[CHNOSZ-commits] r387 - in pkg/CHNOSZ: . man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Feb 8 10:15:08 CET 2019 

Author: jedick
Date: 2019-02-08 10:15:07 +0100 (Fri, 08 Feb 2019)
New Revision: 387

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/man/mosaic.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
anintro.Rmd: revise section on Optional data


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-02-08 08:07:59 UTC (rev 386)
+++ pkg/CHNOSZ/DESCRIPTION	2019-02-08 09:15:07 UTC (rev 387)
@@ -1,6 +1,6 @@
 Date: 2019-02-08
 Package: CHNOSZ
-Version: 1.1.3-94
+Version: 1.1.3-95
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
@@ -14,23 +14,21 @@
 Depends: R (>= 3.1.0)
 Suggests: limSolve, testthat, knitr, rmarkdown, tufte
 Imports: grDevices, graphics, stats, utils
-Description: An integrated set of tools for thermodynamic calculations in geochemistry and compositional
-  biology. The thermodynamic properties of liquid water are calculated using Fortran code from
-  SUPCRT92 (Johnson et al., 1992 <doi:10.1016/0098-3004(92)90029-Q>) or an implementation
-  in R of the IAPWS-95 formulation (Wagner and Pruß, 2002 <doi:10.1063/1.1461829>).
-  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 (Dick et al., 2006 <doi:10.5194/bg-3-311-2006>). High-temperature properties are
-  calculated using the Berman-Brown (1985) <doi:10.1007/BF00379451> equations for minerals
-  and the revised Helgeson-Kirkham-Flowers (1981) <doi:10.2475/ajs.281.10.1249> equations for
-  aqueous species. The HKF equations are augmented with the Deep Earth Water (DEW) model
-  (Sverjensky et al., 2014 <doi:10.1016/j.gca.2013.12.019>) and estimates of parameters in the
-  extended Debye-Hückel equation (Manning et al., 2013 <doi:10.2138/rmg.2013.75.5>)
-  to calculate standard-state properties and activity coefficients for given ionic strength at high
-  pressure (to 6 GPa). Functions are provided to calculate standard-state properties of species and
-  reactions, define the basis species of a chemical system, automatically balance reactions, calculate
-  the chemical affinities of formation reactions for selected species, calculate the equilibrium
-  activities of those species, and plot the results on chemical activity diagrams.
+Description: An integrated set of tools for thermodynamic calculations in
+  aqueous geochemistry and geobiochemistry. Functions are provided for writing
+  balanced reactions to form species from user-selected basis species and for
+  calculating the standard molal properties of species and reactions, including
+  the standard Gibbs energy and equilibrium constant. Calculations of the
+  non-equilibrium chemical affinity and equilibrium chemical activity of species
+  can be portrayed on diagrams as a function of temperature, pressure, or
+  activity of basis species; in two dimensions, this gives a maximum affinity or
+  predominance diagram. The diagrams have formatted chemical formulas and axis
+  labels, and water stability limits can be added to Eh-pH, logfO2-T, and other
+  diagrams with a redox variable. The package has been developed to handle common
+  calculations in aqueous geochemistry, such as solubility due to complexation of
+  metal ions, mineral buffers of redox or pH, and changing the basis species
+  across a diagram ("mosaic diagrams"). CHNOSZ also has unique capabilities for
+  comparing the compositional and thermodynamic properties of different proteins.
 Encoding: UTF-8
 License: GPL (>= 2)
 BuildResaveData: no

Modified: pkg/CHNOSZ/man/mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/mosaic.Rd	2019-02-08 08:07:59 UTC (rev 386)
+++ pkg/CHNOSZ/man/mosaic.Rd	2019-02-08 09:15:07 UTC (rev 387)
@@ -56,8 +56,8 @@
 \dontshow{data(thermo)}# Fe-minerals and aqueous species in Fe-S-O-H system
 # speciate SO4-2, HSO4-, HS-, H2S as a function of Eh and pH
 # after Garrels and Christ, 1965 Figure 7.20
-pH <- c(0, 14, 500)
-Eh <- c(-1, 1, 500)
+pH <- c(0, 14, 250)
+Eh <- c(-1, 1, 250)
 T <- 25
 basis(c("FeO", "SO4-2", "H2O", "H+", "e-"))
 basis("SO4-2", -6)
@@ -78,6 +78,7 @@
 diagram(m2$A.species, add = TRUE, names = NULL)
 title(main=paste("Iron oxides and sulfides in water, log(total S) = -6",
   "After Garrels and Christ, 1965", sep="\n"))
+legend("bottomleft", c("log(act_Fe) = -4", "log(act_Fe) = -6"), lwd = c(2, 1), bty = "n")
 # we could overlay the basis species predominance fields
 #diagram(m1$A.bases, add=TRUE, col="blue", col.names="blue", lty=3)
 }

