From noreply at r-forge.r-project.org Sun Apr 8 14:30:45 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sun, 8 Apr 2018 14:30:45 +0200 (CEST) Subject: [CHNOSZ-commits] r314 - pkg/CHNOSZ Message-ID: <20180408123045.A77A71899E4@r-forge.r-project.org> Author: jedick Date: 2018-04-08 14:30:45 +0200 (Sun, 08 Apr 2018) New Revision: 314 Modified: pkg/CHNOSZ/DESCRIPTION Log: change package title Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2018-03-31 04:45:08 UTC (rev 313) +++ pkg/CHNOSZ/DESCRIPTION 2018-04-08 12:30:45 UTC (rev 314) @@ -1,7 +1,7 @@ -Date: 2018-03-31 +Date: 2018-04-08 Package: CHNOSZ -Version: 1.1.3-21 -Title: Thermodynamic Calculations for Geobiochemistry +Version: 1.1.3-22 +Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors at R: c( person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0687-5890")), From noreply at r-forge.r-project.org Wed Apr 11 16:43:38 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Apr 2018 16:43:38 +0200 (CEST) Subject: [CHNOSZ-commits] r315 - in pkg/CHNOSZ: . inst Message-ID: <20180411144338.E6837188DE1@r-forge.r-project.org> Author: jedick Date: 2018-04-11 16:43:37 +0200 (Wed, 11 Apr 2018) New Revision: 315 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/CITATION Log: update DESCRIPTION and CITATION Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2018-04-08 12:30:45 UTC (rev 314) +++ pkg/CHNOSZ/DESCRIPTION 2018-04-11 14:43:37 UTC (rev 315) @@ -1,6 +1,6 @@ -Date: 2018-04-08 +Date: 2018-04-11 Package: CHNOSZ -Version: 1.1.3-22 +Version: 1.1.3-23 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors at R: c( person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"), @@ -14,15 +14,20 @@ Depends: R (>= 3.1.0) Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice Imports: grDevices, graphics, stats, utils -Description: An integrated set of tools for thermodynamic calculations in geochemistry and - compositional biology. Thermodynamic properties are taken from a database for minerals - and inorganic and organic aqueous species including biomolecules, or from amino acid - group additivity for proteins. High-temperature properties are calculated using the - revised Helgeson-Kirkham-Flowers equations of state for aqueous species, and activity - coefficients can be calculated for specified ionic strength. Functions are - provided to define a system using basis species, automatically balance reactions, - calculate the chemical affinities of formation reactions for selected species, calculate - equilibrium activities, and plot the results on chemical activity diagrams. +Description: An integrated set of tools for thermodynamic calculations in geochemistry and compositional + biology. Thermodynamic properties are taken from a database for minerals and inorganic and + organic aqueous species including biomolecules, or from amino acid group additivity for proteins + (Dick et al., 2006 ). High-temperature properties are calculated + using the Berman-Brown (1985) equations for minerals and the + revised Helgeson-Kirkham-Flowers (1981) equations of state for + aqueous species. The HKF equations are augmented with the Deep Earth Water (DEW) model + (Sverjensky et al., 2014 ) and estimates of parameters in the + extended Debye-H?ckel equation (Manning et al., 2013 ) + to calculate standard-state properties and activity coefficients for given ionic strength at high + pressure (to 60 kb). Functions are provided to define a system using basis species, automatically + balance reactions, calculate the chemical affinities of formation reactions for selected species, + calculate equilibrium activities, and plot the results on chemical activity diagrams. +Encoding: UTF-8 License: GPL (>= 2) BuildResaveData: no VignetteBuilder: knitr Modified: pkg/CHNOSZ/inst/CITATION =================================================================== --- pkg/CHNOSZ/inst/CITATION 2018-04-08 12:30:45 UTC (rev 314) +++ pkg/CHNOSZ/inst/CITATION 2018-04-11 14:43:37 UTC (rev 315) @@ -1,6 +1,4 @@ -citHeader("To cite CHNOSZ in publications use:") - -citEntry(entry = "Article", +bibentry(bibtype = "Article", title = "Calculation of the relative metastabilities of proteins using the CHNOSZ software package", author = person(given = c("Jeffrey", "M."), family = "Dick", email="jmdick at asu.edu"), journal = "Geochemical Transactions", @@ -8,12 +6,5 @@ volume = "9", number = "10", pages = "", - month = "October", doi = "10.1186/1467-4866-9-10", - textVersion = - paste("Dick, J. M. (2008). ", - "Calculation of the relative metastabilities of proteins using the CHNOSZ software package. ", - "Geochemical Transactions, Vol. 9 Art. 10.",sep="") ) - -citFooter("See",sQuote("citation()"),"for