[CHNOSZ-commits] r248 - in pkg/CHNOSZ: . demo man

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2017-10-09 05:14:34 +0200 (Mon, 09 Oct 2017)
New Revision: 248

Removed:
   pkg/CHNOSZ/demo/berman.R
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/00Index
   pkg/CHNOSZ/man/berman.Rd
Log:
delete demo/berman.R; move diagram to man/berman.Rd


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-10-08 23:36:32 UTC (rev 247)
+++ pkg/CHNOSZ/DESCRIPTION	2017-10-09 03:14:34 UTC (rev 248)
@@ -1,6 +1,6 @@
 Date: 2017-10-09
 Package: CHNOSZ
-Version: 1.1.0-46
+Version: 1.1.0-47
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index	2017-10-08 23:36:32 UTC (rev 247)
+++ pkg/CHNOSZ/demo/00Index	2017-10-09 03:14:34 UTC (rev 248)
@@ -21,4 +21,3 @@
 adenine         HKF parameters regressed from heat capacity and volume of aqueous adenine
 DEW             Deep Earth Water (DEW) model for high pressures
 lambda          Effects of lambda transtion on thermodynamic properties of quartz
-berman          Mineral stability diagrams calculated using Berman's equations

Deleted: pkg/CHNOSZ/demo/berman.R
===================================================================
--- pkg/CHNOSZ/demo/berman.R	2017-10-08 23:36:32 UTC (rev 247)
+++ pkg/CHNOSZ/demo/berman.R	2017-10-09 03:14:34 UTC (rev 248)
@@ -1,31 +0,0 @@
-# CHNOSZ/demo/berman.R  20171003
-# make some mineral activity diagrams using Berman (1988) and related data
-
-res <- 200
-
-# using the Helgeson data
-# set up basis species
-basis(c("K+", "Al+3", "quartz", "H2O", "O2", "H+"))
-# use pH = 0 so that aK+ = aK+/aH+
-basis("pH", 0)
-# load the species
-species(c("K-feldspar", "muscovite", "kaolinite", "pyrophyllite", "andalusite"), "cr")
-# calculate affinities in aK+ - temperature space
-a <- affinity(`K+`=c(0, 5, res), T=c(200, 650, res), P=1000)
-# note that we go just past the quartz transition, but it has no effect on the diagram
-diagram(a)
-
-# now using the Berman data
-basis("SiO2", "cr_Berman")
-# it might be good to check that we have Berman's quartz and not coesite or some other SiO2 phase
-info(basis()$ispecies[3])
-# remove the Helgeson minerals
-species(delete=TRUE)
-# load the Berman minerals
-species(c("K-feldspar", "muscovite", "kaolinite", "pyrophyllite", "andalusite"), "cr_Berman")
-# calculate affinities in aK+ - temperature space
-a <- affinity(`K+`=c(0, 5, res), T=c(200, 650, res), P=1000)
-diagram(a, add=TRUE, names="", col="blue", lwd=2)
-
-legend("topleft", lty=c(1, 1), lwd=c(1, 2), col=c("black", "blue"),
-       legend=c("Helgeson et al., 1978 (unadjusted)", "Berman, 1988 (adjusted by Sverjensky et al., 1991)"))

Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd	2017-10-08 23:36:32 UTC (rev 247)
+++ pkg/CHNOSZ/man/berman.Rd	2017-10-09 03:14:34 UTC (rev 248)
@@ -64,6 +64,39 @@
 species(c("quartz", "quartz,beta", "coesite"), "cr_Berman")
 a <- affinity(T=c(200, 1700, 200), P=c(0, 50000, 200))
 diagram(a)
+
+## a longer example, comparing diagrams made using the
+## Berman and Helgeson datasets, after Sverjensky et al., 1991
+res <- 200
+# using the Helgeson data
+# set up basis species
+basis(c("K+", "Al+3", "quartz", "H2O", "O2", "H+"))
+# use pH = 0 so that aK+ = aK+/aH+
+basis("pH", 0)
+# load the species
+species(c("K-feldspar", "muscovite", "kaolinite",
+          "pyrophyllite", "andalusite"), "cr")
+# calculate affinities in aK+ - temperature space
+a <- affinity(`K+`=c(0, 5, res), T=c(200, 650, res), P=1000)
+# note that we go just past the quartz transition,
+# but it has no effect on the diagram
+diagram(a, xlab=ratlab("K+"))
+# now using the Berman data
+basis("SiO2", "cr_Berman")
+# it might be good to check that we have Berman's quartz
+# and not coesite or some other SiO2 phase
+info(basis()$ispecies[3])
+# remove the Helgeson minerals
+species(delete=TRUE)
+# load the Berman minerals
+species(c("K-feldspar", "muscovite", "kaolinite",
+          "pyrophyllite", "andalusite"), "cr_Berman")
+a <- affinity(`K+`=c(0, 5, res), T=c(200, 650, res), P=1000)
+diagram(a, add=TRUE, names="", col="blue", lwd=2)
+legend("topleft", lty=c(1, 1, NA), lwd=c(1, 2, 0), col=c("black", "blue", ""),
+       legend=c("Helgeson et al., 1978 (unadjusted)",
+       "Berman, 1988", "    (adjusted by Sverjensky et al., 1991)"), bty="n")
+title(main="Comparison of Helgeson and Berman datasets at 1000 bar")
 }
 
 \references{
@@ -72,6 +105,8 @@
 Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O–K{\s2}O–CaO–MgO–FeO–Fe{\s2}O{\s3}–Al{\s2}O{\s3}–SiO{\s2}–TiO{\s2}–H{\s2}O–CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
 
 Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{http://www.worldcat.org/oclc/13594862}
+
+Sverjensky, D. A., Hemley, J. J. and D'Angelo, W. M. (1991) Thermodynamic assessment of hydrothermal alkali feldspar-mica-aluminosilicate equilibria. \emph{Geochim. Cosmochim. Acta} \bold{55}, 989-1004. \url{https://doi.org/10.1016/0016-7037(91)90157-Z}
 }
 
 \concept{Secondary thermodynamic modeling}