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2019-02-08 08:07:59 UTC (rev 386)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2019-02-08 09:15:07 UTC (rev 387)
@@ -251,6 +251,9 @@
 ```
 
 Multiple entries exist for methane; the index of the `aq` (aqueous) species is returned by default.
+```{marginfigure}
+This convention applies to organic species, but for inorganic species, the English name refers to the gas (<span style='color:green'>`info("oxygen")`</span>) while the chemical formula is used to identify the aqueous species (<span style='color:green'>`info("O2")`</span>).
+```
 A second argument can be used to specify a different physical state:
 ```{r info_methane_gas}
 info("methane", "gas")
@@ -1962,18 +1965,24 @@
 Thermodynamic properties of minerals in the default database are mostly taken from @Ber88 (including silicates, aluminosilicates, calcite, dolomite, hematite, and magnetite) and @HDNB78 (native elements, sulfides, halides, sulfates, and selected carbonates and oxides that do not duplicate any in the Berman dataset).
 Minerals are identified by the state `cr`, and (for the Helgeson dataset) `cr2`, `cr3`, etc. for higher-temperature polymorphs.
 
-Two optional datasets can be activated by using <span style="color:red">`add.obigt()`</span>:
+Some optional datasets can be activated by using <span style="color:red">`add.obigt()`</span>. The first three of these contain data that have been replaced by or are incompatible with later updates; the superseded data are kept here to reproduce published calculations and for comparison with the newer data:
 
+<span style="color:red">`add.obigt("SUPCRT92")`</span> -- This file contains data for minerals from SUPCRT92 (mostly Helgeson et al., 1978) that have been replaced by the Berman data set.
+
+<span style="color:red">`add.obigt("SLOP98")`</span> -- This file contains data from `slop98.dat` or later slop files, from Everett Shock's GEOPIG group at Arizona State University, that were previously used in CHNOSZ but have been replaced by newer data.
+This includes updates for aqueous Au species as summarized by @PAB_14, and aqueous SiO<sub>2</sub>, aqueous aluminum species, and arsenic-bearing aqueous species and minerals, as compiled in the [SUPCRTBL package](http://www.indiana.edu/~hydrogeo/supcrtbl.html) [@ZZL_16].
+Some calculations using the older data are shown in [this vignette](#complete-equilibrium-solubility) and [<span style="color:blue">`demo(go-IU)`</span>](../demo); see [<span style="color:blue">`demo(gold)`</span>](../demo) for calculations that depend exclusively on the newer data that are now loaded by default in CHNOSZ.
+
+<span style="color:red">`add.obigt("OldAA")`</span> -- This file contains superseded data for amino acids (methionine and glycine) and related species, particularly the [Met], [Gly], and protein backbone groups, as well as metal-glycinate complexes.
+The updates for these data have been taken from various publications ([LaRowe and Dick, 2012](https://doi.org/10.1016/j.gca.2011.11.041); [Kitadai, 2014](https://doi.org/10.1007/s00239-014-9616-1); [Azadi et al., 2019](https://doi.org/10.1016/j.fluid.2018.10.002))
+A comparison of log*K* of metal-glycinate complexes using the updated data is in [<span style="color:blue">`demo(glycinate)`</span>](../demo).
+
 <span style="color:red">`add.obigt("DEW")`</span> -- These are aqueous species, with modified parameters, that are intended for use with the [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model [@SHA14].
 You should also run <span style="color:red">`water("DEW")`</span> to activate the equations in the model; then, they will be used by <span style="color:green">`subcrt()`</span> and <span style="color:green">`affinity()`</span>.
 Examples are in [<span style="color:blue">`demo(DEW)`</span>](../demo).
 
-<span style="color:red">`add.obigt("SLOP98")`</span> -- This file contains data that have been replaced by or are incompatible with more recent data updates.
-This includes updates for aqueous Au species as summarized by @PAB_14, and aqueous SiO<sub>2</sub>, aqueous aluminum species, and arsenic-bearing aqueous species and minerals, as compiled in the [SUPCRTBL package](http://www.indiana.edu/~hydrogeo/supcrtbl.html) [@ZZL_16].
-These updates have been applied to the default database in CHNOSZ; some calculations using the updated data are shown in [<span style="color:blue">`demo(go-IU)`</span>](../demo) and [<span style="color:blue">`demo(gold)`</span>](../demo).
+Detailed references for these optional datasets are in the vignette [<span style="color:blue">*Thermodynamic data in CHNOSZ*</span>](obigt.html) (look under **Optional Data**).
 
-Detailed references for these optional datasets are in the vignette [<span style="color:blue">*Thermodynamic data in CHNOSZ*</span>](obigt.html) (look under **Optional Data** / **DEW** and **Optional Data** / **SLOP98**).
-
 ## Adding data
 
 You can also use <span style="color:red">`add.obigt()`</span> to add data from a user-specified file to the database in the current session.

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