[CHNOSZ-commits] r538 - in pkg/CHNOSZ: . demo inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jul 4 04:00:42 CEST 2020
Author: jedick
Date: 2020-07-04 04:00:42 +0200 (Sat, 04 Jul 2020)
New Revision: 538
Removed:
pkg/CHNOSZ/.Rinstignore
pkg/CHNOSZ/vignettes/obigt.css
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/DEW.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/vignettes/
pkg/CHNOSZ/vignettes/obigt.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
Log:
Update obigt.Rmd (generated HTML is now much smaller)
Deleted: pkg/CHNOSZ/.Rinstignore
===================================================================
--- pkg/CHNOSZ/.Rinstignore 2020-06-30 16:41:21 UTC (rev 537)
+++ pkg/CHNOSZ/.Rinstignore 2020-07-04 02:00:42 UTC (rev 538)
@@ -1,2 +0,0 @@
-vig.bib
-.*.lyx
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-06-30 16:41:21 UTC (rev 537)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-04 02:00:42 UTC (rev 538)
@@ -1,6 +1,6 @@
-Date: 2020-06-30
+Date: 2020-07-02
Package: CHNOSZ
-Version: 1.3.6-12
+Version: 1.3.6-13
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/DEW.R
===================================================================
--- pkg/CHNOSZ/demo/DEW.R 2020-06-30 16:41:21 UTC (rev 537)
+++ pkg/CHNOSZ/demo/DEW.R 2020-07-04 02:00:42 UTC (rev 538)
@@ -95,32 +95,34 @@
## (Nature Geoscience, https://doi.org/10.1038/NGEO2291)
###########
-# define system with loga.species = 0
+# define system
basis("CHNOS+")
-species(c("CO2", "HCO3-", "CO3-2", "acetic acid", "acetate", "CH4"))
-species(1:6, 0)
+inorganic <- c("CO2", "HCO3-", "CO3-2", "CH4")
+organic <- c("formic acid", "formate", "acetic acid", "acetate", "propanoic acid", "propanoate")
+species(c(inorganic, organic), 0)
+fill <- c(rep("aliceblue", length(inorganic)), rep("aquamarine", length(organic)))
# a function to make the diagrams
-dfun <- function(T = 600, P = 50000, res=300) {
+dfun <- function(T = 600, P = 50000, res = 300) {
a <- affinity(pH = c(0, 10, res), O2 = c(-24, -12, res), T = T, P = P)
- diagram(a, limit.water = FALSE, fill=tail(topo.colors(7), -1))
+ # set total C concentration to 0.03 molal
+ # (from EQ3NR model for eclogite [Supporting Information of SSH14])
+ e <- equilibrate(a, loga.balance = log10(0.03))
+ diagram(e, limit.water = FALSE, fill = fill)
dp <- describe.property(c(" T", " P"), c(T, P), digits=0)
legend("bottomleft", legend=dp, bty="n")
}
obigt()
-## (not run) make diagram using CHNOSZ default database
+## (not run: make diagram using CHNOSZ default database;
+## not recommended for high P)
#dfun()
-#t1 <- quote("CHNOSZ default database"[])
-#t2 <- quote("(not recommended for high"~italic(P)*")")
-#mtitle(as.expression(c(t1, t2)))
# make diagram using CO2, HCO3-, CO3-2, CH4, and acetic acid data from DEW spreadsheet
# (the acetate field disappears if we also use the data for acetate from the spreadsheet 20200629)
-add.obigt("DEW_aq", c("CO2", "HCO3-", "CO3-2", "CH4", "acetic acid"))
+#add.obigt("DEW_aq", c("CO2", "HCO3-", "CO3-2", "CH4", "acetic acid"))
+add.obigt("DEW")
dfun()
-CO2quote <- quote(list(CO[2], HCO[3]^"-", CO[3]^"-2"))
-DEWexpr <- substitute("DEW data for"~x, list(x=CO2quote))
-mtitle(as.expression(c(DEWexpr, "and methane")))
+mtitle(c("Inorganic and organic species", "C[total] = 0.03 molal"))
###########
#### plot 4: speciation of carbon as a function T, logfO2 and pH (added 20171008)
@@ -140,10 +142,9 @@
reset()
water("DEW")
# add species data for DEW
-inorganics <- c("methane", "CO2", "HCO3-", "CO3-2")
-organics <- c("formic acid", "formate", "acetic acid", "acetate")
-# skip updating acetate because the new data from the DEW spreadsheet give different logK
