[CHNOSZ-commits] r448 - in pkg/CHNOSZ: . demo inst inst/extdata/OBIGT inst/extdata/thermo man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Apr 16 11:50:20 CEST 2019 

Author: jedick
Date: 2019-04-16 11:50:20 +0200 (Tue, 16 Apr 2019)
New Revision: 448

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/aluminum.R
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/man/add.obigt.Rd
   pkg/CHNOSZ/vignettes/eos-regress.Rmd
   pkg/CHNOSZ/vignettes/mklinks.sh
   pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
OBIGT: move H4SiO4 to AS04.csv (optional data)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/DESCRIPTION	2019-04-16 09:50:20 UTC (rev 448)
@@ -1,6 +1,6 @@
 Date: 2019-04-16
 Package: CHNOSZ
-Version: 1.3.1-28
+Version: 1.3.1-29
 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/aluminum.R
===================================================================
--- pkg/CHNOSZ/demo/aluminum.R	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/demo/aluminum.R	2019-04-16 09:50:20 UTC (rev 448)
@@ -89,12 +89,18 @@
 # plot line: default database
 invTK <- seq(3.5, 1.6, -0.02)
 T <- 1000/invTK - 273.15
-sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "H4SiO4"), c(-1, -2, -5, 2, 2), T = T)
+sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2", "H2O"), c(-1, -2, -5, 2, 2, 4), T = T)
 pK <- -sres$out$logK
 lines(invTK, pK, lwd = 1.5)
+# plot line: default database with AS04 SiO2
+add.obigt("AS04")
+sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2", "H2O"), c(-1, -2, -5, 2, 2, 4), T = T)
+pK <- -sres$out$logK
+lines(invTK, pK, col = "red", lty = 2)
+reset()
 # plot line: SUPCRT92
 add.obigt("SUPCRT92")
-sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "H4SiO4"), c(-1, -2, -5, 2, 2), T = T)
+sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2", "H2O"), c(-1, -2, -5, 2, 2, 4), T = T)
 pK <- -sres$out$logK
 lines(invTK, pK, col = "blue", lty = 2)
 # add title and legend
@@ -102,8 +108,8 @@
 title(main = describe.reaction(sres$reaction), cex.main = 1.1)
 par(xpd = FALSE)
 legend("topright", c("Kaolinite solubility", "After Tutolo et al., 2014 Fig. 2"), bty = "n")
-legend("bottomleft", lty = c(0, 2, 1), pch = c(1, NA, NA), lwd = c(1, 1, 1.5), col = c("black", "blue", "black"),
-       legend = c("Tutolo et al., 2014", "SUPCRT92", "CHNOSZ"), bty = "n", cex = 0.9)
+legend("bottomleft", lty = c(0, 2, 1, 2), pch = c(1, NA, NA, NA), lwd = c(1, 1, 1.5, 1), col = c("black", "blue", "black", "red"),
+       legend = c("Tutolo et al., 2014", "SUPCRT92", "CHNOSZ", 'add.obigt("AS04")'), bty = "n", cex = 0.9)
 reset()
 
 ###########

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-04-16 09:50:20 UTC (rev 448)
@@ -33,7 +33,7 @@
 - vignettes/obigt.bib: check correct year for CHNOSZ reference
 
 - documentation links: after installation, run doc/mklinks.sh
-  and insert the modified anintro.html in the package
+  and put the modified anintro.html and obigt.html in the package
 
 - backwards compatibility: build and check the package with the
   *minimum* R version (from the DESCRIPTION file)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/inst/NEWS	2019-04-16 09:50:20 UTC (rev 448)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.1-26 (2019-04-16)
+CHANGES IN CHNOSZ 1.3.1-29 (2019-04-16)
 ---------------------------------------
 
 - Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
@@ -45,6 +45,8 @@
 
 - OBIGT: use dawsonite Cp coefficients from Tutolo et al., 2014.
 
