From noreply at r-forge.r-project.org Wed Mar 1 14:12:28 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 1 Mar 2017 14:12:28 +0100 (CET) Subject: [CHNOSZ-commits] r178 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man tests/testthat vignettes Message-ID: <20170301131228.4137A187E0D@r-forge.r-project.org> Author: jedick Date: 2017-03-01 14:12:27 +0100 (Wed, 01 Mar 2017) New Revision: 178 Added: pkg/CHNOSZ/inst/extdata/OBIGT/Majzlan_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Tardy_cr.csv Removed: pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Tardy_aq.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/NAMESPACE pkg/CHNOSZ/R/swap.basis.R pkg/CHNOSZ/R/util.data.R pkg/CHNOSZ/R/util.misc.R pkg/CHNOSZ/data/buffer.csv pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/data/thermo.R pkg/CHNOSZ/demo/sources.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Other_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Wagman_gas.csv pkg/CHNOSZ/man/data.Rd pkg/CHNOSZ/man/subcrt.Rd pkg/CHNOSZ/man/util.misc.Rd pkg/CHNOSZ/tests/testthat/test-protein.info.R pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd pkg/CHNOSZ/vignettes/obigt.bib Log: obigt.Rmd: document sprons92.dat additions Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-01 13:12:27 UTC (rev 178) @@ -1,6 +1,6 @@ -Date: 2017-02-27 +Date: 2017-03-01 Package: CHNOSZ -Version: 1.0.8-67 +Version: 1.0.8-68 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/NAMESPACE =================================================================== --- pkg/CHNOSZ/NAMESPACE 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/NAMESPACE 2017-03-01 13:12:27 UTC (rev 178) @@ -55,7 +55,9 @@ "feldspar", "apc", "EOSlab", "EOScalc", "basis.elements", "element.mu", "ibasis", "water.SUPCRT92", "water.props", "eqdata", "plot_findit", - "nonideal", "anim.TCA", "uniprot.aa", "run.guess" + "nonideal", "anim.TCA", "uniprot.aa", "run.guess", +# added 20170301 or later + "GHS_Tr" ) # Load shared objects Modified: pkg/CHNOSZ/R/swap.basis.R =================================================================== --- pkg/CHNOSZ/R/swap.basis.R 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/R/swap.basis.R 2017-03-01 13:12:27 UTC (rev 178) @@ -13,8 +13,8 @@ # matrix part of the basis definition basis.mat <- basis.elements(basis) # the standard Gibbs energies of the basis species - if(T==25) G <- get("thermo")$obigt$G[basis$ispecies] - else G <- unlist(subcrt(basis$ispecies, T=T, property="G")$out) + # don't take it from thermo$obigt, even at 25 degC, because G for H2O is NA there + G <- unlist(subcrt(basis$ispecies, T=T, property="G")$out) # chemical potentials of the basis species species.mu <- G - convert(basis$logact, "G", T=convert(T, "K")) # chemical potentials of the elements @@ -35,8 +35,8 @@ # check that elements of basis.mat and emu are identical if(any(is.na(ielem))) stop(paste("element(s)", paste(names(emu)[is.na(ielem)], collapse=" "), "not found in basis")) # the standard Gibbs energies of the basis species - if(T==25) G <- get("thermo")$obigt$G[basis$ispecies] - else G <- unlist(subcrt(basis$ispecies, T=T, property="G")$out) + # don't take it from thermo$obigt, even at 25 degC, because G for H2O is NA there + G <- unlist(subcrt(basis$ispecies, T=T, property="G")$out) # the chemical potentials of the basis species in equilibrium # with the chemical potentials of the elements basis.mu <- colSums((t(basis.mat)*emu)) - G Modified: pkg/CHNOSZ/R/util.data.R =================================================================== --- pkg/CHNOSZ/R/util.data.R 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/R/util.data.R 2017-03-01 13:12:27 UTC (rev 178) @@ -238,6 +238,8 @@ cat("thermo.refs: table of references is shown in browser\n") } else if(is.character(key)) { # return citation information for the given source(s) + # we omit the [S92] in "HDNB78 [S92]" etc. + key <- gsub("\ .