-add.obigt("DEW", c(inorganics, organics[-4]))
+inorganics <- c("CH4", "CO2", "HCO3-", "CO3-2")
+organics <- c("formic acid", "formate", "acetic acid", "acetate", "propanoic acid", "propanoate")
+add.obigt("DEW")
## set basis species
basis(c("Fe", "SiO2", "CO3-2", "H2O", "oxygen", "H+"))
## calculate logfO2 in QFM buffer
@@ -174,7 +175,6 @@
diagram(e, alpha = "balance", names = names, col = col, ylim = c(0, 0.8), ylab="carbon fraction")
}
-
## add legend and title
ltxt1 <- "P = 50000 bar"
ltxt2 <- substitute(logfO2=="QFM-2", list(logfO2 = axis.label("O2")))
@@ -196,8 +196,8 @@
# calculate equilibrium constants of the reactions in CHNOSZ; use a negative sign to change from formation to dissociation
logK.calc <- -unlist(affinity(T = 600, P = 50000, property = "logK")$values)
logK.calc - c(inorganic.logK, organic.logK)
-## check that we're within 0.021 of the logK values used by SSH14
-stopifnot(maxdiff(logK.calc, c(inorganic.logK, organic.logK)) < 0.021)
+## except for acetate, we're within 0.021 of the logK values used by SSH14
+stopifnot(maxdiff(logK.calc[-8], c(inorganic.logK, organic.logK)[-8]) < 0.021)
## check that we get similar activity coefficients
# activity coefficients for monovalent species from EQ3NR output
@@ -207,12 +207,3 @@
stopifnot(maxdiff(sres$out[[1]]$loggam, loggamma) < 0.023)
# if m_star in nonideal() was zero, we could decrease the tolerance here
#stopifnot(maxdiff(sres$out[[1]]$loggam, loggamma) < 0.004)
-
-###########
-### all done!
-# reset the database and previous water computational option
-obigt()
-water(oldwat)
-###########
-
-par(opar)
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2020-06-30 16:41:21 UTC (rev 537)
+++ pkg/CHNOSZ/inst/CHECKLIST 2020-07-04 02:00:42 UTC (rev 538)
@@ -5,8 +5,8 @@
- run examples() and demos() and inspect their output (especially plots)
-- use test_package("CHNOSZ", reporter = "progress") to find warnings
- from tests that aren't shown in R CMD check
+- use testthat::test_package("CHNOSZ", reporter = "progress") to find
+ warnings from tests that aren't shown in R CMD check
- check that uniprot.aa() works with current UniProt web pages
@@ -44,10 +44,15 @@
updating vignettes
******************
-- Customize rmarkdown to reduce the size of vignettes:
- after installing/upgrading rmarkdown, replace files in
- rmarkdown/rmd/h/bootstrap/fonts/ with empty files
+- Customize rmarkdown installation (in R library directory)
+ - to reduce size of vignettes: replace files in
+ rmd/h/bootstrap/fonts/ with empty files
+
+ - to enable offset anchor position in obigt.Rmd:
+ remove padding-top: 10px; from h2 in
+ rmarkdown/templates/html_vignette/resources/vignette.css
+
- Build the package using both qpdf and ghostscript to compact vignettes:
R CMD build --compact-vignettes=both chnosz/
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2020-06-30 16:41:21 UTC (rev 537)
+++ pkg/CHNOSZ/inst/NEWS 2020-07-04 02:00:42 UTC (rev 538)
@@ -1,6 +1,8 @@
-CHANGES IN CHNOSZ 1.3.6-10 (2020-06-29)
+CHANGES IN CHNOSZ 1.3.6-13 (2020-07-04)
--------------------------------------
+- Use updated data for the 2019 Deep Earth Water (DEW) model.
+
- OBIGT/organic_aq.csv, AkDi.csv, DEW_aq.csv: Remove "methane" as the
name of CH4(aq). Consequently, info("methane") refers to the gas
rather than aqueous species. This is consistent with the behavior for
@@ -27,6 +29,9 @@
- Changing the water model with water() now updates the literature
reference in thermo()$obigt.
+- Revise obigt.Rmd to reduce the size of the HTML file and make
+ deep linking to individual sections work.
+
- TODO: thermo.refs(): add current date, write 'thermo()$obigt'.
- TODO: use degree sign in messages from subcrt().
