From noreply at r-forge.r-project.org Sun Dec 1 12:40:00 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sun, 1 Dec 2024 12:40:00 +0100 (CET) Subject: [CHNOSZ-commits] r853 - in pkg/CHNOSZ: . R inst vignettes Message-ID: <20241201114000.1E44C180061@r-forge.r-project.org> Author: jedick Date: 2024-12-01 12:39:59 +0100 (Sun, 01 Dec 2024) New Revision: 853 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/util.expression.R pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/vignettes/FAQ.Rmd pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/equilibrium.Rmd pkg/CHNOSZ/vignettes/multi-metal.Rmd Log: Don't subscript formulas of species in expr.species() and ratlab() Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-11-30 08:23:48 UTC (rev 852) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-01 11:39:59 UTC (rev 853) @@ -1,6 +1,6 @@ -Date: 2024-11-30 +Date: 2024-12-01 Package: CHNOSZ -Version: 2.1.0-25 +Version: 2.1.0-26 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/R/util.expression.R =================================================================== --- pkg/CHNOSZ/R/util.expression.R 2024-11-30 08:23:48 UTC (rev 852) +++ pkg/CHNOSZ/R/util.expression.R 2024-12-01 11:39:59 UTC (rev 853) @@ -58,7 +58,8 @@ var <- "a" if(molality) var <- "m" if(state %in% c("g", "gas")) var <- "f" - expr <- substitute(italic(a)[b], list(a = var, b = expr)) + # For better readability, no longer using subscripts for species formulas 20241201 + expr <- substitute(italic(a)*b, list(a = var, b = expr)) # Use the logarithm? if(log) expr <- substitute(log ~ a, list(a = expr)) # Write the value if not NULL or NA @@ -311,7 +312,8 @@ # With molality, change a to m a <- ifelse(molality, "m", "a") # The final expression - substitute(log~(italic(a)[expr.top]^exp.top / italic(a)[expr.bottom]^exp.bottom), + # For better readability, no longer using subscripts for species formulas 20241201 + substitute(log~(italic(a)^exp.top*expr.top / italic(a)^exp.bottom*expr.bottom), list(a = a, expr.top = expr.top, exp.top = exp.top, expr.bottom = expr.bottom, exp.bottom = exp.bottom)) } Modified: pkg/CHNOSZ/inst/NEWS.Rd =================================================================== --- pkg/CHNOSZ/inst/NEWS.Rd 2024-11-30 08:23:48 UTC (rev 852) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-01 11:39:59 UTC (rev 853) @@ -15,11 +15,12 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{?G?}}} -\section{Changes in CHNOSZ version 2.1.0-25 (2024-11-30)}{ +\section{Changes in CHNOSZ version 2.1.0-26 (2024-12-01)}{ \itemize{ - \item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to canprot package with different names. + \item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to + canprot package with different names. \item Remove \code{seq2aa()}. @@ -26,37 +27,53 @@ \item Remove \code{add.alpha()}. Now \code{grDevices::adjustcolor()} is used in \code{stack_mosaic()} to add transparency. - \item Add FAQ question: Why are mineral stability boundaries curved on mosaic diagrams? + \item Add FAQ question: Why are mineral stability boundaries curved on + mosaic diagrams? - \item \code{check.EOS()} now uses values of Born coefficients \emph{X} and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending on the \code{model} defined in OBIGT (HKF or DEW, respectively). + \item \code{check.EOS()} now uses values of Born coefficients \emph{X} + and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending + on the \code{model} defined in OBIGT (HKF or DEW, respectively). - \item Add aqueous uranyl complexes from \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)} and related U-bearing minerals from \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}. + \item Add aqueous uranyl complexes from + \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)} + and related U-bearing minerals from + \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}. - \item Except for HUO\s{4}\S{-}, aqueous uranium species from \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} have been moved to \file{SLOP98.csv}. + \item Except for HUO\s{4}\S{-}, aqueous uranium species from + \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} + have been moved to \file{SLOP98.csv}. - \item Remove \code{ispecies} from output of \code{check.OBIGT()} to avoid superfluous diffs. + \item Remove \code{ispecies} from output of \code{check.OBIGT()} to avoid + superfluous diffs. - \item Move americium complexes from \file{slop98.dat} back to \file{inorganic_aq.csv} (entropy of the element Am has been available for checking GHS self-consistency since version 1.4.0). + \item Move americium complexes from \file{slop98.dat} back to + \file{inorganic_aq.csv} (entropy of the element Am has been available for + checking GHS self-consistency since version 1.4.0). - \item Add alkylamines, benzylamines, and aminiums from \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}. + \item Add alkylamines, benzylamines, and aminiums from + \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}. \item \samp{OBIGT/inorganic_cr.csv}: Add cerianite (CeO\s{2}) and chromite (FeCr\s{2}O\s{4}) from \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}. - \item Add \file{demo/total_S.R} (total activity of S--pH diagram for Fe-S-O-C minerals). + \item Add \file{demo/total_S.R} (total activity of S--pH diagram for + Fe-S-O-C minerals). - \item Restore \code{lines} to the output of \code{diagram()} for the x and y values of predominance field boundaries. + \item Restore \code{lines} to the output of \code{diagram()} for the x + and y values of predominance field boundaries. \item OBIGT: Restore steam (H\s{2}O,g) in \file{inorganic_gas.csv}. - \item OBIGT: Fix sign of \emph{c} parameter for nesquehonite. Thanks to James Leong and Grayson Boyer. + \item OBIGT: Fix sign of \emph{c} parameter for nesquehonite. Thanks to + James Leong and Grayson Boyer. \item Add \file{demo/uranyl.R}, total (carbonate|sulfate)-pH diagrams for uranyl species, after \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. - \item Adjust \code{axis.label()} to show sum symbol. + \item Adjust \code{axis.label()} to show sum symbol for + \code{mosaic()}-ed basis species used as a plot variable. \item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes, and add solubility contours for Fe and Au. @@ -64,6 +81,11 @@ \item Add \file{OBIGT/IGEM24.csv} with updated data for Au and Cu complexes and SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS. + + \item For better readability, formulas of species are no longer + subscripted by \code{axis.label()} (via \code{expr.species()}). An + example of the new formatting is log \emph{f}O\s{2}). Similar formatting + for other expressions has been used in the vignettes. } Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/FAQ.Rmd 2024-11-30 08:23:48 UTC (rev 852) +++ pkg/CHNOSZ/vignettes/FAQ.Rmd 2024-12-01 11:39:59 UTC (rev 853) @@ -185,14 +185,14 @@ O2 <- "O2" S2 <- "S2" log <- "log " -aHCO2_ <- "aHCO2?" -aHCO3_ <- "aHCO3?" -logfO2 <- "log fO2" +aHCO2_ <- "aHCO2?" +aHCO3_ <- "aHCO3?" +logfO2 <- "log fO2" Ctot <- "Ctot" C3H5O2_ <- "C3H5O2?" -a3HCO3_ <- "a3HCO3?" -aC3H5O2_ <- "aC3H5O2?" -a2HCO3_ <- "a2HCO3?" +a3HCO3_ <- "a3HCO3?" +aC3H5O2_ <- "aC3H5O2?" +a2HCO3_ <- "a2HCO3?" logCtot <- "log Ctot" CO2 <- "CO2" H2O <- "H2O" Modified: pkg/CHNOSZ/vignettes/anintro.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/anintro.Rmd 2024-11-30 08:23:48 UTC (rev 852) +++ pkg/CHNOSZ/vignettes/anintro.Rmd 2024-12-01 11:39:59 UTC (rev 853) @@ -643,7 +643,7 @@ diagram(acr, add = TRUE, bold = acr$species$state=="cr", limit.water = FALSE) # Add legend legend <- c( - bquote(log * italic(a)["Mn(aq)"] == .(logact)), + bquote(log ~ italic(a)*"Mn(aq)" == .(logact)), bquote(italic(T) == .(T) ~ degree*C) ) legend("topright", legend = as.expression(legend), bty = "n") @@ -761,7 +761,7 @@ ``` ```{r rainbow_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, out.width="100%", echo=FALSE, message=FALSE, cache=TRUE, fig.cap="Affinities of organic synthesis in a hydrothermal system, after Shock and Canovas (2010).", pngquant=pngquant, timeit=timeit} -diagram(a, balance = 1, ylim = c(-100, 100), ylab = quote(italic(A)*", kcal/mol"), +diagram(a, balance = 1, ylim = c(-100, 100), ylab = quote(italic(A)~"(kcal/mol)"), col = rainbow(8), lwd = 2, bg = "slategray3") abline(h = 0, lty = 2, lwd = 2) ``` @@ -1160,7 +1160,7 @@ Let's compare experimental values of heat capacity of four proteins, from @PM90, with those calculated using group additivity. We divide Privalov and Makhatadze's experimental values by the lengths of the proteins to get per-residue values, then plot them. -```{r protein_Cp, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", echo=FALSE, message=FALSE, fig.cap='The heat capacity calculated by group additivity closely approximates experimental values for aqueous proteins. For a related figure showing the effects of ionization in the calculations, see `?ionize.aa`.', cache=TRUE, pngquant=pngquant, timeit=timeit} +```{r protein_Cp, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", echo=FALSE, message=FALSE, fig.cap='The heat capacity calculated by group additivity closely approximates experimental values for aqueous proteins.', cache=TRUE, pngquant=pngquant, timeit=timeit} PM90 <- read.csv(system.file("extdata/cpetc/PM90.csv", package = "CHNOSZ")) plength <- protein.length(colnames(PM90)[2:5]) Cp_expt <- t(t(PM90[, 2:5]) / plength) @@ -1193,7 +1193,7 @@ Charged and uncharged sets of basis species are used to to activate and suppress the ionization calculations. The calculation of affinity for the ionized proteins returns multiple values (as a function of pH), but there is only one value of affinity returned for the nonionized proteins, so we need to use R's `as.numeric()` to avoid subtracting nonconformable arrays: -```{r protein_ionization, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap='Affinity of ionization of proteins. See [demo(ionize)](../demo) for ionization properties calculated as a function of temperature and pH.', cache=TRUE, pngquant=pngquant, timeit=timeit} +```{r protein_ionization, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap='Affinity of ionization of proteins. See [demo(ionize)](../demo) for ionization properties calculated as a function of temperature and pH.', cache=TRUE, pngquant=pngquant, timeit=timeit} ip <- pinfo(c("CYC_BOVIN", "LYSC_CHICK", "MYG_PHYCA", "RNAS1_BOVIN")) basis("CHNOS+") a_ion <- affinity(pH = c(0, 14), iprotein = ip) @@ -1309,20 +1309,20 @@ Let's look at different ways of representing the chemical compositions of the proteins. `protein.basis()` returns the stoichiometry for the formation reaction of each proteins. Dividing by `protein.length()` gives the per-residue reaction coefficients. -Using the set of basis species we have seen before (CO2, NH3, H2S, `r h2o`, `r o2`) there is a noticeable correlation between *n*`r o2` and `r zc`, but even more so between *n*`r h2o` and `r zc` (shown in the plots on the left). +Using the set of basis species we have seen before (CO2, NH3, H2S, `r h2o`, `r o2`) there is a noticeable correlation between *n*`r o2` and `r zc`, but even more so between *n*`r h2o` and `r zc` (shown in the plots on the left). ```{marginfigure} The calculation of *Z*C, which sums elemental ratios, is not affected by the choice of basis species. ``` The `QEC` keyword to `basis()` loads basis species including three amino acids (glutamine, glutamic acid, cysteine, `r h2o`, `r o2`). -This basis strengthens the relationship between `r zc` and *n*`r o2`, but weakens that between `r zc` and *n*`r h2o` (shown in the plots on the right). +This basis strengthens the relationship between `r zc` and *n*`r o2`, but weakens that between `r zc` and *n*`r h2o` (shown in the plots on the right). -```{r rubisco_O2, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap="Chemical metrics (*n*O2 and *n*H2O) calculated with different sets of basis species, compared to carbon oxidation state (*Z*C) which does not depend on the basis species.", cache=TRUE, pngquant=pngquant, timeit=timeit} +```{r rubisco_O2, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap="Chemical metrics (*n*O2 and *n*H2O) calculated with different sets of basis species, compared to carbon oxidation state (*Z*C) which does not depend on the basis species.", cache=TRUE, pngquant=pngquant, timeit=timeit} layout(matrix(1:4, nrow = 2)) par(mgp = c(1.8, 0.5, 0)) pl <- protein.length(aa) ZClab <- axis.label("ZC") -nO2lab <- expression(italic(n)[O[2]]) -nH2Olab <- expression(italic(n)[H[2]*O]) +nO2lab <- expression(italic(n)*O[2]) +nH2Olab <- expression(italic(n)*H[2]*O) lapply(c("CHNOS", "QEC"), function(thisbasis) { basis(thisbasis) pb <- protein.basis(aa) @@ -1336,10 +1336,10 @@ ```{r rubisco_O2, eval=FALSE} ``` -By projecting the compositions of proteins into the `QEC` set of basis species, *n*`r o2` emerges as a strong indicator of oxidation state, while *n*`r h2o` is a relatively uncorrelated (i.e. independent) variable. +By projecting the compositions of proteins into the `QEC` set of basis species, *n*`r o2` emerges as an indicator of oxidation state, while *n*`r h2o` is a relatively uncorrelated (i.e. independent) variable. These independent variables make it easier to distinguish the effects of oxidation and hydration state in proteomic datasets [@DYT20]. -- The [canprot](https://github.com/jedick/canprot) package has functions to calculate chemical metrics (*Z*C, *n*`r o2`, and *n*`r h2o`) directly from amino acid compositions of proteins, and to read amino acid compositions from FASTA files (`canprot::read_fasta()`). +- The [canprot](https://github.com/jedick/canprot) package has functions to calculate chemical metrics (*Z*C, *n*`r o2`, and *n*`r h2o`) directly from amino acid compositions of proteins, and to read amino acid compositions from FASTA files (`canprot::read_fasta()`). ## Normalization to residues Modified: pkg/CHNOSZ/vignettes/equilibrium.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/equilibrium.Rmd 2024-11-30 08:23:48 UTC (rev 852) +++ pkg/CHNOSZ/vignettes/equilibrium.Rmd 2024-12-01 11:39:59 UTC (rev 853) @@ -292,13 +292,13 @@ than two species. * Diagrams **E** and **F** both use the equilibration method to calculate - activities of species as a function of log*a*~H2O~ at log*f*~O2~ = -66. - Diagram **F** shows the default setting, where *a*~CO2~ is taken from the sum + activities of species as a function of log*a*H~2~O at log*f*O~2~ = -66. + Diagram **F** shows the default setting, where *a*CO~2~ is taken from the sum of initial activities of species (each 10^-3^). The positions of equal activities (where the lines cross) are the same as in Diagram **D** at - log*f*~O2~ = -66. + log*f*O~2~ = -66. -* Diagram **F** is drawn for a lower total activity of *a*~CO2~. Not only are +* Diagram **F** is drawn for a lower total activity of *a*CO~2~. Not only are the activities of all amino acids decreased, but glycine starts to become predominant at some conditions. This is because, compared to other amino acids, it is smaller and has a lower coefficient on CO~2~ in its formation @@ -425,7 +425,7 @@ Diagrams **A**, **C**, and **E** are predominance (equal-activity) diagrams made with different balancing constraints. Diagrams **B**, **D**, and **F** -show a cross-section of the same system at log*a*~H2O~ = 0. +show a cross-section of the same system at log*a*H~2~O = 0. * In Diagrams **A** and **B**, the reactions are balanced on protein length. The drastic transitions between proteins in **B** result from the large @@ -473,7 +473,7 @@ Although it is below the stability limit of H~2~O (vertical dashed line), there is an interesting convergence of the metastable equilibrium activities of some -proteins at low log *f*~O2~. +proteins at low log *f*O~2~. ## Document history Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2024-11-30 08:23:48 UTC (rev 852) +++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2024-12-01 11:39:59 UTC (rev 853) @@ -122,7 +122,7 @@ Mashing or simple overlay refers to independent calculations for two different systems that are displayed on the same diagram. -This example starts with a log*f*~O2~--pH base diagram for the C-O-H system then overlays a diagram for S-O-H. +This example starts with a log f*O2--pH base diagram for the C-O-H system then overlays a diagram for S-O-H. The second call to `affinity()` uses the argument recall feature, where the arguments after the first are taken from the previous command. This allows calculations to be run at the same conditions for a different system. This feature is also used in other examples in this vignette. @@ -915,7 +915,7 @@ The higher stability of these complexes from @Hel69 causes the 35 ppm contour to move closer to the position shown by @Sve87. -Interestingly, the calculation here also predict substantial increases of Cu concentration of Cu at high *f*~S2~ and low *f*~O2~, due to the formation of bisulfide complexes with Cu. +Interestingly, the calculation here also predict substantial increases of Cu concentration of Cu at high *f*S2 and low *f*O2, due to the formation of bisulfide complexes with Cu. The aqueous species considered in the calculation can be seen like this: ```{r iCu.aq} names(iCu.aq) @@ -923,7 +923,7 @@ CuHS and Cu(HS)~2~^-^ can be excluded by removing S from the `retrieve()` call above (i.e. only `c("O", "H", "Cl")` as the elements in possible ligands); doing so precludes a high concentration of aqueous Cu in the highly reduced, sulfidic region. -The third plot for the concentation of SO~4~^-2^ is simply made by using `affinity()` to calculate the affinity of its formation reaction as a function of *f*~S2~ and *f*~O2~ at pH 6 and 125 ?C, then using `solubility()` to calculate the solubility of S~2~(gas), expressed in terms of moles of SO~4~^-2^ in order to calculate parts per million (ppm) by weight. +The third plot for the concentation of SO~4~^-2^ is simply made by using `affinity()` to calculate the affinity of its formation reaction as a function of *f*S2 and *f*O2 at pH 6 and 125 ?C, then using `solubility()` to calculate the solubility of S~2~(gas), expressed in terms of moles of SO~4~^-2^ in order to calculate parts per million (ppm) by weight. ## Secondary Balancing @@ -1058,8 +1058,8 @@ This example was prompted by Figure 3 of @MH85; earlier