citing R itself.") From noreply at r-forge.r-project.org Fri Apr 20 16:45:18 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 20 Apr 2018 16:45:18 +0200 (CEST) Subject: [CHNOSZ-commits] r316 - in pkg/CHNOSZ: . inst vignettes Message-ID: <20180420144518.E8D1C18813A@r-forge.r-project.org> Author: jedick Date: 2018-04-20 16:45:18 +0200 (Fri, 20 Apr 2018) New Revision: 316 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd Log: update DESCRIPTION and reduce vignette size Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2018-04-11 14:43:37 UTC (rev 315) +++ pkg/CHNOSZ/DESCRIPTION 2018-04-20 14:45:18 UTC (rev 316) @@ -1,6 +1,6 @@ -Date: 2018-04-11 +Date: 2018-04-20 Package: CHNOSZ -Version: 1.1.3-23 +Version: 1.1.3-24 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors at R: c( person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"), @@ -15,11 +15,14 @@ Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice Imports: grDevices, graphics, stats, utils Description: An integrated set of tools for thermodynamic calculations in geochemistry and compositional - biology. Thermodynamic properties are taken from a database for minerals and inorganic and - organic aqueous species including biomolecules, or from amino acid group additivity for proteins - (Dick et al., 2006 ). High-temperature properties are calculated - using the Berman-Brown (1985) equations for minerals and the - revised Helgeson-Kirkham-Flowers (1981) equations of state for + biology. The thermodynamic properties of liquid water are calculated using Fortran code from + SUPCRT92 (Johnson et al., 1992 ) or an implementation + in R of the IAPWS-95 formulation (Wagner and Pru?, 2002 doi:10.1063/1.1461829). + Thermodynamic properties of other species are taken from a database for minerals and inorganic + and organic aqueous species including biomolecules, or from amino acid group additivity for + proteins (Dick et al., 2006 ). High-temperature properties are + calculated using the Berman-Brown (1985) equations for minerals + and the revised Helgeson-Kirkham-Flowers (1981) equations for aqueous species. The HKF equations are augmented with the Deep Earth Water (DEW) model (Sverjensky et al., 2014 ) and estimates of parameters in the extended Debye-H?ckel equation (Manning et al., 2013 ) Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2018-04-11 14:43:37 UTC (rev 315) +++ pkg/CHNOSZ/inst/NEWS 2018-04-20 14:45:18 UTC (rev 316) @@ -14,7 +14,7 @@ Al-bearing minerals, as well as calcite, dolomite, hematite, and magnetite) are in the file extdata/OBIGT/SUPCRT92.csv, which can be loaded with add.obigt("SUPCRT92"). This is used in some examples for - comparing the datasets (see ?berman and demo(go-IU.R)), but should not + comparing the datasets (see ?berman and demo("go-IU")), but should not be needed by most users. - In thermo$obigt, the minerals using the Berman equations are @@ -27,8 +27,8 @@ winTWQ). - Multipliers on values in the Berman data files (extdata/Berman/*.csv) - have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4 - (to be consistent with the winTWQ data format). + have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4, + to be consistent with the winTWQ data format. - berman() now reads data from a user-supplied file specified in thermo$opt$Berman. @@ -61,7 +61,7 @@ - TODO: fix overly long message for info("SiO2"). -- In equilibrate(), accept a length > 1 'normalize' argument in order +- In equilibrate(), accept a length > 1 'normalize' argument to normalize the chemical formulas of only the selected species. - Export thermo.axis(), as it is useful for adding major and minor tick Modified: pkg/CHNOSZ/vignettes/anintro.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/anintro.Rmd 2018-04-11 14:43:37 UTC (rev 315) +++ pkg/CHNOSZ/vignettes/anintro.Rmd 2018-04-20 14:45:18 UTC (rev 316) @@ -67,8 +67,8 @@ # save space by using a lower resolution dpi <- 50 } else { - pngquant <- "--speed=1 --quality=0-50" - dpi <- 72 + pngquant <- "--speed=1 --quality=0-25" + dpi <- 50 } ## http://stackoverflow.com/questions/23852753/knitr-with-gridsvg @@ -1868,7 +1868,7 @@ ```{r smoker_plot, eval=FALSE, echo=23:25} ``` -```{r smoker_plot, fig.fullwidth=TRUE, fig.width=9, fig.height=5, small.mar=TRUE, dpi=100, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Optimization of a thermodynamic model for relative abundances of amino acids in a 270 ?C black smoker fluid using 1, 2, or 3 variables (left to right).", pngquant=pngquant, timeit=timeit} +```{r smoker_plot, fig.fullwidth=TRUE, fig.width=9, fig.height=5, small.mar=TRUE, dpi=dpi, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Optimization of a thermodynamic model for relative abundances of amino acids in a 270 ?C black smoker fluid using 1, 2, or 3 variables (left to right).", pngquant=pngquant, timeit=timeit} ``` The calculation using `findit()`, in which the added variable log*a*`r h2o` optimizes to ca. -2.4, shows that measured concentrations of 6 amino acids fall within 1--2 log units of the relative abundances in metastable equilibrium. Modified: pkg/CHNOSZ/vignettes/obigt.