@@ -37,12 +42,16 @@
- TODO: describe default logact in basis.Rd
-- TODO: change references for water for different models (IAPWS, DEW)
-
- TODO: change \url to \doi in Rd files
- TODO: use all caps OBIGT in function and variable names
+- TODO: incorporate community uploaded data
+
+- TODO: move DEW_aq.csv to DEW.csv
+
+- TODO: remove suffixed references (supcrt92, slop98)
+
CHANGES IN CHNOSZ 1.3.6 (2020-03-16)
------------------------------------
Index: pkg/CHNOSZ/vignettes
===================================================================
--- pkg/CHNOSZ/vignettes 2020-06-30 16:41:21 UTC (rev 537)
+++ pkg/CHNOSZ/vignettes 2020-07-04 02:00:42 UTC (rev 538)
Property changes on: pkg/CHNOSZ/vignettes
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.html
Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd 2020-06-30 16:41:21 UTC (rev 537)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd 2020-07-04 02:00:42 UTC (rev 538)
@@ -1,11 +1,8 @@
---
title: "Thermodynamic data in [CHNOSZ](http://www.chnosz.net)"
output:
- html_document:
+ html_vignette:
mathjax: null
- theme: default
- css: obigt.css
- highlight: null
vignette: >
%\VignetteIndexEntry{Thermodynamic data in CHNOSZ}
%\VignetteEngine{knitr::rmarkdown}
@@ -16,16 +13,104 @@
@SPRONS92, @SLOP98, @SLOP07, @SLOP16, @CHNOSZ, @JOH92, @WP02, @CWM89, @PRPG97, @TH88, @Kul06, @Sho09, @HP11
csl: elementa.csl
---
+<style>
+/* for CHNOSZ link */
+h1 a:link {
+ color: red;
+ text-decoration: none;
+}
+/* https://css-tricks.com/hash-tag-links-padding/ */
+a.anchor::before {
+ display: block;
+ content: " ";
+ margin-top: -190px;
+ height: 190px;
+ visibility: hidden;
+ pointer-events: none;
+}
+</style>
+<script>
+function ToggleDiv(ID) {
+ var D = document.getElementById("D-" + ID);
+ if (D.style.display === "none") {
+ // close all divs then open this one
+ CloseAllDivs();
+ OpenDiv(ID);
+ // hide the message about nothing open
+ document.getElementById("nothing-open").style.display = "none";
+ } else {
+ // close all divs
+ CloseAllDivs();
+ // hide the message about nothing open
+ document.getElementById("nothing-open").style.display = "block";
+ }
+}
+function OpenDiv(ID) {
+ // open the div
+ var D = document.getElementById("D-" + ID);
+ D.style.display = "block";
+ // style the button
+ var B = document.getElementById("B-" + ID);
+ var Btext = ID.split("-")[1];
+ B.innerHTML = "<b>" + Btext + "</b>";
+ B.style.color = "red";
+}
+function CloseDiv(ID) {
+ // close the div
+ var D = document.getElementById("D-" + ID);
+ D.style.display = "none";
+ // style the button
+ var B = document.getElementById("B-" + ID);
+ var Btext = ID.split("-")[1];
+ B.innerHTML = Btext;
+ B.style.color = "black";
+}
+function OpenAllDivs() {
+ OpenDiv("aqueous-H2O");
+ OpenDiv("aqueous-inorganic");
+ OpenDiv("aqueous-organic");
+ OpenDiv("aqueous-biotic");
+ OpenDiv("solid-inorganic");
+ OpenDiv("solid-berman");
+ OpenDiv("solid-organic");
+ OpenDiv("gas-inorganic");
+ OpenDiv("gas-organic");
+ OpenDiv("liquid-organic");
+ OpenDiv("optional-DEW");
+ OpenDiv("optional-SUPCRT92");
+ OpenDiv("optional-SLOP98");
+ OpenDiv("optional-OldAA");
+ OpenDiv("optional-AS04");
+ OpenDiv("optional-AkDi");
+ document.getElementById("all-open").style.display = "block";
+}
+function CloseAllDivs() {
+ CloseDiv("aqueous-H2O");
+ CloseDiv("aqueous-inorganic");
+ CloseDiv("aqueous-organic");
+ CloseDiv("aqueous-biotic");
+ CloseDiv("solid-inorganic");
+ CloseDiv("solid-berman");
+ CloseDiv("solid-organic");
+ CloseDiv("gas-inorganic");
+ CloseDiv("gas-organic");
+ CloseDiv("liquid-organic");
+ CloseDiv("optional-DEW");
+ CloseDiv("optional-SUPCRT92");
+ CloseDiv("optional-SLOP98");
+ CloseDiv("optional-OldAA");
+ CloseDiv("optional-AS04");
+ CloseDiv("optional-AkDi");
+ document.getElementById("all-open").style.display = "none";
+}
+</script>
-```{r library_CHNOSZ, include=FALSE}
+```{r CHNOSZ_reset, include=FALSE}
library(CHNOSZ)
-```
-
-```{r data_thermo, include=FALSE}
reset()
```
-```{r nspecies, include=FALSE}
+```{r setfile, include=FALSE}
