[CHNOSZ-commits] r813 - in pkg/CHNOSZ: . demo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 28 11:01:02 CET 2023
Author: jedick
Date: 2023-11-28 11:01:01 +0100 (Tue, 28 Nov 2023)
New Revision: 813
Added:
pkg/CHNOSZ/vignettes/elementa.csl.orig
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/gold.R
pkg/CHNOSZ/vignettes/FAQ.Rmd
pkg/CHNOSZ/vignettes/elementa.csl
pkg/CHNOSZ/vignettes/vig.bib
Log:
Add reference for revised HKF to FAQ.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2023-11-15 13:18:19 UTC (rev 812)
+++ pkg/CHNOSZ/DESCRIPTION 2023-11-28 10:01:01 UTC (rev 813)
@@ -1,6 +1,6 @@
Date: 2023-11-15
Package: CHNOSZ
-Version: 2.0.0-32
+Version: 2.0.0-33
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/demo/gold.R
===================================================================
--- pkg/CHNOSZ/demo/gold.R 2023-11-15 13:18:19 UTC (rev 812)
+++ pkg/CHNOSZ/demo/gold.R 2023-11-28 10:01:01 UTC (rev 813)
@@ -98,7 +98,7 @@
title(main=("After Stef\u00e1nsson and Seward, 2004, Fig. 12b"), font.main = 1, cex.main = 1.1)
}
-# Dstimate the Cl- molality and ionic strength for a hypothetical
+# Estimate the Cl- molality and ionic strength for a hypothetical
# NaCl solution with total chloride equal to specified NaCl + KCl solution,
# then estimate the molality of K+ in that solution 20181109
chloride <- function(T, P, m_NaCl, m_KCl) {
Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-11-15 13:18:19 UTC (rev 812)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-11-28 10:01:01 UTC (rev 813)
@@ -229,20 +229,20 @@
reset()
```
-* Additional minerals from @HDNB78, which were available in SUPCRT92 but may conflict with the @Ber88 compilation, can be loaded from an optional database with `add.OBIGT("SUPCRT92")`. When using these data, it is appropriate to cite @HDNB78 rather than SUPCRT92.
+* Additional minerals from @HDNB78, that were available in SUPCRT92 but may conflict with the @Ber88 compilation, can be loaded from an optional database with `add.OBIGT("SUPCRT92")`. When using these data, it is appropriate to cite @HDNB78 rather than SUPCRT92.
*Answered on 2023-05-27; PPM example added on 2023-11-15.*
## 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].
+* The thermodynamic properties of liquid water are calculated using Fortran code from SUPCRT92 [@JOH92] or optionally 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).
+* The corresponding high-temperature properties are calculated using the @BB85 equations for minerals and the revised [@TH88;@SH88] Helgeson-Kirkham-Flowers [@HKF81] equations for aqueous species.
+* The revised 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].
+* A related adjustment is available to convert standard Gibbs energies for gases from the 1 bar standard state used in SUPCRT92 to a variable-pressure standard state [@AC93,Ch.12].
-*Answered on 2018-11-13; moved from <https://chnosz.net/> on 2023-05-27.*
+*Answered on 2018-11-13; moved to FAQ from <https://chnosz.net/> website on 2023-05-27; added references for **revised** HKF on 2023-11-17.*
## When and why do equal-activity boundaries depend on total activity?
@@ -701,7 +701,7 @@
This feature is intended to make it harder to obtain potentially unreliable results at temperatures where a mineral (or an organic solid or liquid) is not stable.
If you want the extrapolated Δ*G*° above the listed phase stability limit, then add `exceed.Ttr = TRUE` to the function call to `subcrt()`.
-OBIGT has a non-exhaustive list of temperatures of melting, decomposition, or other phase change, some of which were taken from `SUPCRT92` while others were taken from @RH95.
+OBIGT has a non-exhaustive list of temperatures of melting, decomposition, or other phase change, some of which were taken from SUPCRT92 while others were taken from @RH95.
These minerals are listed below:
```{r mineral_Ttr, collapse = TRUE}
@@ -739,7 +739,7 @@
Notably, SUPCRT92 outputs Δ*G*° and other standard thermodynamic properties at temperatures higher than Tmax despite the warning.
This is a new feature in the development version of CHNOSZ (to be 2.0.1).
-In previous versions of CHNOSZ, values of Δ*G*° above the *C~p~* equation limit were set to NA without a warning (as with the phase stability limit described above).
+In previous versions of CHNOSZ, values of Δ*G*° above the *C~p~* equation limit were set to NA without a warning, as with the phase stability limit described above.
**4. Finally, if `T` is NA or 0, then no upper temerature limit is imposed by `subcrt()`.**
Modified: pkg/CHNOSZ/vignettes/elementa.csl
===================================================================
--- pkg/CHNOSZ/vignettes/elementa.csl 2023-11-15 13:18:19 UTC (rev 812)
+++ pkg/CHNOSZ/vignettes/elementa.csl 2023-11-28 10:01:01 UTC (rev 813)
@@ -17,7 +17,7 @@
<category citation-format="author-date"/>
<category field="science"/>
<eissn>2325-1026</eissn>
- <summary>Based on The Council of Science Editors style, Name-Year system: author-date in text, sorted in alphabetical order by author. Modified by Jeffrey Dick on 2020-06-29 to change disambiguation style.</summary>
+ <summary>Based on The Council of Science Editors style, Name-Year system: author-date in text, sorted in alphabetical order by author. Modified by Jeffrey Dick on 2020-06-29 to change disambiguation style and on 2023-11-17 to turn off sorting in citations.</summary>
<updated>2016-07-26T01:00:00+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
@@ -415,10 +415,6 @@
</choose>
</macro>
<citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="false" disambiguate-add-givenname="false">
- <sort>
- <key macro="year-date"/>
- <key macro="author-short"/>
- </sort>
<layout prefix="(" suffix=")" delimiter="; ">
<group delimiter=", ">
<text macro="author-short"/>
Added: pkg/CHNOSZ/vignettes/elementa.csl.orig
===================================================================
--- pkg/CHNOSZ/vignettes/elementa.csl.orig (rev 0)
+++ pkg/CHNOSZ/vignettes/elementa.csl.orig 2023-11-28 10:01:01 UTC (rev 813)
@@ -0,0 +1,453 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
+ <info>
+ <title>Elementa</title>
+ <title-short>Elementa</title-short>
+ <id>http://www.zotero.org/styles/elementa</id>
+ <link href="http://www.zotero.org/styles/elementa" rel="self"/>
+ <link href="http://www.zotero.org/styles/council-of-science-editors-author-date" rel="template"/>
+ <link href="http://www.zotero.org/styles/apa" rel="template"/>
+ <link href="https://home.elementascience.org/for-authors/style-guide/" rel="documentation"/>
+ <link href="http://lynn-library.libguides.com/cse" rel="documentation"/>
+ <link href="http://writing.wisc.edu/Handbook/DocCSE_CitationSystems.html" rel="documentation"/>
+ <author>
+ <name>Akos Kokai</name>
+ <email>akokai at berkeley.edu</email>
+ </author>
+ <category citation-format="author-date"/>
+ <category field="science"/>
+ <eissn>2325-1026</eissn>
+ <summary>Based on The Council of Science Editors style, Name-Year system: author-date in text, sorted in alphabetical order by author.</summary>
+ <updated>2016-07-26T01:00:00+00:00</updated>
+ <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+ </info>
+ <locale xml:lang="en">
+ <terms>
+ <term name="editortranslator" form="long">
+ <single>editor and translator</single>
+ <multiple>editors and translators</multiple>
+ </term>
+ <term name="collection-editor" form="long">
+ <single>editor</single>
+ <multiple>editors</multiple>
+ </term>
+ <term name="no date">n.d.</term>
+ </terms>
+ </locale>
+ <macro name="author">
+ <names variable="author" delimiter="; ">
+ <name name-as-sort-order="all" sort-separator=" " initialize-with="" delimiter=", " delimiter-precedes-last="always"/>
+ <label form="long" prefix=", " strip-periods="true"/>
+ <substitute>
+ <names variable="editor translator"/>
+ <names variable="editor"/>