versions of the diagram are in @HBL69 and @Hel70a. In some ways this is like the inverse of the **mosaic stacking** example. -There, reactions were balanced on Fe or Cu, and *f*~O2~ and pH were used as plotting variables. -Here, the reactions are balanced on O~2~ and implicitly on H^+^ through the activity ratios with *a*~Fe^+2^~ and *a*~Cu^+^~, which are the plotting variables. +There, reactions were balanced on Fe or Cu, and *f*O2 and pH were used as plotting variables. +Here, the reactions are balanced on O~2~ and implicitly on H^+^ through the activity ratios with *a*Fe^+2^ and *a*Cu^+^, which are the plotting variables. More common diagrams of this type are balanced on Si or Al. See `demo(saturation)` for an example in the H~2~O-CO~2~-CaO-MgO-SiO~2~ system. From noreply at r-forge.r-project.org Mon Dec 23 10:49:41 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Dec 2024 10:49:41 +0100 (CET) Subject: [CHNOSZ-commits] r854 - in pkg/CHNOSZ: . R demo man Message-ID: <20241223094942.0CA8818032C@r-forge.r-project.org> Author: jedick Date: 2024-12-23 10:49:41 +0100 (Mon, 23 Dec 2024) New Revision: 854 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/stack_mosaic.R pkg/CHNOSZ/R/util.expression.R pkg/CHNOSZ/R/util.legend.R pkg/CHNOSZ/demo/sum_S.R pkg/CHNOSZ/man/stack_mosaic.Rd Log: Update stack_mosaic() Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-01 11:39:59 UTC (rev 853) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-23 09:49:41 UTC (rev 854) @@ -1,6 +1,6 @@ -Date: 2024-12-01 +Date: 2024-12-23 Package: CHNOSZ -Version: 2.1.0-26 +Version: 2.1.0-27 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/R/stack_mosaic.R =================================================================== --- pkg/CHNOSZ/R/stack_mosaic.R 2024-12-01 11:39:59 UTC (rev 853) +++ pkg/CHNOSZ/R/stack_mosaic.R 2024-12-23 09:49:41 UTC (rev 854) @@ -5,11 +5,11 @@ # col: Colors for species1, species2, and species12 # (default of NA for col[3] means to plot species12 boundaries with color for species2) # ...: Arguments for mosaic() (including affinity() arguments) -stack_mosaic <- function(bases, species1, species2, species12, names = NULL, col = list(4, 3, 6), col.names = list(4, 3, 6), - fill = NULL, dx = list(0, 0, 0), dy = list(0, 0, 0), srt = list(0, 0, 0), lwd = list(1, 1, 1), lty = list(1, 1, 1), +stack_mosaic <- function(bases, species1, species2, species12, names = NULL, col = list(1, 4, 4), col.names = list(1, 4, 4), + fill = list(NA, NA, NA), dx = list(0, 0, 0), dy = list(0, 0, 0), srt = list(0, 0, 0), lwd = list(1, 1, 1), lty = list(1, 1, 1), loga_aq = NULL, plot.it = TRUE, ...) { - # Default is to use semi-transparent fill for bimetallic species + # Set fill = NULL to use semi-transparent color for bimetallic species if(is.null(fill)) fill <- list(NA, NA, adjustcolor(col.names[3], alpha.f = 0.312)) # Load species1 (first metal-bearing species) Modified: pkg/CHNOSZ/R/util.expression.R =================================================================== --- pkg/CHNOSZ/R/util.expression.R 2024-12-01 11:39:59 UTC (rev 853) +++ pkg/CHNOSZ/R/util.expression.R 2024-12-23 09:49:41 UTC (rev 854) @@ -143,7 +143,7 @@ if(T.units() == "C") expr <- substitute(degree*a, list(a = expr)) } # Eh - electrical potential - if(grepl("Eh", property)) expr <- substitute(a, list(a = "volt")) + if(grepl("Eh", property)) expr <- substitute(a, list(a = "V")) # IS - ionic strength if(grepl("IS", property)) expr <- substitute(a, list(a = mol~kg^-1)) if(!expr == "") { Modified: pkg/CHNOSZ/R/util.legend.R =================================================================== --- pkg/CHNOSZ/R/util.legend.R 2024-12-01 11:39:59 UTC (rev 853) +++ pkg/CHNOSZ/R/util.legend.R 2024-12-23 09:49:41 UTC (rev 854) @@ -2,7 +2,7 @@ # Functions for making legend text # 20190530 jmd first version -lNaCl <- function(x, digits = 2) substitute(italic(m)[NaCl] == x~mol~kg^-1, list(x = round(x, digits))) +lNaCl <- function(x, digits = 2) substitute(NaCl == x~mol~kg^-1, list(x = round(x, digits))) lS <- function(x, digits = 3) substitute(sum(S) == x~mol~kg^-1, list(x = round(x, digits))) Modified: pkg/CHNOSZ/demo/sum_S.R =================================================================== --- pkg/CHNOSZ/demo/sum_S.R 2024-12-01 11:39:59 UTC (rev 853) +++ pkg/CHNOSZ/demo/sum_S.R 2024-12-23 09:49:41 UTC (rev 854) @@ -67,7 +67,7 @@ diagram(sp, type = "loga.balance", contour.method = "flattest", levels = 10^(-3:5), add = TRUE, col = col, lty = 3, lwd = 1.8, cex = 1.2) } - # Add legends and title + # Add legend and title T_P <- describe.property(c("T", "P"), c(T, P)) P_Cl <- c(bquote(pH == .(pH)), bquote(NaCl == .(m_NaCl)~mol~kg^-1)) legend <- lex(T_P, P_Cl) Modified: pkg/CHNOSZ/man/stack_mosaic.Rd =================================================================== --- pkg/CHNOSZ/man/stack_mosaic.Rd 2024-12-01 11:39:59 UTC (rev 853) +++ pkg/CHNOSZ/man/stack_mosaic.Rd 2024-12-23 09:49:41 UTC (rev 854) @@ -9,7 +9,7 @@ \usage{ stack_mosaic(bases, species1, species2, species12, names = NULL, - col = list(4, 3, 6), col.names = list(4, 3, 6), fill = NULL, + col = list(1, 4, 4), col.names = list(1, 4, 4), fill = list(NA, NA, NA), dx = list(0, 0, 0), dy = list(0, 0, 0), srt = list(0, 0, 0), lwd = list(1, 1, 1), lty = list(1, 1, 1), loga_aq = NULL, plot.it = TRUE, ...) @@ -74,7 +74,7 @@ basis(c("pyrite", "Cu", "Cl-", "H2S", "H2O", "oxygen", "H+")) basis("H2S", -2) # Calculate solution composition for 1 mol/kg NaCl -NaCl <- NaCl(T = T, P = P, m_tot = 1) +NaCl <- NaCl(m_tot = 1, T = T, P = P) basis("Cl-", log10(NaCl$m_Cl)) # Define arguments for stack_mosaic: Speciate aqueous sulfur @@ -84,20 +84,12 @@ # Calculate stabilities of Cu-bearing and FeCu-bearing minerals second species2 <- c("copper", "cuprite", "tenorite", "chalcocite", "covellite") species12 <- c("chalcopyrite", "bornite") -# Use abbreviations for Fe-bearing minerals and formulas for Cu-bearing minerals -names1 <- c("Py", "Po", "Mag", "Hem") -names2 <- info(info(species2))$formula -names12 <- info(info(species12))$formula -names <- list(names1, names2, names12) # Adjust x-position for one species (chalcocite, Cu2S) dx <- list(c(0, 0, 0, 0), c(0, 0, 0, 1, 0), c(0, 0)) -# Use thick dashed lines for the bimetallic species -lwd <- list(1, 1, 2) -lty <- list(1, 1, 2) # Make the diagram -stack_mosaic(bases, species1, species2, species12, names = names, - dx = dx, lwd = lwd, lty = lty, +stack_mosaic(bases, + species1, species2, species12, dx = dx, pH = pH, O2 = O2, T = T, P = P, IS = NaCl$IS) # Add legend and title lTP <- lex(lTP(T, P)) From noreply at r-forge.r-project.org Mon Dec 23 11:30:11 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Dec 2024 11:30:11 +0100 (CET) Subject: [CHNOSZ-commits] r855 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes Message-ID: <20241223103011.8C654183945@r-forge.r-project.org> Author: jedick Date: 2024-12-23 11:30:11 +0100 (Mon, 23 Dec 2024) New Revision: 855 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz pkg/CHNOSZ/vignettes/OBIGT.bib Log: Add Mg(OH)2-MgCl2-H2O phases from Knight et al. (2024) Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-23 09:49:41 UTC (rev 854) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-23 10:30:11 UTC (rev 855) @@ -1,6 +1,6 @@ Date: 2024-12-23 Package: CHNOSZ -Version: 2.1.0-27 +Version: 2.1.0-28 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 2024-12-23 09:49:41 UTC (rev 854) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-23 10:30:11 UTC (rev 855) @@ -15,7 +15,7 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{?G?}}} -\section{Changes in CHNOSZ version 2.1.0-26 (2024-12-01)}{ +\section{Changes in CHNOSZ version 2.1.0-28 (2024-12-23)}{ \itemize{ @@ -87,6 +87,10 @@ example of the new formatting is log \emph{f}O\s{2}). Similar formatting for other expressions has been used in the vignettes. + \item OBIGT: Add Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from + \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al. + (2024)}. + } } Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2024-12-23 09:49:41 UTC (rev 854) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2024-12-23 10:30:11 UTC (rev 855) @@ -8,7 +8,6 @@ anorthite,An,Al2CaSi2O8,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA anthophyllite,Ath,Mg7Si8O24H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA antigorite,Atg,Mg48Si34O99H62O48,cr,Ber88,BDat17.1,2017-10-09,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -brucite,Brc,MgO2H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA Ca-Al-pyroxene,CTs,CaAl2SiO6,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA calcite,Cal,CaCO3,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA chrysotile,Ctl,Mg3Si2O9H4,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-12-23 09:49:41 UTC (rev 854) +++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-12-23 10:30:11 UTC (rev 855) @@ -160,3 +160,10 @@ Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL,J,-3011454,-3203800,275.9,227.3,0,262.83,0.014653,-3549000,0,0,0,0,1273 chromite,Chr,FeCr2O4,cr,RH95,NA,2024-05-23,CGL,J,-1344500,-1445500,146,133.58,44.01,301.8,-0.04157,487700,-2803,1.147E-05,0,0,-1800 cerianite,Cei,CeO2,cr,RH95,NA,2024-05-23,CGL,J,-1024600,-1088700,62.3,61.63,23.85,80.29,0.005699,-729400,-209.9,0,0,0,-1800 +brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000 +bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000 +"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000 +"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000 +"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000 +"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000 +"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-12-23 09:49:41 UTC (rev 854) +++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-12-23 10:30:11 UTC (rev 855) @@ -67,6 +67,7 @@ RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://doi.org/10.3133/b2131 RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (melting temperature and G and H not in SUPCRT92)",https://doi.org/10.3133/b2131 RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","phase stability limit",https://doi.org/10.3133/b2131 +RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","brucite V",https://doi.org/10.3133/b2131 SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8 Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496 DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)4,https://doi.org/10.1016/0016-7037(95)00403-3 @@ -285,16 +286,18 @@ SPD+19,"B. St Clair et al.",2019,"ACS Earth Space Chem 3, 905-921","metal carbonate and bicarbonate complexes and FeSO4",https://doi.org/10.1021/acsearthspacechem.9b00016 AKK+20,"N. N. Akinfiev et al.",2020,"Geochim. Cosmochim. Acta 280, 102-115","Nb and Ta species",https://doi.org/10.1016/j.gca.2020.04.009 LX20,"Liu and Xiao",2020,"Ore Geol. Rev. 117, 103289","huebnerite Cp",https://doi.org/10.1016/j.oregeorev.2019.103289 +NEA20,"Grenthe et al.",2020,"Second Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium","rutherfordine, beta-UO2(OH)2, and Na2U2O7",https://doi.org/10.1787/bf86a907-en +NEA20.1,"Grenthe et al.",2020,"Second Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium",UO3,https://doi.org/10.1787/bf86a907-en LXW21,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488",H2WO4,https://doi.org/10.1016/j.chemgeo.2021.120488 LXW21.1,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","scheelite Cp",https://doi.org/10.1016/j.chemgeo.2021.120488 WV22,"A. E. Williams-Jones and O. V. Vasyukova",2022,"Econ. Geol. 117, 513-528","parameters listed here",https://doi.org/10.5382/econgeo.4895 -HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93",carrollite,https://doi.org/10.3749/2300028 -NEA20,"Grenthe et al.",2020,"Second Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium","rutherfordine, beta-UO2(OH)2, and Na2U2O7",https://doi.org/10.1787/bf86a907-en -NEA20.1,"Grenthe et al.",2020,"Second Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium",UO3,https://doi.org/10.1787/bf86a907-en AZ23,"N. N. Akinfiev and A. V. Zotov",2023,"Geol. Ore Deposits 65, 1-10","Cu+ and CuO-",https://doi.org/10.1134/S1075701523010026 TTA+23,"N. D. Trofimov, B. R. Tagirov et al.",2023,"Chem. Geol. 625, 121413","Cu hydrosulfide and chloride complexes",https://doi.org/10.1016/j.chemgeo.2023.121413 +HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93",carrollite,https://doi.org/10.3749/2300028 +KBJ24,"A. W. Knight, C. R. Bryan and C. F. Jov?-Col?n",2024,"Appl. Geochem. 169, 106032","Mg(OH)2-MgCl2-H2O phases",https://doi.org/10.1016/j.apgeochem.2024.106032 MBA+24,"A. Migdisov,?E.?Bastrakov et al.",2024,"Geochim. Cosmochim. Acta","uranyl-carbonate, -chloride, -sulfate, and -hydroxide complexes",https://doi.org/10.1016/j.gca.2024.04.023 RSS+24,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","alkylamines, benzylamines, and aminiums",https://doi.org/10.1016/j.gca.2024.03.013 RSS+24.1,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","corrected V for tripropylaminium",https://doi.org/10.1016/j.gca.2024.03.013 TAT+24,"B. R. Tagirov, N. N. Akinfiev et al.",2024,"Geochim. Cosmochim. Acta","Au-(hydro)sulfide species and SO4-2-bearing species",https://doi.org/10.1016/j.gca.2024.08.022 TAZ24,"B. R. Tagirov, N. N. Akinfiev and A. V. Zotov",2024,"Geol. Ore Deposits 66, 581--597","Au hydroxide and chloride complexes",https://doi.org/10.1134/S1075701524600403 + Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-23 09:49:41 UTC (rev 854) +++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-23 10:30:11 UTC (rev 855) @@ -310,6 +310,7 @@ "OBIGT","ferberite","cr","J",1.21,, "OBIGT","willemite","cr","J",-1.47,, "OBIGT","rutherfordine","cr","J",-14.37,, +"OBIGT","2-1-4 phase","cr","J",-4.39,, "OBIGT","octadecane","cr","cal",-2.63,, "OBIGT","nonadecane","cr","cal",-13.32,, "OBIGT","eicosane","cr","cal",-2.79,, Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz =================================================================== (Binary files differ) Modified: pkg/CHNOSZ/vignettes/OBIGT.bib =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-23 09:49:41 UTC (rev 854) +++ pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-23 10:30:11 UTC (rev 855) @@ -1837,6 +1837,16 @@ doi = {10.1016/j.gca.2024.04.023}, } + at Article{KBJ24, + author = {Andrew W. Knight and Charles R. Bryan and Carlos F. Jov?-Col?n}, + journal = {Applied Geochemistry}, + title = {Development of a consistent geochemical model of the {Mg(OH)\textsubscript{2}}?{MgCl\textsubscript{2}}?{H\textsubscript{2}O} system from 25?{C} to 120?{C}}, + year = {2024}, + pages = {106032}, + volume = {169}, + doi = {10.1016/j.apgeochem.2024.106032}, +} + @Article{RH72, author = {Robie, Richard A. and Hemingway, Bruce S.}, journal = {American Mineralogist}, From noreply at r-forge.r-project.org Tue Dec 24 14:16:35 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 24 Dec 2024 14:16:35 +0100 (CET) Subject: [CHNOSZ-commits] r856 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes Message-ID: <20241224131635.285B6181836@r-forge.r-project.org> Author: jedick Date: 2024-12-24 14:16:34 +0100 (Tue, 24 Dec 2024) New Revision: 856 Added: pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/util.data.R pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz pkg/CHNOSZ/vignettes/OBIGT.Rmd Log: Move Knight et al. (2024) to optional data Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-23 10:30:11 UTC (rev 855) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-24 13:16:34 UTC (rev 856) @@ -1,6 +1,6 @@ -Date: 2024-12-23 +Date: 2024-12-24 Package: CHNOSZ -Version: 2.1.0-28 +Version: 2.1.0-29 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/R/util.data.R =================================================================== --- pkg/CHNOSZ/R/util.data.R 2024-12-23 10:30:11 UTC (rev 855) +++ pkg/CHNOSZ/R/util.data.R 2024-12-24 13:16:34 UTC (rev 856) @@ -272,6 +272,7 @@ else if(what == "AD") tdata <- read.csv(system.file("extdata/OBIGT/AD.csv", package = "CHNOSZ"), as.is = TRUE) else if(what == "GEMSFIT") tdata <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package = "CHNOSZ"), as.is = TRUE) else if(what == "IGEM24") tdata <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE) + else if(what == "KBJ24") tdata <- read.csv(system.file("extdata/OBIGT/KBJ24.csv", package = "CHNOSZ"), as.is = TRUE) ntot <- nrow(tdata) # Where to keep the results DCp <- DV <- DG <- rep(NA, ntot) @@ -310,6 +311,7 @@ out <- rbind(out, checkfun("AS04")) out <- rbind(out, checkfun("GEMSFIT")) out <- rbind(out, checkfun("IGEM24")) + out <- rbind(out, checkfun("KBJ24")) # Set differences within a tolerance to NA out$DCp[abs(out$DCp) < 1] <- NA out$DV[abs(out$DV) < 1] <- NA @@ -394,8 +396,10 @@ GEMSFIT <- cbind(source = "GEMSFIT", dat) dat <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE) IGEM24 <- cbind(source = "IGEM24", dat) + dat <- read.csv(system.file("extdata/OBIGT/KBJ24.csv", package = "CHNOSZ"), as.is = TRUE) + KBJ24 <- cbind(source = "KBJ24", dat) # Put it all together - out <- rbind(OBIGT, SUPCRT92, SLOP98, AS04, AD, DEW, GEMSFIT, IGEM24) + out <- rbind(OBIGT, SUPCRT92, SLOP98, AS04, AD, DEW, GEMSFIT, IGEM24, KBJ24) # Quote columns 2 (name) and 3 (abbrv) because they have commas for some entries if(!is.null(file)) write.csv(out, file, row.names = FALSE, quote = c(2, 3)) else(return(out)) Modified: pkg/CHNOSZ/inst/NEWS.Rd =================================================================== --- pkg/CHNOSZ/inst/NEWS.Rd 2024-12-23 10:30:11 UTC (rev 855) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-24 13:16:34 UTC (rev 856) @@ -15,10 +15,55 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{?G?}}} -\section{Changes in CHNOSZ version 2.1.0-28 (2024-12-23)}{ +\section{Changes in CHNOSZ version 2.1.0-29 (2024-12-24)}{ + \subsection{OBIGT DEFAULT DATA}{ \itemize{ + \item Add aqueous uranyl complexes from + \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)} + and related U-bearing minerals from + \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}. + + \item Move americium complexes from \file{slop98.dat} back to + \file{inorganic_aq.csv} (entropy of the element Am has been available for + checking GHS self-consistency since version 1.4.0). + + \item Add alkylamines, benzylamines, and aminiums from + \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}. + + \item \samp{OBIGT/inorganic_cr.csv}: Add cerianite (CeO\s{2}) and + chromite (FeCr\s{2}O\s{4}) from + \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}. + + \item Restore steam (H\s{2}O,g) in \file{inorganic_gas.csv}. + + \item Fix sign of \emph{c} parameter for nesquehonite. Thanks to + James Leong and Grayson Boyer. + + } + } + + \subsection{OBIGT OPTIONAL DATA}{ + \itemize{ + + \item Except for HUO\s{4}\S{-}, aqueous uranium species from + \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} + have been moved to \file{SLOP98.csv}. + + \item \file{IGEM24.csv}: updated data for Au and Cu complexes and + SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS. + + \item \file{KBJ24.