# assign the file name to a variable and print the file name and number of species
setfile <- function(csvfile, dat=NULL) {
# assign csvfile outside this function
@@ -36,10 +121,17 @@
dat <- read.csv(file, as.is=TRUE)
## exclude entries for phase transitions
#dat <- dat[!dat$state %in% c("cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9"), ]
- # the class of substance (used as section header), followed by number of species
- class <- gsub(".csv", "", gsub("_.*", "", csvfile))
+ # the state and class of substance (used as section header), followed by number of species
+ basename <- gsub(".csv", "", csvfile)
+ class <- strsplit(basename, "_")[[1]][1]
substr(class, 1, 1) <- toupper(substr(class, 1, 1))
- paste0("`", class, "` (", nrow(dat), ")")
+ state <- strsplit(basename, "_")[[1]][2]
+ if(identical(state, "aq")) state <- "Aqueous "
+ else if(identical(state, "cr")) state <- "Solid "
+ else if(identical(state, "gas")) state <- "Gas "
+ else if(identical(state, "liq")) state <- "Liquid "
+ else state <- "Optional "
+ paste0(state, class, " (", nrow(dat), " species)")
}
```
@@ -58,7 +150,7 @@
#dat <- dat[!dat$state %in% c("cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9"), ]
# count number of times each reference is used
tab <- table(dat[, whichref])
- # there are no references in H2O_aq.csv so we return the species here
+ # in case there are not references (previously for H2O_aq.csv) we return the species here
if(length(tab)==0) return(paste(dat$name, dat$state))
# the keys only (no [S92] etc.)
keys <- sapply(strsplit(names(tab), " "), "[", 1)
@@ -103,285 +195,234 @@
}
```
-This [vignette](index.html), produced on `r Sys.Date()`, documents the sources of thermodynamic data in CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
-All of these data, except for Optional Data, are used in the default database, which is loaded when the package is attached, or by running <span style='color:red'>`reset()`</span>.
+```{r used, include=FALSE}
+# initialize the list of used species
+used <- character()
+# initialize the list of used optional species
+optused <- character()
+```
-The sections below correspond to CSV data files that are stored in the `extdata/OBIGT` package directory and read by <span style='color:red'>`reset()`</span> to create the database in the R session (`thermo()$obigt`).
-In each section, the primary references (`ref1` in `thermo()$obigt`) are listed in chronological order.
-Any secondary references (`ref2`) are listed with bullet points.
+This [vignette](index.html), produced on `r Sys.Date()`, documents the sources of thermodynamic data in the OBIGT database in CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
+Except for Optional Data, all data are present in the default database, which is loaded when the package is attached, or by running <span style='color:red'>`reset()`</span> or <span style='color:red'>`obigt()`</span>.
+
+Each of the buttons below corresponds to one of the CSV data files that are stored in the `extdata/OBIGT` package directory.
+Clicking on a button opens a list of the primary references (`ref1` in `thermo()$obigt`) in chronological order; any secondary references (`ref2`) are listed with bullet points.
Each reference is followed by the number of species, and a note (from `thermo()$refs`).
-Symbols show whether the data were present in the earliest of the sprons92.dat (ø), slop98.dat (\*), slop07.dat (†), or slop16.dat (‡) datafiles for the SUPCRT92 package.
-Any additional comments are placed at the beginning of the sections.
Abbreviations used below are: Cp (heat capacity), GHS (standard Gibbs energy, enthalpy, entropy), HKF (Helgeson-Kirkham-Flowers equations), V (volume), T (temperature), P (pressure).
+Parenthetical marks show if the data were present in the earliest of the sprons92.dat (ø), slop98.dat (\*), slop07.dat (†), or slop16.dat (‡) datafiles for the SUPCRT92 package.
-# Recent changes (2018 - 2019)
+<!-- All buttons at top -->
-* Data from SUPCRT92 which have been superseded by the Berman data are listed under **Optional Data** / **SUPCRT92**.
