[CHNOSZ-commits] r717 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 6 08:25:32 CEST 2022
Author: jedick
Date: 2022-04-06 08:25:32 +0200 (Wed, 06 Apr 2022)
New Revision: 717
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/man/logB_to_OBIGT.Rd
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Add disclaimer about classification of CH4 (methane) to OBIGT.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-03-27 03:25:02 UTC (rev 716)
+++ pkg/CHNOSZ/DESCRIPTION 2022-04-06 06:25:32 UTC (rev 717)
@@ -1,6 +1,6 @@
-Date: 2022-03-27
+Date: 2022-04-06
Package: CHNOSZ
-Version: 1.9.9-9
+Version: 1.9.9-10
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 2022-03-27 03:25:02 UTC (rev 716)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-04-06 06:25:32 UTC (rev 717)
@@ -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 1.9.9-9 (2022-03-27)}{
+\section{Changes in CHNOSZ version 1.9.9-10 (2022-04-06)}{
\subsection{MAJOR CHANGE}{
\itemize{
@@ -28,12 +28,38 @@
}
}
+ \subsection{OBIGT DATABASE}{
+ \itemize{
+
+ \item Add the following \emph{Disclaimer} to the Aqueous Inorganic
+ section of \strong{OBIGT.Rmd}: The maintenance of separate data files for
+ inorganic and organic species is done only for convenience, and is not
+ meant to imply a preference for any substrate, mechanism, or process. In
+ particular, CH\s{4} (methane) is an organic compound that can also be
+ formed abiotically (\href{https://doi.org/10.1002/rog.20011}{Etiope and
+ Sherwood Lollar, 2013}). The words \emph{organic} and \emph{inorganic}
+ (for substrates), \emph{biological} and \emph{thermochemical} (for
+ mechanisms), and \emph{methanogenesis}, \emph{pyrolysis}, and
+ \emph{synthesis} (for processes) can be used to describe different
+ methane-generating pathways in nature
+ (\href{https://doi.org/10.1007/978-3-319-39312-4_166}{Strąpoć, 2018}).
+ The details of this classification system are out of scope for the OBIGT
+ database. For practical reasons, CH\s{4} is placed in the
+ \dQuote{inorganic} data files in OBIGT simply so that the database can be
+ pruned of organic compounds \emph{except} CH\s{4} by running
+ \code{OBIGT(no.organics = TRUE)}. The ability to remove hundreds of
+ less-common organic species while keeping CH\s{4} is useful for some
+ models of inorganic reactions in hydrothermal systems.
+
+ }
+ }
+
\subsection{NEW FEATURES}{
\itemize{
\item Add \code{logB_to_OBIGT()} to fit three thermodynamic parameters
- (\samp{G}, \samp{S}, and \samp{Cp}) to formation constants of aqueous
- species as a function of temperature.
+ (\samp{G}, \samp{S}, and \samp{Cp} at 25 \degC) to formation constants of
+ aqueous species as a function of temperature.
\item Add \code{zap} argument to \code{mod.OBIGT()} to clear parameters
of preexisting species.