+- OBIGT: Move H4SiO4 (Stefánsson, 2001) to AS04.csv (optional data).
+
 CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv	2019-04-16 09:50:20 UTC (rev 448)
@@ -1,3 +1,4 @@
 name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+H4SiO4,NA,H4SiO4,aq,Ste01,NA,31.Aug.06,-312919.933078394,-348676.147227533,45.1003824091778,15.0095602294455,52.3,18.7299235181644,-21.2600382409178,18.6199808795411,-1.20004780114723,58.0305927342256,-20.789913957935,0.0869024856596558,0
 SiO2,NA,SiO2,aq,AS04,NA,08.Feb.19,-199540,-212179,11.128325,-22.324515,15.575422,1.9,1.7,20,-2.7,32.221331,-25.288582,0.342671,0
 HSiO3-,HSiO3-,HSiO3-,aq,"SSH97.2 [S98]",CHNOSZ.8,08.Feb.19,-243151,-276276,-1.871675,-21,5,2.9735,-0.5158,5.9467,-2.7575,8.1489,-7.3123,1.5511,-1

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2019-04-16 09:50:20 UTC (rev 448)
@@ -1,4 +1,4 @@
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+Ò¤›¼iIÇ%ÄñVªG5»J†{À⢘Ý:ú\ψEB°uí}F„ܤ¨˜˜ÆÿÚÿ´ôBR¤y/ñ“?ZàÈŒ¦v1ÿ¸5ë€åWëãË•×?$œvbòÑrö¶w“ÇŸoº¸P)úÊ«ÔuhG!ŸYPƒÂRû—åPŽý홍AÿÝé  ^ká-©«ô ”€ÈߌC2.±Ägû    YZ
\ No newline at end of file

Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)

Modified: pkg/CHNOSZ/man/add.obigt.Rd
===================================================================
--- pkg/CHNOSZ/man/add.obigt.Rd	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/man/add.obigt.Rd	2019-04-16 09:50:20 UTC (rev 448)
@@ -125,13 +125,40 @@
 title(main = "AABB = UPBB + H2O; after Figure 9 of Kitadai, 2014")
 # reset to default database
 obigt()
+
+# Another use of add.obigt(): calculate Delta G of
+# H4SiO4 = SiO2 + 2H2O using different data for SiO2.
+# first, get H4SiO4 from Stefansson, 2001
+add.obigt("AS04", "H4SiO4")
+T <- seq(0, 350, 10)
+s1 <- subcrt(c("H4SiO4", "SiO2", "H2O"), c(-1, 1, 2), T = T)
+# now, get SiO2 from Apps and Spycher, 2004
+add.obigt("AS04", "SiO2")
+s2 <- subcrt(c("H4SiO4", "SiO2", "H2O"), c(-1, 1, 2), T = T)
+# plot logK from the first and second calculations
+plot(T, s1$out$G, type = "l", xlab = axis.label("T"),
+  ylab = axis.label("DG"), ylim = c(-100, 600))
+lines(T, s2$out$G, lty = 2)
+# add title and legend
+title(main = describe.reaction(s1$reaction))
+stxt <- lapply(c("H4SiO4", "SiO2", "SiO2"), expr.species)
+legend("top", legend = as.expression(stxt), bty = "n")
+legend("topright", c("Stef\u00e1nsson, 2001", "Shock et al., 1989",
+  "Apps and Spycher, 2004"), lty = c(0, 1, 2), bty = "n")
+reset()
 }
 
 \references{
+Apps, J. and Spycher, N. (2004) \emph{Data qualification for thermodynamic data used to support THC calculations}. DOC.20041118.0004 ANL-NBS-HS-000043 REV 00. Bechtel SAIC Company, LLC.
+
 Bazarkina, E. F., Zotov, A. V., and Akinfiev, N. N. (2010)  Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1-1000 bar and 25°C. \emph{Geology of Ore Deposits} \bold{52}, 167--178. \url{https://doi.org/10.1134/S1075701510020054}
 
 Kitadai, N. (2014)  Thermodynamic prediction of glycine polymerization as a function of temperature and pH consistent with experimentally obtained results. \emph{J. Mol. Evol.} \bold{78}, 171--187. \url{https://doi.org/10.1007/s00239-014-9616-1}
 
+Shock, E. L., Helgeson, H. C. and Sverjensky, D. A. (1989) Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of inorganic neutral species. \emph{Geochim. Cosmochim. Acta} \bold{53}, 2157--2183. \url{https://doi.org/10.1016/0016-7037(89)90341-4}
+
+Stef{\aacute}nsson, A. (2001) Dissolution of primary minerals of basalt in natural waters. I. Calculation of mineral solubilities from 0\degC to 350\degC. \emph{Chem. Geol.} \bold{172}, 225--250. \url{https://doi.org/10.1016/S0009-2541(00)00263-1}
+
 Sverjensky, D. A., Shock, E. L., and Helgeson, H. C. (1997) Prediction of the thermodynamic properties of aqueous metal complexes to 1000 °C and 5 kbar. \emph{Geochim. Cosmochim. Acta} \bold{61}, 1359--1412. \url{https://doi.org/10.1016/S0016-7037(97)00009-4}
 }
 