+### Aqueous Species <button id="B-aqueous-H2O" onclick='ToggleDiv("aqueous-H2O")'>H2O</button> <button id="B-aqueous-inorganic" onclick='ToggleDiv("aqueous-inorganic")'>Inorganic</button> <button id="B-aqueous-organic" onclick='ToggleDiv("aqueous-organic")'>Organic</button> <button id="B-aqueous-biotic" onclick='ToggleDiv("aqueous-biotic")'>Biotic</button>
+### Solids <button id="B-solid-inorganic" onclick='ToggleDiv("solid-inorganic")'>Inorganic</button> <button id="B-solid-berman" onclick='ToggleDiv("solid-berman")'>Berman</button> <button id="B-solid-organic" onclick='ToggleDiv("solid-organic")'>Organic</button>
+### Gases <button id="B-gas-inorganic" onclick='ToggleDiv("gas-inorganic")'>Inorganic</button> <button id="B-gas-organic" onclick='ToggleDiv("gas-organic")'>Organic</button> Liquids <button id="B-liquid-organic" onclick='ToggleDiv("liquid-organic")'>Organic</button>
+### Optional Data <button id="B-optional-DEW" onclick='ToggleDiv("optional-DEW")'>DEW</button> <button id="B-optional-SUPCRT92" onclick='ToggleDiv("optional-SUPCRT92")'>SUPCRT92</button> <button id="B-optional-SLOP98" onclick='ToggleDiv("optional-SLOP98")'>SLOP98</button> <button id="B-optional-OldAA" onclick='ToggleDiv("optional-OldAA")'>OldAA</button> <button id="B-optional-AS04" onclick='ToggleDiv("optional-AS04")'>AS04</button> <button id="B-optional-AkDi" onclick='ToggleDiv("optional-AkDi")'>AkDi</button>
-* Superseded data from SLOP98 (including Al, As, and Au species) are listed under **Optional Data** / **SLOP98**.
+<div id="all-open" style="display: none">
+*Showing citations in all data files.*
+*Press any button above to hide them.*
+</div>
-# Sources of data {.tabset .tabset-fade}
+<!-- Aqueous species divs -->
-Use the tabs below to select a section for viewing.
-Select "All at once" to show all sections.
-
-## Aqueous species {.tabset .tabset-pills}
-
-### `r setfile("H2O_aq.csv")`
-```{r H2O_aq, results="asis", echo=FALSE}
-cat('This file contains H<sub>2</sub>O, *e*<sup>-</sup>, and H<sup>+</sup>.\n')
-cat('The properties of H<sub>2</sub>O are listed as NA; CHNOSZ calculates its properties using a Fortran subroutine taken from SUPRCT92 ([Johnson et al., 1992](https://doi.org/10.1016/0098-3004(92)90029-Q)) (default) or using the IAPWS-95 equations ([Wagner and Pruß, 2002](https://doi.org/10.1063/1.1461829)) or the [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model ([Sverjensky et al., 2014](https://doi.org/10.1016/j.gca.2013.12.019)).\n\n')
-cat('By convention, the standard Gibbs energy of formation, entropy, and heat capacity of the aqueous proton (H<sup>+</sup>) are 0 at all *T* and *P* ([e.g. Cox et al., 1989](http://www.worldcat.org/oclc/18559968)).\n')
-cat('The formation reaction of the proton can be expressed as ½H<sub>2,(*g*)</sub> + Z = H<sup>+</sup>, where Z is the "element" of positive charge.\n')
-cat('Because the conventional standard Gibbs energy of this reaction is 0 at all *T*, the standard entropy of the reaction is also constrained to be zero (cf. [Puigdomenech et al., 1997](http://www.oecd-nea.org/dbtdb/pubs/book-pdf/427-494.pdf)).\n')
-cat('Therefore, the "element" of positive charge (Z) has zero thermodynamic properties except for an entropy, *S*°<sub>*T*<sub>r</sub></sub>, that is negative one-half that of H<sub>2,(*g*)</sub>.\n')
-cat('The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by *e*<sup>-</sup> = -Z, is opposite that of Z.<span style="color:red">**</span>\n\n')
-cat('Despite these considerations, the final column of the thermodynamic database (`thermo()$obigt`) lists a charge of "0" for both the aqueous proton and electron.\n')
-cat('Data in this this column are used in CHNOSZ only to specify the charge that is input to the "*g*-function" ([Tanger and Helgeson, 1988](https://doi.org/10.2475/ajs.288.1.19); [Shock and Helgeson, 1988](https://doi.org/10.1016/0016-7037(88)90181-0)).\n')
-cat('Setting it to zero prevents activation of the *g*-function, which would result in non-zero contributions to thermodynamic properties, conflicting with the conventions mentioned above.\n')
-cat('All other calculations in CHNOSZ obtain the elemental makeup, including the correct charge for the species, by parsing the chemical formulas stored in the database.<span style="color:red">^^</span>\n\n')
-cat('<span style="color:red">**</span>Likewise, [GEM-Selektor](http://gems.web.psi.ch/) defines "independent components" to be stoichiometric units usually consisting of elements and charge; the latter, [which is named Zz](http://gems.web.psi.ch/tests/TestNaCl-dep.html) and has a standard molal entropy of -65.34 J/mol/K and heat capacity of -14.418 J/mol/K (negative one-half those of gaseous hydrogen), is negated in the formula of the fictive "aqueous electron" ([Kulik, 2006](https://doi.org/10.1016/j.chemgeo.2005.08.014)).\n\n')
-cat('<span style="color:red">^^</span> Relatedly, charged amino acid sidechain groups have a charge that is tabulated as zero, because other values would be incompatible with group additivity of cations and anions (which have derivatives of the omega parameter (ω) in the revised HKF equations of state that are not opposites of each other) to give a neutral species (for which the derivatives of ω are taken to be zero) (cf. [Dick et al., 2006](https://doi.org/10.5194/bg-3-311-2006)).\n')
-```
-```{r used, include=FALSE}
-# initialize the list of used species
-used <- character()
-```
+<div id="D-aqueous-H2O" style="display: none">
+## <a id="aqueous-H2O" class="anchor"></a> `r setfile("H2O_aq.csv")`
```{r reflist, results="asis", echo=FALSE}
used <- c(used, filerefs(csvfile))
```
-### `r setfile("inorganic_aq.csv")`
-```{r inorganic_aq, results="asis", echo=FALSE}
-```
+This file contains H<sub>2</sub>O, *e*<sup>-</sup>, and H<sup>+</sup>.
