[CHNOSZ-commits] r30 - in pkg/CHNOSZ: . R inst inst/tests man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 27 15:04:22 CET 2012
Author: jedick
Date: 2012-11-27 15:04:22 +0100 (Tue, 27 Nov 2012)
New Revision: 30
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/zzz.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/tests/test-revisit.R
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/anim.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/eos.Rd
pkg/CHNOSZ/man/eqdata.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/ionize.aa.Rd
pkg/CHNOSZ/man/iprotein.Rd
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/read.expr.Rd
pkg/CHNOSZ/man/revisit.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/swap.basis.Rd
pkg/CHNOSZ/man/transfer.Rd
pkg/CHNOSZ/man/util.affinity.Rd
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/man/util.formula.Rd
pkg/CHNOSZ/man/util.units.Rd
pkg/CHNOSZ/man/water.Rd
pkg/CHNOSZ/man/wjd.Rd
Log:
use degree symbol in Rd \eqn text (UTF-8)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/DESCRIPTION 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,6 +1,6 @@
-Date: 2012-11-20
+Date: 2012-11-27
Package: CHNOSZ
-Version: 0.9.8-4
+Version: 0.9.8-5
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey M. Dick
Maintainer: Jeffrey M. Dick <jmdick at asu.edu>
Modified: pkg/CHNOSZ/R/zzz.R
===================================================================
--- pkg/CHNOSZ/R/zzz.R 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/R/zzz.R 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,4 +1,4 @@
-# CHNOSZ/xxx.R
+# CHNOSZ/zzz.R
# this has the .onAttach function for package startup message and data initialization
.onAttach <- function(libname,pkgname) {
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/inst/CHECKLIST 2012-11-27 14:04:22 UTC (rev 30)
@@ -8,6 +8,8 @@
- run demos() to run all demos
+- run test_package("CHNOSZ") to run all tests
+
- check output of demo("sources") to make sure all data sources are cited
- recreate extdata/thermo/obigt_check.csv after all data updates:
@@ -30,6 +32,6 @@
- clean up all TODO, XXX, etc. in Rd files (and hopefully R files too)
-- all Rd files have \keyword{...}
+- ensure all Rd files have \keyword{...}
- test read.supcrt(), write.supcrt() on e.g. slop98.dat
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/inst/NEWS 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 0.9.8-4 (2012-11-20)
+CHANGES IN CHNOSZ 0.9.8-5 (2012-11-27)
--------------------------------------
SIGNIFICANT USER-VISIBLE CHANGES:
@@ -282,6 +282,8 @@
- Add TODO and CHECKLIST to the installation directory of the package.
+- Use UTF-8 degree symbol in second argument of \eqn{}{}.
+
PERFORMANCE AND CODE CLEAN-UPS:
- A matrix is now returned by makeup(), GHS() and some other functions
Modified: pkg/CHNOSZ/inst/tests/test-revisit.R
===================================================================
--- pkg/CHNOSZ/inst/tests/test-revisit.R 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/inst/tests/test-revisit.R 2012-11-27 14:04:22 UTC (rev 30)
@@ -82,10 +82,13 @@
expect_equal(min(r1$H), 0)
expect_equal(r1$xopt, -7.5)
# we can even go into 2 dimensions
- a2 <- affinity(H2=c(-10, -5, 101), T=c(0, 100, 101), exceed.Ttr=TRUE)
- e2 <- equilibrate(a2)
- r2 <- revisit(e2, "DGtr", loga2=loga2, plot.it=FALSE)
- # we should DGtr=0 at the temperature of the reference distribution (25 degC)
- expect_equal(min(r2$H), 0)
- expect_equal(r2$yopt, 25)
+ # (it's a slightly longer test, so don't run it on CRAN)
+ if(!any(grepl("R_CHECK_TIMINGS", names(Sys.getenv())))) {
+ a2 <- affinity(H2=c(-10, -5, 101), T=c(0, 100, 101), exceed.Ttr=TRUE)
+ e2 <- equilibrate(a2)
+ r2 <- revisit(e2, "DGtr", loga2=loga2, plot.it=FALSE)
+ # we should DGtr=0 at the temperature of the reference distribution (25 degC)
+ expect_equal(min(r2$H), 0)
+ expect_equal(r2$yopt, 25)
+ }
})
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
\name{EOSregress}
\alias{EOSregress}
\alias{EOSvar}
@@ -68,7 +69,7 @@