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from + \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al. + (2024)}. + + } + } + + \subsection{NEW FEATURES}{ + \itemize{ + \item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to canprot package with different names. @@ -34,29 +79,9 @@ and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending on the \code{model} defined in OBIGT (HKF or DEW, respectively). - \item Add aqueous uranyl complexes from - \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)} - and related U-bearing minerals from - \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}. - - \item Except for HUO\s{4}\S{-}, aqueous uranium species from - \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} - have been moved to \file{SLOP98.csv}. - \item Remove \code{ispecies} from output of \code{check.OBIGT()} to avoid superfluous diffs. - \item Move americium complexes from \file{slop98.dat} back to - \file{inorganic_aq.csv} (entropy of the element Am has been available for - checking GHS self-consistency since version 1.4.0). - - \item Add alkylamines, benzylamines, and aminiums from - \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}. - - \item \samp{OBIGT/inorganic_cr.csv}: Add cerianite (CeO\s{2}) and - chromite (FeCr\s{2}O\s{4}) from - \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}. - \item Add \file{demo/total_S.R} (total activity of S--pH diagram for Fe-S-O-C minerals). @@ -63,11 +88,6 @@ \item Restore \code{lines} to the output of \code{diagram()} for the x and y values of predominance field boundaries. - \item OBIGT: Restore steam (H\s{2}O,g) in \file{inorganic_gas.csv}. - - \item OBIGT: Fix sign of \emph{c} parameter for nesquehonite. Thanks to - James Leong and Grayson Boyer. - \item Add \file{demo/uranyl.R}, total (carbonate|sulfate)-pH diagrams for uranyl species, after \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. @@ -78,20 +98,13 @@ \item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes, and add solubility contours for Fe and Au. - \item Add \file{OBIGT/IGEM24.csv} with updated data for Au and Cu - complexes and SO\s{4}\S{-2}-bearing species from - researchers at IGEM RAS. - \item For better readability, formulas of species are no longer subscripted by \code{axis.label()} (via \code{expr.species()}). An example of the new formatting is log \emph{f}O\s{2}). Similar formatting for other expressions has been used in the vignettes. - \item OBIGT: Add Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from - \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al. - (2024)}. - } + } } Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2024-12-23 10:30:11 UTC (rev 855) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2024-12-24 13:16:34 UTC (rev 856) @@ -8,6 +8,7 @@ anorthite,An,Al2CaSi2O8,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA anthophyllite,Ath,Mg7Si8O24H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA antigorite,Atg,Mg48Si34O99H62O48,cr,Ber88,BDat17.1,2017-10-09,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +brucite,Brc,MgO2H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA Ca-Al-pyroxene,CTs,CaAl2SiO6,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA calcite,Cal,CaCO3,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA chrysotile,Ctl,Mg3Si2O9H4,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA Added: pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv 2024-12-24 13:16:34 UTC (rev 856) @@ -0,0 +1,8 @@ +name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T +brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000 +bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000 +"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000 +"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000 +"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000 +"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000 +"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-12-23 10:30:11 UTC (rev 855) +++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-12-24 13:16:34 UTC (rev 856) @@ -160,10 +160,3 @@ Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL,J,-3011454,-3203800,275.9,227.3,0,262.83,0.014653,-3549000,0,0,0,0,1273 chromite,Chr,FeCr2O4,cr,RH95,NA,2024-05-23,CGL,J,-1344500,-1445500,146,133.58,44.01,301.8,-0.04157,487700,-2803,1.147E-05,0,0,-1800 cerianite,Cei,CeO2,cr,RH95,NA,2024-05-23,CGL,J,-1024600,-1088700,62.3,61.63,23.85,80.29,0.005699,-729400,-209.9,0,0,0,-1800 -brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000 -bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000 -"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000 -"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000 -"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000 -"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000 -"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000 Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-23 10:30:11 UTC (rev 855) +++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-24 13:16:34 UTC (rev 856) @@ -310,7 +310,6 @@ "OBIGT","ferberite","cr","J",1.21,, "OBIGT","willemite","cr","J",-1.47,, "OBIGT","rutherfordine","cr","J",-14.37,, -"OBIGT","2-1-4 phase","cr","J",-4.39,, "OBIGT","octadecane","cr","cal",-2.63,, "OBIGT","nonadecane","cr","cal",-13.32,, "OBIGT","eicosane","cr","cal",-2.79,, @@ -400,3 +399,4 @@ "SUPCRT92","greenalite","cr","cal",,,142507 "SUPCRT92","grunerite","cr","cal",9.72,, "SUPCRT92","halloysite","cr","cal",-1.6,, +"KBJ24","2-1-4 phase","cr","J",-4.39,, Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz =================================================================== (Binary files differ) Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-23 10:30:11 UTC (rev 855) +++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-24 13:16:34 UTC (rev 856) @@ -206,7 +206,7 @@ ### Aqueous Species ### Solids ### Gases    Liquids -### Optional Data +### Optional Data @@ -397,6 +397,15 @@ ``` + +
Total count of species: References were found for `r length(used)` of `r nrow(thermo()$OBIGT)` species in the default OBIGT database and `r length(optused)` optional species. From noreply at r-forge.r-project.org Wed Dec 25 03:21:19 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 25 Dec 2024 03:21:19 +0100 (CET) Subject: [CHNOSZ-commits] r857 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT inst/extdata/OBIGT/testing inst/tinytest vignettes Message-ID: <20241225022119.26B5C180042@r-forge.r-project.org> Author: jedick Date: 2024-12-25 03:21:18 +0100 (Wed, 25 Dec 2024) New Revision: 857 Added: pkg/CHNOSZ/inst/extdata/OBIGT/testing/ pkg/CHNOSZ/inst/extdata/OBIGT/testing/AS04.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/GEMSFIT.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM24.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/KBJ24.csv Removed: pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv pkg/CHNOSZ/inst/extdata/OBIGT/GEMSFIT.csv pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/add.OBIGT.R pkg/CHNOSZ/R/util.data.R pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/inst/tinytest/test-util.data.R pkg/CHNOSZ/vignettes/OBIGT.Rmd Log: Move some optional data files to OBIGT/testing Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-25 02:21:18 UTC (rev 857) @@ -1,6 +1,6 @@ Date: 2024-12-24 Package: CHNOSZ -Version: 2.1.0-29 +Version: 2.1.0-30 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors at R: c( person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"), Modified: pkg/CHNOSZ/R/add.OBIGT.R =================================================================== --- pkg/CHNOSZ/R/add.OBIGT.R 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/R/add.OBIGT.R 2024-12-25 02:21:18 UTC (rev 857) @@ -115,11 +115,22 @@ thermo <- get("thermo", CHNOSZ) to1 <- thermo$OBIGT id1 <- paste(to1$name,to1$state) - # We match system files with the file suffixes (.csv) removed - sysfiles <- dir(system.file("extdata/OBIGT/", package = "CHNOSZ")) - sysnosuffix <- sapply(strsplit(sysfiles, "\\."), "[", 1) - isys <- match(file, sysnosuffix) - if(!is.na(isys)) file <- system.file(paste0("extdata/OBIGT/", sysfiles[isys]), package = "CHNOSZ") + + # `file` should be the path to a CSV file, or the name (without path or .csv) of a file in the package's OBIGT or OBIGT/testing + if(!file.exists(file)) { + + # List all files in OBIGT and OBIGT/testing + OBIGT_files <- dir(system.file("extdata/OBIGT/", package = "CHNOSZ"), full.names = TRUE) + testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), full.names = TRUE) + all_files <- c(OBIGT_files, testing_files) + # Match argument to file names without path or .csv suffix + all_names <- gsub(".csv", "", basename(all_files)) + ifile <- match(file, all_names) + if(is.na(ifile)) stop(paste(file, "is not a file and doesn't match any files in the OBIGT database")) + file <- all_files[ifile] + + } + # Read data from the file to2 <- read.csv(file, as.is = TRUE) Etxt <- paste(unique(to2$E_units), collapse = " and ") Modified: pkg/CHNOSZ/R/util.data.R =================================================================== --- pkg/CHNOSZ/R/util.data.R 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/R/util.data.R 2024-12-25 02:21:18 UTC (rev 857) @@ -265,14 +265,11 @@ message(paste("check.OBIGT: checking", what)) # Looking at thermo$OBIGT if(what == "OBIGT") tdata <- get("thermo", CHNOSZ)$OBIGT - else if(what == "DEW") tdata <- read.csv(system.file("extdata/OBIGT/DEW.csv", package = "CHNOSZ"), as.is = TRUE) - else if(what == "SLOP98") tdata <- read.csv(system.file("extdata/OBIGT/SLOP98.csv", package = "CHNOSZ"), as.is = TRUE) - else if(what == "SUPCRT92") tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package = "CHNOSZ"), as.is = TRUE) - else if(what == "AS04") tdata <- read.csv(system.file("extdata/OBIGT/AS04.csv", package = "CHNOSZ"), as.is = TRUE) - else if(what == "AD") tdata <- read.csv(system.file("extdata/OBIGT/AD.csv", package = "CHNOSZ"), as.is = TRUE) - else if(what == "GEMSFIT") tdata <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package = "CHNOSZ"), as.is = TRUE) - else if(what == "IGEM24") tdata <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE) - else if(what == "KBJ24") tdata <- read.csv(system.file("extdata/OBIGT/KBJ24.csv", package = "CHNOSZ"), as.is = TRUE) + else { + if(what %in% c("DEW", "SLOP98", "SUPCRT92" ,"AD")) file <- paste0("extdata/OBIGT/", what, ".csv") + else file <- paste0("extdata/OBIGT/testing/", what, ".csv") + tdata <- read.csv(system.file(file, package = "CHNOSZ"), as.is = TRUE) + } ntot <- nrow(tdata) # Where to keep the results DCp <- DV <- DG <- rep(NA, ntot) @@ -305,13 +302,11 @@ # Check default database (OBIGT) out <- checkfun("OBIGT") # Check optional data - out <- rbind(out, checkfun("DEW")) - out <- rbind(out, checkfun("SLOP98")) - out <- rbind(out, checkfun("SUPCRT92")) - out <- rbind(out, checkfun("AS04")) - out <- rbind(out, checkfun("GEMSFIT")) - out <- rbind(out, checkfun("IGEM24")) - out <- rbind(out, checkfun("KBJ24")) + for(what in c("DEW", "SLOP98", "SUPCRT92" ,"AD")) out <- rbind(out, checkfun(what)) + # Check testing data + testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), full.names = TRUE) + sources <- gsub(".csv", "", basename(testing_files)) + for(what in sources) out <- rbind(out, checkfun(what)) # Set differences within a tolerance to NA out$DCp[abs(out$DCp) < 1] <- NA out$DV[abs(out$DV) < 1] <- NA @@ -387,19 +382,18 @@ SLOP98 <- cbind(source = "SLOP98", dat) dat <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package = "CHNOSZ"), as.is = TRUE) SUPCRT92 <- cbind(source = "SUPCRT92", dat) - # More optional data 20220929 - dat <- read.csv(system.file("extdata/OBIGT/AS04.csv", package = "CHNOSZ"), as.is = TRUE) - AS04 <- cbind(source = "AS04", dat) dat <- read.csv(system.file("extdata/OBIGT/AD.csv", package = "CHNOSZ"), as.is = TRUE) AD <- cbind(source = "AD", dat) - dat <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package = "CHNOSZ"), as.is = TRUE) - GEMSFIT <- cbind(source = "GEMSFIT", dat) - dat <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE) - IGEM24 <- cbind(source = "IGEM24", dat) - dat <- read.csv(system.file("extdata/OBIGT/KBJ24.csv", package = "CHNOSZ"), as.is = TRUE) - KBJ24 <- cbind(source = "KBJ24", dat) + # Testing data 20220929 + testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), full.names = TRUE) + testing_list <- lapply(testing_files, function(file) { + dat <- read.csv(file, as.is = TRUE) + source <- gsub(".csv", "", basename(file)) + cbind(source = source, dat) + }) + testing <- do.call(rbind, testing_list) # Put it all together - out <- rbind(OBIGT, SUPCRT92, SLOP98, AS04, AD, DEW, GEMSFIT, IGEM24, KBJ24) + out <- rbind(OBIGT, SUPCRT92, SLOP98, AD, DEW, testing) # Quote columns 2 (name) and 3 (abbrv) because they have commas for some entries if(!is.null(file)) write.csv(out, file, row.names = FALSE, quote = c(2, 3)) else(return(out)) Modified: pkg/CHNOSZ/inst/NEWS.Rd =================================================================== --- pkg/CHNOSZ/inst/NEWS.Rd 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 02:21:18 UTC (rev 857) @@ -15,7 +15,7 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{?G?}}} -\section{Changes in CHNOSZ version 2.1.0-29 (2024-12-24)}{ +\section{Changes in CHNOSZ version 2.1.0-30 (2024-12-25)}{ \subsection{OBIGT DEFAULT DATA}{ \itemize{ @@ -32,7 +32,7 @@ \item Add alkylamines, benzylamines, and aminiums from \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}. - \item \samp{OBIGT/inorganic_cr.csv}: Add cerianite (CeO\s{2}) and + \item \file{inorganic_cr.csv}: Add cerianite (CeO\s{2}) and chromite (FeCr\s{2}O\s{4}) from \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}. @@ -47,14 +47,18 @@ \subsection{OBIGT OPTIONAL DATA}{ \itemize{ - \item Except for HUO\s{4}\S{-}, aqueous uranium species from + \item Aqueous uranium species other than HUO\s{4}\S{-} from \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} have been moved to \file{SLOP98.csv}. - \item \file{IGEM24.csv}: updated data for Au and Cu complexes and + \item Make new directory \file{OBIGT/testing} to hold optional data files + for testing (currently \file{AS04.csv}, \file{GEMSFIT.csv}, + \file{IGEM24.csv}, and \file{KBJ24.csv}). + + \item Add \file{IGEM24.csv}: updated data for Au and Cu complexes and SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS. - \item \file{KBJ24.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from + \item Add \file{KBJ24.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al. (2024)}. @@ -61,20 +65,31 @@ } } - \subsection{NEW FEATURES}{ + \subsection{DOCUMENTATION}{ + \itemize{ - \item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to - canprot package with different names. - - \item Remove \code{seq2aa()}. - - \item Remove \code{add.alpha()}. Now \code{grDevices::adjustcolor()} is - used in \code{stack_mosaic()} to add transparency. - \item Add FAQ question: Why are mineral stability boundaries curved on mosaic diagrams? + \item Add \file{demo/total_S.R}: total activity of S--pH diagram for + Fe-S-O-C minerals. + + \item Add \file{demo/uranyl.R}: total (carbonate|sulfate)-pH diagrams + for uranyl species, after + \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. + + \item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes, + and add solubility contours for Fe and Au. + + } + + } + + + \subsection{OTHER CHANGES}{ + \itemize{ + \item \code{check.EOS()} now uses values of Born coefficients \emph{X} and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending on the \code{model} defined in OBIGT (HKF or DEW, respectively). @@ -82,22 +97,13 @@ \item Remove \code{ispecies} from output of \code{check.OBIGT()} to avoid superfluous diffs. - \item Add \file{demo/total_S.R} (total activity of S--pH diagram for - Fe-S-O-C minerals). - \item Restore \code{lines} to the output of \code{diagram()} for the x and y values of predominance field boundaries. - \item Add \file{demo/uranyl.R}, total (carbonate|sulfate)-pH diagrams - for uranyl species, after - \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. - - \item Adjust \code{axis.label()} to show sum symbol for - \code{mosaic()}-ed basis species used as a plot variable. + \item Adjust \code{axis.label()} to show sum symbol (?) for total + activity or molality of basis species used as a plotting variable in + \code{mosaic()}. - \item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes, - and add solubility contours for Fe and Au. - \item For better readability, formulas of species are no longer subscripted by \code{axis.label()} (via \code{expr.species()}). An example of the new formatting is log \emph{f}O\s{2}). Similar formatting @@ -106,6 +112,20 @@ } } + \subsection{REMOVED FEATURES}{ + \itemize{ + + \item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to + canprot package with different names. + + \item Remove \code{seq2aa()}. + + \item Remove \code{add.alpha()}. Instead, \code{grDevices::adjustcolor()} + is now used in \code{stack_mosaic()} to add transparency. + + } + } + } \section{Changes in CHNOSZ version 2.1.0 (2024-02-11)}{ Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -1,4 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,model,E_units,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,2006-08-31,HKF,cal,-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,2019-02-08,HKF,cal,-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,OBIGT.8,2019-02-08,HKF,cal,-243151,-276276,-1.871675,-21,5,2.9735,-0.5158,5.9467,-2.7575,8.1489,-7.3123,1.5511,-1 Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/GEMSFIT.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/GEMSFIT.csv 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/inst/extdata/OBIGT/GEMSFIT.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -1,43 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -Al+3,NA,Al+3,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-116298.8,,-81.2,-28.523,-45.3,-3.3984,-16.0789,12.0699,-2.1143,14.4295,-8.8523,2.7403,3 -AlOH+2,NA,AlOH+2,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-166238.3,,-43.291,-8.948,-20.6,-0.4532,-8.8878,9.2434,-2.4116,15.4131,-4.8618,1.5897,2 -Al(OH)2+,NA,Al(OH)2+,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-214696.9,,-6.58,9.766,3.85,2.4944,-1.6909,6.4146,-2.7091,16.7439,-1.0465,0.5324,1 -Al(OH)3,NA,Al(OH)3,aq,MWKH16.1,MWKL17.1,2022-02-01,HKF,cal,-264295.7,,1.233,59.407,30.7,6.1977,8.2816,2.495,-3.1214,71.1003,-1.0644,1.0461,0 -Al(OH)4-,NA,Al(OH)4-,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-311925.7,,24.749,23.074,46.3,8.4938,12.9576,0.657,-3.3147,55.7265,-11.4047,1.0403,-1 -NaAl(OH)4,NA,NaAl(OH)4,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-373346.8,,48.8,32.161,53.6,9.1267,14.3411,0.1121,-3.3719,60.7157,-14.0523,0,0 -AlH3SiO4+2,NA,AlH3SiO4+2,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-426008.8,,13.571,-71.862,-13.96,0.16,-7.23,8.61,-2.48,37.07,-49.66,0.88,2 -KAlO2,NA,KAlO2,aq,PH97,MWKL17.1,2022-02-01,HKF,cal,-262938.3,,35.7,4.314,31.14,6.007,6.8858,3.0436,-3.0637,1.394,1.212,-0.05,0 -K+,NA,K+,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-66173.5,,24.149,2.005,9.01,3.559,-1.473,5.435,-2.712,7.4,-1.791,0.1927,1 -KOH,NA,KOH,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-103162.8,,21.654,9.912,14.1,3.7562,1.39,5.2037,-2.8365,13.499,-1.0192,0.1665,0 -KCl,NA,KCl,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-96204.8,,43.537,7.964,29.9,5.8341,7.055,2.9771,-3.0707,-5.7084,7.6228,0.1996,0 -Na+,NA,Na+,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-61219.4,,13.96,9.111,-1.21,1.839,-2.285,3.256,-2.726,18.18,-2.981,0.3306,1 -NaOH,NA,NaOH,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-98366.9,,10.134,27.127,-0.23,1.7792,-3.4372,7.101,-2.6369,22.8222,2.6543,0.1189,0 -NaCl,NA,NaCl,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-91554.5,,26.482,11.358,24,5.0828,4.629,3.9306,-2.9704,13.6339,-0.7212,0.0889,0 -NaHSiO3,NA,NaHSiO3,aq,SSH97.5,MWKL17.1,2022-02-01,HKF,cal,-306641.3,,10,24.606,12.73,3.4928,0.75,5.4483,-2.81,20.2395,1.9785,-0.038,0 -HSiO3-,NA,HSiO3-,aq,MWKH16.1,MWKL17.1,2022-02-01,HKF,cal,-242632.6,,4.708,-9.195,5,3.309,-0.5201,5.9467,-2.7575,15,-4.9202,1.5583,-1 -SiO2,NA,SiO2,aq,SHS89.1,MWKL17.1,2022-02-01,HKF,cal,-199340.6,,18,-76.119,16.1,1.9,1.7,20,-2.7,29.1,-51.2,0.1291,0 -Cl-,NA,Cl-,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-31379.1,,13.561,-29.276,17.34,4.032,4.801,5.563,-2.847,-4.4,-5.714,1.456,-1 -HCl,NA,HCl,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-30411.1,,0.421,35.731,16.4,16.1573,-11.4311,-46.1866,-2.3036,46.4716,-5.2811,0,0 -OH-,NA,OH-,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-37594.9,,-2.56,-32.586,-4.71,1.2527,0.0738,1.8423,-2.7821,4.15,-10.346,1.7246,-1 -CaOH+,NA,CaOH+,aq,MWKL17,NA,2022-02-01,HKF,cal,-171307.4,,8.717,-18.74,10.96,3.9385,-1.1019,6.1831,-2.7334,-9.5888,-2.6253,0.419,1 -CaCl+,NA,CaCl+,aq,MWKL17,NA,2022-02-01,HKF,cal,-164745.9,,-0.71,17.526,5.56,2.7406,-1.0897,6.1783,-2.734,21.588,0.524,0.5626,1 -CaCl2,NA,CaCl2,aq,MWKL17,NA,2022-02-01,HKF,cal,-190246.2,,16.188,30.956,32.65,6.2186,7.4024,2.8406,-3.085,23.9609,3.272,-0.038,0 -CaHCO3+,NA,CaHCO3+,aq,MWKL17,NA,2022-02-01,HKF,cal,-273712.7,,15.839,55.992,13.28,3.7,1.2579,5.252,-2.831,43.112,7.7228,0.3113,1 -CaCO3,NA,CaCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-262687.4,,4.806,-29.603,-15.65,-0.3907,-8.7325,9.1753,-2.4179,-11.5309,-9.0641,-0.038,0 -MgOH+,NA,MgOH+,aq,MWKL17,NA,2022-02-01,HKF,cal,-149737.8,,-16.099,30.856,1.66,2.2937,-2.1809,6.6072,-2.6888,31.5415,3.2394,0.795,1 -MgCl+,NA,MgCl+,aq,MWKL17,NA,2022-02-01,HKF,cal,-141540.2,,-19.001,25.086,1.25,2.2809,-2.3585,6.677,-2.6815,28.5471,2.0579,0.8389,1 -MgCl2,NA,MgCl2,aq,MWKL17,NA,2022-02-01,HKF,cal,-166483.3,,-2.765,40.815,28.25,5.6165,5.9323,3.4184,-3.0242,29.7395,5.2804,-0.038,0 -MgHCO3+,NA,MgHCO3+,aq,MWKL17,NA,2022-02-01,HKF,cal,-250682.8,,-4.567,60.872,9.34,3.3,0.1608,5.6868,-2.7875,47.5204,9.3524,0.6204,1 -MgCO3,NA,MgCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-239242.8,,-24.515,-27.4,-18.27,-0.7355,-9.5745,9.5062,-2.3831,-9.8914,-8.616,0,0 -NaCO3-,NA,NaCO3-,aq,MWKL17,NA,2022-02-01,HKF,cal,-188774.6,,13.406,-19.673,-1.52,2,-2.335,6.6714,-2.6825,7.7693,-7.1095,1.4265,-1 -NaHCO3,NA,NaHCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-201258.4,,37.921,48.241,31.82,6.1192,7.1597,2.9359,-3.075,34.4381,6.7919,0,0 -KCO3-,NA,KCO3-,aq,MWKL17,NA,2022-02-01,HKF,cal,-193772.9,,18.241,-26.972,8.29,3.4128,0.554,5.5266,-2.8018,2.739,-8.5569,1.3525,-1 -KHCO3,NA,KHCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-206090.8,,49.89,32.249,43.2,7.6623,10.9298,1.4497,-3.2307,24.7193,3.5355,-0.038,0 -CO3-2,NA,CO3-2,aq,MWKL17,NA,2022-02-01,HKF,cal,-126191,,-11.95,-77.115,-6.06,2.8524,-3.9844,6.4142,-2.6143,-7.9872,-18.8139,3.3914,-2 -HCO3-,NA,HCO3-,aq,MWKL17,NA,2022-02-01,HKF,cal,-140261.7,,23.093,-8.329,24.21,2.9936,4.9787,23.5905,-2.9848,12.994,-4.7579,1.2792,-1 -CaSiO3,NA,CaSiO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-362130.5,,-4.909,-42.782,15.7,3.1272,-10.5859,42.3257,-2.3414,61.911,-51.1046,0.0935,0 -MgSiO3,NA,MgSiO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-338990.2,,-24.379,-40.607,12.1,0.8426,-11.069,52.9604,-2.3216,68.7194,-53.9981,-0.0445,0 -Ca+2,NA,Ca+2,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-132127.4,,-13.5,-7.53,-18.06,-0.1947,-7.252,5.2966,-2.4792,9,-2.522,1.2366,2 -Mg+2,NA,Mg+2,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-108987.8,,-33,-5.34,-21.55,-0.8217,-8.599,8.39,-2.39,20.8,-5.892,1.5372,2 -CaHSiO3+,NA,CaHSiO3+,aq,SSH97.5,MWKL17.1,2022-02-01,HKF,cal,-376457.2,,-1.99,32.87,-6.56,1.0647,-5.1787,7.7785,-2.5649,30.8048,3.6619,0.5831,1 -MgHSiO3+,NA,MgHSiO3+,aq,SSH97.5,MWKL17.1,2022-02-01,HKF,cal,-353658.7,,-23.78,37.82,-10.57,0.6289,-6.2428,8.1967,-2.5209,36.7882,4.6702,0.9177,1 Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -1,17 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -KHSO4,NA,KHSO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-246551,NA,52.892,43.67,36.82,6.8032,8.8337,2.278,-3.1442,31.8025,5.8381,0,0 -KSO4-,NA,KSO4-,aq,TAT+24,NA,2024-11-30,HKF,cal,-246636,NA,60.893,-136.37,30.4,6.8612,6.0072,3.3889,-3.0273,-63.7366,-30.8131,1.0996,-1 -H2SO4,NA,H2SO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-178211,NA,28.058,67.18,83.42,13.1225,24.5891,-3.9144,-3.7955,45.8348,10.5047,0,0 -AuHS,NA,AuHS,aq,TAT+24,NA,2024-11-30,HKF,cal,8208,NA,38.583,26.25,45.73,8.0227,11.8073,1.1093,-3.2671,-49.3817,37.2185,0,0 -AuHS(H2S)3,NA,AuHS(H2S)3,aq,TAT+24,NA,2024-11-30,HKF,cal,-13146,NA,174.161,111.89,145.3,21.6476,45.0745,-11.966,-4.6424,-48.4088,78.8834,0,0 -Au(HS)2-,NA,Au(HS)2-,aq,TAT+24,NA,2024-11-30,HKF,cal,3532,NA,71.791,-30.47,67.97,11.5845,20.504,-2.3089,-3.6266,1.6472,-8.8534,1.5338,-1 -Au2S2-2,NA,Au2S2-2,aq,TAT+24,NA,2024-11-30,HKF,cal,28054,NA,78.65,-119.3,83.58,14.2429,26.9949,-4.86,-3.895,-35.3863,-27.3368,3.079,-2 -AuOH,NA,AuOH,aq,TAZ24,NA,2024-11-30,HKF,cal,-25947,NA,33.492,18.03,46.58,8.1395,12.0926,0.9972,-3.2789,1.6058,8.0824,0,0 -AuCl,NA,AuCl,aq,TAZ24,NA,2024-11-30,HKF,cal,-1900,NA,52.2,-71.9,50.8,8.7165,13.5013,0.4435,-3.3371,-35.9711,-17.6806,0,0 -AuCl2-,NA,AuCl2-,aq,TAZ24,NA,2024-11-30,HKF,cal,-36572,NA,43.5,9.5,68.52,11.4087,20.0747,-2.1401,-3.6089,16.8432,-0.463,0.7031,-1 -CuHS,NA,CuHS,aq,TTA+23,NA,2024-11-30,HKF,cal,-2969,NA,59.1,-67.713,44.85,7.9477,11.6243,1.1812,-3.2596,-32.4272,-16.8275,0.1197,0 -Cu(HS)2-,NA,Cu(HS)-2,aq,TTA+23,NA,2024-11-30,HKF,cal,-5665,NA,56.647,7.274,79.573,13.0153,23.9975,-3.6819,-3.7711,18.2332,-1.1267,0.9517,-1 -CuCl,NA,CuCl,aq,TTA+23,NA,2024-11-30,HKF,cal,-23360,NA,61.777,-101.336,26.967,5.4552,5.5383,3.5732,-3.008,-52.5985,-23.9839,0,0 -CuCl2-,NA,CuCl2-,aq,TTA+23,NA,2024-11-30,HKF,cal,-58026,NA,53.111,-19.991,32.604,6.6297,8.406,2.4461,-3.1265,4.1186,-7.1067,1.0612,-1 -Cu+,NA,Cu+,aq,AZ23,NA,2024-11-30,HKF,cal,11945,NA,9.7,13.66,-7.99,0.9243,-5.5244,7.9213,-2.5506,37.8578,-8.925,0.6653,1 -CuO-,NA,CuO-,aq,AZ23,NA,2024-11-30,HKF,cal,-19574,NA,-2.45,-12.69,-13.11,0.3673,-6.8845,8.4559,-2.4944,-55.4517,25.7204,1.0433,-1 Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv 2024-12-24 13:16:34 UTC (rev 856) +++ pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -1,8 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000 -bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000 -"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000 -"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000 -"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000 -"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000 -"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000 Copied: pkg/CHNOSZ/inst/extdata/OBIGT/testing/AS04.csv (from rev 856, pkg/CHNOSZ/inst/extdata/OBIGT/AS04.csv) =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/testing/AS04.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/AS04.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -0,0 +1,4 @@ +name,abbrv,formula,state,ref1,ref2,date,model,E_units,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,2006-08-31,HKF,cal,-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,2019-02-08,HKF,cal,-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,OBIGT.8,2019-02-08,HKF,cal,-243151,-276276,-1.871675,-21,5,2.9735,-0.5158,5.9467,-2.7575,8.1489,-7.3123,1.5511,-1 Copied: pkg/CHNOSZ/inst/extdata/OBIGT/testing/GEMSFIT.csv (from rev 856, pkg/CHNOSZ/inst/extdata/OBIGT/GEMSFIT.csv) =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/testing/GEMSFIT.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/GEMSFIT.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -0,0 +1,43 @@ +name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T +Al+3,NA,Al+3,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-116298.8,,-81.2,-28.523,-45.3,-3.3984,-16.0789,12.0699,-2.1143,14.4295,-8.8523,2.7403,3 +AlOH+2,NA,AlOH+2,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-166238.3,,-43.291,-8.948,-20.6,-0.4532,-8.8878,9.2434,-2.4116,15.4131,-4.8618,1.5897,2 +Al(OH)2+,NA,Al(OH)2+,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-214696.9,,-6.58,9.766,3.85,2.4944,-1.6909,6.4146,-2.7091,16.7439,-1.0465,0.5324,1 +Al(OH)3,NA,Al(OH)3,aq,MWKH16.1,MWKL17.1,2022-02-01,HKF,cal,-264295.7,,1.233,59.407,30.7,6.1977,8.2816,2.495,-3.1214,71.1003,-1.0644,1.0461,0 +Al(OH)4-,NA,Al(OH)4-,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-311925.7,,24.749,23.074,46.3,8.4938,12.9576,0.657,-3.3147,55.7265,-11.4047,1.0403,-1 +NaAl(OH)4,NA,NaAl(OH)4,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-373346.8,,48.8,32.161,53.6,9.1267,14.3411,0.1121,-3.3719,60.7157,-14.0523,0,0 +AlH3SiO4+2,NA,AlH3SiO4+2,aq,TS01.1,MWKL17.1,2022-02-01,HKF,cal,-426008.8,,13.571,-71.862,-13.96,0.16,-7.23,8.61,-2.48,37.07,-49.66,0.88,2 +KAlO2,NA,KAlO2,aq,PH97,MWKL17.1,2022-02-01,HKF,cal,-262938.3,,35.7,4.314,31.14,6.007,6.8858,3.0436,-3.0637,1.394,1.212,-0.05,0 +K+,NA,K+,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-66173.5,,24.149,2.005,9.01,3.559,-1.473,5.435,-2.712,7.4,-1.791,0.1927,1 +KOH,NA,KOH,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-103162.8,,21.654,9.912,14.1,3.7562,1.39,5.2037,-2.8365,13.499,-1.0192,0.1665,0 +KCl,NA,KCl,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-96204.8,,43.537,7.964,29.9,5.8341,7.055,2.9771,-3.0707,-5.7084,7.6228,0.1996,0 +Na+,NA,Na+,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-61219.4,,13.96,9.111,-1.21,1.839,-2.285,3.256,-2.726,18.18,-2.981,0.3306,1 +NaOH,NA,NaOH,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-98366.9,,10.134,27.127,-0.23,1.7792,-3.4372,7.101,-2.6369,22.8222,2.6543,0.1189,0 +NaCl,NA,NaCl,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-91554.5,,26.482,11.358,24,5.0828,4.629,3.9306,-2.9704,13.6339,-0.7212,0.0889,0 +NaHSiO3,NA,NaHSiO3,aq,SSH97.5,MWKL17.1,2022-02-01,HKF,cal,-306641.3,,10,24.606,12.73,3.4928,0.75,5.4483,-2.81,20.2395,1.9785,-0.038,0 +HSiO3-,NA,HSiO3-,aq,MWKH16.1,MWKL17.1,2022-02-01,HKF,cal,-242632.6,,4.708,-9.195,5,3.309,-0.5201,5.9467,-2.7575,15,-4.9202,1.5583,-1 +SiO2,NA,SiO2,aq,SHS89.1,MWKL17.1,2022-02-01,HKF,cal,-199340.6,,18,-76.119,16.1,1.9,1.7,20,-2.7,29.1,-51.2,0.1291,0 +Cl-,NA,Cl-,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-31379.1,,13.561,-29.276,17.34,4.032,4.801,5.563,-2.847,-4.4,-5.714,1.456,-1 +HCl,NA,HCl,aq,MWKH16,MWKL17.1,2022-02-01,HKF,cal,-30411.1,,0.421,35.731,16.4,16.1573,-11.4311,-46.1866,-2.3036,46.4716,-5.2811,0,0 +OH-,NA,OH-,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-37594.9,,-2.56,-32.586,-4.71,1.2527,0.0738,1.8423,-2.7821,4.15,-10.346,1.7246,-1 +CaOH+,NA,CaOH+,aq,MWKL17,NA,2022-02-01,HKF,cal,-171307.4,,8.717,-18.74,10.96,3.9385,-1.1019,6.1831,-2.7334,-9.5888,-2.6253,0.419,1 +CaCl+,NA,CaCl+,aq,MWKL17,NA,2022-02-01,HKF,cal,-164745.9,,-0.71,17.526,5.56,2.7406,-1.0897,6.1783,-2.734,21.588,0.524,0.5626,1 +CaCl2,NA,CaCl2,aq,MWKL17,NA,2022-02-01,HKF,cal,-190246.2,,16.188,30.956,32.65,6.2186,7.4024,2.8406,-3.085,23.9609,3.272,-0.038,0 +CaHCO3+,NA,CaHCO3+,aq,MWKL17,NA,2022-02-01,HKF,cal,-273712.7,,15.839,55.992,13.28,3.7,1.2579,5.252,-2.831,43.112,7.7228,0.3113,1 +CaCO3,NA,CaCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-262687.4,,4.806,-29.603,-15.65,-0.3907,-8.7325,9.1753,-2.4179,-11.5309,-9.0641,-0.038,0 +MgOH+,NA,MgOH+,aq,MWKL17,NA,2022-02-01,HKF,cal,-149737.8,,-16.099,30.856,1.66,2.2937,-2.1809,6.6072,-2.6888,31.5415,3.2394,0.795,1 +MgCl+,NA,MgCl+,aq,MWKL17,NA,2022-02-01,HKF,cal,-141540.2,,-19.001,25.086,1.25,2.2809,-2.3585,6.677,-2.6815,28.5471,2.0579,0.8389,1 +MgCl2,NA,MgCl2,aq,MWKL17,NA,2022-02-01,HKF,cal,-166483.3,,-2.765,40.815,28.25,5.6165,5.9323,3.4184,-3.0242,29.7395,5.2804,-0.038,0 +MgHCO3+,NA,MgHCO3+,aq,MWKL17,NA,2022-02-01,HKF,cal,-250682.8,,-4.567,60.872,9.34,3.3,0.1608,5.6868,-2.7875,47.5204,9.3524,0.6204,1 +MgCO3,NA,MgCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-239242.8,,-24.515,-27.4,-18.27,-0.7355,-9.5745,9.5062,-2.3831,-9.8914,-8.616,0,0 +NaCO3-,NA,NaCO3-,aq,MWKL17,NA,2022-02-01,HKF,cal,-188774.6,,13.406,-19.673,-1.52,2,-2.335,6.6714,-2.6825,7.7693,-7.1095,1.4265,-1 +NaHCO3,NA,NaHCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-201258.4,,37.921,48.241,31.82,6.1192,7.1597,2.9359,-3.075,34.4381,6.7919,0,0 +KCO3-,NA,KCO3-,aq,MWKL17,NA,2022-02-01,HKF,cal,-193772.9,,18.241,-26.972,8.29,3.4128,0.554,5.5266,-2.8018,2.739,-8.5569,1.3525,-1 +KHCO3,NA,KHCO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-206090.8,,49.89,32.249,43.2,7.6623,10.9298,1.4497,-3.2307,24.7193,3.5355,-0.038,0 +CO3-2,NA,CO3-2,aq,MWKL17,NA,2022-02-01,HKF,cal,-126191,,-11.95,-77.115,-6.06,2.8524,-3.9844,6.4142,-2.6143,-7.9872,-18.8139,3.3914,-2 +HCO3-,NA,HCO3-,aq,MWKL17,NA,2022-02-01,HKF,cal,-140261.7,,23.093,-8.329,24.21,2.9936,4.9787,23.5905,-2.9848,12.994,-4.7579,1.2792,-1 +CaSiO3,NA,CaSiO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-362130.5,,-4.909,-42.782,15.7,3.1272,-10.5859,42.3257,-2.3414,61.911,-51.1046,0.0935,0 +MgSiO3,NA,MgSiO3,aq,MWKL17,NA,2022-02-01,HKF,cal,-338990.2,,-24.379,-40.607,12.1,0.8426,-11.069,52.9604,-2.3216,68.7194,-53.9981,-0.0445,0 +Ca+2,NA,Ca+2,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-132127.4,,-13.5,-7.53,-18.06,-0.1947,-7.252,5.2966,-2.4792,9,-2.522,1.2366,2 +Mg+2,NA,Mg+2,aq,SH88.4,MWKL17.1,2022-02-01,HKF,cal,-108987.8,,-33,-5.34,-21.55,-0.8217,-8.599,8.39,-2.39,20.8,-5.892,1.5372,2 +CaHSiO3+,NA,CaHSiO3+,aq,SSH97.5,MWKL17.1,2022-02-01,HKF,cal,-376457.2,,-1.99,32.87,-6.56,1.0647,-5.1787,7.7785,-2.5649,30.8048,3.6619,0.5831,1 +MgHSiO3+,NA,MgHSiO3+,aq,SSH97.5,MWKL17.1,2022-02-01,HKF,cal,-353658.7,,-23.78,37.82,-10.57,0.6289,-6.2428,8.1967,-2.5209,36.7882,4.6702,0.9177,1 Copied: pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM24.csv (from rev 856, pkg/CHNOSZ/inst/extdata/OBIGT/IGEM24.csv) =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM24.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM24.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -0,0 +1,17 @@ +name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T +KHSO4,NA,KHSO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-246551,NA,52.892,43.67,36.82,6.8032,8.8337,2.278,-3.1442,31.8025,5.8381,0,0 +KSO4-,NA,KSO4-,aq,TAT+24,NA,2024-11-30,HKF,cal,-246636,NA,60.893,-136.37,30.4,6.8612,6.0072,3.3889,-3.0273,-63.7366,-30.8131,1.0996,-1 +H2SO4,NA,H2SO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-178211,NA,28.058,67.18,83.42,13.1225,24.5891,-3.9144,-3.7955,45.8348,10.5047,0,0 +AuHS,NA,AuHS,aq,TAT+24,NA,2024-11-30,HKF,cal,8208,NA,38.583,26.25,45.73,8.0227,11.8073,1.1093,-3.2671,-49.3817,37.2185,0,0 +AuHS(H2S)3,NA,AuHS(H2S)3,aq,TAT+24,NA,2024-11-30,HKF,cal,-13146,NA,174.161,111.89,145.3,21.6476,45.0745,-11.966,-4.6424,-48.4088,78.8834,0,0 +Au(HS)2-,NA,Au(HS)2-,aq,TAT+24,NA,2024-11-30,HKF,cal,3532,NA,71.791,-30.47,67.97,11.5845,20.504,-2.3089,-3.6266,1.6472,-8.8534,1.5338,-1 +Au2S2-2,NA,Au2S2-2,aq,TAT+24,NA,2024-11-30,HKF,cal,28054,NA,78.65,-119.3,83.58,14.2429,26.9949,-4.86,-3.895,-35.3863,-27.3368,3.079,-2 +AuOH,NA,AuOH,aq,TAZ24,NA,2024-11-30,HKF,cal,-25947,NA,33.492,18.03,46.58,8.1395,12.0926,0.9972,-3.2789,1.6058,8.0824,0,0 +AuCl,NA,AuCl,aq,TAZ24,NA,2024-11-30,HKF,cal,-1900,NA,52.2,-71.9,50.8,8.7165,13.5013,0.4435,-3.3371,-35.9711,-17.6806,0,0 +AuCl2-,NA,AuCl2-,aq,TAZ24,NA,2024-11-30,HKF,cal,-36572,NA,43.5,9.5,68.52,11.4087,20.0747,-2.1401,-3.6089,16.8432,-0.463,0.7031,-1 +CuHS,NA,CuHS,aq,TTA+23,NA,2024-11-30,HKF,cal,-2969,NA,59.1,-67.713,44.85,7.9477,11.6243,1.1812,-3.2596,-32.4272,-16.8275,0.1197,0 +Cu(HS)2-,NA,Cu(HS)-2,aq,TTA+23,NA,2024-11-30,HKF,cal,-5665,NA,56.647,7.274,79.573,13.0153,23.9975,-3.6819,-3.7711,18.2332,-1.1267,0.9517,-1 +CuCl,NA,CuCl,aq,TTA+23,NA,2024-11-30,HKF,cal,-23360,NA,61.777,-101.336,26.967,5.4552,5.5383,3.5732,-3.008,-52.5985,-23.9839,0,0 +CuCl2-,NA,CuCl2-,aq,TTA+23,NA,2024-11-30,HKF,cal,-58026,NA,53.111,-19.991,32.604,6.6297,8.406,2.4461,-3.1265,4.1186,-7.1067,1.0612,-1 +Cu+,NA,Cu+,aq,AZ23,NA,2024-11-30,HKF,cal,11945,NA,9.7,13.66,-7.99,0.9243,-5.5244,7.9213,-2.5506,37.8578,-8.925,0.6653,1 +CuO-,NA,CuO-,aq,AZ23,NA,2024-11-30,HKF,cal,-19574,NA,-2.45,-12.69,-13.11,0.3673,-6.8845,8.4559,-2.4944,-55.4517,25.7204,1.0433,-1 Copied: pkg/CHNOSZ/inst/extdata/OBIGT/testing/KBJ24.csv (from rev 856, pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv) =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/testing/KBJ24.