+The properties of H<sub>2</sub>O are listed as NA; CHNOSZ calculates its properties using a Fortran subroutine taken from SUPRCT92 ([Johnson et al., 1992](https://doi.org/10.1016/0098-3004(92)90029-Q)) (default) or using the IAPWS-95 equations ([Wagner and Pruß, 2002](https://doi.org/10.1063/1.1461829)) or the [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model ([Sverjensky et al., 2014](https://doi.org/10.1016/j.gca.2013.12.019)).
-```{r reflist, results="asis", echo=FALSE}
-```
+By convention, the standard Gibbs energy of formation, entropy, and heat capacity of the aqueous proton (H<sup>+</sup>) are 0 at all *T* and *P* ([e.g. Cox et al., 1989](http://www.worldcat.org/oclc/18559968)).
+The formation reaction of the proton can be expressed as ½H<sub>2,(*g*)</sub> + Z = H<sup>+</sup>, where Z is the "element" of positive charge.
+Because the conventional standard Gibbs energy of this reaction is 0 at all *T*, the standard entropy of the reaction is also constrained to be zero (cf. [Puigdomenech et al., 1997](http://www.oecd-nea.org/dbtdb/pubs/book-pdf/427-494.pdf)).
+Therefore, the "element" of positive charge (Z) has zero thermodynamic properties except for an entropy, *S*°<sub>*T*<sub>r</sub></sub>, that is negative one-half that of H<sub>2,(*g*)</sub>.
+The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by *e*<sup>-</sup> = -Z, is opposite that of Z.
-### `r setfile("organic_aq.csv")`
-```{r reflist, results="asis", echo=FALSE}
-```
+Likewise, [GEM-Selektor](http://gems.web.psi.ch/) defines "independent components" to be stoichiometric units usually consisting of elements and charge; the latter, [which is named Zz](http://gems.web.psi.ch/tests/TestNaCl-dep.html) and has a standard molal entropy of -65.34 J/mol/K and heat capacity of -14.418 J/mol/K (negative one-half those of gaseous hydrogen), is negated in the formula of the fictive "aqueous electron" ([Kulik, 2006](https://doi.org/10.1016/j.chemgeo.2005.08.014)).
-### `r setfile("biotic_aq.csv")`
-```{r reflist, results="asis", echo=FALSE}
-```
+Despite these considerations, the final column of the thermodynamic database (`thermo()$obigt`) lists a charge of "0" for both the aqueous proton and electron.
+Data in this this column are used in CHNOSZ only to specify the charge that is input to the "*g*-function" ([Tanger and Helgeson, 1988](https://doi.org/10.2475/ajs.288.1.19); [Shock and Helgeson, 1988](https://doi.org/10.1016/0016-7037(88)90181-0)).
+Setting it to zero prevents activation of the *g*-function, which would result in non-zero contributions to thermodynamic properties, conflicting with the conventions mentioned above.
+All other calculations in CHNOSZ obtain the elemental makeup, including the correct charge for the species, by parsing the chemical formulas stored in the database.