\code{EOScoeffs} retrieves coefficients in the Helgeson-Kirkham-Flowers equations from the thermodynamic database (\code{\link{thermo}$obigt}) for the given aqueous \code{species}. If the \code{property} is \samp{Cp}, the resulting dataframe has column names of \samp{(Intercept)}, \samp{invTTheta2} and \samp{TX}, respectively holding the coefficients \eqn{c_1}{c1}, \eqn{c_2}{c2} and \eqn{\omega}{omega} in equation \eqn{Cp^\circ = c_1 + c_2/(T-\Theta)^2 + {\omega}TX}{Cp = c1 + c2/(T-Theta)^2 + omega*TX}. If the \code{property} is \samp{V}, the data frame has column names of \samp{(Intercept)}, \samp{invTTheta} and \samp{Q}, respectively holding the coefficients \eqn{\sigma}{sigma}, \eqn{\xi}{xi} and \eqn{-\omega}{-omega} in \eqn{V^\circ = \sigma + \xi/(T-\Theta) - {\omega}Q}{V = sigma + xi/(T-Theta) - omega*Q}.
- The motivation for writing these functions is to explore alternatives or possible modifications to the revised Helgeson-Kirkham-Flowers equations applied to aqueous nonelectrolytes. As pointed out by Schulte et al., 2001, the functional forms of the equations do not permit retrieving values of the solvation parameter (\eqn{\omega}{omega}) that closely represent the observed trends in both heat capacity and volume at high temperatures (above ca. 200 degrees C).
+ The motivation for writing these functions is to explore alternatives or possible modifications to the revised Helgeson-Kirkham-Flowers equations applied to aqueous nonelectrolytes. As pointed out by Schulte et al., 2001, the functional forms of the equations do not permit retrieving values of the solvation parameter (\eqn{\omega}{omega}) that closely represent the observed trends in both heat capacity and volume at high temperatures (above ca. 200 \eqn{^{\circ}}{°}C).
}
Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/affinity.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
\name{affinity}
\alias{affinity}
\title{Chemical Affinities of Formation Reactions}
@@ -28,7 +29,7 @@
Valid properties are \samp{A} or NULL for chemical affinity, \samp{logK} or \samp{logQ} for logarithm of equilibrium constant and reaction activity product, or any of the properties available in \code{\link{subcrt}} except for \samp{rho}. The properties returned are those of the formation reactions of the species of interest from the basis species. It is also possible to calculate the properties of the species of interest themselves (not their formation reactions) by setting the \code{property} to \samp{G.species}, \samp{Cp.species}, etc. Except for \samp{A}, the properties of proteins or their reactions calculated in this manner are restricted to nonionized proteins.
- Zero, one, or more leading arguments to the function identify which of the chemical activities of basis species, temperature, pressure and/or ionic strength to vary. The names of each of these arguments may be the formula of any of the basis species of the system, or \samp{T}, \samp{P}, \samp{pe}, \samp{pH}, \samp{Eh}, or \samp{IS} (but names may not be repeated). To use the names of charged basis species such as \samp{K+} and \samp{SO4-2} as the arguments, they should be enclosed in quotes (see the example for aluminum speciation in \code{\link{diagram}}). The value of each argument is of the form \code{c(min,max)} or \code{c(min,max,res)} where \code{min} and \code{max} refer to the minimimum and maximum values of variable identified by the name of the argument, and \code{res} denotes the resolution, or number of points along which to do the calculations (this is assigned a default value of 128 if it is missing). For any arguments that refer to basis species, the numerical values are the logarithms of the activities of that basis species, or logarithms of fugacities if it is a gas. Unlike the \code{energy} function, the units of \samp{T} and \samp{P} in \code{affinity} are those the user has set using \code{\link{T.units}} and \code{\link{P.units} }(on program start-up these are \eqn{^{\circ}}{degrees }C and bar, respectively).