+ <names variable="collection-editor"/>
+ <names variable="translator"/>
+ <choose>
+ <if type="report">
+ <text variable="publisher"/>
+ <text macro="title"/>
+ </if>
+ <else>
+ <text macro="title"/>
+ </else>
+ </choose>
+ </substitute>
+ </names>
+ </macro>
+ <macro name="author-short">
+ <names variable="author">
+ <name form="short" delimiter=", " initialize-with="" and="text"/>
+ <substitute>
+ <names variable="editor"/>
+ <names variable="collection-editor"/>
+ <names variable="translator"/>
+ <choose>
+ <if type="report">
+ <text variable="publisher"/>
+ <text macro="title"/>
+ </if>
+ <else>
+ <text macro="title"/>
+ </else>
+ </choose>
+ </substitute>
+ </names>
+ </macro>
+ <macro name="container-contributors">
+ <names variable="editor translator" delimiter="; ">
+ <name delimiter-precedes-last="always" initialize-with="" name-as-sort-order="all" sort-separator=" "/>
+ <label prefix=", "/>
+ </names>
+ </macro>
+ <macro name="year">
+ <choose>
+ <if variable="issued">
+ <date variable="issued" delimiter=" ">
+ <date-part name="year"/>
+ </date>
+ </if>
+ <else>
+ <text term="no date"/>
+ </else>
+ </choose>
+ </macro>
+ <macro name="year-date">
+ <choose>
+ <if variable="issued">
+ <group delimiter=" ">
+ <date variable="issued" delimiter=" ">
+ <date-part name="year"/>
+ </date>
+ <choose>
+ <if type="patent article-newspaper webpage" match="any">
+ <date variable="issued" delimiter=" ">
+ <date-part name="month" form="short" strip-periods="true"/>
+ <date-part name="day"/>
+ </date>
+ </if>
+ <else-if type="article-journal article-magazine" match="any">
+ <choose>
+ <if variable="volume issue" match="none">
+ <date variable="issued" delimiter=" ">
+ <date-part name="month" form="short" strip-periods="true"/>
+ <date-part name="day"/>
+ </date>
+ </if>
+ </choose>
+ </else-if>
+ </choose>
+ </group>
+ </if>
+ <else>
+ <text term="no date"/>
+ </else>
+ </choose>
+ </macro>
+ <macro name="title">
+ <group delimiter=" ">
+ <choose>
+ <if type="book">
+ <text variable="title" font-style="italic" text-case="title"/>
+ </if>
+ <else>
+ <text variable="title"/>
+ </else>
+ </choose>
+ <choose>
+ <if type="thesis dataset speech interview broadcast" match="any">
+ <text variable="genre" form="long" prefix="[" suffix="]"/>
+ </if>
+ </choose>
+ <choose>
+ <!-- Book reviews -->
+ <if variable="reviewed-author">
+ <choose>
+ <if variable="reviewed-title">
+ <group delimiter=" ">
+ <text variable="title"/>
+ <group delimiter=", " prefix="[" suffix="]">
+ <text variable="reviewed-title" font-style="italic" prefix="Review of "/>
+ <names variable="reviewed-author" delimiter=", ">
+ <label form="verb-short" suffix=" "/>
+ <name and="text" initialize-with="" delimiter=", "/>
+ </names>
+ </group>
+ </group>
+ </if>
+ <else>
+ <!-- assume `title` is title of reviewed work -->
+ <group delimiter=", " prefix="[" suffix="]">
+ <text variable="title" font-style="italic" prefix="Review of "/>
+ <names variable="reviewed-author" delimiter=", ">
+ <label form="verb-short" suffix=" "/>
+ <name and="text" initialize-with="" delimiter=", "/>
+ </names>
+ </group>
+ </else>
+ </choose>
+ </if>
+ </choose>
+ </group>
+ </macro>
+ <macro name="container-title">
+ <choose>
+ <if type="chapter">
+ <text variable="container-title" font-style="italic" text-case="title"/>
+ </if>
+ <else-if type="article-magazine article-newspaper">
+ <text variable="container-title" font-style="italic"/>
+ </else-if>
+ <else-if type="article-journal">
+ <text variable="container-title" form="short" font-style="italic" strip-periods="true"/>
+ </else-if>
+ <else>
+ <text variable="container-title"/>
+ </else>
+ </choose>
+ </macro>
+ <macro name="container">
+ <group>
+ <choose>