+</div>
-## Solids {.tabset .tabset-pills}
+<div id="D-aqueous-inorganic" style="display: none">
+## <a id="aqueous-inorganic" class="anchor"></a> `r setfile("inorganic_aq.csv")`
-### `r setfile("inorganic_cr.csv")`
-```{r inorganic_cr, results="asis", echo=FALSE}
-cat("Chamosite,7A and witherite were present in sprons92.dat but not in slop98.dat or later files, and are not included in CHNOSZ.\n\n")
-cat("The source of parameters used here for goethite is different from that in the slop files ([Shock, 2009](https://doi.org/10.2113/gsecongeo.104.8.1235)).<hr>")
-```
-
```{r reflist, results="asis", echo=FALSE}
```
+</div>
-### `r setfile("organic_cr.csv")`
+<div id="D-aqueous-organic" style="display: none">
+## <a id="aqueous-organic" class="anchor"></a> `r setfile("organic_aq.csv")`
+
```{r reflist, results="asis", echo=FALSE}
```
+</div>
-### `r setfile("Berman_cr.csv")`
-```{r Berman_cr, results="asis", echo=FALSE}
-cat("This file gives the identifiying information for minerals whose properties are calculated using the formulation of [Berman (1988)](https://doi.org/10.1093/petrology/29.2.445).\n")
-cat("Note that thermodynamic properties for these minerals are listed as NA in `thermo()$obigt`; the actual data are stored separately, as CSV files in `extdata/Berman/*.csv`.\n")
-```
+<div id="D-aqueous-biotic" style="display: none">
+## <a id="aqueous-biotic" class="anchor"></a> `r setfile("biotic_aq.csv")`
+Charged amino acid sidechain groups have a Z parameter that is tabulated as zero; their chemical formulas indicate the correct charge.
+Non-zero values of Z would yield derivatives of the omega parameter (ω) in the revised HKF equations of state for the cations and anions *that are not opposites of each other*.
+This would be incompatible with group additivity of cations and anions to give a neutral species, for which the derivatives of ω are taken to be zero (cf. [Dick et al., 2006](https://doi.org/10.5194/bg-3-311-2006)).
```{r reflist, results="asis", echo=FALSE}
```
+</div>
-## Liquids {.tabset .tabset-pills}
+<!-- Solid species divs -->
-### `r setfile("organic_liq.csv")`
+<div id="D-solid-inorganic" style="display: none">
+## <a id="solid-inorganic" class="anchor"></a> `r setfile("inorganic_cr.csv")`
+Chamosite,7A and witherite were present in sprons92.dat but not in slop98.dat or later files, and are not included in CHNOSZ.
+The source of parameters used here for goethite is different from that in the slop files ([Shock, 2009](https://doi.org/10.2113/gsecongeo.104.8.1235)).
+
```{r reflist, results="asis", echo=FALSE}
```
+</div>
-## Gases {.tabset .tabset-pills}
+<div id="D-solid-berman" style="display: none">
+## <a id="solid-berman" class="anchor"></a> `r setfile("Berman_cr.csv")`
+This file gives the identifiying information for minerals whose properties are calculated using the formulation of [Berman (1988)](https://doi.org/10.1093/petrology/29.2.445).
+Thermodynamic properties for these minerals are listed as NA in `thermo()$obigt`; the actual data are stored separately, as CSV files in `extdata/Berman/*.csv`.
-### `r setfile("inorganic_gas.csv")`
```{r reflist, results="asis", echo=FALSE}
```
+</div>
-### `r setfile("organic_gas.csv")`
+<div id="D-solid-organic" style="display: none">
+## <a id="solid-organic" class="anchor"></a> `r setfile("organic_cr.csv")`
+
```{r reflist, results="asis", echo=FALSE}
```
+</div>
-## Optional Data {.tabset .tabset-pills}
+<!-- Gas species divs -->
-### `r setfile("DEW_aq.csv")`
-```{r DEW_aq, results="asis", echo=FALSE}
-cat("The [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model extends the applicability of the revised HKF equations of state to 60 kbar. Accuracy of the thermodynamic calculations at these conditions is improved by revised correlations for the <i>a</i><sub>1</sub> HKF parameter, as described by [Sverjensky et al., 2014](https://doi.org/10.1016/j.gca.2013.12.019). The data here were taken from the May 2017 version of the DEW spreadsheet ([Dew Model, 2017](http://www.dewcommunity.org/resources.html)). The following species are present in the spreadsheet, but are not used here because the parameters are unchanged from the default database in CHNOSZ: B(OH)<sub>3</sub>, Br<sup>-</sup>, Ca<sup>+2</sup>, Cl<sup>-</sup>, Cs<sup>+</sup>, F<sup>-</sup>, H<sup>+</sup>, H<sub>2</sub>, He, I<sup>-</sup>, K<sup>+</sup>, Kr, Li<sup>+</sup>, Mg<sup>+2</sup>, Na<sup>+</sup>, Ne, O<sub>2</sub>, Rb<sup>+</sup>, Rn, SO<sub>4</sub><sup>-2</sup>.\n\n")