+ Zero, one, or more leading arguments to the function identify which of the chemical activities of basis species, temperature, pressure and/or ionic strength to vary. The names of each of these arguments may be the formula of any of the basis species of the system, or \samp{T}, \samp{P}, \samp{pe}, \samp{pH}, \samp{Eh}, or \samp{IS} (but names may not be repeated). To use the names of charged basis species such as \samp{K+} and \samp{SO4-2} as the arguments, they should be enclosed in quotes (see the example for aluminum speciation in \code{\link{diagram}}). The value of each argument is of the form \code{c(min,max)} or \code{c(min,max,res)} where \code{min} and \code{max} refer to the minimimum and maximum values of variable identified by the name of the argument, and \code{res} denotes the resolution, or number of points along which to do the calculations (this is assigned a default value of 128 if it is missing). For any arguments that refer to basis species, the numerical values are the logarithms of the activities of that basis species, or logarithms of fugacities if it is a gas. Unlike the \code{energy} function, the units of \samp{T} and \samp{P} in \code{affinity} are those the user has set using \code{\link{T.units}} and \code{\link{P.units} }(on program start-up these are \eqn{^{\circ}}{°}C and bar, respectively).
If one or more buffers are assigned to the definition of \code{\link{basis}} species, \code{affinity} calls \code{\link{buffer}} to calculate the logarithms of activities of these basis species from the buffer.
@@ -53,8 +54,7 @@
}
\examples{
-\dontshow{data(thermo)}
-## set up a system and calculate
+\dontshow{data(thermo)}## set up a system and calculate
## chemical affinities of formation reactions
basis(c("SiO2","MgO","H2O","O2"),c(-5,-5,0,999))
species(c("quartz","enstatite","forsterite"))
@@ -76,8 +76,7 @@
# Standard molal Gibbs energies of reactions
affinity(property="G")
-\donttest{
-## amino acid synthesis at low and high temperatures
+\donttest{## amino acid synthesis at low and high temperatures
## after Amend and Shock, 1998
# select the basis species and species of interest
# and set their activities, first for the 18 degree C case
@@ -123,7 +122,6 @@
E.units("cal")
species(delete=TRUE)
-
## affinities of metabolic reactions
## after Amend and Shock, 2001, Fig. 7
# use aq state for all basis species (including O2)
Modified: pkg/CHNOSZ/man/anim.Rd
===================================================================
--- pkg/CHNOSZ/man/anim.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/anim.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
\name{anim.TCA}
\alias{anim}
\alias{anim.TCA}
@@ -32,9 +33,9 @@
To ensure the results described below, each function here does remove any existing system definition by calling \code{data(thermo)}.
- \code{anim.TCA} creates a series of figures showing how a logaH2O - logfO2 activity diagram for various species involved in the tricarboxylic acid (TCA) cycle changes as a function of pH. Alternatively, set \code{redox} to \code{list(H2=c(-20,0))} to draw a logaH2O - logaH2 diagram. The diagrams are made at 25 degrees C unless \code{high.T} is TRUE, in which case high-temperature (100 degrees C) stability fields are overlain. The number of frames to be used for the animation (as pH increases ranges between the values specified in \code{pHlim}) is given by \code{nframes}.
+ \code{anim.TCA} creates a series of figures showing how a logaH2O - logfO2 activity diagram for various species involved in the tricarboxylic acid (TCA) cycle changes as a function of pH. Alternatively, set \code{redox} to \code{list(H2=c(-20,0))} to draw a logaH2O - logaH2 diagram. The diagrams are made at 25 \eqn{^{\circ}}{°}C unless \code{high.T} is TRUE, in which case high-temperature (100 \eqn{^{\circ}}{°}C) stability fields are overlain. The number of frames to be used for the animation (as pH increases ranges between the values specified in \code{pHlim}) is given by \code{nframes}.