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/KBJ24.csv 2024-12-25 02:21:18 UTC (rev 857) @@ -0,0 +1,8 @@ +name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T +brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000 +bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000 +"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000 +"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000 +"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000 +"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000 +"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 857 From noreply at r-forge.r-project.org Wed Dec 25 04:04:02 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 25 Dec 2024 04:04:02 +0100 (CET) Subject: [CHNOSZ-commits] r858 - in pkg/CHNOSZ: . R demo inst inst/extdata inst/extdata/OBIGT inst/extdata/OBIGT/testing man vignettes Message-ID: <20241225030402.94E05183905@r-forge.r-project.org> Author: jedick Date: 2024-12-25 04:04:01 +0100 (Wed, 25 Dec 2024) New Revision: 858 Added: pkg/CHNOSZ/demo/references.R pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/Sandia.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/SiO2.csv pkg/CHNOSZ/inst/extdata/refs.csv Removed: pkg/CHNOSZ/demo/sources.R pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/AS04.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM24.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/KBJ24.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/add.OBIGT.R pkg/CHNOSZ/R/examples.R pkg/CHNOSZ/R/thermo.R pkg/CHNOSZ/demo/00Index pkg/CHNOSZ/demo/aluminum.R pkg/CHNOSZ/inst/CHECKLIST pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/man/add.OBIGT.Rd pkg/CHNOSZ/man/examples.Rd pkg/CHNOSZ/vignettes/OBIGT.Rmd pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/custom_data.Rmd pkg/CHNOSZ/vignettes/eos-regress.Rmd Log: Rename some files in OBIGT/testing Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-25 03:04:01 UTC (rev 858) @@ -1,6 +1,6 @@ -Date: 2024-12-24 +Date: 2024-12-25 Package: CHNOSZ -Version: 2.1.0-30 +Version: 2.1.0-31 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/R/add.OBIGT.R =================================================================== --- pkg/CHNOSZ/R/add.OBIGT.R 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/R/add.OBIGT.R 2024-12-25 03:04:01 UTC (rev 858) @@ -120,8 +120,8 @@ if(!file.exists(file)) { # List all files in OBIGT and OBIGT/testing - OBIGT_files <- dir(system.file("extdata/OBIGT/", package = "CHNOSZ"), full.names = TRUE) - testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), full.names = TRUE) + OBIGT_files <- dir(system.file("extdata/OBIGT", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE) + testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE) all_files <- c(OBIGT_files, testing_files) # Match argument to file names without path or .csv suffix all_names <- gsub(".csv", "", basename(all_files)) Modified: pkg/CHNOSZ/R/examples.R =================================================================== --- pkg/CHNOSZ/R/examples.R 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/R/examples.R 2024-12-25 03:04:01 UTC (rev 858) @@ -30,7 +30,7 @@ cat("Time elapsed: ", proc.time() - .ptime, "\n") } -demos <- function(which = c("sources", "protein.equil", "affinity", "NaCl", "density", +demos <- function(which = c("references", "protein.equil", "affinity", "NaCl", "density", "ORP", "ionize", "buffer", "protbuff", "glycinate", "mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "minsol", "Shh", "saturation", "adenine", "DEW", "lambda", "potassium", "TCA", "aluminum", Modified: pkg/CHNOSZ/R/thermo.R =================================================================== --- pkg/CHNOSZ/R/thermo.R 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/R/thermo.R 2024-12-25 03:04:01 UTC (rev 858) @@ -78,7 +78,7 @@ # Create OBIGT data frame OBIGT <- do.call(rbind, datalist) # Also read references file - refs <- read.csv(file.path(OBIGTdir, "refs.csv"), as.is = TRUE) + refs <- read.csv(file.path(OBIGTdir, "../refs.csv"), as.is = TRUE) # Get thermo from CHNOSZ environment thermo <- get("thermo", CHNOSZ) # Set OBIGT and refs Modified: pkg/CHNOSZ/demo/00Index =================================================================== --- pkg/CHNOSZ/demo/00Index 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/demo/00Index 2024-12-25 03:04:01 UTC (rev 858) @@ -1,4 +1,4 @@ -sources Cross-check the reference list with the thermodynamic database +references Cross-check the references in refs.csv with the thermodynamic database protein.equil Chemical activities of two proteins in metastable equilibrium affinity Affinities of metabolic reactions and amino acid synthesis NaCl Equilibrium constant for aqueous NaCl dissociation Modified: pkg/CHNOSZ/demo/aluminum.R =================================================================== --- pkg/CHNOSZ/demo/aluminum.R 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/demo/aluminum.R 2024-12-25 03:04:01 UTC (rev 858) @@ -25,7 +25,7 @@ # boehmite from Hemingway et al., 1991 r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) ## Second calculation: get SiO2(aq) from Apps and Spycher, 2004 -add.OBIGT("AS04") +add.OBIGT("SiO2") r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) reset() ## Third calculation: get Si(OH)4 from Akinfiev and Plyasunov, 2014 @@ -48,7 +48,7 @@ title(main = describe.reaction(r4$reaction), cex.main = 1.1) legend("bottomright", lty = c(0, 0, 1, 2, 3, 0), pch = c(1, 4, NA, NA, NA, NA), lwd = c(1, 1, 1.5, 1, 1, 0), col = c("black", "red", "black", "red", "purple", NA), bty = "n", cex = 0.9, - legend = c("Hemley et al., 1980", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("AS04")', 'add.OBIGT("AD")', "")) + legend = c("Hemley et al., 1980", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("SiO2")', 'add.OBIGT("AD")', "")) legend("bottomright", lty = 4, pch = NA, lwd = 1, col = "blue", legend = 'add.OBIGT("SUPCRT92")', bty = "n", cex = 0.9) legend("topleft", c("Boehmite - Kaolinite", "After Zhu and Lu, 2009 Fig. A1"), bty = "n") # Helgeson et al., 1978 (HDNB78): http://www.worldcat.org/oclc/13594862 @@ -105,7 +105,7 @@ pK <- -sres$out$logK lines(invTK, pK, lwd = 1.5) # Plot line: SiO2 from Apps and Spycher, 2004 -add.OBIGT("AS04") +add.OBIGT("SiO2") sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2"), c(-1, -2, -1, 2, 2), T = T) pK <- -sres$out$logK lines(invTK, pK, col = "red", lty = 2) @@ -133,7 +133,7 @@ legend("topright", c("Kaolinite solubility", "After Tutolo et al., 2014 Fig. 2"), bty = "n") legend("bottomleft", lty = c(0, 0, 0, 1, 2, 3, 4), pch = c(1, NA, 4, NA, NA, NA, NA), lwd = c(1, 1, 1, 1.5, 1, 1, 1), col = c("black", "black", "red", "black", "red", "purple", "blue"), - legend = c("Various sources \u2013", " see Tutolo et al., 2014", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("AS04")', 'add.OBIGT("AD")', 'add.OBIGT("SUPCRT92")'), + legend = c("Various sources \u2013", " see Tutolo et al., 2014", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("SiO2")', 'add.OBIGT("AD")', 'add.OBIGT("SUPCRT92")'), bty = "n", cex = 0.9) ########### Copied: pkg/CHNOSZ/demo/references.R (from rev 857, pkg/CHNOSZ/demo/sources.R) =================================================================== --- pkg/CHNOSZ/demo/references.R (rev 0) +++ pkg/CHNOSZ/demo/references.R 2024-12-25 03:04:01 UTC (rev 858) @@ -0,0 +1,36 @@ +# CHNOSZ/demo/reference.R +## Cross-checking references +library(CHNOSZ) + +# The available reference keys +available_refs <- thermo()$refs$key + +# The used reference keys +# List all files in OBIGT and OBIGT/testing +OBIGT_files <- dir(system.file("extdata/OBIGT", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE) +testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE) +all_files <- c(OBIGT_files, testing_files) +all_data <- lapply(all_files, read.csv) +all_data <- do.call(rbind, all_data) +used_refs <- na.omit(c(all_data$ref1, all_data$ref2)) + +# Print messages for unavailable and unused refs +unavailable_refs <- used_refs[!used_refs %in% available_refs] +unused_refs <- available_refs[!available_refs %in% used_refs] +if(length(unavailable_refs) > 0 | length(unused_refs) > 0) { + + if(length(unavailable_refs) > 0) { + print("References used in database but not available in refs.csv:") + print(unique(unavailable_refs)) + } + + if(length(unused_refs) > 0) { + print("References available in refs.csv but not used in database:") + print(unique(unused_refs)) + } + +} else { + + print("All references accounted for!") + +} Deleted: pkg/CHNOSZ/demo/sources.R =================================================================== --- pkg/CHNOSZ/demo/sources.R 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/demo/sources.R 2024-12-25 03:04:01 UTC (rev 858) @@ -1,40 +0,0 @@ -# CHNOSZ/demo/sources.R -## Cross-checking sources -library(CHNOSZ) - -# The reference sources -ref.source <- thermo()$refs$key -# Sources in the primary thermodynamic database -# Se omit the [S92] in "HDNB78 [S92]" etc. -tdata <- thermo()$OBIGT -ps1 <- gsub("\ .*", "", tdata$ref1) -ps2 <- gsub("\ .*", "", tdata$ref2) -# Sources in the optional datafiles -tdata <- read.csv(system.file("extdata/OBIGT/DEW.csv", package="CHNOSZ"), as.is=TRUE) -os1 <- gsub("\ .*", "", tdata$ref1) -os2 <- gsub("\ .*", "", tdata$ref2) -tdata <- read.csv(system.file("extdata/OBIGT/SLOP98.csv", package="CHNOSZ"), as.is=TRUE) -os3 <- gsub("\ .*", "", tdata$ref1) -os4 <- gsub("\ .*", "", tdata$ref2) -tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE) -os5 <- gsub("\ .*", "", tdata$ref1) -os6 <- gsub("\ .*", "", tdata$ref2) -tdata <- read.csv(system.file("extdata/OBIGT/AS04.csv", package="CHNOSZ"), as.is=TRUE) -os7 <- gsub("\ .*", "", tdata$ref1) -os8 <- gsub("\ .*", "", tdata$ref2) -tdata <- read.csv(system.file("extdata/OBIGT/AD.csv", package="CHNOSZ"), as.is=TRUE) -os9 <- gsub("\ .*", "", tdata$ref1) -os10 <- gsub("\ .*", "", tdata$ref2) -tdata <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package="CHNOSZ"), as.is=TRUE) -os11 <- gsub("\ .*", "", tdata$ref1) -os12 <- gsub("\ .*", "", tdata$ref2) -# All of the thermodynamic data sources - some of them might be NA -OBIGT.source <- unique(c(ps1, ps2, os1, os2, os3, os4, os5, os6, os7, os8, os9, os10, os11, os12)) -OBIGT.source <- OBIGT.source[!is.na(OBIGT.source)] -# These all produce character(0) if the sources are all accounted for -print("missing these sources for thermodynamic properties:") -print(unique(OBIGT.source[!(OBIGT.source %in% ref.source)])) -# Determine if all the reference sources are cited -# This should produce character(0) -print("these sources are present but not cited:") -print(ref.source[!(ref.source %in% OBIGT.source)]) Modified: pkg/CHNOSZ/inst/CHECKLIST =================================================================== --- pkg/CHNOSZ/inst/CHECKLIST 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/inst/CHECKLIST 2024-12-25 03:04:01 UTC (rev 858) @@ -1,6 +1,6 @@ **************************** Release checklist for CHNOSZ - (updated 2024-02-11) + (updated 2024-12-25) **************************** - Run examples() and demos() and inspect their output (especially plots) @@ -19,11 +19,11 @@ - Add BibTeX references to vignettes/OBIGT.bib (used in the OBIGT.Rmd vignette). -- Add references and notes to extdata/OBIGT/refs.csv +- Add references and notes to extdata/refs.csv (also used in the OBIGT.Rmd vignette and thermo.refs()). -- Check output of demo/sources.R to make sure all references - are cited (printed results should be character(0)). +- Check output of demo/references.R to cross-check references in refs.csv with + OBIGT files. - Rebuild extdata/thermo/stoich.csv.xz after all data updates (used in retrieve() to search the databse by element): Modified: pkg/CHNOSZ/inst/NEWS.Rd =================================================================== --- pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 03:04:01 UTC (rev 858) @@ -52,13 +52,13 @@ have been moved to \file{SLOP98.csv}. \item Make new directory \file{OBIGT/testing} to hold optional data files - for testing (currently \file{AS04.csv}, \file{GEMSFIT.csv}, - \file{IGEM24.csv}, and \file{KBJ24.csv}). + for testing (currently \file{SiO2.csv}, \file{GEMSFIT.csv}, + \file{IGEM.csv}, and \file{Sandia.csv}). - \item Add \file{IGEM24.csv}: updated data for Au and Cu complexes and + \item Add \file{IGEM.csv}: updated data for Au and Cu complexes and SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS. - \item Add \file{KBJ24.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from + \item Add \file{Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al. (2024)}. Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-12-25 02:21:18 UTC (rev 857) +++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-12-25 03:04:01 UTC (rev 858) @@ -1,303 +0,0 @@ -key,author,year,citation,note,URL -Kel60,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gases Cp",https://www.worldcat.org/oclc/693388901 -Kel60.2,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","iron Cp",https://www.worldcat.org/oclc/693388901 -Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https://www.worldcat.org/oclc/693388901 -Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,https://www.worldcat.org/oclc/14154245 -PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",https://www.worldcat.org/oclc/14154292 -RH72,"R. A. Robie and B. S. Hemingway",1972,"Am. Mineral. 57, 1768-1781","nesquehonite Cp",https://pubs.geoscienceworld.org/msa/ammin/article-pdf/57/11-12/1768/4256711/am-1972-1768.pdf -BKK77,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","willemite Cp",https://www.worldcat.org/oclc/695258 -HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229",minerals,https://www.worldcat.org/oclc/13594862 -HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",https://www.worldcat.org/oclc/13594862 -RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,https://doi.org/10.3133/b1452 -RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://doi.org/10.3133/b1452 -RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://doi.org/10.3133/b1452 -RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://doi.org/10.3133/b1452 -PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4 -WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf -WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","Mn(OH)2 (amorphous) and MgSO4",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf -BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,https://doi.org/10.1016/0016-7037(83)90066-2 -HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",H2O,https://www.worldcat.org/oclc/858456124 -Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845 -JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365 -PMW87,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","cattierite, linnaeite, and Co-pentlandite",https://www.worldcat.org/oclc/16131757 -RA87,"E. J. Reardon and D. K. Armstrong",1987,"Geochim. Cosmochim. Acta 51, 63-72","celestite GHS",https://doi.org/10.1016/0016-7037(87)90007-X -RS87,"J. R. Ruaya and T. M. Seward",1987,"Geochim. Cosmochim. Acta 51, 121-130",HCl,https://doi.org/10.1016/0016-7037(87)90013-5 -Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522",minerals,https://doi.org/10.1093/petrology/29.2.445 -OH88,"E. H. Oelkers and H. C. Helgeson",1988,"J. Phys. Chem. 92, 1631-1639",KCl,https://doi.org/10.1016/0016-7037(88)90181-0 -SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",https://doi.org/10.1016/0016-7037(88)90181-0 -SH88.1,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","values of GHS",https://doi.org/10.1016/0016-7037(88)90181-0 -SH88.2,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",H2AsO3-,https://doi.org/10.1016/0016-7037(88)90181-0 -SH88.3,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",Ag+,https://doi.org/10.1016/0016-7037(88)90181-0 -SH88.4,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","K+, Na+, Ca+2, Mg+2, Cl-, and OH-",https://doi.org/10.1016/0016-7037(88)90181-0 -SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4 -SHS89.1,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183",SiO2,https://doi.org/10.1016/0016-7037(89)90341-4 -Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344",annite,http://ammin.geoscienceworld.org/content/75/3-4/328 -Ber90.1,"R. G. Berman",1990,"Am. Mineral. 75, 328-344","almandine and ilmenite: modified H and/or S",http://ammin.geoscienceworld.org/content/75/3-4/328 -Eva90,"B. W. Evans",1990,"Lithos 25, 3-23","glaucophane and pumpellyite",https://doi.org/10.1016/0024-4937(90)90003-J -Pol90,"D. A. Polya",1990,"Trans. Inst. Min. Metall. 99, B120-B124","ferberite G, S and Cp (Cp coefficients multiplied by 4.184 to convert to J, as listed in @WS00, but who give a 2nd term that is off by a factor of 10). Cp at 25 °C is from @LW74.", -OH90,"E. H. Oelkers and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 727-738","Debye-H?ckel extended term parameter (b$\gamma$)",https://doi.org/10.1016/0016-7037(90)90368-U -SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O -HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,https://pubs.usgs.gov/publication/70016664 -SHD91,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","G and H revisions for K- and Al-bearing silicates",https://doi.org/10.1016/0016-7037(89)90341-4 -SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4 -SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4 -JUN92,"C. de Capitani",1992,"JUN92.bs database supplied with Theriak/Domino software","data as listed in `JUN92.bs` data file",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html -JOH92,"J. W. Johnson and E. H. Oelkers and H. C. Helgeson",1992,"Comp. Geosci. 