-cat("Besides using <span style='color:red'>`add.obigt('DEW')`</span> to load these data, you should also run <span style='color:red'>`water('DEW')`</span> to activate the DEW equations in CHNOSZ. See [<span style='color:blue'>`demo(DEW)`</span>](../demo) for some examples.<hr>")
-```
+<div id="D-gas-inorganic" style="display: none">
+## <a id="gas-inorganic" class="anchor"></a> `r setfile("inorganic_gas.csv")`
-```{r optused, include=FALSE}
-# initialize the list of used optional data
-optused <- character()
+```{r reflist, results="asis", echo=FALSE}
```
-```{r optreflist, results="asis", echo=FALSE}
-# run filerefs for optional data sources
-optused <- c(optused, filerefs(csvfile))
-```
+</div>
-### `r setfile("SUPCRT92.csv")`
-```{r SUPCRT92, results="asis", echo=FALSE}
-cat('These minerals and aqueous species, taken from the SUPCRT92 database, were present in earlier versions of CHNOSZ but have since been superseded by @Ber88 (minerals) and @NA03 (H<sub>2</sub>AsO<sub>3</sub><sup>-</sup>). The thermodynamic properties and parameters are kept here as optional data for reproducing published calculations and making comparisons with newer data. The minerals here include all of the silicates and Al-bearing minerals from @HDNB78, as well as calcite, dolomite, hematite, and magnetite. Use <span style="color:red">`add.obigt("SUPCRT92")`</span> to load the data. **NOTE:** Other minerals from SUPCRT92, including native elements, sulfides, halides, sulfates, and selected carbonates and oxides that do not duplicate those in the Berman dataset, are still present in the default database (**inorganic_cr.csv**).\n\n')
-```
+<div id="D-gas-organic" style="display: none">
+## <a id="gas-organic" class="anchor"></a> `r setfile("organic_gas.csv")`
-```{r optreflist, results="asis", echo=FALSE}
+```{r reflist, results="asis", echo=FALSE}
```
+</div>
-### `r setfile("SLOP98.csv")`
-```{r SLOP98, results="asis", echo=FALSE}
-cat('These species, which were taken from or are linked to slop98.dat (or later versions) and were present in earlier versions of CHNOSZ, have been replaced by or are incompatible with species currently in the default database, including aqueous Al species [@TS01], As species [@NA03], Au, Ag, and Cu species [@AZ01; @AZ10], Pd species [@TBZ+13], Zn species [@AT14], and Pt species [@TBB15]. This file also contains aqueous transuranic actinide complexes, for which estimated thermodynamic properties have been reported, but no entropies of the corresponding elements at 298.15 K are available to check the self-consistency of the GHS values for the complexes. Use <span style="color:red">`add.obigt("SLOP98")`</span> to load the data. **NOTE:** Many other species found in slop98.dat and later versions are still present in the default database.\n\n')
-```
+<!-- Liquid species divs -->
-```{r optreflist, results="asis", echo=FALSE}
-```
+<div id="D-liquid-organic" style="display: none">
+## <a id="liquid-organic" class="anchor"></a> `r setfile("organic_liq.csv")`
-### `r setfile("OldAA.csv")`
-```{r OldAA, results="asis", echo=FALSE}
-cat('Data for these amino acids and related species were present in earlier versions of CHNOSZ but have been replaced by or are incompatible with later updates [@LD12; @Kit14; @AKAE19]. Use <span style="color:red">`add.obigt("OldAA")`</span> to load the data.\n\n')
+```{r reflist, results="asis", echo=FALSE}
```
+</div>
-```{r optreflist, results="asis", echo=FALSE}
-```
+<!-- Optional species divs -->
-### `r setfile("AS04.csv")`
-```{r AS04, results="asis", echo=FALSE}
-cat('This file has data for aqueous SiO<sub>2</sub> from @AS04 and a modified HSiO<sub>3</sub><sup>-</sup> to be consistent with the SiO<sub>2</sub> here. This file also has H<sub>4</sub>SiO<sub>4</sub> from an earlier publication [@Ste01] that is roughly consistent with SiO<sub>2</sub> here (see <span style="color:red">`?add.obigt`</span>). Use <span style="color:red">`add.obigt("AS04")`</span> to load the data; see [<span style="color:blue">*Regressing thermodynamic data*</span>](eos-regress.html) for an example.\n\n')
-```
+<div id="D-optional-DEW" style="display: none">
+## <a id="optional-DEW" class="anchor"></a> `r setfile("DEW_aq.csv")`
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 538
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