@@ -231,7 +257,6 @@
}
}
-
\subsection{OTHER CHANGES}{
\itemize{
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2022-03-27 03:25:02 UTC (rev 716)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2022-04-06 06:25:32 UTC (rev 717)
@@ -700,10 +700,10 @@
Rh(SO4)3-3,Rh(SO4)3-3,Rh(SO4)3-3,aq,SS98a,NA,1995-03-30,cal,-483700,-583100,37.9,-73.3,37.5,8.3237,12.5416,0.8232,-3.2974,2.2248,-17.9739,4.2376,-3
RhOH+2,Rh(OH)+2,Rh(OH)+2,aq,SS98a,NA,1995-07-13,cal,-820,-14620,-32.5,-0.1,-0.3,2.247,-2.2946,6.6503,-2.684,20.365,-3.0549,1.5475,2
RhO+,RhO+,RhO+,aq,SS98a,NA,1994-07-25,cal,3140,-10010,-18.7,-39.5,1.9,2.3067,-2.1515,6.6002,-2.69,-9.3049,-11.0806,0.8334,1
-Ar,Ar,Ar,aq,PS01,NA,2000-10-04,cal,3890,-2880,14.3,52.82,32.6,11.71,-2.39,-44.93,1.91,27.96,9.56,-0.46,0
-Xe,Xe,Xe,aq,PS01,NA,2000-10-04,cal,3215,-4540,14.5,64.77,42.5,18.4,-2.39,-59.03,1.43,35.85,13.86,-0.39,0
-CH4,NA,CH4,aq,PS01,NA,2000-10-04,cal,-8140,-20930,21,60.23,36,17.69,-15.3,-67.88,11.47,40.87,6.45,-0.4,0
-CO2,NA,CO2,aq,PS01,NA,2005-08-18,cal,-92250,-98900,28.1,51.86,33.5,15.2964,-10.0382,-55.4493,7.4092,36.8069,3.5851,-0.3107,0
+Ar,Ar,Ar,aq,PS01.1,NA,2000-10-04,cal,3890,-2880,14.3,52.82,32.6,11.71,-2.39,-44.93,1.91,27.96,9.56,-0.46,0
+Xe,Xe,Xe,aq,PS01.1,NA,2000-10-04,cal,3215,-4540,14.5,64.77,42.5,18.4,-2.39,-59.03,1.43,35.85,13.86,-0.39,0
+CH4,NA,CH4,aq,PS01.1,NA,2000-10-04,cal,-8140,-20930,21,60.23,36,17.69,-15.3,-67.88,11.47,40.87,6.45,-0.4,0
+CO2,NA,CO2,aq,PS01.1,NA,2005-08-18,cal,-92250,-98900,28.1,51.86,33.5,15.2964,-10.0382,-55.4493,7.4092,36.8069,3.5851,-0.3107,0
CF4,NA,CF4,aq,SSW01,NA,2006-09-01,cal,-202700,-224680,32.4,105.4,0,0,0,0,0,51.2936,28.0572,-0.3282,0
SF6,NA,SF6,aq,SSW01,NA,2006-09-01,cal,-259240,-293780,37.2,146.4,0,0,0,0,0,61.295,40.7143,-0.2601,0
NF3,NA,NF3,aq,SSW01,NA,2006-09-01,cal,-15660,-33515,35.7,82.8,0,0,0,0,0,43.4774,18.2721,-0.2406,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2022-03-27 03:25:02 UTC (rev 716)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2022-04-06 06:25:32 UTC (rev 717)
@@ -122,7 +122,8 @@
AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x
AZ01,"N. N. Akinfiev and A. V. Zotov",2001,"Geochem. Int. 39, 990-1006","M<sup>+</sup>, MCl<sub>2</sub><sup>-</sup>, M(OH)<sub>2</sub><sup>-</sup>, MCl, and MOH (M = Au<sup>+</sup>, Ag<sup>+</sup>, or Cu<sup>+</sup>)",http://pleiades.online/cgi-perl/search.pl?type=abstract&name=geochem&number=10&year=1&page=990
MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","polymorphs of ice",https://doi.org/10.1016/S0883-2927(00)00025-1
-PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes",https://doi.org/10.1016/S0016-7037(01)00678-0
+PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes (organic species)",https://doi.org/10.1016/S0016-7037(01)00678-0
+PS01.1,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes (Ar, Xe, CH<sub>4</sub>, and CO<sub>2</sub>)",https://doi.org/10.1016/S0016-7037(01)00678-0
Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",https://doi.org/10.1016/S0016-7037(01)00761-X
Ste01,"A. Stefansson",2001,"Chem. Geol. 172, 225-250","aqueous H<sub>4</sub>SiO<sub>4</sub>",https://doi.org/10.1016/S0009-2541(00)00263-1
SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
Modified: pkg/CHNOSZ/man/logB_to_OBIGT.Rd
===================================================================
--- pkg/CHNOSZ/man/logB_to_OBIGT.Rd 2022-03-27 03:25:02 UTC (rev 716)
+++ pkg/CHNOSZ/man/logB_to_OBIGT.Rd 2022-04-06 06:25:32 UTC (rev 717)
@@ -64,7 +64,7 @@
legend("topleft", legend, pch = c(19, NA), lty = c(0, 1), col = c(1, 4), pt.cex = 2)
## ZnCl+ from Mei et al. (2015)
-# These are values calculated from the modified Ryzhenko-Bryzgalin model
+# These are values for 5000 bar calculated from the modified Ryzhenko-Bryzgalin model
logB <- c(-1.93, -1.16, -0.38, 0.45, 1.15, 1.76, 2.30, 2.80, 3.26, 3.70, 4.12, 4.53, 4.92)
species <- c("Zn+2", "Cl-", "ZnCl+")