18, 899-947",H2O,https://doi.org/10.1016/0098-3004(92)90029-Q -Joh92,"J. W. Johnson",1992,"Personal calculation","steam: "Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."", -SPRONS92.1,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "", -SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "", -Sho92.1,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diketopiperazine GHS",https://doi.org/10.1016/0016-7037(92)90392-V -VGT92,"O. Vidal, B. Goff? and T. Theye",1992,"J. Metamorphic Geol. 10, 603-614",sudoite,https://doi.org/10.1111/j.1525-1314.1992.tb00109.x -ZS92,"C. Zhu and D. A. Sverjensky",1982,"Geochim. Cosmochim. Acta 56, 3435-3467","F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of @ZS92; heat capacity and volume parameters from `berman.dat`.",https://doi.org/10.1016/0016-7037(92)90390-5 -Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",https://doi.org/10.1016/0016-7037(93)90542-5 -Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",https://doi.org/10.1016/0016-7037(93)90542-5 -SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal-acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J -SK93.1,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","Ag-, Au-, Cu(I)- and Al-acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J -SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",https://doi.org/10.1006/icar.1993.1185 -SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,https://doi.org/10.1016/0016-7037(93)90337-V -HDM+94,"A. W. Hakin et al.",1994,"J. Chem. Soc., Faraday Trans. 90, 2027-2035","glutamic acid",https://doi.org/10.1039/FT9949002027 -HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P -PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255 -PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964 -RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bixbyite, cattierite, cerianite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, zinc",https://doi.org/10.3133/b2131 -RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://doi.org/10.3133/b2131 -RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://doi.org/10.3133/b2131 -RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, halloysite, pyrope: GHS and Cp at 25 °C",https://doi.org/10.3133/b2131 -RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",https://doi.org/10.3133/b2131 -RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://doi.org/10.3133/b2131 -RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (melting temperature and G and H not in SUPCRT92)",https://doi.org/10.3133/b2131 -RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","phase stability limit",https://doi.org/10.3133/b2131 -RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","brucite V",https://doi.org/10.3133/b2131 -SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8 -Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496 -DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)4,https://doi.org/10.1016/0016-7037(95)00403-3 -AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F -DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3 -DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3 -DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3 -HP97,"P. C. Ho and D. A. Palmer",1997,"Geochim. Cosmochim. Acta 61, 3027-3040",KOH,https://doi.org/10.1016/S0016-7037(97)00146-4 -MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","MgSO4, NaSO4-, and HCl",https://doi.org/10.1016/S0016-7037(97)00241-X -MS97.1,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",sulfur,https://doi.org/10.1016/S0016-7037(97)00241-X -MS97.2,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00241-X -PH97,"V. A. Pokrovskii and H. C. Helgeson",1997,"Chem. Geol. 137, 221-242",KAl2O,https://doi.org/10.1016/S0009-2541(96)00167-2 -SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","aqueous ions and hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0 -SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","zincite and litharge",https://doi.org/10.1016/S0016-7037(96)00339-0 -SSWS97.2,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Au+ and Cu+",https://doi.org/10.1016/S0016-7037(96)00339-0 -SSWS97.3,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","arsenate and arsenite species",https://doi.org/10.1016/S0016-7037(96)00339-0 -SSWS97.4,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Al+3 and Al-hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0 -SSWS97.5,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Zn+2 and Zn-hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0 -SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",https://doi.org/10.1016/S0016-7037(97)00009-4 -SSH97.1,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au(HS)2- and Ag(HS)2-",https://doi.org/10.1016/S0016-7037(97)00009-4 -SSH97.2,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412",HSiO3-,https://doi.org/10.1016/S0016-7037(97)00009-4 -SSH97.3,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au-, Ag-, Cu- and Zn-chloride complexes",https://doi.org/10.1016/S0016-7037(97)00009-4 -SSH97.4,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Zn-acetate complexes",https://doi.org/10.1016/S0016-7037(97)00009-4 -SSH97.5,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","NaHSiO3, CaHSiO3+, and MgHSiO3+",https://doi.org/10.1016/S0016-7037(97)00009-4 -SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",https://doi.org/10.1016/S0016-7037(97)00240-8 -SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,https://doi.org/10.1016/S0016-7037(97)00240-8 -TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",https://doi.org/10.1016/S1251-8050(97)83981-X -TZA97,"B. R. Tagirov, A. V. Zotov and N. N. Akinfiev",2007,"Geochim. Cosmochim. Acta 61, 4267-4280","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00274-3 -ST97,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylammonium chloride HKF parameters",https://doi.org/10.1023/A:1022977006327 -proton,OBIGT,1997,"Hydrogen-ion convention","""The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature"" [@JOH92]",https://chnosz.net -HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6 -HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6 -RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1 -SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools -SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "Gf and Hf from @SS93a TMM"",http://geopig.asu.edu/?q=tools -SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools -SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",http://geopig.asu.edu/?q=tools -SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",http://geopig.asu.edu/?q=tools -SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",https://doi.org/10.1016/S0016-7037(98)00049-0 -SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",https://doi.org/10.1016/S0016-7037(98)00049-0 -SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh+3,https://doi.org/10.1016/S0016-7037(98)00049-0 -SS98a.3,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","Pd+2 and Pt+2 and their complexes",https://doi.org/10.1016/S0016-7037(98)00049-0 -SUF+98,"H. Senoh et al.",1998,"J. Alloys Compd. 280, 114-124","Mn(OH)2: Cp coefficients from linear fit to values estimated by @SUF+98",https://doi.org/10.1016/S0925-8388(98)00739-7 -HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",https://doi.org/10.1016/S0016-7037(99)00276-8 -MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253","americium species",http://rimg.geoscienceworld.org/content/38/1/221 -PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5 -PSK99.1,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","Al(Mal)+ and Al(Oxal)+",https://doi.org/10.1016/S0016-7037(99)00146-5 -SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",https://doi.org/10.2138/rmg.2000.40.9 -TDDZ00,"B. R. Tagirov et al.",2000,"Chem. Geol. 162, 193-219",FeCl+2,https://doi.org/10.2138/rmg.2000.40.9 -WS00,"S. A. Wood and I. M. Samson",2000,"Econ. Geol. 95, 143-182","scheelite and ferberite; GHS and V of scheelite and V of ferberite are from @RHF78.",https://doi.org/10.2113/gsecongeo.95.1.143 -AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,https://doi.org/10.1016/S0016-7037(01)00707-4 -AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N2O",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x -AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x -AZ01,"N. N. Akinfiev and A. V. Zotov",2001,"Geochem. Int. 39, 990-1006","M+, MCl2-, M(OH)2-, MCl, and MOH (M = Au+, Ag+, or Cu+)",http://pleiades.online/cgi-perl/search.pl?type=abstract&name=geochem&number=10&year=1&page=990 -MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","polymorphs of ice",https://doi.org/10.1016/S0883-2927(00)00025-1 -PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes (organic species)",https://doi.org/10.1016/S0016-7037(01)00678-0 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 858 From noreply at r-forge.r-project.org Wed Dec 25 07:05:31 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 25 Dec 2024 07:05:31 +0100 (CET) Subject: [CHNOSZ-commits] r859 - in pkg/CHNOSZ: . inst inst/extdata inst/extdata/OBIGT/testing inst/extdata/adds vignettes Message-ID: <20241225060531.2A0991805DB@r-forge.r-project.org> Author: jedick Date: 2024-12-25 07:05:30 +0100 (Wed, 25 Dec 2024) New Revision: 859 Added: pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv pkg/CHNOSZ/inst/extdata/refs.csv pkg/CHNOSZ/vignettes/OBIGT.Rmd pkg/CHNOSZ/vignettes/OBIGT.bib Log: OBIGT/testing: add REE from Migdisov et al. (2009) Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-25 03:04:01 UTC (rev 858) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-25 06:05:30 UTC (rev 859) @@ -1,6 +1,6 @@ Date: 2024-12-25 Package: CHNOSZ -Version: 2.1.0-31 +Version: 2.1.0-32 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 2024-12-25 03:04:01 UTC (rev 858) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 06:05:30 UTC (rev 859) @@ -15,7 +15,7 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{?G?}}} -\section{Changes in CHNOSZ version 2.1.0-30 (2024-12-25)}{ +\section{Changes in CHNOSZ version 2.1.0-31 (2024-12-25)}{ \subsection{OBIGT DEFAULT DATA}{ \itemize{ @@ -25,7 +25,12 @@ and related U-bearing minerals from \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}. - \item Move americium complexes from \file{slop98.dat} back to + \item For compatibility with the above change, aqueous uranium species + other than HUO\s{4}\S{-} from + \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} + have been moved to optional data (\file{SLOP98.csv}). + + \item Move americium complexes from \file{SLOP98.csv} back to \file{inorganic_aq.csv} (entropy of the element Am has been available for checking GHS self-consistency since version 1.4.0). @@ -47,46 +52,24 @@ \subsection{OBIGT OPTIONAL DATA}{ \itemize{ - \item Aqueous uranium species other than HUO\s{4}\S{-} from - \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} - have been moved to \file{SLOP98.csv}. - \item Make new directory \file{OBIGT/testing} to hold optional data files - for testing (currently \file{SiO2.csv}, \file{GEMSFIT.csv}, - \file{IGEM.csv}, and \file{Sandia.csv}). + for testing, including \file{SiO2.csv} and \file{GEMSFIT.csv} in addition + to those listed below. - \item Add \file{IGEM.csv}: updated data for Au and Cu complexes and + \item Add \file{testing/IGEM.csv}: Au and Cu complexes and SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS. - \item Add \file{Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from + \item Add \file{testing/Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al. (2024)}. - } - } + \item Add \file{testing/REE.csv}: REE(III) fluoride and chloride complexes from + \href{https://doi.org/10.1016/j.gca.2009.08.023}{Migdisov et al. (2009)} + (previously available in CHNOSZ verisons 0.9-5 to 1.0.8). - \subsection{DOCUMENTATION}{ - - \itemize{ - - \item Add FAQ question: Why are mineral stability boundaries curved on - mosaic diagrams? - - \item Add \file{demo/total_S.R}: total activity of S--pH diagram for - Fe-S-O-C minerals. - - \item Add \file{demo/uranyl.R}: total (carbonate|sulfate)-pH diagrams - for uranyl species, after - \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. - - \item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes, - and add solubility contours for Fe and Au. - } - } - \subsection{OTHER CHANGES}{ \itemize{ @@ -106,12 +89,33 @@ \item For better readability, formulas of species are no longer subscripted by \code{axis.label()} (via \code{expr.species()}). An - example of the new formatting is log \emph{f}O\s{2}). Similar formatting + example of the new formatting is log \emph{f}O\s{2}. Similar formatting for other expressions has been used in the vignettes. } } + \subsection{DOCUMENTATION}{ + + \itemize{ + + \item Add FAQ question: Why are mineral stability boundaries curved on + mosaic diagrams? + + \item Add \file{demo/total_S.R}: total activity of S--pH diagram for + Fe-S-O-C minerals. + + \item Add \file{demo/uranyl.R}: total (carbonate|sulfate)-pH diagrams + for uranyl species, after + \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. + + \item Revise \file{demo/sum_S.R} for log \emph{f}O\s{2} - log \emph{m} ?S + diagram and add solubility contours for Fe and Au. + + } + + } + \subsection{REMOVED FEATURES}{ \itemize{ Added: pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv 2024-12-25 06:05:30 UTC (rev 859) @@ -0,0 +1,43 @@ +name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T +LaF+2,NA,LaF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-236290,NA,-28.9,38.62,-36.67,-2.6763,-14.316,11.377,-2.1872,42.7211,4.8321,1.5259,2 +CeF+2,NA,CeF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-234190,NA,-24.92,25.38,-42.85,-3.5448,-16.4364,12.2104,-2.0995,34.4101,2.1345,1.4656,2 +PrF+2,NA,PrF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-235200,NA,-25.4,21.48,-40.63,-3.2382,-15.6879,11.9162,-2.1305,32.1968,1.3417,1.473,2 +NdF+2,NA,NdF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-233150,NA,-26.48,24.73,-41.72,-3.3812,-16.0371,12.0534,-2.116,34.2449,2.0023,1.4892,2 +SmF+2,NA,SmF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232090,NA,-27.08,-5.4,-40.5,-3.2108,-15.621,11.8899,-2.1332,16.6719,-4.1344,1.4983,2 +EuF+2,NA,EuF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-210450,NA,-28.85,-11.08,-39.73,-3.0953,-15.339,11.7791,-2.1449,13.5854,-5.2922,1.5251,2 +GdF+2,NA,GdF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-231710,NA,-25.91,-11.83,-38.73,-2.9753,-15.046,11.6639,-2.157,12.7413,-5.4446,1.4806,2 +TbF+2,NA,TbF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232790,NA,-30.21,-21.45,-38.53,-2.9233,-14.919,11.614,-2.1622,7.7005,-7.4034,1.5458,2 +DyF+2,NA,DyF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232030,NA,-29.52,-27.14,-39.08,-3.0025,-15.1125,11.69,-2.1543,4.2664,-8.5636,1.5353,2 +HoF+2,NA,HoF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-234580,NA,-28.53,-22.87,-40.09,-3.1464,-15.4638,11.8281,-2.1397,6.6315,-7.6938,1.5203,2 +ErF+2,NA,ErF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-233060,NA,-32.54,-26.35,-41.66,-3.3383,-15.9323,12.0123,-2.1204,5.1506,-8.4013,1.581,2 +TmF+2,NA,TmF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-233080,NA,-31.84,-30.14,-41.66,-3.3423,-15.942,12.0161,-2.12,2.8337,-9.1731,1.5705,2 +YbF+2,NA,YbF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-226300,NA,-30.41,-36.41,-43.34,-3.5804,-16.5233,12.2446,-2.0959,-1.0405,-10.4509,1.5488,2 +LuF+2,NA,LuF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232530,NA,-36.16,-32.88,-43.9,-3.6241,-16.6301,12.2865,-2.0915,1.8202,-9.7329,1.6359,2 +LaCl+2,NA,LaCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-196390,NA,-47.06,94.49,-17.46,0.0563,-7.6438,8.7545,-2.463,77.9764,16.2138,1.8009,2 +CeCl+2,NA,CeCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-193910,NA,-46.15,111.04,-23.65,-0.796,-9.7248,9.5724,-2.377,87.5448,19.5834,1.7871,2 +PrCl+2,NA,PrCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-194950,NA,-54.19,148.14,-21.42,-0.4448,-8.8673,9.2354,-2.4124,110.4007,27.1413,1.9089,2 +NdCl+2,NA,NdCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-192950,NA,-51.92,122.49,-22.51,-0.607,-9.2633,9.391,-2.3961,95.0531,21.916,1.8745,2 +SmCl+2,NA,SmCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191390,NA,-44.42,76.88,-21.3,-0.4843,-8.9637,9.2732,-2.4084,67.2886,12.6257,1.761,2 +EuCl+2,NA,EuCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-169620,NA,-42.31,55.98,-20.52,-0.3896,-8.7326,9.1824,-2.418,54.746,8.3675,1.729,2 +GdCl+2,NA,GdCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-190950,NA,-34.69,31.25,-19.52,-0.2964,-8.505,9.0929,-2.4274,39.2045,3.3318,1.6136,2 +TbCl+2,NA,TbCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191790,NA,-38.16,26.39,-19.33,-0.2506,-8.3931,9.0489,-2.432,36.8323,2.3408,1.6661,2 +DyCl+2,NA,DyCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191030,NA,-40.82,34.88,-19.88,-0.3106,-8.5396,9.1065,-2.426,42.1744,4.0696,1.7064,2 +HoCl+2,NA,HoCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-193750,NA,-41.14,43.23,-20.88,-0.4456,-8.8692,9.2361,-2.4123,47.1123,5.7705,1.7113,2 +ErCl+2,NA,ErCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-192230,NA,-41.84,29.13,-22.45,-0.6564,-9.384,9.4384,-2.3911,38.9461,2.8986,1.7219,2 +TmCl+2,NA,TmCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-192250,NA,-42.84,14.93,-22.46,-0.652,-9.3733,9.4342,-2.3915,30.7668,0.0075,1.7371,2 +YbCl+2,NA,YbCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-185320,NA,-38.84,-7.59,-24.13,-0.9035,-9.9872,9.6755,-2.3661,17.0158,-4.5799,1.6765,2 +LuCl+2,NA,LuCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191690,NA,-42.08,-32.19,-24.69,-0.9615,-10.129,9.7313,-2.3603,3.0453,-9.5913,1.7255,2 +LaCl2+,NA,LaCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-227450,NA,-2.02,-8.19,6.83,2.9168,-0.6596,6.0093,-2.7517,6.6097,-4.7029,0.5747,1 +CeCl2+,NA,CeCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-224990,NA,9.64,-54.21,-0.06,1.9073,-3.1244,6.9781,-2.6498,-21.9709,-14.0772,0.3982,1 +PrCl2+,NA,PrCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-225970,NA,1.82,-22.59,2.42,2.2914,-2.1866,6.6095,-2.6886,-2.3592,-7.6362,0.5166,1 +NdCl2+,NA,NdCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-224000,NA,-1.36,-34.48,1.21,2.144,-2.5465,6.7509,-2.6737,-8.8885,-10.0582,0.5647,1 +SmCl2+,NA,SmCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222430,NA,-3.21,-34.9,2.56,2.3393,-2.0696,6.5635,-2.6934,-8.8795,-10.1437,0.5927,1 +EuCl2+,NA,EuCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-200660,NA,-10.02,-5.48,3.42,2.4959,-1.6871,6.4131,-2.7093,9.3035,-4.1509,0.6958,1 +GdCl2+,NA,GdCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-221990,NA,-7.61,-2.41,4.53,2.634,-1.3499,6.2806,-2.7232,10.7695,-3.5255,0.6593,1 +TbCl2+,NA,TbCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222840,NA,-12.4,-2.81,4.75,2.6916,-1.2094,6.2254,-2.729,11.1974,-3.607,0.7319,1 +DyCl2+,NA,DyCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222050,NA,-17.33,16.06,4.14,2.6363,-1.3444,6.2785,-2.7234,22.9371,0.2368,0.8065,1 +HoCl2+,NA,HoCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-224770,NA,-15.26,9.04,3.02,2.4712,-1.7476,6.4369,-2.7068,18.5365,-1.1932,0.7751,1 +ErCl2+,NA,ErCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-223270,NA,-20.65,4.65,1.27,2.2626,-2.2569,6.6371,-2.6857,16.7094,-2.0874,0.8569,1 +TmCl2+,NA,TmCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-223290,NA,-20.2,4.66,1.26,2.2586,-2.2666,6.6409,-2.6853,16.6521,-2.0854,0.85,1 +YbCl2+,NA,YbCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-216360,NA,-19.22,-4.55,-0.6,1.9985,-2.9017,6.8906,-2.659,11.1191,-3.9614,0.8351,1 +LuCl2+,NA,LuCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222750,NA,-30.31,11.26,-1.23,1.9757,-2.9572,6.9124,-2.6567,21.9175,-0.7409,1.0031,1 Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-25 03:04:01 UTC (rev 858) +++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-25 06:05:30 UTC (rev 859) @@ -399,4 +399,4 @@ "SUPCRT92","greenalite","cr","cal",,,142507 "SUPCRT92","grunerite","cr","cal",9.72,, "SUPCRT92","halloysite","cr","cal",-1.6,, -"KBJ24","2-1-4 phase","cr","J",-4.39,, +"Sandia","2-1-4 phase","cr","J",-4.39,, Modified: pkg/CHNOSZ/inst/extdata/refs.