- \code{anim.plasma} produces a series of equilibrium activity diagrams for proteins in human blood plasma, as a function of log aO2 and log aH2, at 25 degrees C. Unlike most other examples in CHNOSZ, the chemical potentials of hydrogen and oxygen in the system are represented by the activities of O2 and H2, and H2O is not used as a basis species. Therefore, the equilibrium activities of H2O vary by many orders of magnitude across these diagrams. The list of proteins is taken from Anderson and Anderson (2003); see the description for the data file AA03.csv in \code{\link{extdata}}. The first diagram shows the equilibrium predominance fields with all 71 listed proteins in the calculation. In each subsequent diagram, the protein whose predominance field occupies the greatest area on the diagram is removed. The range of \code{\link{heat.colors}} indicates the reported reference abundances of the proteins, with the deepest (reddest) colors corresponding to the highest abundances.
+ \code{anim.plasma} produces a series of equilibrium activity diagrams for proteins in human blood plasma, as a function of log aO2 and log aH2, at 25 \eqn{^{\circ}}{°}C. Unlike most other examples in CHNOSZ, the chemical potentials of hydrogen and oxygen in the system are represented by the activities of O2 and H2, and H2O is not used as a basis species. Therefore, the equilibrium activities of H2O vary by many orders of magnitude across these diagrams. The list of proteins is taken from Anderson and Anderson (2003); see the description for the data file AA03.csv in \code{\link{extdata}}. The first diagram shows the equilibrium predominance fields with all 71 listed proteins in the calculation. In each subsequent diagram, the protein whose predominance field occupies the greatest area on the diagram is removed. The range of \code{\link{heat.colors}} indicates the reported reference abundances of the proteins, with the deepest (reddest) colors corresponding to the highest abundances.
\code{anim.carboxylase} animates equilibrium rank-activity diagrams along a combined temperature and logaH2 gradient, or makes a single plot on the default device (without conversion to animated GIF) if a single \code{temperature} is provided. The proteins in the calculation are 24 carboxylases from a variety of organisms. There are 12 ribulose phosphate carboxylase and 12 acetyl-coenzyme A carboxylase; 6 of each type are from nominally mesophilic organisms and 6 from nominally thermophilic organisms, shown as blue and red symbols on the diagrams. The activities of hydrogen at each temperature are calculated using \eqn{\log a_{\mathrm{H_{2}}_{\left(aq\right)}}=-11+3/\left(40\times T\left(^{\circ}C\right)\right)}{logaH2 = -11 + 3/40 * T(degC)}; this equation comes from a model of relative stabilities of proteins in a hot-spring environment (Dick and Shock, 2011).
@@ -42,13 +43,13 @@
\examples{
\dontrun{
- # animate a stability diagram with a high-temperature overlay
- anim.TCA(high.T=TRUE)
- # using H2 instead of O2
- anim.TCA(list(H2=c(-20,0))) }
+# animate a stability diagram with a high-temperature overlay
+anim.TCA(high.T=TRUE)
+# using H2 instead of O2
+anim.TCA(list(H2=c(-20,0))) }
- # using anim.carboxylase in non-animation mode
- anim.carboxylase(T=100)
+# using anim.carboxylase in non-animation mode
+anim.carboxylase(T=100)
}
\references{
Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/basis.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -85,6 +85,7 @@
basis(c("H2O", "O2", "H+"))
## clear the basis species
basis(delete=TRUE)
+
\dontrun{
## marked dontrun because they produce errors
# fewer species than elements
@@ -92,7 +93,8 @@
# more species than elements
basis(c("H2O", "O2", "H2", "H+"))
# non-independent species
-basis(c("CO2", "H2O", "HCl", "Cl-", "H+")) }
+basis(c("CO2", "H2O", "HCl", "Cl-", "H+"))}
+
## specify activities and states
basis(c("H2O", "O2", "CO2"), c(-2, -78, -3), c("liq", "aq", "aq"))
# change logarithms of activities/fugacities
Modified: pkg/CHNOSZ/man/buffer.Rd
===================================================================
--- pkg/CHNOSZ/man/buffer.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/buffer.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -94,8 +94,8 @@
exceed.Ttr=TRUE)$values)
for(i in 1:length(a)) stopifnot(isTRUE(
all.equal(as.numeric(a[[i]]),rep(0,length(a[[i]])))))
