[CHNOSZ-commits] r606 - in pkg/CHNOSZ: . inst inst/extdata/adds inst/extdata/thermo man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 15 09:02:15 CEST 2020
Author: jedick
Date: 2020-09-15 09:02:15 +0200 (Tue, 15 Sep 2020)
New Revision: 606
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/element.csv
pkg/CHNOSZ/man/thermo.Rd
Log:
Add entropies for Am, Pu, Cm, Np from Thoenen et al., 2014
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-09-10 01:48:18 UTC (rev 605)
+++ pkg/CHNOSZ/DESCRIPTION 2020-09-15 07:02:15 UTC (rev 606)
@@ -1,6 +1,6 @@
-Date: 2020-09-10
+Date: 2020-09-15
Package: CHNOSZ
-Version: 1.3.6-79
+Version: 1.3.6-80
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 2020-09-10 01:48:18 UTC (rev 605)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-09-15 07:02:15 UTC (rev 606)
@@ -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 1.3.6-79 (2020-09-10)}{
+\section{Changes in CHNOSZ version 1.3.6-80 (2020-09-15)}{
\subsection{MAJOR CHANGES}{
\itemize{
@@ -127,6 +127,10 @@
database (\samp{docs/OBIGT.bib}), which is used by the \pkg{logKcalc}
package (\url{https://github.com/jedick/logKcalc}).
+ \item \samp{thermo/element.csv}: Add entropies for Am, Pu, Cm, Np from
+ Thoenen et al., 2014 (\href{https://www.psi.ch/en/les/database}{The
+ PSI/Nagra Chemical Thermodynamic Database 12/07}).
+
}
}
@@ -274,8 +278,6 @@
\item TODO: move H2O92D.f and R wrapper to a separate package (so people
don't have to compile anything to install CHNOSZ updates).
- \item TODO: get entropies for Am, Pu, Cm, Np.
-
\item TODO: add empty diagram -> exceed.Ttr hint to anintro.Rmd.
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-09-10 01:48:18 UTC (rev 605)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-09-15 07:02:15 UTC (rev 606)
@@ -312,16 +312,27 @@
"SLOP98",45,"AsO4-3","aq","cal",,-1.65,
"SLOP98",52,"Al+3","aq","cal",1.74,,
"SLOP98",59,"ZnO2-2","aq","cal",,-1.17,
+"SLOP98",61,"AmOH+2","aq","cal",,,11642
+"SLOP98",62,"AmO+","aq","cal",,,11636
+"SLOP98",63,"HAmO2","aq","cal",,,23273
+"SLOP98",81,"AmCO3+","aq","cal",,,-9689
+"SLOP98",82,"Am(CO3)2-","aq","cal",,,69826
+"SLOP98",83,"AmSO4+","aq","cal",,,46571
+"SLOP98",84,"Am(SO4)2-","aq","cal",,,93130
"SLOP98",101,"Al(Mal)+","aq","cal",,-2.19,
"SLOP98",102,"Al(Oxal)+","aq","cal",,-2.62,
-"SLOP98",104,"Pu(Oxal)+2","aq","cal",-1.2,-4.44,
-"SLOP98",106,"Am(Oxal)+","aq","cal",,-1.8,
-"SLOP98",107,"Cm(Oxal)+","aq","cal",,-1.8,
-"SLOP98",108,"Np(Oxal)+2","aq","cal",-1.27,-4.69,
-"SLOP98",109,"NpO2(Oxal)","aq","cal",,-1.94,
-"SLOP98",110,"NpO2(Succ)","aq","cal",,-3.16,
+"SLOP98",103,"PuO2(Oxal)","aq","cal",,,2913
+"SLOP98",104,"Pu(Oxal)+2","aq","cal",-1.2,-4.44,-1743
+"SLOP98",105,"PuO2(Succ)","aq","cal",,,2912
+"SLOP98",106,"Am(Oxal)+","aq","cal",,-1.8,3036
+"SLOP98",107,"Cm(Oxal)+","aq","cal",,-1.8,3834
+"SLOP98",108,"Np(Oxal)+2","aq","cal",-1.27,-4.69,2753
+"SLOP98",109,"NpO2(Oxal)","aq","cal",,-1.94,2729
+"SLOP98",110,"NpO2(Succ)","aq","cal",,-3.16,2728
+"SLOP98",111,"NpO2(Glut)","aq","cal",,,2728
"SLOP98",142,"MgAsO4-","aq","cal",1.3,,
"SLOP98",145,"MnAsO4-","aq","cal",-1.45,,
+"SLOP98",165,"AmCrO4+2","aq","cal",,,-4654
"SLOP98",169,"PdCl4-2","aq","cal",,-1.05,
