4*2H2O,cr,RH95,Kel60.3,22.Nov.15,cal,-429493,-483509,46.32,NA,74.69,21.84,76,0,0,0,0,0,400
+gypsum,NA,CaSO4*2H2O,cr,RH95.7,Kel60.3,22.Nov.15,cal,-429493,-483509,46.32,NA,74.69,21.84,76,0,0,0,0,0,400
MgSO4,NA,MgSO4,cr,WEP+82.2,NA,24.Nov.15,cal,-279780,-307100,21.89,NA,NA,23.06,0,0,0,0,0,0,NA
"arsenic,alpha",NA,As,cr,NA03,ZZL+16.1,16.Oct.17,J,0,0,35.63,24.43,12.96,NA,NA,NA,NA,NA,NA,NA,NA
arsenolite,NA,As2O3,cr,NA03,NA,16.Oct.17,J,-576340,-657270,107.38,96.88,NA,NA,NA,NA,NA,NA,NA,NA,NA
@@ -137,3 +136,7 @@
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
+manganosite,Mng,MnO,cr,RH95,NA,15.Aug.20,J,-362900,-385200,59.71,44.1,13.22,60.28,3.51,0,-297.5,0,0,0,2000
+pyrolusite,NA,MnO2,cr,RH95,NA,15.Aug.20,J,-465000,-520000,52.8,54.76,16.61,290.4,-144.2,20.12,-3787,4.541,0,0,850
+bixbyite,NA,Mn2O3,cr,RH95,NA,15.Aug.20,J,-882100,-959000,113.7,101.81,31.37,162.4,12.11,10.46,-1317,0.3462,0,0,1400
+hausmannite,NA,Mn3O4,cr,RH95,NA,15.Aug.20,J,-1282500,-1384500,164.1,142.02,46.95,-7.432,94.87,-67.12,3396,0,0,0,1400
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-08-15 00:13:56 UTC (rev 596)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-08-15 02:15:16 UTC (rev 597)
@@ -59,7 +59,7 @@
HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P
PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255
PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964
-RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",https://pubs.er.usgs.gov/publication/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","manganosite, pyrolusite, bixbyite, and hausmannite",https://pubs.er.usgs.gov/publication/b2131
RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://pubs.er.usgs.gov/publication/b2131
RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://pubs.er.usgs.gov/publication/b2131
RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, pyrope (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
@@ -66,6 +66,7 @@
RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://pubs.er.usgs.gov/publication/b2131
RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
+RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",https://pubs.er.usgs.gov/publication/b2131
SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes with metals. Values are taken from slop98.dat, which notes corrected values for some species.",https://doi.org/10.1016/0016-7037(95)00058-8
Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-08-15 00:13:56 UTC (rev 596)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-08-15 02:15:16 UTC (rev 597)
@@ -242,31 +242,31 @@
"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",2007,"octadecane","cr","cal",-2.63,,
-"OBIGT",2008,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2009,"eicosane","cr","cal",-2.79,,
-"OBIGT",2010,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2011,"docosane","cr","cal",-2.63,,
-"OBIGT",2012,"tricosane","cr","cal",-5.22,,
-"OBIGT",2013,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2014,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2015,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2016,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2068,"carbazole","cr","cal",-43.39,,
