[CHNOSZ-commits] r788 - in pkg/CHNOSZ: . vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat May 27 12:33:31 CEST 2023
Author: jedick
Date: 2023-05-27 12:33:30 +0200 (Sat, 27 May 2023)
New Revision: 788
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/vignettes/FAQ.Rmd
pkg/CHNOSZ/vignettes/mklinks.sh
pkg/CHNOSZ/vignettes/vig.bib
Log:
FAQ.Rmd: Add citations and thermodynamic models
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2023-05-22 09:37:36 UTC (rev 787)
+++ pkg/CHNOSZ/DESCRIPTION 2023-05-27 10:33:30 UTC (rev 788)
@@ -1,6 +1,6 @@
-Date: 2023-05-22
+Date: 2023-05-27
Package: CHNOSZ
-Version: 2.0.0-7
+Version: 2.0.0-8
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/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-05-22 09:37:36 UTC (rev 787)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-05-27 10:33:30 UTC (rev 788)
@@ -43,6 +43,8 @@
NOTE <- '<span style="background-color: yellow;">NOTE</span>'
# CHNOSZ functions
equilibrate_ <- '<code>equilibrate()</code>'
+info_ <- '<code>info()</code>'
+thermo.refs_ <- '<code>thermo.refs()</code>'
# Math stuff
logK <- "log <i>K</i>"
Hplus <- "H<sup>+</sup>"
@@ -65,7 +67,6 @@
This vignette was compiled on `r Sys.Date()` with CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
-<!-- ######## SECTION MARKER ######## -->
## How is 'CHNOSZ' pronounced?
As one syllable, starting with an *sh* sound and [rhyming with *Oz*](https://en.wiktionary.org/wiki/Rhymes:English/%C9%92z).
@@ -73,7 +74,32 @@
*Answered on 2023-05-22.*
-<!-- ######## SECTION MARKER ######## -->
+## How can CHNOSZ be cited?
+
+* This paper is the general reference for CHNOSZ: @Dic19.
+* This paper describes the features for making diagrams with multiple metals: @Dic21b.
+* This paper describes the features for calculations involving proteins: @Dic08.
+* The [<span style="color:blue">*OBIGT thermodynamic database*</span>](OBIGT.html) represents the work of many researchers.
+**If you publish results that depend on any of these data, please cite the primary sources.**
+Use `r info_` to show the reference keys for particular species and `r thermo.refs_` to list the bibliographic details:
+```{r alanine, message = FALSE}
+info(info("alanine"))[c("ref1", "ref2")]
+thermo.refs(info("alanine"))
+```
+
+*Answered on 2023-05-27.*
+
+## What thermodynamic models are used in CHNOSZ?
+
+* The thermodynamic properties of liquid water are calculated using Fortran code from SUPCRT92 [@JOH92] or an implementation in R of the IAPWS-95 formulation [@WP02].
+* Thermodynamic properties of other species are taken from a database for minerals and inorganic and organic aqueous species including biomolecules, or from amino acid group additivity for proteins [@DLH06].
+* The corresponding high-temperature properties are calculated using the @BB85 equations for minerals and the revised Helgeson-Kirkham-Flowers [@HKF81] equations for aqueous species.
+* The HKF equations are augmented with the Deep Earth Water (DEW) model [@SHA14] and estimates of parameters in the extended Debye-Hückel equation [@MSS13] to calculate standard-state properties and activity coefficients for given ionic strength at high pressure (to 6 GPa).
+* Activity coefficients are implemented via adjusted standard Gibbs energies at specified ionic strength [@Alb96], which converts all activity variables in the workflow to molalities.
+* A related adjustment is available to convert standard Gibbs energies for gases from the 1 bar standard state used in SUPCRT to a variable-pressure standard state [@AC93,Ch.12].
+
+*Answered on 2018-11-13; moved from <https://chnosz.net/> on 2023-05-27.*
+
## When and why do equal-activity boundaries depend on total activity?
Short answer: When the species have the same number of the conserved element (let's take C for example),
Modified: pkg/CHNOSZ/vignettes/mklinks.sh
===================================================================
--- pkg/CHNOSZ/vignettes/mklinks.sh 2023-05-22 09:37:36 UTC (rev 787)
+++ pkg/CHNOSZ/vignettes/mklinks.sh 2023-05-27 10:33:30 UTC (rev 788)
@@ -140,3 +140,5 @@
# Add links to FAQ.html 20230517
sed -i 's/<code>equilibrate()<\/code>/<code><a href="..\/html\/equilibrate.html" style="color:\ green;">equilibrate()<\/a><\/code>/g' FAQ.html
+sed -i 's/<code>info()<\/code>/<code><a href="..\/html\/info.html" style="color:\ green;">info()<\/a><\/code>/g' FAQ.html
+sed -i 's/<code>thermo.refs()<\/code>/<code><a href="..\/html\/util.data.html" style="color:\ green;">thermo.refs()<\/a><\/code>/g' FAQ.html
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2023-05-22 09:37:36 UTC (rev 787)
+++ pkg/CHNOSZ/vignettes/vig.bib 2023-05-27 10:33:30 UTC (rev 788)
@@ -19,6 +19,15 @@
doi = {10.1016/S0301-4622(00)00116-2},
}
+ at Book{AC93,
+ author = {Anderson, Greg M. and Crerar, David A.},
+ publisher = {Oxford University Press},
+ title = {{T}hermodynamics in {G}eochemistry: {T}he {E}quilibrium {M}odel},
+ year = {1993},
+ address = {New York},
+ doi = {10.1093/oso/9780195064643.001.0001},
+}
+
@Article{BZA10,
author = {Bazarkina, E. F. and Zotov, A. V. and Akinfiev, N. N.},
journal = {Geology of Ore Deposits},
@@ -544,6 +553,17 @@
doi = {10.1371/journal.pone.0029529},
}
+ at Article{BB85,
+ author = {Berman, Robert G. and Brown, Thomas H.},
+ journal = {Contributions to Mineralogy and Petrology},
+ title = {Heat capacity of minerals in the system {Na\textsubscript{2}O--K\textsubscript{2}O--CaO--MgO--FeO--Fe\textsubscript{2}O\textsubscript{3}--Al\textsubscript{2}O\textsubscript{3}--SiO\textsubscript{2}--TiO\textsubscript{2}--H\textsubscript{2}O--CO\textsubscript{2}}: representation, estimation, and high temperature extrapolation},
+ year = {1985},
+ number = {2},
+ pages = {168--183},
+ volume = {89},
+ doi = {10.1007/BF00379451},
+}
+
@Article{Dic19,
author = {Dick, Jeffrey M.},
journal = {Frontiers in Earth Science},
@@ -736,6 +756,16 @@
url = {https://www.worldcat.org/oclc/563921897},
}
+ at Article{Dic21b,
+ author = {Dick, Jeffrey M.},
+ journal = {Applied Computing and Geosciences},
+ title = {Diagrams with multiple metals in {CHNOSZ}},
+ year = {2021},
+ pages = {100059},
+ volume = {10},
+ doi = {10.1016/j.acags.2021.100059},
+}
+
@Article{MWKL17,
author = {Miron, George D. and Wagner, Thomas and Kulik, Dmitrii A. and Lothenbach, Barbara},
journal = {American Journal of Science},
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