"SUPCRT92",26,"antigorite","cr","cal",,,812
"SUPCRT92",41,"clinochlore,7A","cr","cal",,,666
Modified: pkg/CHNOSZ/inst/extdata/thermo/element.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/element.csv 2020-09-10 01:48:18 UTC (rev 605)
+++ pkg/CHNOSZ/inst/extdata/thermo/element.csv 2020-09-15 07:02:15 UTC (rev 606)
@@ -129,3 +129,7 @@
Rb,cr,WEP+82,85.4678,18.3508604206501,1
Cs,cr,WEP+82,132.9054,20.3704588910134,1
Fr,cr,WEP+82,223,22.8011472275335,1
+Pu,cr,THBC14,NA,13.01625,1
+Am,cr,THBC14,NA,13.24092,1
+Np,cr,THBC14,NA,12.06023,1
+Cm,cr,THBC14,NA,16.92161,1
Modified: pkg/CHNOSZ/man/thermo.Rd
===================================================================
--- pkg/CHNOSZ/man/thermo.Rd 2020-09-10 01:48:18 UTC (rev 605)
+++ pkg/CHNOSZ/man/thermo.Rd 2020-09-15 07:02:15 UTC (rev 606)
@@ -64,7 +64,7 @@
}
\item \code{thermo()$element}
- Dataframe containing the thermodynamic properties of elements taken from Cox et al., 1989 and Wagman et al., 1982.
+ Dataframe containing the thermodynamic properties of elements taken from Cox et al., 1989, Wagman et al., 1982, and (for Am, Pu, Np, Cm) Thoenen et al., 2014.
The standard molal entropy (\eqn{S}(\code{Z})) at 25 \degC and 1 bar for the \dQuote{element} of charge (\code{Z}) was calculated from \eqn{S}(H2,g) + 2\eqn{S}(\code{Z}) = 2\eqn{S}(H+), where the standard molal entropies of H2,g and H+ were taken from Cox et al., 1989.
The mass of \code{Z} is taken to be zero.
Accessing this data frame using \code{\link{mass}} or \code{\link{entropy}} will select the first entry found for a given element; i.e., values from Wagman et al., 1982 will only be retrieved if the properties of the element are not found from Cox et al., 1989.
@@ -73,9 +73,9 @@
\code{state} \tab character \tab Stable state of element at 25 \degC and 1 bar\cr
\code{source} \tab character \tab Source of data\cr
\code{mass} \tab numeric \tab Mass of element (in natural isotopic distribution;\cr
- \tab \tab referenced to a mass of 12 for \eqn{^{12}}{12}C)\cr
+ \tab \tab referenced to a mass of 12 for \S{12}C)\cr
\code{s} \tab numeric \tab Entropy of the compound of the element in its stable\cr
- \tab \tab state at 25 \degC and 1 bar (cal K\eqn{^{-1}}{^-1} mol\eqn{^{-1}}{^-1})\cr
+ \tab \tab state at 25 \degC and 1 bar (cal K\S{-1} mol\S{-1})\cr
\code{n} \tab numeric \tab Number of atoms of the element in its stable\cr
\tab \tab compound at 25 \degC and 1 bar
}
@@ -282,6 +282,8 @@
Shock, E. L. et al. {1998} \emph{SLOP98.dat} (computer data file). \url{https://doi.org/10.5281/zenodo.2630820}
+Thoenen, T., Hummel, W., Berner, U. and Curti, E. (2014) \emph{The PSI/Nagra Chemical Thermodynamic Database 12/07}. Paul Scherrer Institut. \url{https://www.psi.ch/en/les/database}
+
Wagman, D. D., Evans, W. H., Parker, V. B., Schumm, R. H., Halow, I., Bailey, S. M., Churney, K. L. and Nuttall, R. L. (1982) The NBS tables of chemical thermodynamic properties. Selected values for inorganic and C\s{1} and C\s{2} organic substances in SI units. \emph{J. Phys. Chem. Ref. Data} \bold{11} (supp. 2), 1--392. \url{https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf}
}
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