-"OBIGT",2109,"triphenylene","cr","cal",,,541
-"OBIGT",2422,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2580,"ethylene","gas","cal",-4.59,,
-"OBIGT",2590,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2900,"nonacontane","liq","cal",,,635
-"OBIGT",2907,"2-methyloctane","liq","cal",10,,
-"OBIGT",3320,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",1963,"jarosite","cr","cal",,,20697
+"OBIGT",1964,"natrojarosite","cr","cal",,,17554
+"OBIGT",1972,"realgar,alpha","cr","J",,,768
+"OBIGT",1973,"realgar,beta","cr","J",,,989
+"OBIGT",1974,"orpiment","cr","J",,,-1036
+"OBIGT",1982,"dawsonite","cr","J",,,19466
+"OBIGT",1984,"ferberite","cr","J",1.21,,
+"OBIGT",2010,"octadecane","cr","cal",-2.63,,
+"OBIGT",2011,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2012,"eicosane","cr","cal",-2.79,,
+"OBIGT",2013,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2014,"docosane","cr","cal",-2.63,,
+"OBIGT",2015,"tricosane","cr","cal",-5.22,,
+"OBIGT",2016,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2017,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2018,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2019,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2071,"carbazole","cr","cal",-43.39,,
+"OBIGT",2112,"triphenylene","cr","cal",,,541
+"OBIGT",2425,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2583,"ethylene","gas","cal",-4.59,,
+"OBIGT",2593,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2903,"nonacontane","liq","cal",,,635
+"OBIGT",2910,"2-methyloctane","liq","cal",10,,
+"OBIGT",3323,"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/man/macros/macros.Rd
===================================================================
--- pkg/CHNOSZ/man/macros/macros.Rd 2020-08-15 00:13:56 UTC (rev 596)
+++ pkg/CHNOSZ/man/macros/macros.Rd 2020-08-15 02:15:16 UTC (rev 597)
@@ -49,6 +49,16 @@
\newcommand{\eacute}{\ifelse{latex}{\out{\'{e}}}{\ifelse{html}{\out{é}}{é}}}
\newcommand{\gamma}{\ifelse{latex}{\eqn{\gamma}}{\ifelse{html}{\out{γ}}{γ}}}
\newcommand{\alpha}{\ifelse{latex}{\eqn{\alpha}}{\ifelse{html}{\out{α}}{α}}}
+\newcommand{\lambda}{\ifelse{latex}{\eqn{\lambda}}{\ifelse{html}{\out{λ}}{α}}}
% links to vignettes 20200716
\newcommand{\viglink}{\ifelse{html}{\out{<a href="../doc/#1.html"><strong>#1</strong></a>}}{\bold{#1.html}}}
+
+% HKF parameters 20200815
+\newcommand{\a1}{\ifelse{latex}{\eqn{a_1}}{\ifelse{html}{\out{<I>a</I><sub>1</sub>}}{a1}}}
+\newcommand{\a2}{\ifelse{latex}{\eqn{a_2}}{\ifelse{html}{\out{<I>a</I><sub>2</sub>}}{a2}}}
+\newcommand{\a3}{\ifelse{latex}{\eqn{a_3}}{\ifelse{html}{\out{<I>a</I><sub>3</sub>}}{a3}}}
+\newcommand{\a4}{\ifelse{latex}{\eqn{a_4}}{\ifelse{html}{\out{<I>a</I><sub>4</sub>}}{a4}}}
+\newcommand{\c1}{\ifelse{latex}{\eqn{c_1}}{\ifelse{html}{\out{<I>c</I><sub>1</sub>}}{c1}}}
+\newcommand{\c2}{\ifelse{latex}{\eqn{c_2}}{\ifelse{html}{\out{<I>c</I><sub>2</sub>}}{c2}}}
+\newcommand{\omega}{\ifelse{latex}{\eqn{\omega}}{\ifelse{html}{\out{ω}}{ω}}}
Modified: pkg/CHNOSZ/man/thermo.Rd
===================================================================
--- pkg/CHNOSZ/man/thermo.Rd 2020-08-15 00:13:56 UTC (rev 596)
+++ pkg/CHNOSZ/man/thermo.Rd 2020-08-15 02:15:16 UTC (rev 597)
@@ -137,26 +137,26 @@