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/refs.csv 2024-12-25 03:04:01 UTC (rev 858) +++ pkg/CHNOSZ/inst/extdata/refs.csv 2024-12-25 06:05:30 UTC (rev 859) @@ -174,6 +174,7 @@ GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805-6815","kieserite, starkeyite, hexahydrite, and epsomite",https://doi.org/10.1016/j.gca.2009.08.005 HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695","kerogens (C128, C292, C406, C415, C515) and pyrobitumen (C54H42)",https://doi.org/10.1016/j.gca.2008.03.004 LRB09,"K. H. Lemke, R. J. Rosenbauer and D. K. Bird",2009,"Astrobiology 9, 141-146","diglycine and diketopiperazine",https://doi.org/10.1089/ast.2008.0166 +MWW09,"A. A. Migdisov, A. E. Williams-Jones and T. Wagner",2009,"Geochim. Cosmochim. Acta 73, 7087-7109","REE F- and Cl- complexes",https://doi.org/10.1016/j.gca.2009.08.023 AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010 AML10.1,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","Np- and Am-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010 AZ10,"N. N. Akinfiev and A. V. Zotov",2010,"Geochem. Int. 48, 714-720","MHS and M(HS)2- (M = Au+, Ag+, or Cu+)",https://doi.org/10.1134/S0016702910070074 Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-25 03:04:01 UTC (rev 858) +++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-25 06:05:30 UTC (rev 859) @@ -405,6 +405,10 @@ This file also has H4SiO4 from an earlier publication [@Ste01] that is roughly consistent with the SiO2 here. See `demo(aluminum)` and the vignette [*Regressing thermodynamic data*](eos-regress.html) for examples. +

REE

+ +Rare earth element (REE(III)) fluoride and chloride complexes [@MWW09]. +

GEMSFIT

Internally consistent dataset for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl obtained with the [GEMSFIT](https://doi.org/10.1016/j.apgeochem.2014.10.013) package [@MWKH16;@MWKL17]. Modified: pkg/CHNOSZ/vignettes/OBIGT.bib =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-25 03:04:01 UTC (rev 858) +++ pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-25 06:05:30 UTC (rev 859) @@ -456,6 +456,17 @@ doi = {10.1016/S0883-2927(00)00025-1}, } + at Article{MWW09, + author = {Migdisov, Art. A. and Williams-Jones, A. E. and Wagner, T.}, + journal = {Geochimica et Cosmochimica Acta}, + title = {An experimental study of the solubility and speciation of the {R}are {E}arth {E}lements ({III}) in fluoride- and chloride-bearing aqueous solutions at temperatures up to 300 ?{C}}, + year = {2009}, + number = {23}, + pages = {7087--7109}, + volume = {73}, + doi = {10.1016/j.gca.2009.08.023}, +} + @Article{OH88, author = {Oelkers, Eric H. and Helgeson, Harold C.}, journal = {Journal of Physical Chemistry}, From noreply at r-forge.r-project.org Wed Dec 25 09:02:37 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 25 Dec 2024 09:02:37 +0100 (CET) Subject: [CHNOSZ-commits] r860 - in pkg/CHNOSZ: . inst inst/extdata inst/extdata/OBIGT/testing inst/extdata/adds vignettes Message-ID: <20241225080237.B3EA91836ED@r-forge.r-project.org> Author: jedick Date: 2024-12-25 09:02:36 +0100 (Wed, 25 Dec 2024) New Revision: 860 Added: pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv pkg/CHNOSZ/inst/extdata/refs.csv pkg/CHNOSZ/vignettes/OBIGT.Rmd pkg/CHNOSZ/vignettes/OBIGT.bib Log: OBIGT/testing: add germanium, indium, gallium, and cadmium species from Huston and Bastrakov (2024) Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-25 06:05:30 UTC (rev 859) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-25 08:02:36 UTC (rev 860) @@ -1,6 +1,6 @@ Date: 2024-12-25 Package: CHNOSZ -Version: 2.1.0-32 +Version: 2.1.0-33 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 2024-12-25 06:05:30 UTC (rev 859) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 08:02:36 UTC (rev 860) @@ -15,7 +15,7 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{?G?}}} -\section{Changes in CHNOSZ version 2.1.0-31 (2024-12-25)}{ +\section{Changes in CHNOSZ version 2.1.0-33 (2024-12-25)}{ \subsection{OBIGT DEFAULT DATA}{ \itemize{ @@ -67,6 +67,10 @@ \href{https://doi.org/10.1016/j.gca.2009.08.023}{Migdisov et al. (2009)} (previously available in CHNOSZ verisons 0.9-5 to 1.0.8). + \item Add \file{testing/GA.csv}: Germanium, indium, gallium, and cadmium + species from \href{https://doi.org/10.1080/08120099.2024.2423772}{Huston + and Bastrakov (2024)}. + } } Added: pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.csv 2024-12-25 08:02:36 UTC (rev 860) @@ -0,0 +1,46 @@ +name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T +CdCl+,NA,CdCl+,aq,BZA10,NA,07.Jul.2023,HKF,cal,-52629,NA,7.06,11.12,2.2,2.2303,-2.3357,6.6681,-2.6824,16.6723,-0.7693,0.4372,1 +CdCl2,NA,CdCl2,aq,BZA10,NA,07.Jul.2023,HKF,cal,-84883,NA,25.72,116.01,42.21,7.5221,10.5852,1.5895,-3.2166,73.7023,20.5956,-0.0495,0 +CdCl3-,NA,CdCl3-,aq,BZA10,NA,07.Jul.2023,HKF,cal,-115399,NA,45.15,97.78,63.47,10.8045,18.5994,-1.5605,-3.5479,72.0244,16.8832,0.9378,-1 +CdCl4-2,NA,CdCl4-2,aq,BZA10,NA,07.Jul.2023,HKF,cal,-145583,NA,50.61,42.52,81.35,13.8329,25.9938,-4.4669,-3.8536,53.6766,5.6267,2.4766,-2 +cadmium,Cd,Cd,cr,RH95.9,NA,07.Jul.2023,CGL,J,0,0,51.8,25.98,13.005,0,-0.038115,-134020,300.44,-1.43E-05,0,0,594.18 +monteponite,Mtp,CdO,cr,Bla17,NA,07.Jul.2023,CGL,J,-228661,-258350,54.8,43.65,15.59,47.26,0.00636,-490000,0,0,0,0,1273 +"Cd(OH)2 (cr)","Cd(OH)2 (cr)",Cd(OH)2,cr,Bla17,NA,07.Jul.2023,CGL,J,-472900,-559850,96,80,29.67,104.67,0.00279,-2267000,0,0,0,0,1273 +greenockite,Gnk,CdS,cr,RH95.9,NA,07.Jul.2023,CGL,J,-146100,-149600,72.2,47.3,29.93,35.38,0.01503,-533300,235.7,-2.4E-06,0,0,1100 +"CdSO4 (cr)","CdSO4 (cr)",CdSO4,cr,Bla17,NA,07.Jul.2023,CGL,J,-822631,-933280,123.04,100.4,44.44,77.32,0.0774,0,0,0,0,0,1273 +otavite,Ota,CdCO3,cr,Bla17,NA,07.Jul.2023,CGL,J,-674698,-75263,103.88,89.11,34.3,57.77,0.11693,-313000,0,0,0,0,1273 +GaOH+2,GaOH+2,GaOH+2,aq,Bla17,NA,07.Jul.2023,HKF,J,-383045,-368550,126.692,170.42,-5.707,0.5188,-31.2921,36.3548,-10.3303,62.4713,11.2717,-10.3303,2 +Ga(OH)2+,Ga(OH)2+,Ga(OH)2+,aq,Bla17,NA,07.Jul.2023,HKF,J,-594881,-672710,50.292,77.94,9.63,12.8156,-1.2636,24.5559,-11.5729,69.4628,3.2217,-0.2343,1 +Ga(OH)3,Ga(OH)3,Ga(OH)3,aq,Bla17,NA,07.Jul.2023,HKF,J,-805462,-928286,132.633,112.46,30.964,25.1124,28.7608,12.7528,-12.8156,91.7091,10.2131,0,0 +Ga(OH)4-,Ga(OH)4-,Ga(OH)4-,aq,Bla17,NA,07.Jul.2023,HKF,J,-1021440,-1212749,136.189,114.19,49.552,34.4996,67.3536,-2.4204,-14.4118,158.148,-4.3221,4.2731,-1 +GaSO4+,GaSO4+,GaSO4+,aq,HB24,NA,07.Jul.2023,HKF,cal,-219750,-262279,-42.5,-47.98,-3.9,1.6345,-3.7905,7.2399,-2.6223,-12.8072,-10.9423,1.1948,1 +Ga(SO4)2-,Ga(SO4)2-,Ga(SO4)2-,aq,HB24,NA,07.Jul.2023,HKF,cal,-400818,-473276,-6,-69.45,32.69,1.9788,-3.3569,7.0695,-2.6402,-17.1818,-27.5761,1.7204,-1 +gallium,Ga,Ga,cr,Pan82,NA,07.Jul.2023,CGL,cal,0,0,9.758,6.25,11.803,6.496,0.0002,0,0,0,0,0,302.9 +"Ga2O3 (cr)","Ga2O3 (cr)",Ga2O3,cr,Pan82,NA,07.Jul.2023,CGL,cal,-238620,-260300,20.31,22.02,31.87,27.135,0.003144,-538000,0,0,0,0,2000 +"GaOOH (cr)","GaOOH (cr)",GaOOH,cr,Bla17,NA,07.Jul.2023,CGL,J,-627893,-705329,51.61,86.24,19.7,54.39,0.06418,1130000,0,0,0,0,1273 +"GaS (cr)","GaS (cr)",GaS,cr,PMW87.1,NA,07.Jul.2023,CGL,cal,-48927,-50000,13.82,11.02,26.37,10.705,0.004912,-102100,0,0,0,0,1000 +"Ga2S3 (cr)","Ga2S3 (cr)",Ga2S3,cr,BKK77.1,NA,07.Jul.2023,CGL,cal,NA,-122800,33.4,24.999,62.505,21.63,0.0113,0,0,0,0,0,1363 +Ge(OH)4,Ge(OH)4,Ge(OH)4,aq,PS98,NA,28.Nov.2019,HKF,cal,-231200,-267000,47.83,50,54.9,9.29,14.9,-0.11,-3.4,57.1,-3.5,0,0 +GeO(OH)3-,GeO(OH)3-,GeO(OH)3-,aq,PS98,NA,28.Nov.2019,HKF,cal,-218500,-260500,27.14,18,27.14,5.96,6.77,3.09,-3.06,27.66,0.63,1.2,-1 +germanium,Ge,Ge,cr,RH95.9,NA,28.Nov.2019,CGL,J,0,0,31.09,5.59,13.63,24.033,0.003049,-157140,0.84921,-2.5E-08,0,0,1211.4 +"GeO2 (hex)","GeO2 (hex)",GeO2,cr,PS98,NA,28.Nov.2019,CGL,cal,-119700,-132600,13.21,12.45,24.44,14.623,0.003296,-280500,0,0,0,0,1273 +argutite,"GeO2 (tetr)",GeO2,cr,PS98,NA,28.Nov.2019,CGL,cal,-124600,-138700,9.49,11.99,17.42,16.457,0.002178,-454900,0,0,0,0,1273 +"GeS (cr)","GeS (cr)",GeS,cr,OC95,NA,28.Nov.2019,CGL,J,-62276,-61195,66.93,47.77,25.53,45.6,0.0146,-197000,0,0,0,0,930 +"GeS2 (cr)","GeS2 (cr)",GeS2,cr,NRH74,NA,28.Nov.2019,CGL,cal,-44800,-45300,20.9,15.7,22.27,15.665,0.002624,-66401,0,0,0,0,1273 +"GeS2 (alpha)","GeS2 (alpha)",GeS2,cr,MMO+11,NA,28.Nov.2019,CGL,J,NA,-124683,87.935,66.191,22.27,-66.63,0.1597,-7672000,0,-5.18E-05,52240,-1,1116 +InCl+2,InCl+2,InCl+2,aq,BS23,NA,07.Jul.2023,HKF,cal,-58530.66,-65513.139,-38.803,44.059,-12.821,-2.446,6.363,-2.992,-3.042,47.137,5.94,1.644,2 +InCl2+,InCl2+,InCl2+,aq,BS23,NA,07.Jul.2023,HKF,cal,-92119.729,-107898.655,-26.056,84.938,12.449,-2.094,5.446,36.329,-3.004,64.639,14.267,0.944,1 +InCl3,InCl3,InCl3,aq,BS23,NA,07.Jul.2023,HKF,cal,-124358.201,-152376.136,-24.855,107.036,40.603,-1.604,4.172,79.3,-2.951,68.62,18.769,-0.03,0 +InF+2,InF+2,InF+2,aq,BS23,NA,07.Jul.2023,HKF,cal,-97424.777,-99126.775,-23.527,48.161,-31.931,-2.328,6.056,-36.052,-3.029,47.381,6.776,1.41,2 +InF2+,InF2+,InF2+,aq,BS23,NA,07.Jul.2023,HKF,cal,-169539.617,-181812.026,-19.166,94.733,-27.953,-2.044,5.317,-31.841,-2.999,69.469,16.262,0.845,1 +InF3,InF3,InF3,aq,BS23,NA,07.Jul.2023,HKF,cal,-240426.641,-268312.027,-31.717,124.115,-23.522,-1.604,4.172,-28.216,-2.951,78.629,22.247,-0.03,0 +InF4-,InF4-,InF4-,aq,BS23,NA,07.Jul.2023,HKF,cal,-308448.762,-358424.759,-65.994,136.307,-18.585,-2.948,7.667,-8.325,-3.096,110.376,24.731,2.64,-1 +InSO4+,InSO4+,InSO4+,aq,HB24,NA,07.Jul.2023,HKF,cal,-205423,-236952,-26.5,-38.05,-1.65,1.8605,-3.2387,7.023,-2.6451,-10.7845,-7.3551,0.9525,1 +In(SO4)2-,In(SO4)2-,In(SO4)2-,aq,HB24,NA,07.Jul.2023,HKF,cal,-386081,-447540,10,-60.49,32.19,2.2048,-2.8051,6.8526,-2.663,-15.3567,-24.9589,1.4781,-1 +InHS+2,InHS+2,InHS+2,aq,BS23,NA,07.Jul.2023,HKF,cal,-34864.521,-41566.732,-41.307,57.552,-9.961,-2.464,6.408,1.951,-3.044,55.357,8.689,1.678,2 +In(HS)2+,In(HS)2+,In(HS)2+,aq,BS23,NA,07.Jul.2023,HKF,cal,-41008.506,-55299.1,-27.954,117.159,18.495,-2.107,5.481,46.584,-3.006,83.771,20.831,0.971,1 +indium,In,In,cr,Pan82,NA,07.Jul.2023,CGL,cal,0,0,13.82,6.389,15.76,2.62,0.009254,82700,0,0,0,0,429.78 +"In2O3 (cr)",In2O3,In2O3,cr,Pan82,NA,07.Jul.2023,CGL,cal,-198537,-221270,24.9,24,38.67,29.323,0.001936,-524500,0,0,0,0,1327 +"InS (cr)",InS,InS,cr,PMW87.1,NA,07.Jul.2023,CGL,cal,-30652,-32000,16.96,11.5,28.36,11.613,0.003112,-92500,0,0,0,0,965 +"In2S3 (cr)",In2S3,In2S3,cr,PMW87.1,NA,07.Jul.2023,CGL,cal,-81564,-85000,39.1,28.2,66.5,30.434,0.001416,-235600,0,0,0,0,660 +"In2(SO4)3 (cr)",In2(SO4)3,In2(SO4)3,cr,BKK77.1,NA,07.Jul.2023,CGL,cal,NA,-651400,72.2,65.739,150.53,47.85,0.06,0,0,0,0,0,943 Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-25 06:05:30 UTC (rev 859) +++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-25 08:02:36 UTC (rev 860) @@ -399,4 +399,22 @@ "SUPCRT92","greenalite","cr","cal",,,142507 "SUPCRT92","grunerite","cr","cal",9.72,, "SUPCRT92","halloysite","cr","cal",-1.6,, +"GA","cadmium","cr","J",-22.72,, +"GA","otavite","cr","J",,,677368 +"GA","GaOH+2","aq","J",9.07,, +"GA","Ga(OH)4-","aq","J",-3.75,, +"GA","GaSO4+","aq","cal",2.05,, +"GA","Ga(SO4)2-","aq","cal",-19.44,-36.42, +"GA","germanium","cr","J",17.63,, +"GA","InCl+2","aq","cal",,,7343 +"GA","InCl2+","aq","cal",,,7350 +"GA","InCl3","aq","cal",,,7358 +"GA","InF+2","aq","cal",,,7346 +"GA","InF2+","aq","cal",,,7357 +"GA","InF3","aq","cal",,,7367 +"GA","InF4-","aq","cal",,,7378 +"GA","InSO4+","aq","cal",3.64,,7358 +"GA","In(SO4)2-","aq","cal",-19.05,-33.6,7380 +"GA","InHS+2","aq","cal",,,7362 +"GA","In(HS)2+","aq","cal",,,7389 "Sandia","2-1-4 phase","cr","J",-4.39,, Modified: pkg/CHNOSZ/inst/extdata/refs.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/refs.csv 2024-12-25 06:05:30 UTC (rev 859) +++ pkg/CHNOSZ/inst/extdata/refs.csv 2024-12-25 08:02:36 UTC (rev 860) @@ -4,8 +4,10 @@ Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https://www.worldcat.org/oclc/693388901 Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,https://www.worldcat.org/oclc/14154245 PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",https://www.worldcat.org/oclc/14154292 +NRH74,"Naumov, G. B., Ryzhenko, B. N., & Khodakovsky, I. L.",1974,"Handbook of Thermodynamic Data (U.S. Geol. Surv.)","GeS2",https://www.worldcat.org/oclc/8139446 RH72,"R. A. Robie and B. S. Hemingway",1972,"Am. Mineral. 57, 1768-1781","nesquehonite Cp",https://pubs.geoscienceworld.org/msa/ammin/article-pdf/57/11-12/1768/4256711/am-1972-1768.pdf BKK77,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","willemite Cp",https://www.worldcat.org/oclc/695258 +BKK77.1,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","Ga2S3 and In2(SO4)3",https://www.worldcat.org/oclc/695258 HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229",minerals,https://www.worldcat.org/oclc/13594862 HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",https://www.worldcat.org/oclc/13594862 RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,https://doi.org/10.3133/b1452 @@ -12,6 +14,7 @@ RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://doi.org/10.3133/b1452 RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://doi.org/10.3133/b1452 RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://doi.org/10.3133/b1452 +Pan82,"L. B. Pankratz",1987,"Thermodynamic Properties of Elements and Oxides (U.S. Bureau of Mines Bull. 672)","gallium, Ga2O3, indium, In2O3",https://catalog.hathitrust.org/Record/102119912 PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4 WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","Mn(OH)2 (amorphous) and MgSO4",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf @@ -20,6 +23,7 @@ Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845 JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365 PMW87,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","cattierite, linnaeite, and Co-pentlandite",https://www.worldcat.org/oclc/16131757 +PMW87.1,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","GaS, InS, and In2S3",https://www.worldcat.org/oclc/16131757 RA87,"E. J. Reardon and D. K. Armstrong",1987,"Geochim. Cosmochim. Acta 51, 63-72","celestite GHS",https://doi.org/10.1016/0016-7037(87)90007-X RS87,"J. R. Ruaya and T. M. Seward",1987,"Geochim. Cosmochim. Acta 51, 121-130",HCl,https://doi.org/10.1016/0016-7037(87)90013-5 Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522",minerals,https://doi.org/10.1093/petrology/29.2.445 @@ -56,6 +60,7 @@ SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",https://doi.org/10.1006/icar.1993.1185 SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,https://doi.org/10.1016/0016-7037(93)90337-V HDM+94,"A. W. Hakin et al.",1994,"J. Chem. Soc., Faraday Trans. 90, 2027-2035","glutamic acid",https://doi.org/10.1039/FT9949002027 +OC95,"P. A. G. O'Hare and L. A. Curtiss",1995,"J. Chem. Thermodynamics 27, 643-662","GeS",https://doi.org/10.1006/jcht.1995.0066 HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255 PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964 @@ -68,6 +73,7 @@ RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (melting temperature and G and H not in SUPCRT92)",https://doi.org/10.3133/b2131 RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","phase stability limit",https://doi.org/10.3133/b2131 RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","brucite V",https://doi.org/10.3133/b2131 +RH95.9,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","germanium, cadmium, and greenockite (CdS)",https://doi.org/10.3133/b2131 SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8 Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496 DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)4,https://doi.org/10.1016/0016-7037(95)00403-3 @@ -100,12 +106,13 @@ proton,OBIGT,1997,"Hydrogen-ion convention","""The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature"" [@JOH92]",https://chnosz.net HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6 HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6 +PS98,"G. S. Pokrovski and J. Schott",1998,"Geochim. Cosmochim. Acta 62, 1631-1642","GeO2 (hex) and (tetr) (augite) and Ge hydroxide and oxyhydroxide complexes",https://doi.org/10.1016/S0016-7037(98)00081-7 RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1 -SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools -SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "Gf and Hf from @SS93a TMM"",http://geopig.asu.edu/?q=tools -SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools -SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",http://geopig.asu.edu/?q=tools -SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",http://geopig.asu.edu/?q=tools +SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",https://doi.org/10.5281/zenodo.2630820 +SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "Gf and Hf from @SS93a TMM"",https://doi.org/10.5281/zenodo.2630820 +SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",https://doi.org/10.5281/zenodo.2630820 +SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",https://doi.org/10.5281/zenodo.2630820 +SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",https://doi.org/10.5281/zenodo.2630820 SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",https://doi.org/10.1016/S0016-7037(98)00049-0 SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",https://doi.org/10.1016/S0016-7037(98)00049-0 SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh+3,https://doi.org/10.1016/S0016-7037(98)00049-0 @@ -144,6 +151,7 @@ SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",https://doi.org/10.1016/j.gca.2003.06.001 VPV05,"O. Vidal, T. Parra and P. Viellard",2005,"Am. Mineral. 