+ <if type="chapter entry-dictionary entry-encyclopedia" match="any">
+ <text term="in" text-case="capitalize-first" suffix=": "/>
+ </if>
+ </choose>
+ <choose>
+ <if type="bill legal_case legislation" match="none">
+ <group delimiter=". ">
+ <text macro="container-contributors"/>
+ <text macro="container-title"/>
+ </group>
+ </if>
+ </choose>
+ </group>
+ </macro>
+ <macro name="edition">
+ <choose>
+ <if is-numeric="edition">
+ <group delimiter=" ">
+ <number variable="edition" form="ordinal"/>
+ <label variable="edition" form="short"/>
+ </group>
+ </if>
+ <else>
+ <text variable="edition"/>
+ </else>
+ </choose>
+ </macro>
+ <macro name="pages">
+ <choose>
+ <if type="chapter entry-dictionary entry-encyclopedia" match="any">
+ <group delimiter="; ">
+ <group>
+ <label variable="page" form="short" suffix=" " plural="never"/>
+ <text variable="page"/>
+ </group>
+ <group>
+ <text variable="number-of-pages"/>
+ <choose>
+ <if is-numeric="number-of-pages">
+ <label variable="number-of-pages" form="short" prefix=" " plural="never"/>
+ </if>
+ </choose>
+ </group>
+ </group>
+ </if>
+ </choose>
+ </macro>
+ <macro name="journal-locators">
+ <group suffix=".">
+ <choose>
+ <if variable="volume issue page" match="none">
+ <choose>
+ <if type="article-journal review review-book">
+ <text term="in press" prefix=", "/>
+ </if>
+ </choose>
+ </if>
+ <else>
+ <group>
+ <text variable="volume" prefix=" " font-weight="bold"/>
+ <text variable="issue" prefix="(" suffix=")"/>
+ <text variable="page" prefix=": "/>
+ </group>
+ </else>
+ </choose>
+ </group>
+ </macro>
+ <macro name="locators">
+ <choose>
+ <if type="article-journal article-magazine article-newspaper review review-book" match="any">
+ <text macro="journal-locators"/>
+ </if>
+ <else-if type="paper-conference">
+ <choose>
+ <if variable="container-title">
+ <text macro="journal-locators"/>
+ </if>
+ <else>
+ <date variable="issued" delimiter=" " suffix=".">
+ <date-part name="year"/>
+ <date-part name="month" form="short" strip-periods="true"/>
+ <date-part name="day"/>
+ </date>
+ </else>
+ </choose>
+ </else-if>
+ <else-if type="bill legal_case legislation" match="none">
+ <text macro="edition" suffix="."/>
+ </else-if>
+ </choose>
+ </macro>
+ <macro name="legal-cites">
+ <!-- Bluebook style; adapted from apa.csl -->
+ <choose>
+ <if type="bill legal_case legislation" match="any">
+ <group delimiter=" ">
+ <choose>
+ <if variable="container-title">
+ <text variable="volume"/>
+ <text variable="container-title"/>
+ <group delimiter=" ">
+ <!--change to label variable="section" as that becomes available -->
+ <text term="section" form="symbol"/>
+ <text variable="section"/>
+ </group>
+ <text variable="section"/>
+ <text variable="page"/>
+ </if>
+ <else>
+ <choose>
+ <if type="legal_case">
+ <text variable="number" prefix="No. "/>
+ </if>
+ <else>
+ <text variable="number" prefix="Pub. L. No. "/>
+ <group delimiter=" ">
+ <!--change to label variable="section" as that becomes available -->
+ <text term="section" form="symbol"/>
+ <text variable="section"/>
+ </group>
+ <text variable="section"/>
+ </else>
+ </choose>
+ </else>
+ </choose>
+ </group>
+ </if>
+ </choose>
+ </macro>
+ <macro name="event">
+ <choose>
+ <if variable="event">
+ <choose>
+ <if variable="container-title" match="none">
+ <!-- Don't give event info if part of a publication
+ (e.g., conference proceedings) -->
+ <choose>
+ <if type="paper-conference" match="none">
+ <group delimiter=" ">
+ <text variable="genre" text-case="capitalize-first"/>
+ <text term="presented at" text-case="capitalize-first"/>
+ </group>
+ </if>
+ </choose>
+ <group prefix=" " suffix="." delimiter="; ">
+ <text variable="event"/>
+ <text variable="event-place"/>