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/obigt.Rmd 2018-04-11 14:43:37 UTC (rev 315) +++ pkg/CHNOSZ/vignettes/obigt.Rmd 2018-04-20 14:45:18 UTC (rev 316) @@ -5,6 +5,7 @@ mathjax: null theme: default css: obigt.css + highlight: null vignette: > %\VignetteIndexEntry{Thermodynamic data in CHNOSZ} %\VignetteEngine{knitr::rmarkdown} From noreply at r-forge.r-project.org Sun Apr 29 10:08:09 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sun, 29 Apr 2018 10:08:09 +0200 (CEST) Subject: [CHNOSZ-commits] r317 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT Message-ID: <20180429080809.95177189A95@r-forge.r-project.org> Author: jedick Date: 2018-04-29 10:08:08 +0200 (Sun, 29 Apr 2018) New Revision: 317 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/basis.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv Log: change abbreviation of grossular to Grs Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2018-04-20 14:45:18 UTC (rev 316) +++ pkg/CHNOSZ/DESCRIPTION 2018-04-29 08:08:08 UTC (rev 317) @@ -1,6 +1,6 @@ -Date: 2018-04-20 +Date: 2018-04-29 Package: CHNOSZ -Version: 1.1.3-24 +Version: 1.1.3-25 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors at R: c( person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"), @@ -27,9 +27,10 @@ (Sverjensky et al., 2014 ) and estimates of parameters in the extended Debye-H?ckel equation (Manning et al., 2013 ) to calculate standard-state properties and activity coefficients for given ionic strength at high - pressure (to 60 kb). Functions are provided to define a system using basis species, automatically - balance reactions, calculate the chemical affinities of formation reactions for selected species, - calculate equilibrium activities, and plot the results on chemical activity diagrams. + pressure (to 60 kb). Functions are provided to calculate standard-state properties of species and + reactions, define the basis species of a chemical system, automatically balance reactions, calculate + the chemical affinities of formation reactions for selected species, calculate the equilibrium + activities of those species, and plot the results on chemical activity diagrams. Encoding: UTF-8 License: GPL (>= 2) BuildResaveData: no Modified: pkg/CHNOSZ/R/basis.R =================================================================== --- pkg/CHNOSZ/R/basis.R 2018-04-20 14:45:18 UTC (rev 316) +++ pkg/CHNOSZ/R/basis.R 2018-04-29 08:08:08 UTC (rev 317) @@ -154,7 +154,7 @@ bufmakeup <- makeup(ispecies) inbasis <- names(bufmakeup) %in% colnames(basis()) if(FALSE %in% inbasis) { - stop(paste("the elements '",c2s(rownames(bufmakeup)[!inbasis]), + stop(paste("the elements '",c2s(names(bufmakeup)[!inbasis]), "' of species '",thermo$buffers$species[ibuff[k]],"' in buffer '",state[i], "' are not in the basis\n",sep="")) } Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2018-04-20 14:45:18 UTC (rev 316) +++ pkg/CHNOSZ/inst/NEWS 2018-04-29 08:08:08 UTC (rev 317) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.1.3-21 (2018-03-31) +CHANGES IN CHNOSZ 1.1.3-25 (2018-04-29) --------------------------------------- THERMODYNAMIC DATA @@ -43,6 +43,8 @@ equation as d0 .. d4, rename "d5" (constant that scales disordering enthalpy to volume) to "Vad" (notation used in Theriak-Domino manual). +- Change abbreviation of grossular to Grs. + OTHER CHANGES - Lines in 1-D diagram()s can optionally be drawn as splines using the Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2018-04-20 14:45:18 UTC (rev 316) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2018-04-29 08:08:08 UTC (rev 317) @@ -28,7 +28,7 @@ ferrosilite,Fsl,SiFeO3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA forsterite,Fo,Mg2SiO4,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA gehlenite,Ge,Al2Ca2SiO7,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -grossular,Gr,Ca3Al2Si3O12,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +grossular,Grs,Ca3Al2Si3O12,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA hematite,Hm,Fe2O3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA ilmenite,Ilm,FeTiO3,cr,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA jadeite,Jd,NaAlSi2O6,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA