[CHNOSZ-commits] r659 - in pkg/CHNOSZ: . inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Mar 20 11:13:33 CET 2021
Author: jedick
Date: 2021-03-20 11:13:33 +0100 (Sat, 20 Mar 2021)
New Revision: 659
Added:
pkg/CHNOSZ/inst/ONEWS.Rd
pkg/CHNOSZ/inst/OONEWS
Removed:
pkg/CHNOSZ/inst/ONEWS
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/solubility.Rd
Log:
Split out ONEWS.Rd (late 2011 to early 2020)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-03-20 08:01:25 UTC (rev 658)
+++ pkg/CHNOSZ/DESCRIPTION 2021-03-20 10:13:33 UTC (rev 659)
@@ -1,6 +1,6 @@
Date: 2021-03-20
Package: CHNOSZ
-Version: 1.4.0-28
+Version: 1.4.0-29
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/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2021-03-20 08:01:25 UTC (rev 658)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2021-03-20 10:13:33 UTC (rev 659)
@@ -345,1992 +345,3 @@
}
}
-
-\section{Changes in CHNOSZ version 1.3.6 (2020-03-16)}{
- \itemize{
-
- \item Fix for R-devel (4.0.0): test-add.protein.R had a test that failed
- with new stringsAsFactors = FALSE default for read.table().
-
- }
-}
-
-\section{Changes in CHNOSZ version 1.3.5 (2020-02-16)}{
- \itemize{
-
- \item Fix for R-devel (4.0.0): remove documentation for unused argument
- '...' in add.protein.Rd.
-
- }
-}
-
-\section{Changes in CHNOSZ version 1.3.4 (2019-12-15)}{
-
- \subsection{THERMODYNAMIC DATA}{
- \itemize{
- \item Change data for dawsonite, scheelite, and ferberite from calories to
- Joules (as originally reported).
-
- \item Use correct Cp coefficients for ferberite (2nd term in equation of
- Wood and Samson, 2000 is off by a factor of 10). Thanks to Xiangchong
- Liu and David Polya for the bug report and assistance.
-
- \item Move more carbonates from SUPCRT92 back into the default database:
- artinite, azurite.
- }
- }
-
- \subsection{DIAGRAMS}{
- \itemize{
- \item Improve the handling of solids in equilibrate(). They are now excluded
- from the equilibrium calculation, but their stability fields are
- calculated using the maximum affinity method (with diagram()). Where
- solids are stable, logarithms of activities of aqueous species are set
- to -999, and vice versa. Thanks to Feng Lai for the request and test
- case.
- }
- }
-
- \subsection{PACKAGE CLEANUP}{
- \itemize{
- \item Remove files Sce.csv.xz and yeastgfp.csv.xz and functions yeastgfp()
- and yeast.aa(). These have been moved to the JMDplots package
- (https://github.com/jedick/JMDplots).
-
- \item Remove protein_refseq.csv.xz (based on RefSeq release 61). An updated
- version, based on RefSeq release 95, is available in JMDplots.
- }
- }
-
- \subsection{BUG FIXES}{
- \itemize{
- \item describe.reaction(): revert the Unicode double arrow. Unlike that, a
- simple equals sign is displayed correctly on all systems.
-
- \item Fix bug in unexported function obigt2eos(): lambda (exponent in heat
- capacity equation) was incorrectly going through a units conversion.
-
- \item subcrt(): properties of minerals are now output at the listed upper
- T limit (or transition temperature, for e.g. cr1 -> cr2). Previously,
- properties were set to NA at, and not only above, the T limit. Thanks
- to Evgeniy Bastrakov for the bug report.
-
- \item In mosaic(), set the activities of only aqueous basis species to the
- total activity, which is taken from the incoming basis() definition.
- This fixes a bug where activities of minerals (particularly, native
- sulfur) were unexpectedly changed; their logarithms are now set to 0.
- Thanks to Evgeniy Bastrakov for the bug report.
-
- \item Fix a bug where berman() returned NA values for K-feldspar below
- 298.15 K, due to improperly initialized values for the disorder
- properties. Thanks to Kaustubh Hakim for the bug report.
-
- \item Use inherits() instead of class() for checking try() errors (don't
- use conditions of length > 1 in if() statements -- fix for R-devel).
-
- \item Fix a bug in affinity() with calculations in IS-T (but not T-IS)
- space. This involves a workaround for the limitation in subcrt() that
- only IS (if present) can be the 'grid' variable.
- }
- }
-
-}
-
-\section{Changes in CHNOSZ version 1.3.3 (2019-08-02)}{
-
- \subsection{NEW FEATURE: ENERGY UNITS}{
- \itemize{
- \item The csv data files in OBIGT now have a column named "E_units", which
- is used to specify the energy units for each species (cal or J).
-
- \item The messages produced by info() (and checkGHS() and checkEOS()) use
- cal or J depending on the units in the database.
-
- \item All properties returned by info() reflect the units in the database
- for each species (no conversion is done).
-
- \item All properties returned by subcrt() continue to follow the user's
- units setting (from E.units(), default cal). The messages from
- subcrt() now include the units used for the output.
-
- \item For backward compatibility, add.obigt() allows reading data from a
- user-supplied file with no "E_units" column. In this case, the units
- are set to cal.
- }
- }
-
- \subsection{NEW FEATURE: SOLUBILITY UNITS}{
- \itemize{
- \item convert() now handles the output from solubility(), for converting
- calculated concentrations to ppm or ppb.
-
- \item diagram() has a new argument 'levels' for specifying the levels at
- which to draw solubility contours.
-
- \item demo/contour.R has been updated to show the 1, 10, 100, 1000 ppb
- contours for Au solubility.
-
- \item Add demo/sphalerite.R for calculations of solubility of sphalerite,
- converted to log ppm (after Akinfiev and Tagirov, 2014).
- }
- }
-
- \subsection{NEW FEATURES: DIAGRAMS}{
- \itemize{
- \item diagram(): add 'lty.cr' argument to specify line type for boundaries
- between minerals (two crystalline phases). Setting lty.cr = 0
- suppresses the lines, which is useful for plotting only the activities
- of aqueous species (can be used to make solubility diagrams for some
- systems).
-
- \item Also add 'lty.aq' to specify the line type between aqueous species.
-
- \item The 'names' argument of diagram() recognizes more values, making it
- easier to use in scripts. A value of NULL or TRUE plots the names, and
- NA or FALSE hides the names.
-
- \item Add functions lNaCl(), lS(), lT(), lP(), lTP(), and lex() for making
- legend text to describe system conditions.
- }
- }
-
- \subsection{BUG FIXES}{
- \itemize{
- \item In mosaic(), constant activities were used for each changing basis
- species, leading to an artificial inflation of the affinities of
- species around the transitions where the basis species become equally
- abundant. Now, affinities of formation of species are calculated using
- activities of basis species that are adjusted (i.e. lowered) according
- to their relative abundances.
-
- \item The 'mixing' argument of mosaic() has been removed; it is no longer
- needed with the improved handling of activities of basis species.
-
- \item Using the "Alberty" method, nonideal() calculated incorrect values of
- adjusted H, S, and Cp at given ionic strength. The correct equations
- are now used (taken from Alberty, 2001), and checks of the self-
- consistency of the calculated values and comparisons with the
- Debye-Hückel limiting slopes for G, H, and Cp have been added to
- test-nonideal.R.
-
- \item For improved calculation of the Debye-Hückel limiting slopes, the
- equation for the Debye-Hückel constant was changed to use the equation
- given by Clarke and Glew, 1980 (valid to 150 °C).
- }
- }
-
- \subsection{IMPROVEMENTS TO MOSAIC}{
- \itemize{
- \item In mosaic(), groups of changing basis species are equilibrated for a
- total activity given by the activity of the starting basis species in
- the incoming basis() definition. This provides a means to specify the
- the amount of a conserved element in the basis species.
-
- \item equilibrate(): make it possible to process the output of mosaic().
- This feature combines the equilibrium activities of the formed species
- with those of the changing basis species to make an object that can be
- plotted with diagram(). This can be useful for conserving two elements
- in a system: one in the basis species, the other in the formed
- species. Thanks to Kirt Robinson for the feature request and test
- system for acetamide, which has been added to ?equilibrate.
-
- \item Add tests to test-mosaic.R to check that activitives produced by
- mosaic() - equilibrate() and mosaic() - solubility() really are
- equilibrium activities, i.e. that the affinities of reactions between
- species are zero everywhere, in particular near the transitions of
- basis species.
-
- \item In mosaic(), include the relative abundances in each group of basis
- species in the output ('E.bases').
- }
- }
-
- \subsection{THERMODYNAMIC DATA}{
- \itemize{
- \item Correct the value of a1 for acetamide (Shock, 1993). Thanks to Kirt
- Robinson.
-
- \item Add properties of aqueous species (dimethylamine, trimethylamine,
- resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane
- carboxylic acid) from LaRowe and Amend, 2019 and HKF parameters for
- dimethylammonium chloride from Shvedov and Tremaine, 1997.
-
- \item Add data for zoisite, clinozoisite, and epidote from Gottschalk, 2004.
- Thanks to Evgeniy Bastrakov for contributing the data file.
-
- \item Move some carbonates from SUPCRT92 back into default database:
- huntite, hydromagnesite, malachite, nesquehonite.
-
- \item Add trisulfur radical ion (S3-) from Pokrovski and Dubessy, 2015.
-
- \item Correct entries for aqueous phenanthrene and methylphenanthrene
- isomers to use Joules (Dick et al., 2013).
- }
- }
-
- \subsection{DOCUMENTATION}{
- \itemize{
- \item demo/aluminum.R: add calculations using Si(OH)4 from the Akinfiev-
- Diamond model (SiO2 in these reactions is replaced by Si(OH)4 - 2 H2O).
-
- \item Modify demo/saturation.R to use the argument recall feature of
- affinity().
-
- \item In anintro.Rmd, include an example of using mod.obigt() to add a
- solid (magnesiochromite, with data from Klemme et al., 2000). Thanks
- to Alan Boudreau for the suggestion.
-
- \item In anintro.Rmd, add description of add.obigt("AkDi") and change
- mod.obigt() example for aqueous species to use CoCl4-2 (Liu et al.,
- 2011).
- }
- }
-
- \subsection{OTHER CHANGES}{
- \itemize{
- \item Add function moles(), to calculate the total number of moles of
- elements in the output from equilibrate().
-
- \item subcrt(): stop with an error if length(logact) is not the same as the
- number of species.
-
- \item Add 'transect' argument to affinity(), to allow forcing transect mode
- for any number of values of the variables.
-
- \item solubility() has a new argument 'codeanal' that when set to TRUE
- indicates the printing of additional diagnostic messages.
-
- \item check.obigt(): add 'E_units' column and fix a bug, also involving
- makeup() and entropy(), where many species with differences between
- database and computed values of Gibbs energy were not listed.
- }
- }
-
-}
-
-\section{Changes in CHNOSZ version 1.3.2 (2019-04-20)}{
-
- \subsection{NEW FEATURES}{
- \itemize{
- \item Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
- precalculated stochiometric matrix for the default database, to speed
- up retrieve().
-
- \item retrieve() now updates the stoichiometric matrix when the database
- changes, instead of performing a full recalculation.
-
- \item Add 'ligands' argument to retrieve(), for getting metal-bearing
- species with a range of possible elements in the ligands.
-
- \item diagram(): Starting with R version 3.6.0, 'fill' can be the name of
- any available HCL-based color palette (see hcl.pals() for a list).
-
- \item Add demo/contour.R for gold solubility contours on logfO2-pH diagram.
-
- \item In the output of affinity(), the list of 'vals' (the values of the
- input variables) now has names corresponding to the variables.
-
- \item In diagram(), a background grid corresponding to major and/or minor
- tick marks can be added using the 'grid' argument. Or, use
- thermo.axis() after diagram() to overlay a grid.
-
- \item Add demo/arsenic.R (Eh-pH diagram after Lu and Zhu, 2011).
-
- \item Rename demo/go-IU.R to aluminum.R, and add plots from Tutolo et al.,
- 2014.
-
- \item Add argument 'plot.box' (default TRUE) to thermo.plot.new() and
- 'plot.line' (default FALSE) to thermo.axis() to prevent unnecessary
- plotting of axis lines. thermo.axis() also avoids plotting tick
- marks at the plot limits.
- }
- }
-
- \subsection{THERMODYNAMIC DATA}{
- \itemize{
- \item OBIGT: use dawsonite Cp coefficients from Tutolo et al., 2014.
-
- \item OBIGT: Move H4SiO4 (Stefánsson, 2001) to AS04.csv (optional data).
-
- \item Berman: rename .csv files to include whole year. berman()
- now uses the years in the filenames to assemble the data in reverse
- chronological order, and keeps only the most recent data for any
- duplicated minerals.
-
- \item Berman: Add data for sudoite, daphnite, Mg-amesite, and Fe-amesite
- (Vidal et al., 1992, 2001, 2005).
-
- \item Berman: make "albite" identical to "albite,low", not "albite,high".
-
- \item Move transuranic actinide complexes to optional data (SLOP98), as
- entropies of the elements at 298.15 K are not available to check the
- self-consistency of the GHS values for the complexes.
-
- \item obigt.Rmd: Use Zenodo DOI for citations of slop98.dat, slop07.dat, and
- slop16.dat.
- }
- }
-
-}
-
-\section{Changes in CHNOSZ version 1.3.1 (2019-03-02)}{
- \itemize{
-
- \item Fix unexported function obigt2eos(), which was affected by "Assignment
- to empty subset of data.frame fails check of length of value"
- (https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17483). The bug
- caused errors in R-release (3.5.2) but not R-devel, when using info()
- for species with the AkDi model.
-
- \item Fixes to maintain compatibility with R version 3.1.0: don't use
- lengths(), and provide explicit colClasses to read.csv() to avoid
- automatic assignment of character for long numeric values.
-
- }
-}
-
-\section{Changes in CHNOSZ version 1.3.0 (2019-02-26)}{
-
- \subsection{CRAN COMPLIANCE}{
- \itemize{
- \item Because data(thermo) and data(OBIGT) did not actually create said
- objects in the user's workspace (the expected behavior for data()),
- the package's data are now loaded by two new functions, reset() and
- obigt(). reset() is automatically run upon loading the package, so
- that existing scripts beginning with data(thermo) still work (this
- command now has no effect other than producing a warning).
- }
- }
-
- \subsection{NEW FEATURES}{
- \itemize{
- \item Add thermo() as a convenience function to access or modify the
- package's data, especially various computational options.
-
- \item Add retrieve() to retrieve all the species having given elements, or
- all species in a given chemical system. Thanks to Evgeniy Bastrakov
- for the suggestion.
-
- \item Add AkDi() to calculate thermodynamic properties of aqueous
- nonelectrolytes using the Akinfiev-Diamond model. Thanks to Evgeniy
- Bastrakov for guidance.
- }
- }
-
- \subsection{THERMODYNAMIC DATA}{
- \itemize{
- \item Revert to using SiO2(aq) from SUPCRT92 (i.e. Shock et al., 1989) in
- the default database.
-
- \item Move SiO2(aq) from Apps and Spycher, 2004 and recalculated HSiO3- to
- new optional data file, OBIGT/AS04.csv.
-
- \item Move H2AsO3- from OBIGT/SLOP98.csv to OBIGT/SUPCRT92.csv.