coeff <- c(-1, -1, 1)
@@ -78,7 +78,8 @@
Tfit <- seq(25, 600, 25)
sres <- subcrt(species, coeff, T = Tfit, P = P)
lines(sres$out$T, sres$out$logK, col = 4)
-title(describe.reaction(sres$reaction))
+title(describe.reaction(sres$reaction), line = 3)
+title("5000 bar", font.main = 1, line = 1)
legend <- c("Mei et al. (2015)", "logB_to_OBIGT()")
legend("topleft", legend, pch = c(19, NA), lty = c(0, 1), col = c(1, 4), pt.cex = 2)
}
Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-03-27 03:25:02 UTC (rev 716)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-04-06 06:25:32 UTC (rev 717)
@@ -246,6 +246,12 @@
<div id="D-aqueous-inorganic" style="display: none">
## <a id="aqueous-inorganic" class="anchor"></a> `r setfile("inorganic_aq.csv")`
+*Disclaimer*: The maintenance of separate data files for inorganic and organic species is done only for convenience, and is not meant to imply a preference for any substrate, mechanism, or process.
+In particular, CH<sub>4</sub> (methane) is an organic compound that can also be formed abiotically [@ES13].
+The words *organic* and *inorganic* (for substrates), *biological* and *thermochemical* (for mechanisms), and *biogenic*, *abiogenic*, and *pyrolytic* (for processes) can be used to describe different methane-generating pathways in nature [@Str18].
+The details of this classification system are out of scope for the OBIGT database.
+For practical reasons, CH<sub>4</sub> is placed in the "inorganic" data files in OBIGT simply so that the database can be pruned of organic compounds *except* CH<sub>4</sub> by running `OBIGT(no.organics = TRUE)`.
+The ability to remove hundreds of less-common organic species while keeping CH<sub>4</sub> is useful for some models of inorganic reactions in hydrothermal systems.
```{r reflist, results="asis", echo=FALSE}
```
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2022-03-27 03:25:02 UTC (rev 716)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2022-04-06 06:25:32 UTC (rev 717)
@@ -32,14 +32,14 @@
}
@Article{AH97b,
- author = {Amend, Jan P. and Helgeson, Harold C.},
- journal = {Journal of the Chemical Society, Faraday Transactions},
- title = {{C}alculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. {P}art 1. \textsc{l}-{$\alpha$}-amino acids},
- year = {1997},
- volume = {93},
- number = {10},
- pages = {1927--1941},
- doi = {10.1039/A608126F},
+ author = {Amend, Jan P. and Helgeson, Harold C.},
+ journal = {Journal of the Chemical Society, Faraday Transactions},
+ title = {{C}alculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. {P}art 1. \textsc{l}-{$\alpha$}-amino acids},
+ year = {1997},
+ number = {10},
+ pages = {1927--1941},
+ volume = {93},
+ doi = {10.1039/A608126F},
}
@Article{AP01,
@@ -221,22 +221,20 @@
}
@Article{HKF81,
- author = {Helgeson, Harold C. and Kirkham, David H. and Flowers, George C.},
- journal = {American Journal of Science},
- title = {{T}heoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures: {IV}. {C}alculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600°{C} and 5 {K}b},
- year = {1981},
- number = {10},
- pages = {1249--1516},
- volume = {281},
- doi = {10.2475/ajs.281.10.1249},
- size = {268 p.},
- sourceid = {ISI:A1981MZ34200001},
+ author = {Helgeson, Harold C. and Kirkham, David H. and Flowers, George C.},
+ journal = {American Journal of Science},
+ title = {{T}heoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures: {IV}. {C}alculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600°{C} and 5 {K}b},
+ year = {1981},
+ number = {10},
+ pages = {1249--1516},
+ volume = {281},
+ doi = {10.2475/ajs.281.10.1249},
}
@Article{HOKR98,
author = {Helgeson, Harold C. and Owens, Christine E. and Knox, Annette M. and Richard, Laurent},
journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the standard molal thermodynamic properties of crystalline, liquid, and gas organic molecules at high temperatures and pressures},