-\donttest{
-## buffer made of one species: show values of logfO2 on an
+
+\donttest{## buffer made of one species: show values of logfO2 on an
## Eh-pH diagram; after Garrels, 1960, Figure 6
basis("CHNOSe")
# here we will buffer the activity of the electron by O2
Modified: pkg/CHNOSZ/man/data.Rd
===================================================================
--- pkg/CHNOSZ/man/data.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/data.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
\name{thermo}
\docType{data}
\alias{thermo}
@@ -14,7 +15,11 @@
The \code{thermo} object holds the thermodynamic database of properties of species, some thermodynamic constants and operational parameters for functions in CHNOSZ, the properties of elements, references to literature sources of thermodynamic data, compositions of chemical activity buffers, and amino acid compositions of proteins. The \code{thermo} object also holds intermediate data used in calculations, in particular the definitions of basis species and species of interest input by the user, and the calculated properties of \code{\link{water}} so that subsequent calculations at the same temperature-pressure conditions can be accelerated.
- The \code{thermo} object is a \code{\link{list}} composed of \code{\link{data.frame}}s or lists each representing a class of data. The object is created in the global environment upon loading the package (by \code{\link{.onAttach}}). At any time, the user can restore the data object to its initial state by calling \code{data(thermo)}. This is sometimes a useful command to use during an interactive session, when previous definitions of basis species and species of interest are longer desired.
+The \code{thermo} object is a \code{\link{list}} composed of \code{\link{data.frame}}s or lists each representing a class of data.
+The object is created in an environment named \code{thermo}; see \code{\link{sideeffects}} for details.
+It is created upon loading the package, through a call to \code{data(thermo)} in \code{\link{.onAttach}}.
+At any time, the user can restore the data object to its initial state by calling \code{data(thermo)}.
+This is sometimes a useful command to use during an interactive session, when previous definitions of basis species and species of interest are longer desired.
The function \code{\link{add.obigt}} is available to update the thermodynamic database in use in a running session. For example, one can run \code{add.obigt("mydata.csv")} after loading the package, and the data in that file will be added to the database. The format of this file must be the same as the \code{OBIGT.csv} file provided with CHNOSZ. Although changes made using \code{add.obigt} are lost when the current \R session is closed, the data can always be restored the next time as long as the user has the \code{mydata.csv} (or other) file available.
@@ -50,17 +55,17 @@
}
\item \code{thermo$element}
- Dataframe containing the thermodynamic properties of elements taken from Cox et al., 1989 and Wagman et al., 1982. The standard molal entropy (\eqn{S}(\code{Z})) at 25 \eqn{^{\circ}}{degrees }C and 1 bar for the element of charge (\code{Z}) was calculated from \eqn{S}(H2,g) + 2\eqn{S}(\code{Z}) = 2\eqn{S}(H+), where the standard molal entropies of H2,g and H+ were taken from Cox et al., 1989. The mass of \code{Z} is taken to be zero. Accessing this data frame using \code{\link{mass}} or \code{\link{entropy}} will select the first entry found for a given element; i.e., values from Wagman et al., 1982 will only be retrieved if the properties of the element are not found from Cox et al., 1989.
+ Dataframe containing the thermodynamic properties of elements taken from Cox et al., 1989 and Wagman et al., 1982. The standard molal entropy (\eqn{S}(\code{Z})) at 25 \eqn{^{\circ}}{°}C and 1 bar for the element of charge (\code{Z}) was calculated from \eqn{S}(H2,g) + 2\eqn{S}(\code{Z}) = 2\eqn{S}(H+), where the standard molal entropies of H2,g and H+ were taken from Cox et al., 1989. The mass of \code{Z} is taken to be zero. Accessing this data frame using \code{\link{mass}} or \code{\link{entropy}} will select the first entry found for a given element; i.e., values from Wagman et al., 1982 will only be retrieved if the properties of the element are not found from Cox et al., 1989.
\tabular{lll}{
\code{element} \tab character \tab Symbol of element\cr
- \code{state} \tab character \tab Stable state of element at 25 \eqn{^{\circ}}{degrees }C and 1 bar\cr
+ \code{state} \tab character \tab Stable state of element at 25 \eqn{^{\circ}}{°}C and 1 bar\cr
\code{source} \tab character \tab Source of data\cr
\code{mass} \tab numeric \tab Mass of element (in natural isotopic distribution;\cr
\tab \tab referenced to a mass of 12 for \eqn{^{12}}{12}C)\cr
\code{s} \tab numeric \tab Entropy of the compound of the element in its stable\cr
- \tab \tab state at 25 \eqn{^{\circ}}{degrees }C and 1 bar (cal K\eqn{^{-1}}{^-1} mol\eqn{^{-1}}{^-1})\cr
+ \tab \tab state at 25 \eqn{^{\circ}}{°}C and 1 bar (cal K\eqn{^{-1}}{^-1} mol\eqn{^{-1}}{^-1})\cr
\code{n} \tab numeric \tab Number of atoms of the element in its stable\cr
- \tab \tab compound at 25 \eqn{^{\circ}}{degrees }C and 1 bar
+ \tab \tab compound at 25 \eqn{^{\circ}}{°}C and 1 bar
}
\item \code{thermo$obigt}
@@ -73,17 +78,17 @@
\itemize{
\item Use corrected values of \eqn{a_2}{a2} and \eqn{a_4}{a4} for [-CH2NH2] (were incorrectly listed as zero in Table 6 of Dick et al., 2006).
- \item The standard molal thermodynamic properties and equations of state parameters of the aqueous electron are zero except for the standard molal entropy at 25 \eqn{^{\circ}}{degrees }C and 1 bar, which is the opposite of that for the element of charge (\code{Z}, see above).
+ \item The standard molal thermodynamic properties and equations of state parameters of the aqueous electron are zero except for the standard molal entropy at 25 \eqn{^{\circ}}{°}C and 1 bar, which is the opposite of that for the element of charge (\code{Z}, see above).
\item The properties and parameters of some reference unfolded proteins used by Dick et al., 2006 are included here. Their names have dashes, instead of underscores, so that they are not confused with proteins whose properties are generated at runtime.
- \item The standard molal Gibbs energies and enthalpies of formation of the elements and entropies at 25 \eqn{^{\circ}}{degrees }C and 1 bar of aqueous metal-amino acid (alanate or glycinate) complexes reported by Shock and Koretsky, 1995 were recalculated by adding to their values the differences in the corresponding properties between the values for aqueous alanate and glycinate used by Shock and Koretsky, 1995, and those used by Amend and Helgeson, 1997b and Dick et al., 2006.
+ \item The standard molal Gibbs energies and enthalpies of formation of the elements and entropies at 25 \eqn{^{\circ}}{°}C and 1 bar of aqueous metal-amino acid (alanate or glycinate) complexes reported by Shock and Koretsky, 1995 were recalculated by adding to their values the differences in the corresponding properties between the values for aqueous alanate and glycinate used by Shock and Koretsky, 1995, and those used by Amend and Helgeson, 1997b and Dick et al., 2006.
\item The standard molal properties and equations-of-state parameters of four phase species (see below) of Fe(cr) were generated from heat capacity data given by Robie and Hemingway, 1995.
}
These modifications are indicated in \code{OBIGT.csv} by having \samp{CHNOSZ} as one of the sources of data. Note also that some data appearing in the \acronym{slop98.dat} file (Shock et al., 1998) were corrected or modified as noted in that file, and are indicated in \code{OBIGT.csv} by having \samp{SLOP98} as one of the sources of data.
- In order to represent thermodynamic data for minerals with phase transitions, the different phases of these minerals are represented as phase species that have states denoted by \samp{cr1}, \samp{cr2}, etc. The standard molar thermodynamic properties at 25 \eqn{^{\circ}}{degrees }C and 1 bar (\eqn{T_r}{Pr} and \eqn{P_r}{Pr}) of the \samp{cr2} phase species of minerals were generated by first calculating those of the \samp{cr1} phase species at the transition temperature (\eqn{T_{tr}}{Ttr}) and 1 bar then taking account of the volume and entropy of transition (the latter can be retrieved by combining the former with the Clausius-Clapeyron equation and values of \eqn{(dP/dT)} of transitions taken from the \acronym{SUPCRT92} data file) to calculate the standard molar entropy of the \samp{cr2} phase species at \eqn{T_{tr}}{Ttr}, and taking account of the enthalpy of transition (\eqn{{\Delta}H^{\circ}}{DeltaH0}, taken from the \acronym{SUPCRT92} data file) to calculate the standard molar enthalpy of the \samp{cr2} phase species at \eqn{T_{tr}}{Ttr}. The standard molar properties of the \samp{cr2} phase species at \eqn{T_{tr}}{Ttr} and 1 bar calculated in this manner were combined with the equations-of-state parameters of the species to generate values of the standard molar properties at 25 \eqn{^{\circ}}{degrees }C and 1 bar. This process was repeated as necessary to generate the standard molar properties of phase species represented by \samp{cr3} and \samp{cr4}, referencing at each iteration the previously calculated values of the standard molar properties of the lower-temperature phase species (i.e., \samp{cr2} and \samp{cr3}). A consequence of tabulating the standard molar thermodynamic properties of the phase species is that the values of \eqn{(dP/dT)} and \eqn{{\Delta}H^{\circ}}{DeltaH0} of phase transitions can be calculated using the equations of state and therefore do not need to be stored in the thermodynamic database. However, the transition temperatures (\eqn{T_{tr}}{Ttr}) generally can not be assessed by comparing the Gibbs energies of phase species and are tabulated in the database.
+ In order to represent thermodynamic data for minerals with phase transitions, the different phases of these minerals are represented as phase species that have states denoted by \samp{cr1}, \samp{cr2}, etc. The standard molar thermodynamic properties at 25 \eqn{^{\circ}}{°}C and 1 bar (\eqn{T_r}{Pr} and \eqn{P_r}{Pr}) of the \samp{cr2} phase species of minerals were generated by first calculating those of the \samp{cr1} phase species at the transition temperature (\eqn{T_{tr}}{Ttr}) and 1 bar then taking account of the volume and entropy of transition (the latter can be retrieved by combining the former with the Clausius-Clapeyron equation and values of \eqn{(dP/dT)} of transitions taken from the \acronym{SUPCRT92} data file) to calculate the standard molar entropy of the \samp{cr2} phase species at \eqn{T_{tr}}{Ttr}, and taking account of the enthalpy of transition (\eqn{{\Delta}H^{\circ}}{DeltaH0}, taken from the \acronym{SUPCRT92} data file) to calculate the standard molar enthalpy of the \samp{cr2} phase species at \eqn{T_{tr}}{Ttr}. The standard molar properties of the \samp{cr2} phase species at \eqn{T_{tr}}{Ttr} and 1 bar calculated in this manner were combined with the equations-of-state parameters of the species to generate values of the standard molar properties at 25 \eqn{^{\circ}}{°}C and 1 bar. This process was repeated as necessary to generate the standard molar properties of phase species represented by \samp{cr3} and \samp{cr4}, referencing at each iteration the previously calculated values of the standard molar properties of the lower-temperature phase species (i.e., \samp{cr2} and \samp{cr3}). A consequence of tabulating the standard molar thermodynamic properties of the phase species is that the values of \eqn{(dP/dT)} and \eqn{{\Delta}H^{\circ}}{DeltaH0} of phase transitions can be calculated using the equations of state and therefore do not need to be stored in the thermodynamic database. However, the transition temperatures (\eqn{T_{tr}}{Ttr}) generally can not be assessed by comparing the Gibbs energies of phase species and are tabulated in the database.
- The identification of species and their standard molal thermodynamic properties at 25 \eqn{{^\circ}}{degrees }C and 1 bar are located in the first 12 columns of \code{thermo$obigt}:
+ The identification of species and their standard molal thermodynamic properties at 25 \eqn{{^\circ}}{°}C and 1 bar are located in the first 12 columns of \code{thermo$obigt}:
\tabular{lll}{
\code{name} \tab character \tab Species name\cr
@@ -227,7 +232,7 @@
Dick, J. M., LaRowe, D. E. and Helgeson, H. C. (2006) Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. \emph{Biogeosciences} \bold{3}, 3110--336. \url{http://www.biogeosciences.net/3/311/2006/bg-3-311-2006.html}
- Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\eqn{^{\circ}}{degrees }C. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{http://dx.doi.org/10.1016/0098-3004(92)90029-Q}
+ Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\eqn{^{\circ}}{°}C. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{http://dx.doi.org/10.1016/0098-3004(92)90029-Q}
Shock, E. L. and Koretsky, C. M. {1995} Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. \emph{Geochim. Cosmochim. Acta} \bold{59}, 1497--1532. \url{http://dx.doi.org/10.1016/0016-7037(95)00058-8}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/diagram.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -150,8 +150,8 @@
"After Seewald, 1997"))
# try it with and without the loga.balance argument (total activity of
# the balanced quantity, in this case H2S aka sulfur)
-\donttest{
-## Degrees of formation of ionized forms of glycine
+
+\donttest{## Degrees of formation of ionized forms of glycine
## After Fig. 1 of Aksu and Doyle, 2001
basis("CHNOS+")
species(ispecies <- info(c("glycinium", "glycine", "glycinate")))
Modified: pkg/CHNOSZ/man/eos.Rd
===================================================================
--- pkg/CHNOSZ/man/eos.Rd 2012-11-20 01:05:45 UTC (rev 29)
+++ pkg/CHNOSZ/man/eos.Rd 2012-11-27 14:04:22 UTC (rev 30)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
\name{eos}
\alias{hkf}
\alias{cgl}
@@ -19,14 +20,14 @@
\item{property}{character, name(s) of properties to calculate}
\item{T}{numeric, temperature(s) at which to calculate properties (K)}
\item{P}{numeric, pressure(s) at which to calculate properties (bar)}
- \item{ghs}{dataframe, values of the standard molal Gibbs energy and enthalpy of formation from the elements and entropy at 25 \eqn{^{\circ}}{degrees }C and 1 bar}
+ \item{ghs}{dataframe, values of the standard molal Gibbs energy and enthalpy of formation from the elements and entropy at 25 \eqn{^{\circ}}{°}C and 1 bar}
\item{eos}{dataframe, values of the equations-of-state parameters}
- \item{contrib}{character, which contributions to consider in the revised HKF equations equations of state: (\code{n})onsolvation, (\code{s})olvation (the \eqn{\omega}{omega} terms), or (o)rigination contributions (i.e., the property itself at 25 \eqn{^{\circ}}{degrees }C and 1 bar). Default is \code{c("n","s","o")}, for all contributions}
+ \item{contrib}{character, which contributions to consider in the revised HKF equations equations of state: (\code{n})onsolvation, (\code{s})olvation (the \eqn{\omega}{omega} terms), or (o)rigination contributions (i.e., the property itself at 25 \eqn{^{\circ}}{°}C and 1 bar). Default is \code{c("n","s","o")}, for all contributions}
\item{H2O.PT}{dataframe, values of the electrostatic properties of water at the temperature(s) and pressure(s) of interest}
\item{H2O.PrTr}{dataframe, values of the electrostatic properties of water at the reference temperature and pressure}
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 30
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