Modified: pkg/CHNOSZ/vignettes/eos-regress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/eos-regress.Rmd	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/vignettes/eos-regress.Rmd	2019-04-16 09:50:20 UTC (rev 448)
@@ -97,7 +97,7 @@
 
 # A note on the algorithms
 
-The regression functions are essentially a wrapper around the [<span style="color:green">`water()`</span>](http://www.chnosz.net/manual/water.html)-related functions in CHNOSZ and [`lm()` in R](http://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html).
+The regression functions are essentially a wrapper around the <span style="color:green">`water()`</span>-related functions in CHNOSZ and `lm()` in R.
 The former provide values of the Born functions.
 Accordingly, numerical values for all of the *variables* in the equations (e.g. 1/(*T* - Θ)<sup>2</sup> and *TX*) can be calculated at each experimental *T* and *P*.
 
@@ -396,12 +396,12 @@
 ```
 
 We just calculated the properties of the `r h4sio4` pseudospecies.
-For comparison, the database in CHNOSZ contains `pseudo-H4SiO4` with parameters from @Ste01:
+For comparison, the database in CHNOSZ contains `H4SiO4` with parameters from @Ste01:
 ```{r width180, include=FALSE}
 options(width = 180)
 ```
 ```{r info_H4SiO4, message=FALSE}
-info(info(c("calc-H4SiO4", "pseudo-H4SiO4")))
+info(info(c("calc-H4SiO4", "H4SiO4")))
 ```
 ```{r width80, include=FALSE}
 ```
@@ -410,28 +410,28 @@
 s1 <- subcrt(c("calc-H4SiO4", "SiO2", "H2O"), c(-1, 1, 2))
 plot(s1$out$T, s1$out$G, type = "l", ylim = c(-100, 600),
   xlab = axis.label("T"), ylab = axis.label("DG0"))
-s2 <- subcrt(c("pseudo-H4SiO4", "SiO2", "H2O"), c(-1, 1, 2))
+s2 <- subcrt(c("H4SiO4", "SiO2", "H2O"), c(-1, 1, 2))
 lines(s2$out$T, s2$out$G, lty = 2)
 abline(h = 0, lty = 3)
 legend("topright", legend = c("calc-H4SiO4 (this vignette)",
-  "pseudo-H4SiO4", "(Stefánsson, 2001)"), lty = c(1, 2, NA), bty = "n")
+  "H4SiO4", "(Stefánsson, 2001)"), lty = c(1, 2, NA), bty = "n")
 text(225, 250, describe.reaction(s1$reaction))
 ```
 
-Let's compare `pseudo-H4SiO4` from Stefánsson (2001) and the `calc-H4SiO4` we just made with the calculated properties of `r sio2` + 2 `r h2o` as a function of temperature:
+Let's compare `H4SiO4` from Stefánsson (2001) and the `calc-H4SiO4` we just made with the calculated properties of `r sio2` + 2 `r h2o` as a function of temperature:
 ```{r subcrt_H4SiO4, eval=FALSE}
 ```
 
 Ideally, the lines would be horizontal with a _y_-interecept of 0.
-However, both the `calc-H4SiO4` we made here and the `pseudo-H4SiO4` from Stefánsson (2001) show deviations that increase at higher temperatures.
+However, both the `calc-H4SiO4` we made here and the `H4SiO4` from Stefánsson (2001) show deviations that increase at higher temperatures.
 While they are not quite negligible, these deviations are comparatively small.
 For example, the almost 200 cal/mol offset in Δ<i>G</i>° at 350 °C corresponds to a difference in log<i>K</i> of only -0.07.
 