+ title = {Calculation of the standard molal thermodynamic properties of crystalline, liquid, and gas organic molecules at high temperatures and pressures},
year = {1998},
number = {6},
pages = {985--1081},
@@ -320,14 +318,14 @@
}
@Article{LH06a,
- author = {LaRowe, Douglas E. and Helgeson, Harold C.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{B}iomolecules in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures},
- year = {2006},
- volume = {70},
- number = {18},
- pages = {4680--4724},
- doi = {10.1016/j.gca.2006.04.010},
+ author = {LaRowe, Douglas E. and Helgeson, Harold C.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{B}iomolecules in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures},
+ year = {2006},
+ number = {18},
+ pages = {4680--4724},
+ volume = {70},
+ doi = {10.1016/j.gca.2006.04.010},
}
@Article{LH06b,
@@ -518,14 +516,14 @@
}
@Article{PS01,
- author = {Plyasunov, Andrey V. and Shock, Everett L.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}orrelation strategy for determining the parameters of the revised {H}elgeson-{K}irkham-{F}lowers model for aqueous nonelectrolytes},
- year = {2001},
- volume = {65},
- number = {21},
- pages = {3879--3900},
- doi = {10.1016/S0016-7037(01)00678-0},
+ author = {Plyasunov, Andrey V. and Shock, Everett L.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{C}orrelation strategy for determining the parameters of the revised {H}elgeson-{K}irkham-{F}lowers model for aqueous nonelectrolytes},
+ year = {2001},
+ number = {21},
+ pages = {3879--3900},
+ volume = {65},
+ doi = {10.1016/S0016-7037(01)00678-0},
}
@Article{PD15,
@@ -612,11 +610,11 @@
@Book{RH95,
author = {Robie, Richard A. and Hemingway, Bruce S.},
- publisher = {U. S. Geological Survey},
+ publisher = {U.S. Geological Survey},
title = {{T}hermodynamic {P}roperties of {M}inerals and {R}elated {S}ubstances at 298.15 {K} and 1 {B}ar (10\textsuperscript{5} {P}ascals) {P}ressure and at {H}igher {T}emperatures},
year = {1995},
+ address = {Washington, D.C.},
series = {Bulletin 2131},
- address = {Washington, D. C.},
doi = {10.3133/b2131},
pages = {461},
}
@@ -880,14 +878,14 @@
}
@Article{TH88,
- author = {Tanger, IV, John C. and Helgeson, Harold C.},
- journal = {American Journal of Science},
- title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {R}evised equations of state for the standard partial molal properties of ions and electrolytes},
- year = {1988},
- volume = {288},
- number = {1},
- pages = {19--98},
- doi = {10.2475/ajs.288.1.19},
+ author = {Tanger, IV, John C. and Helgeson, Harold C.},
+ journal = {American Journal of Science},
+ title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {R}evised equations of state for the standard partial molal properties of ions and electrolytes},
+ year = {1988},
+ number = {1},
+ pages = {19--98},
+ volume = {288},
+ doi = {10.2475/ajs.288.1.19},
}
@Article{TSD97,
@@ -903,7 +901,7 @@
@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 = {J. Phys. Chem. Ref. Data},
+ journal = {Journal of Physical and Chemical Reference 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},
@@ -1768,3 +1766,26 @@
volume = {317},
doi = {10.2475/07.2017.01},
}
+
+ at Article{ES13,
+ author = {Etiope, Giuseppe and Sherwood Lollar, Barbara},
+ journal = {Reviews of Geophysics},
+ title = {Abiotic methane on {E}arth},
+ year = {2013},
+ number = {2},
+ pages = {276--299},
+ volume = {51},
+ doi = {10.1002/rog.20011},
+}
+
+ at InBook{Str18,
+ author = {Str{\k{a}}po{\'{c}}, Dariusz},
+ editor = {White, William M.},
+ pages = {100--107},
+ publisher = {Springer International Publishing},
+ title = {Biogenic Methane},
+ year = {2018},
+ address = {Cham},
+ booktitle = {Encyclopedia of Geochemistry},
+ doi = {10.1007/978-3-319-39312-4_166},
+}
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