Columns 14-21 for aqueous species (parameters in the revised HKF equations of state):
\tabular{lll}{
- \code{a1} \tab numeric \tab \eqn{a_1\times10}{a1 * 10} (cal mol\eqn{^{-1}}{^-1} bar\eqn{^{-1}}{^-1})\cr
- \code{a2} \tab numeric \tab \eqn{a_2\times10^{-2}}{a2 * 10^{-2}} (cal mol\eqn{^{-1}}{^-1})\cr
- \code{a3} \tab numeric \tab \eqn{a_3}{a3} (cal K mol\eqn{^{-1}}{^-1} bar\eqn{^{-1}}{^-1})\cr
- \code{a4} \tab numeric \tab \eqn{a_4\times10^{-4}}{a4 * 10^-4} (cal mol\eqn{^{-1}}{^-1} K)\cr
- \code{c1} \tab numeric \tab \eqn{c_1}{c1} (cal mol\eqn{^{-1}}{^-1} K\eqn{^{-1}}{^-1})\cr
- \code{c2} \tab numeric \tab \eqn{c_2\times10^{-4}}{c2 * 10^-4} (cal mol\eqn{^{-1}}{^-1} K)\cr
- \code{omega} \tab numeric \tab \eqn{\omega\times10^{-5}}{omega * 10^-5} (cal mol\eqn{^{-1}}{^-1})\cr
+ \code{a1} \tab numeric \tab \a1 * 10 (cal mol\S{-1} bar\S{-1})\cr
+ \code{a2} \tab numeric \tab \a2 * 10\S{-2} (cal mol\S{-1})\cr
+ \code{a3} \tab numeric \tab \a3 (cal K mol\S{-1} bar\S{-1})\cr
+ \code{a4} \tab numeric \tab \a4 * 10\S{-4} (cal mol\S{-1} K)\cr
+ \code{c1} \tab numeric \tab \c1 (cal mol\S{-1} K\S{-1})\cr
+ \code{c2} \tab numeric \tab \c2 * 10\S{-4} (cal mol\S{-1} K)\cr
+ \code{omega} \tab numeric \tab \omega * 10\S{-5} (cal mol\S{-1})\cr
\code{Z} \tab numeric \tab Charge
}
-Columns 14-21 for crystalline, gas and liquid species (\eqn{Cp=a+bT+cT^{-2}+dT^{-0.5}+eT^2+fT^{\lambda}}{Cp = a + bT + cT^-2 + dT^-0.5 + eT^2 + fT^lambda}).
+Columns 14-21 for crystalline, gas and liquid species (\eqn{Cp} = \eqn{a} + \eqn{bT} + \eqn{cT}\S{-2} + \eqn{dT}\S{-0.5} + \eqn{eT}\S{2} + \eqn{fT}\S{lambda})
\tabular{lll}{
- \code{a} \tab numeric \tab \eqn{a} (cal K\eqn{^{-1}}{^-1} mol\eqn{^{-1}}{^-1})\cr
- \code{b} \tab numeric \tab \eqn{b\times10^3}{b * 10^3} (cal K\eqn{^{-2}}{^-2} mol\eqn{^{-1}}{^-1})\cr
- \code{c} \tab numeric \tab \eqn{c\times10^{-5}}{c * 10^-5} (cal K mol\eqn{^{-1}}{^-1})\cr
- \code{d} \tab numeric \tab \eqn{d} (cal K\eqn{^{-0.5}}{^-0.5} mol\eqn{^{-1}}{^-1})\cr
- \code{e} \tab numeric \tab \eqn{e\times10^5}{e * 10^5} (cal K\eqn{^{-3}}{^-3} mol\eqn{^{-1}}{^-1})\cr
- \code{f} \tab numeric \tab \eqn{f} (cal K\eqn{^{-\lambda-1}}{-lambda-1} mol\eqn{^{-1}}{^-1})\cr
- \code{lambda} \tab numeric \tab \eqn{\lambda}{lambda} (exponent on the \eqn{f} term)\cr
+ \code{a} \tab numeric \tab \eqn{a} (cal K\S{-1} mol\S{-1})\cr
+ \code{b} \tab numeric \tab \eqn{b} * 10\S{3} (cal K\S{-2} mol\S{-1})\cr
+ \code{c} \tab numeric \tab \eqn{c} * 10\S{-5} (cal K mol\S{-1})\cr
+ \code{d} \tab numeric \tab \eqn{d} (cal K\S{-0.5} mol\S{-1})\cr
+ \code{e} \tab numeric \tab \eqn{e} * 10\S{5} (cal K\S{-3} mol\S{-1})\cr
+ \code{f} \tab numeric \tab \eqn{f} (cal K\S{-lambda-1} mol\S{-1})\cr
+ \code{lambda} \tab numeric \tab \lambda (exponent on the \eqn{f} term)\cr
\code{T} \tab numeric \tab Temperature of phase transition or upper\cr
\tab \tab temperature limit of validity of extrapolation (K)
}
@@ -175,7 +175,7 @@
}
\item \code{thermo()$refs}
- Dataframe of references to sources of thermodynamic data.
+ References for thermodynamic data.
\tabular{lll}{
\code{key} \tab character \tab Source key\cr
\code{author} \tab character \tab Author(s)\cr
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