-The following example uses the `pseudo-H4SiO4` from Stefánsson (2001) to make an activity diagram for the K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O system.
+The following example uses the `H4SiO4` from Stefánsson (2001) to make an activity diagram for the K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O system.
 This is similar to diagrams found, for example, on p. 361 of [Garrels and Christ, 1965](http://www.worldcat.org/oclc/517586) and Figure 3 of [Steinmann et al., 1994](http://ccm.geoscienceworld.org/content/42/2/197), but is quantitatively a closer match to the diagram in the [User's Guide to PHREEQC](https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/html/final-75.html).
 
 ```{r activity_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, echo=TRUE, results="hide", message=FALSE, dpi=dpi, out.width="100%", cache=TRUE, fig.cap="Activity diagram for K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O.", pngquant=pngquant}
-basis(c("Al+3", "pseudo-H4SiO4", "K+", "H2O", "H+", "O2"))
+basis(c("Al+3", "H4SiO4", "K+", "H2O", "H+", "O2"))
 species(c("gibbsite", "muscovite", "kaolinite", "pyrophyllite", "K-feldspar"))
 a <- affinity(H4SiO4 = c(-8, 0, 300), `K+` = c(-1, 8, 300))
 diagram(a, ylab = ratlab("K+"), fill = "terrain", yline = 1.7)

Modified: pkg/CHNOSZ/vignettes/mklinks.sh
===================================================================
--- pkg/CHNOSZ/vignettes/mklinks.sh	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/vignettes/mklinks.sh	2019-04-16 09:50:20 UTC (rev 448)
@@ -37,7 +37,7 @@
 sed -i '120,$s/<code>diagram()<\/code>/<code><a href="..\/html\/diagram.html" style="background-image:none;">diagram()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>basis()<\/code>/<code><a href="..\/html\/basis.html" style="background-image:none;">basis()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>species()<\/code>/<code><a href="..\/html\/species.html" style="background-image:none;">species()<\/a><\/code>/g' anintro.html
-sed -i '120,$s/<code>reset()<\/code>/<code><a href="..\/html\/thermo.html" style="background-image:none;">reset()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>reset()<\/code>/<code><a href="..\/html\/reset.html" style="background-image:none;">reset()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>describe.reaction()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">describe.reaction()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>swap.basis()<\/code>/<code><a href="..\/html\/swap.basis.html" style="background-image:none;">swap.basis()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>water.lines()<\/code>/<code><a href="..\/html\/util.plot.html" style="background-image:none;">water.lines()<\/a><\/code>/g' anintro.html
@@ -45,6 +45,7 @@
 sed -i '120,$s/<code>mosaic()<\/code>/<code><a href="..\/html\/mosaic.html" style="background-image:none;">mosaic()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>convert()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">convert()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>mod.buffer()<\/code>/<code><a href="..\/html\/buffer.html" style="background-image:none;">mod.buffer()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>reset\$/<code><a href="..\/html\/thermo.html" style="background-image:none;">reset<\/a>\$/g' anintro.html
 sed -i '120,$s/<code>solubility()<\/code>/<code><a href="..\/html\/solubility.html" style="background-image:none;">solubility()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>ZC.col()<\/code>/<code><a href="..\/html\/util.plot.html" style="background-image:none;">ZC.col()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>aminoacids(\"\")<\/code>/<code><a href="..\/html\/util.seq.html" style="background-image:none;">aminoacids(\"\")<\/a><\/code>/g' anintro.html
@@ -95,3 +96,8 @@
 sed -i '120,$s/substitute()/<a href="..\/..\/base\/html\/substitute.html" style="background-image:none;">substitute()<\/a>/g' anintro.html
 sed -i '120,$s/for()/<a href="..\/..\/base\/html\/Control.html" style="background-image:none;">for()<\/a>/g' anintro.html
 sed -i '120,$s/browseURL()/<a href="..\/..\/utils\/html\/browseURL.html" style="background-image:none;">browseURL()<\/a>/g' anintro.html
+
+# add links to obigt.Rmd
+sed -i '120,$s/<code>add.obigt()<\/code>/<code><a href="..\/html\/add.obigt.html" style="color:red;">add.obigt()<\/a><\/code>/g' obigt.html
+sed -i '120,$s/<code>reset()<\/code>/<code><a href="..\/html\/reset.html" style="color:red;">reset()<\/a><\/code>/g' obigt.html
+sed -i 's/<code>?add.obigt<\/code>/<code><a href="..\/html\/add.obigt.html" style="color:red;">?add.obigt<\/a><\/code>/g' obigt.html

Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd	2019-04-16 06:07:08 UTC (rev 447)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd	2019-04-16 09:50:20 UTC (rev 448)
@@ -250,7 +250,7 @@
 
 ### `r setfile("AS04.csv")`
 ```{r AS04, results="asis", echo=FALSE}
-cat('This file has data for aqueous SiO<sub>2</sub> from @AS04 and modified HSiO<sub>3</sub><sup>-</sup>. Use <span style="color:red">`add.obigt("AS04")`</span> to load the data; see [<span style="color:blue">`demo(aluminum)`</span>](../demo) for an example.\n\n')
+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')
 ```
 
 ```{r optreflist, results="asis", echo=FALSE}

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