+ </group>
+ </if>
+ </choose>
+ </if>
+ </choose>
+ </macro>
+ <macro name="publisher">
+ <group delimiter=": ">
+ <choose>
+ <if type="thesis">
+ <text variable="publisher-place" prefix="[" suffix="]"/>
+ </if>
+ <else-if variable="event" match="none">
+ <text variable="publisher-place"/>
+ </else-if>
+ </choose>
+ <text variable="publisher"/>
+ </group>
+ </macro>
+ <macro name="collection">
+ <!-- This is to appear at the end of the citation:
+ after publisher, before access. -->
+ <choose>
+ <if type="report">
+ <group prefix=" " suffix="." delimiter=" ">
+ <text variable="collection-title"/>
+ <text variable="number" prefix="Report No.: "/>
+ </group>
+ </if>
+ <else-if type="book">
+ <group prefix=" (" suffix=")." delimiter=" ">
+ <names variable="collection-editor" suffix=". ">
+ <name delimiter-precedes-last="always" initialize-with="" name-as-sort-order="all" sort-separator=" "/>
+ <label prefix="; "/>
+ </names>
+ <group delimiter="; ">
+ <text variable="collection-title"/>
+ <choose>
+ <if variable="collection-number">
+ <group>
+ <text term="volume" form="short" text-case="capitalize-first" suffix=". "/>
+ <text variable="collection-number"/>
+ </group>
+ </if>
+ <else>
+ <group>
+ <label variable="volume" form="short" text-case="capitalize-first" suffix=". "/>
+ <text variable="volume"/>
+ </group>
+ </else>
+ </choose>
+ </group>
+ </group>
+ </else-if>
+ <!-- Add other types that need collection info after publisher. -->
+ </choose>
+ </macro>
+ <macro name="access">
+ <choose>
+ <if variable="DOI">
+ <text variable="DOI" prefix="doi: "/>
+ </if>
+ <else-if variable="URL">
+ <group suffix=". " delimiter=" ">
+ <text term="available at" text-case="capitalize-first"/>
+ <text variable="URL"/>
+ </group>
+ <group suffix=". " delimiter=" ">
+ <text term="accessed" text-case="capitalize-first"/>
+ <date variable="accessed" delimiter=" ">
+ <date-part name="year"/>
+ <date-part name="month" form="short" strip-periods="true"/>
+ <date-part name="day"/>
+ </date>
+ </group>
+ </else-if>
+ </choose>
+ </macro>
+ <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true">
+ <sort>
+ <key macro="year-date"/>
+ <key macro="author-short"/>
+ </sort>
+ <layout prefix="(" suffix=")" delimiter="; ">
+ <group delimiter=", ">
+ <text macro="author-short"/>
+ <text macro="year"/>
+ </group>
+ <text variable="locator" prefix=": "/>
+ </layout>
+ </citation>
+ <bibliography hanging-indent="true" et-al-min="11" et-al-use-first="10">
+ <sort>
+ <key macro="author"/>
+ <key macro="year-date"/>
+ </sort>
+ <layout>
+ <group delimiter=". " suffix=".">
+ <text macro="author"/>
+ <text macro="year-date"/>
+ <text macro="title"/>
+ <group delimiter="">
+ <text macro="container"/>
+ <text macro="locators"/>
+ </group>
+ <text macro="legal-cites"/>
+ <text macro="event"/>
+ <text macro="publisher"/>
+ <text macro="pages"/>
+ <text macro="collection"/>
+ </group>
+ <text prefix=" " macro="access"/>
+ </layout>
+ </bibliography>
+</style>
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2023-11-15 13:18:19 UTC (rev 812)
+++ pkg/CHNOSZ/vignettes/vig.bib 2023-11-28 10:01:01 UTC (rev 813)
@@ -371,6 +371,17 @@
doi = {10.1111/j.1468-8123.2010.00277.x},
}
+ at Article{SH88,
+ author = {Shock, Everett L. and Helgeson, Harold C.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Correlation algorithms for ionic species and equation of state predictions to 5 kb and 1000°{C}},
+ year = {1988},
+ number = {8},
+ pages = {2009--2036},
+ volume = {52},
+ doi = {10.1016/0016-7037(88)90181-0},
+}
+
@Article{SHS89,
author = {Shock, Everett L. and Helgeson, Harold C. and Sverjensky, Dimitri A.},
journal = {Geochimica et Cosmochimica Acta},
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