-
- \item Add OBIGT/AkDi.csv as optional data file for aqueous species from
- Akinfiev and Diamond, 2003 and Akinfiev and Plyasunov, 2014.
-
- \item Add gaseous HF and HCl to as requirements for the Akinfiev-Diamond
- model for dissolved gases.
-
- \item Move Au+3, AuCl3-2, and AuCl4-3 back into default database.
-
- \item Add/replace data for Ag+ and Cu+ and their complexes from Akinfiev
- and Zotov, 2001 and 2010.
-
- \item Update HCl(aq) with data from Tagirov et al., 1997.
-
- \item Update Pd+2 and complexes with data from Tagirov et al., 2013.
-
- \item Update Pt+2 and complexes with data from Tagirov et al., 2015.
-
- \item Update Zn+2 and complexes with data from Akinfiev and Tagirov, 2015.
- }
- }
-
- \subsection{DOCUMENTATION}{
- \itemize{
- \item In demo/NaCl.R, indicate region not considered by Shock et al., 1992
- in developing the "g function" applicable to electrolytes in the
- revised HKF model, and note presence of resulting discontinuities (see
- man/examples.Rd).
-
- \item Add demo/AkDi.R showing calculations of Henry's constant of dissolved
- gases, after Figure 1 of Akinfiev and Diamond, 2003.
- }
- }
-
- \subsection{OTHER CHANGES}{
- \itemize{
- \item In describe.reaction(), change equals sign to reaction double arrow.
-
- \item water() and water.SUPCRT92(): add 'P1' argument to choose whether to
- output 1 bar for Psat at temperatures less than 100 degrees C
- (default is TRUE).
-
- \item diagram(): 'xlim' and 'ylim' arguments now apply to 2-variable
- diagrams. Thanks to Evgeniy Bastrakov for the suggestion.
- }
- }
-
-}
-
-\section{Changes in CHNOSZ version 1.2.0 (2019-02-09)}{
-
- \subsection{BUG FIXES}{
- \itemize{
- \item Fix bug in nonideal() where "Zn" in formula was identified as charge.
- Thanks to Feng Lai for the bug report.
-
- \item Fix a bug where subcrt()$reaction$coeffs was incorrect for reactions
- involving minerals with phase transitions. Also ensure that the output
- reaction stoichiometry is correct for duplicated species in reactions.
- Thanks to Grayson Boyer for the bug report.
-
- \item For species in the revised HKF model, subcrt() now sets properties to
- NA where the density of H2O is less than 0.35 g/cm3, avoiding the
- output of bogus values in this region. Thanks to Evgeniy Bastrakov.
-
- \item For systems where no basis species is present in all formation
- reactions, and the user hasn't provided balance coefficients, stop
- with an error instead of setting the balance cofficients to 1.
- Thanks to Shuang Kong for an example calculation and Tucker Ely for
- a previous suggestion to produce an error here. The affected code is
- in balance(), an unexported function used in equilibrate() and
- diagram() (and now also solubility()).
- }
- }
-
- \subsection{NEW FEATURE: SOLUBILITY CALCULATIONS}{
- \itemize{
- \item Add solubility(). Run this after affinity() to calculate the
- solubility of a solid or gas defined as the conserved basis species,
- which is involved in the formation of one or more dissolved species.
-
- \item Features include automatic detection of dissociation reactions and
- finding the final ionic strength for dissolution of a mineral into
- pure water (find.IS argument).
-
- \item find.IS depends on the new argument recall feature of affinity() (or
- mosaic() if that is used instead). This allows a calculation to be
- re-run with the same settings except for particular additions or
- modifications, in this case modified values of ionic strength.
-
- \item Revise demo/solubility.R to show solubility calculations for CO2(gas)
- and calcite as a function of T and pH.
- }
- }
-
- \subsection{NEW FEATURE: EXPANDED ACTIVITY COEFFICIENT CALCULATIONS}{
- \itemize{
- \item Reorganize and expand options for activity coefficient calculations
- (set in thermo$opt$nonideal: Bdot, Bdot0, bgamma, bgamma0, or Alberty).
- The previous default, which corresponds to 'bgamma' (T- and
- P-dependent extended term parameter with single ion-size parameter),
- has been replaced by 'Bdot' (T-dependent extended term parameter and
- species-dependent ion-size parameter; see below).
-
- \item nonideal() with the 'Bdot' or 'Bdot0' equation uses specific
- ion-size parameters for different ions, in accord with the HCh package
- (Shvarov and Bastrakov, 1999). Parameters are from Table 2.7 of
- Garrels and Christ, 1965.
-
- \item nonideal() now calulates activity coefficients of neutral species,
- using the Setchénow equation. Whether the extended-term parameter in
- this equation is taken to be zero or is taken from the value for
- charged species (see above) is controlled by setting
- 'thermo$opt$Setchenow' to bgamma0 (default) or bgamma.
-
- \item Add NaCl(), implementing a first-order calculation of the speciation
- of NaCl in water, taking account of activity coefficients and the
- reaction Na+ + Cl- = NaCl(aq).
- }
- }
-
- \subsection{OTHER NEW FEATURES}{
- \itemize{
- \item Add dumpdata() for returning/writing all packaged thermodynamic data
- (including default database and optional data files). The file is
- also available on the website (chnosz.net/download/alldata.csv).
-
- \item mosaic() has been rewritten to handle more than two changing groups
- of basis species.
-
- \item mosaic() gets a new argument 'mixing' (default TRUE), indicating
- whether the Gibbs energy of ideal mixing should be included in the
- calculations with blend = TRUE. As a test of this change, an example
- using mosaic() to calculate the pH-dependent solubility of calcite
- has been added to solubility.Rd.
- }
- }
-
- \subsection{DOCUMENTATION}{
- \itemize{
- \item Add demo/gold.R for calculations of Au solubility in hydrothermal
- chloride and sulfide solutions (based on diagrams from Akinfiev and
- Zotov, 2001, Stefánsson and Seward, 2004, and Williams-Jones et al.,
- 2009). This depends on the revised nonideal() and new NaCl() functions
- described above.
-
- \item anintro.Rmd: add section on solubility calculations. Add cuprite to
- mosaic diagram example, and note about implications of changing
- balance coefficients to 1. Add 'mklinks.sh' script for adding links
- to CHNOSZ and R documentation.
-
- \item Add demo/bison.R (average oxidation state of carbon of metagenome-
- derived proteins in different microbial phyla at Bison Pool)
-
- \item demo/saturation.R replaces the previous activity_ratios.R, and
- includes not only activity ratios on the axes but also saturation
- limits for calcite, dolomite, magnesite, and brucite in the
- H2O-CO2-CaO-MgO-SiO2 system.
-
- \item Add demo/glycinate.R showing logK of complexation of glycinate with
- divalent and monovalent metals.
-
- \item Remove vignette wjd.Rnw (Winding journey down in Gibbs energy).
- }
- }
-
- \subsection{THERMODYNAMIC DATA}{
- \itemize{
- \item The Berman data (Berman, 1988 and later additions) have replaced the
- SUPCRT92 data (based on Helgeson et al., 1978) for most minerals in
- the default database (i.e. the one loaded by data(thermo)). Only
- native elements, sulfides, halides, sulfates, and selected carbonates
- and oxides from SUPCRT92 that do not duplicate any in the Berman
- dataset are loaded by default.
-
- \item The superseded SUPCRT92 minerals (primarily the silicates and
- Al-bearing minerals, as well as calcite, dolomite, hematite, and
- magnetite) are in the file extdata/OBIGT/SUPCRT92.csv, which can be
- loaded with add.obigt("SUPCRT92"). This is used in some examples for
- comparing the datasets (see ?berman and demo("go-IU")), but should not
- be needed by most users.
-
- \item In thermo$obigt, the minerals using the Berman equations are
- identified as those having NA values for all thermodynamic properties
- (columns 8-20). These minerals have the state of "cr" (not "cr_Berman"
- as before).
-
- \item The heat capacity equation in berman() has been expanded to
- Cp = k0 + k1T-1/2 + k2T-2 + k3T-3 + k4T-1 + k5T + k6T2 (as used in
- winTWQ).
-
- \item Multipliers on values in the Berman data files (extdata/Berman/*.csv)
- have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4,
- to be consistent with the winTWQ data format.
-
- \item berman() now reads data from a user-supplied file specified in
- thermo$opt$Berman.
-
- \item Add mineral data from Berman and Aranovich, 1996 to
- extdata/Berman/testing and an example of loading these data via
- add.obigt() and thermo$opt$Berman (see ?berman).
-
- \item Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
-
- \item To reduce confusion that "d5" might be a coefficient in the same
- equation as d0 .. d4, rename "d5" (constant that scales disordering
- enthalpy to volume) to "Vad" (notation used in Theriak-Domino manual).
-
- \item Change abbreviation of grossular to Grs.
-
- \item Make names for dicarboxylic acid anions from Shock, 1995 (in
- organic_aq.csv) consistent with those used in later papers, e.g.
- H-succinate and succinate-2 for the -1 and -2 charged ions. Remove
- duplicated entries for H-succinate and succinate-2 from biotic_aq.csv.
-
- \item Update G, H, and S of celestite using properties of the dissolution
- reaction given by Reardon and Armstrong, 1987.
-
- \item Add scheelite (CaWO4) and ferberite (FeWO4) using data adopted by
- Wood and Samson, 2000.
-
- \item Update aqueous Au species with data from Akinfiev and Zotov, 2001
- and 2010, and Pokrovski et al., 2014.
-
- \item Move SUPCRTBL updates (As and Al minerals and aqueous species and
- SiO2(aq)) into default database.
-
- \item Values for SiO2(aq) are taken from Apps and Spycher, 2004. Thanks
- to John Apps for providing the document.
-
- \item Recalculate GHS for HSiO3- by adding difference from SiO2(aq)
- (Sverjensky et al., 1997) to updated values for SiO2(aq).
-
- \item Add test-recalculate.R to check that recalculated values are correctly
- entered in OBIGT.
-
- \item Move superseded data for aqueous Au, As, and Al species, SiO2 and
- HSiO3- to OBIGT/SLOP98.csv.
-
- \item Add or update glycine, diglycine, and triglycine (zwitterions and
- ions), and diketopiperazine, [Gly] and [UPBB] groups from Kitadai,
- 2014.
-
- \item Add data for metal-glycinate complexes from Azadi et al., 2019,
- superseding Shock and Koretsky, 1995.
-
- \item For reproducing previous calculations, superseded data for [Gly] and
- [UPBB], as well as [Met] (earlier superseded by LaRowe and Dick,
- 2012), and metal-glycinate complexes have been moved to
- OBIGT/OldAA.csv.
- }
- }
-
- \subsection{DIAGRAMS}{
- \itemize{
- \item Lines in 1-D diagram()s can optionally be drawn as splines using the
- method for splinefun() given in the 'spline.method' argument (the
- default of NULL means no splines).
-
- \item Add 'srt' argument to diagram() (rotation of line labels).
-
- \item Export thermo.axis(), as it is useful for adding major and minor tick
- marks after (above) other plot elements such as legends.
-
- \item diagram(): rename 'what' argument to 'type'.
-
- \item diagram(): add new type of diagram, 'saturation', which is used to
- plot saturation lines for minerals (where their affinity equals
- zero).
-
- \item thermo.plot.new() and, by extension, diagram(), now "listen" to the
- setting of par("mar"). However, if a new plot is being made, or the
- device has the default setting of mar from par(), mar is (re)set to
- the default value in thermo.plot.new().
-
- \item diagram(): numeric 'names' now indicates subset of species names to
- include as labels on the plot.
-
- \item diagram(): new argument 'family' to select the font family for species
- names (labels on the plot). New arguments 'bold' and 'italic' apply to
- formatted names (e.g. chemical formulas), and 'font' applies to those
- without formatting.
-
- \item 'lines' is added to the return list of diagram(), giving the
- coordinates of lines (field boundaries) on 2-D diagrams (these are
- taken from the output of contourLines()).
- }
- }
-
- \subsection{COMPUTATIONAL OPTIONS}{
- \itemize{
- \item Add 'exceed.rhomin' argument to subcrt() and affinity() to enable
- output of properties for species in the revised HKF model below 0.35
- g/cm3.
-
- \item In equilibrate(), accept a length > 1 'normalize' argument to
- normalize the chemical formulas of only the selected species.
-
- \item Add thermo$opt$maxcores (default 2) to specify maximum number of
- cores for parallel calculations with palply().
-
- \item Keywords in basis(): Change 'CHNOPS+' to use O2 instead of e-, and add
- 'CHNOPSe' and 'MgCHNOPSe' for sets of basis species that have e-.
-
- \item Add 'keep.duplicates' argument to thermo.refs(). Set it to TRUE to
- output a single primary reference for each species, keeping any
- duplicated references (but not including any secondary references in
- thermo$obigt$ref2). Thanks to Evgeniy Bastrakov for the suggestion.
- }
- }
-
- \subsection{USABILITY ENHANCEMENTS}{
- \itemize{
- \item To provide better diagnostics for other apps using CHNOSZ, warning
- messages produced by subcrt() are now available in the output of
- affinity(), under 'sout$warnings'.
-
- \item Change internal variable names in subcrt() for better readability
- (sinfo -> ispecies, inpho -> iphases, sinph -> phasespecies).
-
- \item info(): display mineral names instead of just "cr" in messages (e.g.
- for info("SiO2")).
-
- \item info(): species with no matches in default database are also
- searched in optional data files.
-
- \item Add C implementation of counting occurrences of all letters in a
- string (src/count_letters.c) to speed up operation of count.aa().
-
- \item read.fasta(): add support for file connections created using
- archive::archive_read (https://github.com/jimhester/archive).
-
- \item The arguments in expr.species() have been reorganized for more
- flexible and concise usage.
-
- \item Reduce message clutter for diagrams showing water stability limits.
-
- \item In subcrt(), improve error message for invalid property names.
-
- \item In affinity(), make invalid variable names an error.
-
- \item Add 'return.sout' argument to affinity(), to return just the values
- calculated with subcrt().
- }
- }
-
-}
-
-\section{Changes in CHNOSZ version 1.1.3 (2017-11-13)}{
-
- \subsection{MAJOR CHANGES}{
- \itemize{
- \item Add berman() function and extdata/Berman/*.csv files for calculating
- thermodynamic properties of minerals using equations of Berman, 1988.
-
- \item Calculations related to Berman's (1988) Figs. 1 and 2 for the lambda
- transition of quartz are available in the new demo lambda.R.
-
- \item Add functions implementing the Deep Earth Water (DEW) model
- (Sverjensky et al., 2014): water.DEW() and its supporting functions
- calculateDensity(), calculateGibbsofWater(), calculateEpsilon(),
- calculateQ().
-
- \item The computational setting for water (thermo$opt$water) can now be set
- using water("DEW"), water("IAPWS"), etc.
-
- \item Usage of the DEW model is shown in the new demo DEW.R. This demo also
- depends on the Berman equations (above) and, for the last diagram in
- the demo, the following *four* NEWS items:
-
- \item In equilibrate(), it is now possible to combine affinity calculations
- with variable activity of the balancing basis species (loga.balance).
- For example, in the last plot of the DEW demo, the calculation
- involves simultaneously varying temperature and logfO2 (given as
- arguments to affinity()) as well as total concentration of carbon
- (given by the loga.balance argument in equilibrate()).
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 659
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