90, 347-358",Fe-amesite,https://doi.org/10.2138/am.2005.1554 ZZX+05,"Y. Zhu et al.",2005,"J. Hazard. Mater. A120, 37-44","barium arsenate and barium hydrogen arsenate: G",https://doi.org/10.1016/j.jhazmat.2004.12.025 +electron,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",https://chnosz.net ARHB06,"C. Akilan et al.",2006,"ChemPhysChem 7, 2319-2330",MgSO4,https://doi.org/10.1002/cphc.200600342 AVZP06,"N. N. Akinfiev et al.",2006,"Geochem. Int. 44, 867-878",AgCl3-2,https://doi.org/10.1134/S0016702906090035 BL06,"A. V. Bandura and S. N. Lvov",2006,"J. Phys. Chem. Ref. Data 35, 15-30",OH-,https://doi.org/10.1063/1.1928231 @@ -162,11 +170,10 @@ LMR06,"D. Langmuir et al.",2006,"Geochim. Cosmochim. Acta 70, 2942-2956","scorodite and amorphous ferric arsenate: G",https://doi.org/10.1016/j.gca.2006.03.006 MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175 SGX+06,"A. V. Sharygin et al.",2006,"Geochim. Cosmochim. Acta 70, 5169-5182",KSO4-,https://doi.org/10.1016/j.gca.2006.07.034 -electron,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",https://chnosz.net Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain", MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes; linked to properties of arsenate and arsenite from @SSWS97",https://doi.org/10.1007/s00254-006-0578-5 -SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)+2",http://geopig.asu.edu/?q=tools -SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high-temperature HKF parameters from @AP01",http://geopig.asu.edu/?q=tools +SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)+2",https://doi.org/10.5281/zenodo.2630820 +SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high-temperature HKF parameters from @AP01",https://doi.org/10.5281/zenodo.2630820 ZW07,"S. P. Ziemer and E. M. Woolley",2007,"J. Chem. Thermodynamics 39, 645-666",glutamate,https://doi.org/10.1016/j.jct.2006.08.008 Ric08,"L. Richard",2008,"personal communication",alkenes, PPB+08,"E. Perfetti et al.",2008,"Geochim. Cosmochim. Acta 72, 713-731","arsenopyrite, loellingite, and westerveldite",https://doi.org/10.1016/j.gca.2007.11.017 @@ -175,6 +182,7 @@ HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695","kerogens (C128, C292, C406, C415, C515) and pyrobitumen (C54H42)",https://doi.org/10.1016/j.gca.2008.03.004 LRB09,"K. H. Lemke, R. J. Rosenbauer and D. K. Bird",2009,"Astrobiology 9, 141-146","diglycine and diketopiperazine",https://doi.org/10.1089/ast.2008.0166 MWW09,"A. A. Migdisov, A. E. Williams-Jones and T. Wagner",2009,"Geochim. Cosmochim. Acta 73, 7087-7109","REE F- and Cl- complexes",https://doi.org/10.1016/j.gca.2009.08.023 +BZA10,"E. F. Bazarkina, A. V. Zotov and N. N. Akinfiev",2010,"Geol. Ore Deposits 52, 167-178","Cd chloride complexes",https://doi.org/10.1134/S1075701510020054 AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010 AML10.1,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","Np- and Am-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010 AZ10,"N. N. Akinfiev and A. V. Zotov",2010,"Geochem. Int. 48, 714-720","MHS and M(HS)2- (M = Au+, Ag+, or Cu+)",https://doi.org/10.1134/S0016702910070074 @@ -182,6 +190,7 @@ MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",https://doi.org/10.1007/s12665-009-0369-x Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",https://doi.org/10.1007/s10498-010-9102-3 LBT+11,"W. Liu et al.",2011,"Geochim. Cosmochim. Acta 75, 1227-1248","Co-chloride complexes",https://doi.org/10.1016/j.gca.2010.12.002 +MMO+11,"Ji?? M?lek, Takefumi Mitsuhashi et al.",2011,"J. Chem. Thermodynamics 43, 405-409","GeS2 (alpha)",https://doi.org/10.1016/j.jct.2010.10.011 RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",https://doi.org/10.1016/j.gca.2011.07.030 LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",https://doi.org/10.1016/j.gca.2011.11.041 LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",https://doi.org/10.1016/j.gca.2011.11.041 @@ -230,6 +239,7 @@ OBIGT.7,"J. M. Dick",2019,"OBIGT database in CHNOSZ","Tl(Gly) and Tl(Gly)2-: change Ti to Tl",https://chnosz.net OBIGT.8,"J. M. Dick",2019,"OBIGT database in CHNOSZ","GHS recalculated by adding difference from SiO2 [@SSH97] to updated values for SiO2 [@AS04]",https://chnosz.net OBIGT.9,"J. M. Dick",2021,"OBIGT database in CHNOSZ","diaminopimelic acid, putrescine and spermidine: parameters recalculated to account for a missing [-CH2NH2] group in the group additivity equations",https://chnosz.net +Bla17,"P. Blanc",2017,"Thermoddem: Update for the 2017 version","monteponite, Cd(OH)2, CdSO4, otavite, GaOOH, and Ga hydroxide complexes",https://thermoddem.brgm.fr/page/brgm-reports LCT17,"A. R. Lowe, J. S. Cox and P. R. Tremaine",2017,"J. Chem. Thermodynamics 112, 129-145","adenine HKF parameters",https://doi.org/10.1016/j.jct.2017.04.005 DEW17.01,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(acetic acid, glycine, methanol, propanoic acid, propanol: parameters in DEW spreadsheet are the same as in @PS01)",http://www.dewcommunity.org DEW17.02,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(ethanol: parameters in DEW spreadsheet are different from @PS01; no comment provided)",http://www.dewcommunity.org @@ -292,6 +302,7 @@ LXW21,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488",H2WO4,https://doi.org/10.1016/j.chemgeo.2021.120488 LXW21.1,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","scheelite Cp",https://doi.org/10.1016/j.chemgeo.2021.120488 WV22,"A. E. Williams-Jones and O. V. Vasyukova",2022,"Econ. Geol. 117, 513-528","parameters listed here",https://doi.org/10.5382/econgeo.4895 +BS23,"G. Boyer and E. Shock",2023,"The Complicator (prototype)","In (indium) complexes",https://doi.org/10.5281/zenodo.8206644 AZ23,"N. N. Akinfiev and A. V. Zotov",2023,"Geol. Ore Deposits 65, 1-10","Cu+ and CuO-",https://doi.org/10.1134/S1075701523010026 TTA+23,"N. D. Trofimov, B. R. Tagirov et al.",2023,"Chem. Geol. 625, 121413","Cu hydrosulfide and chloride complexes",https://doi.org/10.1016/j.chemgeo.2023.121413 HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93",carrollite,https://doi.org/10.3749/2300028 @@ -301,3 +312,4 @@ RSS+24.1,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","corrected V for tripropylaminium",https://doi.org/10.1016/j.gca.2024.03.013 TAT+24,"B. R. Tagirov, N. N. Akinfiev et al.",2024,"Geochim. Cosmochim. Acta","Au-(hydro)sulfide species and SO4-2-bearing species",https://doi.org/10.1016/j.gca.2024.08.022 TAZ24,"B. R. Tagirov, N. N. Akinfiev and A. V. Zotov",2024,"Geol. Ore Deposits 66, 581--597","Au hydroxide and chloride complexes",https://doi.org/10.1134/S1075701524600403 +HB24,"D. L. Huston and?E.?Bastrakov",2024,"Aust. J. Earth Sci.","Ga and In sulfate complexes [algorithms based on @SSH97]",https://doi.org/10.1080/08120099.2024.2423772 Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-25 06:05:30 UTC (rev 859) +++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-25 08:02:36 UTC (rev 860) @@ -421,6 +421,10 @@ Model for the Mg(OH)2-MgCl2-H2O system at 25 to 150 °C from researchers at Sandia National Laboratories [@KBJ24]. +

GA

+ +Germanium, indium, gallium, and cadmium species from researchers at Geoscience Australia [@HB24]. +

Citations

```{r optreflist, results="asis", echo=FALSE} Modified: pkg/CHNOSZ/vignettes/OBIGT.bib =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-25 06:05:30 UTC (rev 859) +++ pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-25 08:02:36 UTC (rev 860) @@ -63,6 +63,17 @@ doi = {10.1111/j.1574-6976.2001.tb00576.x}, } + at Article{BZA10, + author = {Bazarkina, E. F. and Zotov, A. V. and Akinfiev, N. N.}, + journal = {Geology of Ore Deposits}, + title = {Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1-1000 bar and 25?{C}}, + year = {2010}, + number = {2}, + pages = {167--178}, + volume = {52}, + doi = {10.1134/S1075701510020054}, +} + @Article{BH83, author = {Bowers, Teresa Suter and Helgeson, Harold C.}, journal = {Geochimica et Cosmochimica Acta}, @@ -565,6 +576,18 @@ doi = {10.1016/j.epsl.2014.11.035}, } + at Article{PS98, + author = {Pokrovski, Gleb S. and Schott, Jacques}, + journal = {Geochimica et Cosmochimica Acta}, + title = {{T}hermodynamic properties of aqueous {G}e({IV}) hydroxide complexes from 25 to 350?{C}: {I}mplications for the behavior of germanium and the {G}e/{S}i ratio in hydrothermal fluids}, + year = {1998}, + number = {9}, + pages = {1631--1642}, + volume = {62}, + doi = {10.1016/S0016-7037(98)00081-7}, + sourceid = {OBIGT06}, +} + @Article{PH95, author = {Pokrovskii, Vitalii A. and Helgeson, Harold C.}, journal = {American Journal of Science}, @@ -756,14 +779,6 @@ doi = {10.2113/gsecongeo.104.8.1235}, } - at Misc{SLOP98, - author = {slop98.dat}, - title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92}, - howpublished = {Last updated on 1998-08-20. Accessed on 2019-04-08.}, - year = {1998}, - doi = {10.5281/zenodo.2630820}, -} - @Article{SH88, author = {Shock, Everett L. and Helgeson, Harold C.}, journal = {Geochimica et Cosmochimica Acta}, @@ -1041,12 +1056,13 @@ volume = {78}, } - at Misc{SLOP07, - author = {slop07.dat}, - title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92}, - howpublished = {Last updated on 2008-04-17. Accessed on 2019-04-08.}, - year = {2007}, - doi = {10.5281/zenodo.2630820}, + at Misc{BS23, + author = {Grayson Boyer and Everett Shock}, + howpublished = {Zenodo}, + note = {Version v0.0.2}, + title = {The Complicator (prototype)}, + year = {2023}, + doi = {10.5281/zenodo.8206644}, } @Misc{SLOP16, @@ -1582,6 +1598,16 @@ doi = {10.1016/j.oregeorev.2019.103289}, } + at TechReport{Bla17, + author = {P. Blanc}, + institution = {Bureau de Recherches G?ologiques et Mini?res}, + title = {Thermoddem: Update for the 2017 version}, + year = {2017}, + number = {BRGM/RP-66811-FR}, + type = {Report}, + url = {https://thermoddem.brgm.fr/page/brgm-reports}, +} + @TechReport{electron, author = {OBIGT}, institution = {OBIGT database in CHNOSZ}, @@ -1896,3 +1922,81 @@ volume = {65}, doi = {10.1134/S1075701523010026}, } + + + + at Article{HB24, + author = {Huston, D. L. and Bastrakov, E.}, + journal = {Australian Journal of Earth Sciences}, + title = {Germanium, indium, gallium and cadmium in zinc ores: a mineral system approach}, + year = {2024}, + doi = {10.1080/08120099.2024.2423772}, +} + + at Misc{slo98, + author = {slop98.dat}, + howpublished = {Last updated on 1998-08-20. Accessed on 2019-04-08.}, + title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92}, + year = {1998}, + doi = {10.5281/zenodo.2630820}, +} + + at Misc{slo07, + author = {slop07.dat}, + howpublished = {Last updated on 2008-04-17. Accessed on 2019-04-08.}, + title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92}, + year = {2007}, + doi = {10.5281/zenodo.2630820}, +} + + at Book{Pan82, + author = {L. B. Pankratz}, + publisher = {Bureau of Mines}, + title = {Thermodynamic Properties of Elements and Oxides}, + year = {1982}, + number = {672}, + series = {Bulletin}, + url = {https://catalog.hathitrust.org/Record/102119912}, +} + + at Article{MMO+11, + author = {Ji?? M?lek and Takefumi Mitsuhashi and Naoki Ohashi and Yuki Taniguchi and Hitoshi Kawaji and Tooru Atake}, + journal = {The Journal of Chemical Thermodynamics}, + title = {Heat capacity and thermodynamic properties of germanium disulfide at temperatures from {\emph{T}} = (2 to 1240) {K}}, + year = {2011}, + number = {3}, + pages = {405--409}, + volume = {43}, + doi = {10.1016/j.jct.2010.10.011}, +} + + at Article{OC95, + author = {P. A. G. O'Hare and L. A. Curtiss}, + journal = {The Journal of Chemical Thermodynamics}, + title = {Thermochemistry of (germanium + sulfur): {IV}. Critical evaluation of the thermodynamic properties of solid and gaseous germanium({II}) sulfide {GeS} and germanium({IV}) disulfide {GeS\textsubscript{2}}, and digermanium disulfide {Ge\textsubscript{2}S\textsubscript{2}}(g). Enthalpies of dissociation of bonds in {GeS}(g), {GeS\textsubscript{2}}(g), and {Ge\textsubscript{2}S\textsubscript{2}}(g)}, + year = {1995}, + number = {6}, + pages = {643--662}, + volume = {27}, + doi = {10.1006/jcht.1995.0066}, +} + + at Article{WS06, + author = {Scott A. Wood and Iain M. Samson}, + journal = {Ore Geology Reviews}, + title = {The aqueous geochemistry of gallium, germanium, indium and scandium}, + year = {2006}, + number = {1}, + pages = {57--102}, [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 860 From noreply at r-forge.r-project.org Thu Dec 26 04:33:13 2024 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 26 Dec 2024 04:33:13 +0100 (CET) Subject: [CHNOSZ-commits] r861 - in pkg/CHNOSZ: . inst inst/extdata inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes Message-ID: <20241226033313.A210A1808F1@r-forge.r-project.org> Author: jedick Date: 2024-12-26 04:33:12 +0100 (Thu, 26 Dec 2024) New Revision: 861 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv pkg/CHNOSZ/inst/extdata/refs.csv pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz pkg/CHNOSZ/vignettes/OBIGT.bib Log: OBIGT: Add tantalum species from Hu et al. (2024) Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2024-12-25 08:02:36 UTC (rev 860) +++ pkg/CHNOSZ/DESCRIPTION 2024-12-26 03:33:12 UTC (rev 861) @@ -1,6 +1,6 @@ -Date: 2024-12-25 +Date: 2024-12-26 Package: CHNOSZ -Version: 2.1.0-33 +Version: 2.1.0-34 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 2024-12-25 08:02:36 UTC (rev 860) +++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-26 03:33:12 UTC (rev 861) @@ -15,7 +15,7 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{?G?}}} -\section{Changes in CHNOSZ version 2.1.0-33 (2024-12-25)}{ +\section{Changes in CHNOSZ version 2.1.0-34 (2024-12-26)}{ \subsection{OBIGT DEFAULT DATA}{ \itemize{ @@ -30,13 +30,16 @@ \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)} have been moved to optional data (\file{SLOP98.csv}). + \item Add alkylamines, benzylamines, and aminiums from + \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}. + + \item Add tantalum species from + \href{https://doi.org/10.1016/j.gca.2024.10.019}{Hu et al. (2024)}. + \item Move americium complexes from \file{SLOP98.csv} back to \file{inorganic_aq.csv} (entropy of the element Am has been available for checking GHS self-consistency since version 1.4.0). - \item Add alkylamines, benzylamines, and aminiums from - \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}. - \item \file{inorganic_cr.csv}: Add cerianite (CeO\s{2}) and chromite (FeCr\s{2}O\s{4}) from \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}. Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2024-12-25 08:02:36 UTC (rev 860) +++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2024-12-26 03:33:12 UTC (rev 861) @@ -912,3 +912,5 @@ UO2CO3,UO2CO3,UO2CO3,aq,MBA+24,NA,2024-04-23,HKF,cal,-367270,-403994,12.78,-59.3,2.31,2.0683,-2.7313,6.8236,-2.6661,-0.8475,-28.9369,-0.038,0 UO2(CO3)2-2,UO2(CO3)2-2,UO2(CO3)2-2,aq,MBA+24,NA,2024-04-23,HKF,cal,-502825,-564657,34.72,-28.8,-1.11,2.521,-1.626,6.3892,-2.7118,-42.4375,18.8896,2.6863,-2 UO2(CO3)3-4,UO2(CO3)3-4,UO2(CO3)3-4,aq,MBA+24,NA,2024-04-23,HKF,cal,-635898,-741562,-6.14,-48.3,-4.53,3.3318,0.3538,5.6111,-2.7936,-59.7866,34.9856,6.4701,-4 +Ta(OH)3F3-,Ta(OH)3F3-,Ta(OH)3F3-,aq,HET+24,NA,2024-12-26,HKF,cal,-464794,NA,49.87,102.537,60.003,8.517,72.6759,-126.173,-6.85,94.3167,6.6323,0.5706,-1 +TaF7-2,TaF7-2,TaF7-2,aq,HET+24,NA,2024-12-26,HKF,cal,-585453,NA,46.13,-57.1404,60.309,4.4045,-109.973,371.972,0.8805,268.318,-150.173,3.3215,-2 Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-25 08:02:36 UTC (rev 860) +++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-26 03:33:12 UTC (rev 861) @@ -133,6 +133,7 @@ "OBIGT","TaO3-","aq","cal",-1.61,, "OBIGT","HTaO3F-","aq","cal",-1.15,-1.91, "OBIGT","UO2(CO3)3-4","aq","cal",,-1.98, +"OBIGT","TaF7-2","aq","cal",-9.97,-4.13, "OBIGT","CH4","aq","cal",-2.61,, "OBIGT","hexane","aq","cal",1.43,3.21, "OBIGT","ethylene","aq","cal",6.12,-3.82, Modified: pkg/CHNOSZ/inst/extdata/refs.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/refs.csv 2024-12-25 08:02:36 UTC (rev 860) +++ pkg/CHNOSZ/inst/extdata/refs.csv 2024-12-26 03:33:12 UTC (rev 861) @@ -313,3 +313,4 @@ TAT+24,"B. R. Tagirov, N. N. Akinfiev et al.",2024,"Geochim. Cosmochim. Acta","Au-(hydro)sulfide species and SO4-2-bearing species",https://doi.org/10.1016/j.gca.2024.08.022 TAZ24,"B. R. Tagirov, N. N. Akinfiev and A. V. Zotov",2024,"Geol. Ore Deposits 66, 581--597","Au hydroxide and chloride complexes",https://doi.org/10.1134/S1075701524600403 HB24,"D. L. Huston and?E.?Bastrakov",2024,"Aust. J. Earth Sci.","Ga and In sulfate complexes [algorithms based on @SSH97]",https://doi.org/10.1080/08120099.2024.2423772 +HET+24,"B. Hu,?B. Etschmann et al.",2024,"Geochim. Cosmochim. Acta","Ta(OH)3F3- and TaF7-2",https://doi.org/10.1016/j.gca.2024.10.019 Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz =================================================================== (Binary files differ) Modified: pkg/CHNOSZ/vignettes/OBIGT.bib =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-25 08:02:36 UTC (rev 860) +++ pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-26 03:33:12 UTC (rev 861) @@ -1912,6 +1912,16 @@ doi = {10.1016/j.gca.2024.08.022}, } + + at Article{HET+24, + author = {Bin Hu and Barbara Etschmann and Denis Testemale and Weihua Liu and Qiushi Guan and Harald M?ller and Jo?l Brugger}, + journal = {Geochimica et Cosmochimica Acta}, + title = {Tantalum in hydrothermal fluids}, + year = {2024}, + doi = {10.1016/j.gca.2024.10.019}, + issn = {0016-7037}, +} + @Article{AZ23, author = {Akinfiev, N. N. and Zotov, A. V.}, journal = {Geology of Ore Deposits},