*", "", key) ix <- match(key, x$key) ina <- is.na(ix) if(any(is.na(ix))) message(paste("thermo.refs: reference key(s)", Modified: pkg/CHNOSZ/R/util.misc.R =================================================================== --- pkg/CHNOSZ/R/util.misc.R 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/R/util.misc.R 2017-03-01 13:12:27 UTC (rev 178) @@ -2,29 +2,74 @@ # some utility functions for the CHNOSZ package # speciate/thermo.R 20051021 jmd -dPdTtr <- function(x) { +dPdTtr <- function(ispecies) { # calculate dP/dT for a phase transition # (argument is index of the lower-T phase) thermo <- get("thermo") - t1 <- subcrt(x, P=0, T=thermo$obigt$z.T[x], convert=FALSE, check.Ttr=FALSE) - t2 <- subcrt(x+1, P=0, T=thermo$obigt$z.T[x], convert=FALSE, check.Ttr=FALSE) + t1 <- subcrt(ispecies, P=0, T=thermo$obigt$z.T[ispecies], convert=FALSE, check.Ttr=FALSE) + t2 <- subcrt(ispecies+1, P=0, T=thermo$obigt$z.T[ispecies], convert=FALSE, check.Ttr=FALSE) # if these aren't the same mineral all we can say is zero # actually, should be infinity ... the volume change is zero if(as.character(t1$species$name) != as.character(t2$species$name)) return(Inf) # we really hope the G's are the same ... - #if(abs(t2$out[[1]]$G - t2$out[[1]]$G) > 0.1) warning('dP.dT: inconsistent values of G for different phases of ',x,call.=FALSE) + #if(abs(t2$out[[1]]$G - t2$out[[1]]$G) > 0.1) warning('dP.dT: inconsistent values of G for different phases of ',ispecies,call.=FALSE) dP.dT <- convert( ( t2$out[[1]]$S - t1$out[[1]]$S ) / ( t2$out[[1]]$V - t1$out[[1]]$V ), 'cm3bar' ) return(dP.dT) } -Ttr <- function(x,P=1,dPdT=NULL) { +Ttr <- function(ispecies,P=1,dPdT=NULL) { # calculate a phase transition temperature # taking account of P (from dP/dT) - T <- get("thermo")$obigt$z.T[x] - if(is.null(dPdT)) dPdT <- dPdTtr(x) + T <- get("thermo")$obigt$z.T[ispecies] + if(is.null(dPdT)) dPdT <- dPdTtr(ispecies) return(T + P / dPdT) } +GHS_Tr <- function(ispecies, Htr) { + # calculate G, H, and S at Tr for cr2, cr3, ... phases 20170301 + # Htr: enthalpy(ies) of transition + # ispecies: the species index for cr1 + thisinfo <- info(ispecies) + name <- thisinfo$name + # start from Tr (T=298.15 K) + Tprev <- 298.15 + # the GHS at T + Gf <- thisinfo$G + Hf <- thisinfo$H + S <- thisinfo$S + # where to store the calculated GHS at Tr + Gf_Tr <- Hf_Tr <- S_Tr <- numeric() + for(i in 1:(length(Htr)+1)) { + # check that we have the correct one of cr1, cr2, ... + thiscr <- paste0("cr", i) + if(thisinfo$state!=thiscr | thisinfo$name!=name) stop(paste("species", thisis, "is not", name, thiscr)) + # if we're above cr1, calculate the equivalent GHS at Tr + if(i > 1) { + # the HS increments from 298.15 to Ttr + HSinc <- cgl(c("H", "S"), T=c(298.15, Ttr), ghs=thisinfo, eos=thisinfo) + Hf_Tr <- c(Hf_Tr, Hf - diff(HSinc[[1]]$H)) + S_Tr <- c(S_Tr, S - diff(HSinc[[1]]$S)) + # plug in the calculated S_Tr to calculate the G increment correctly + thisinfo$S <- tail(S_Tr, 1) + Ginc <- cgl("G", T=c(298.15, Ttr), ghs=thisinfo, eos=thisinfo) + Gf_Tr <- c(Gf_Tr, Gf - diff(Ginc[[1]]$G)) + } + # the temperature of the next transition + Ttr <- thisinfo$T + # the GHS increments from Tprev to Ttr + GHCinc <- cgl(c("G", "H", "S"), T=c(Tprev, Ttr), ghs=thisinfo, eos=thisinfo) + # the GHS + transition at Tr + Gf <- Gf + diff(GHCinc[[1]]$G) + Hf <- Hf + diff(GHCinc[[1]]$H) + Htr[i] + S <- S + diff(GHCinc[[1]]$S) + Htr[i] / Ttr + # prepare next phase + thisis <- ispecies + i + thisinfo <- info(thisis) + Tprev <- Ttr + } + list(Gf_Tr=Gf_Tr, Hf_Tr=Hf_Tr, S_Tr=S_Tr) +} + unitize <- function(logact=NULL,length=NULL,logact.tot=0) { # scale the logarithms of activities given in loga # so that the logarithm of total activity of residues Modified: pkg/CHNOSZ/data/buffer.csv =================================================================== --- pkg/CHNOSZ/data/buffer.csv 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/data/buffer.csv 2017-03-01 13:12:27 UTC (rev 178) @@ -14,7 +14,7 @@ MAMINE,methanamine,aq,-3 HM,hematite,cr1,0 HM,magnetite,cr1,0 -FeFeO,Fe,cr1,0 +FeFeO,iron,cr1,0 FeFeO,FeO,cr,0 CO2-AC,CO2,aq,-3 CO2-AC,"acetic acid",aq,-3 Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/data/refs.csv 2017-03-01 13:12:27 UTC (rev 178) @@ -4,7 +4,8 @@ Kel60.2,"K. K. Kelley",1960,"gypsum Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 Pan70,"L. B. Pankratz",1970,chlorargyrite,"U. S. Bureau of Mines Report of Investigations 7430",http://www.worldcat.org/oclc/14154245 PK70,"L. B. Pankratz and E. G. King",1970,"bornite and chalcopyrite","U. S. Bureau of Mines Report of Investigations 7435",http://www.worldcat.org/oclc/14154292 -HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,minerals,"Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862 +HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"minerals and phase transitions","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862 +HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"litharge S, V, and Cp parameters","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862 RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"chlorargyrite, rutile, and titanite","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"dickite, fluorphlogopite, halloysite, and pyrope","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 PB82,"L. N. Plummer and E. Busenberg",1982,"aragonite and calcite","Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4 @@ -16,22 +17,21 @@ JH85,"K. J. Jackson and H. C. Helgeson",1985,"Sn minerals","Econ. Geol. 80, 1365-1378",http://dx.doi.org/10.2113/gsecongeo.80.5.1365 Nei86,"F. C. Neidhardt",1986,,"Escherichia coli and Salmonella typhimurium, 3-5",http://www.worldcat.org/oclc/15280827 SH88,"E. L. Shock and H. C. Helgeson",1988,"ionic species","Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0 -SH88.1,"E. L. Shock and H. C. Helgeson",1988,"corrections for Ca-bearing minerals","Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0 -SH88.2,"E. L. Shock and H. C. Helgeson",1988,titanite,"Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0 CWM89,"J. D. Cox, D. D. Wagman and V. A. Medvedev, eds.",1989,,"CODATA Key Values for Thermodynamics",http://www.worldcat.org/oclc/18559968 SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"inorganic neutral species","Geochim. Cosmochim. Acta 53, 2157-2183",http://dx.doi.org/10.1016/0016-7037(89)90341-4 SH90,"E. L. Shock and H. C. Helgeson",1990,"organic species","Geochim. Cosmochim. Acta 54, 915-945",http://dx.doi.org/10.1016/0016-7037(90)90429-O Joh92a,"J. W. Johnson",1992,"steam, Cp represented by Maier-Kelley equation","personal communication", +SPRONS92.1,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", +SPRONS92.2,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", Sho92,"E. L. Shock",1992,dipeptides,"Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V Sho93,"E. L. Shock",1993,ethylacetate,"Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 Sho93.1,"E. L. Shock",1993,"carbon monoxide and ethylene","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 SK93,"E. L. Shock and C. M. Koretsky",1993,"metal-acetate complexes","Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J SM93,"E. L. Shock and W. B. McKinnon",1993,"CO, HCN, urea","Icarus 106, 464-477",http://dx.doi.org/10.1006/icar.1993.1185 SS93,"M. D. Schulte and E. L. Shock",1993,aldehydes,"Geochim. Cosmochim. Acta 57, 3835-3846",http://dx.doi.org/10.1016/0016-7037(93)90337-V -HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"REE complexes","Geochim. Cosmochim. Acta 59, 4329-4350",http://dx.doi.org/10.1016/0016-7037(95)00314-P +HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"complexes of rare earth elements","Geochim. Cosmochim. Acta 59, 4329-4350",http://dx.doi.org/10.1016/0016-7037(95)00314-P PK95,"V. B. Parker and I. L. Khodakovskii",1995,melanterite,"J. Phys. Chem. Ref. Data 24, 1699-1745",http://dx.doi.org/10.1063/1.555964 RH95,"R. A. Robie and B. S. Hemingway",1995,"gypsum GHS","U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131 -RH95.1,"R. A. Robie and B. S. Hemingway",1995,iron,"U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131 SK95,"E. L. Shock and C. M. Koretsky",1995,"metal-organic acid complexes","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8 Sho95,"E. L. Shock",1995,"carboxylic acids","Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496 Gur96,"S. Gurrieri",1996,sulfur,"personal communication", @@ -41,11 +41,14 @@ SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uranium species","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8 SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"metal complexes","Geochim. Cosmochim. Acta 61, 1359-1412",http://dx.doi.org/10.1016/S0016-7037(97)00009-4 SSW+97,"E. L. Shock, D. C. Sassani et al.",1997,"inorganic ions and hydroxide complexes","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 +SSW+97.1,"E. L. Shock, D. C. Sassani et al.",1997,"zincite and litharge","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"humic acid, microflora, and plants","C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 RH98,"L. Richard and H. C. Helgeson",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 3591-3636",http://dx.doi.org/10.1016/S0016-7037(97)00345-1 SLOP98,"E. L. Shock et al.",1998,,"slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.1,"E. L. Shock et al.",1998,"zincite and litharge; "These data were used in @SSW+97, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.2,"E. L. Shock et al.",1998,"daphnite; "Gf and Hf from @SS93a TMM"","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"metal-dicarboxylate complexes","Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5 SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"jarosite, natroalunite, and natrojarosite","Rev. Mineral. Geochem. 40, 453-479",http://dx.doi.org/10.2138/rmg.2000.40.9 @@ -67,9 +70,9 @@ LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Mg-complexed adenosine nucleotides (ATP), NAD, and NADP","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008 LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"pyridine and piperidine","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008 MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"coquimbite, ferricopiapite, rhomboclase","Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175 -CHNOSZ.1,"J. M. Dick",2007,"recalculated GHS","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.2,"J. M. Dick",2007,"calculated Cp coefficients","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.3,"J. M. Dick",2007,pseudo-H4SiO4,"CHNOSZ package documentation",http://chnosz.net +CHNOSZ.1,"J. M. Dick",2017,"GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.2,"J. M. Dick",2017,"The standard molal Gibbs energies and enthalpies of formation from the elements and entropies at 25 °C and 1 bar of aqueous metal-amino acid (alanate or glycinate) complexes reported by @SK95 were recalculated by adding the differences between values reported by @AH97b and @DLH06 for alanate or glycinate.","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.3,"J. M. Dick",2017,pseudo-H4SiO4,"CHNOSZ package documentation",http://chnosz.net Dic07,"J. M. Dick",2007,"glutathione, cystine, and cystine sidechain","Ph.D. Dissertation, U.C. Berkeley", MA07,"L. Marini and M. Accornero",2007,"metal-arsenate and metal-arsenite complexes","Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5 Ric08,"L. Richard",2008,alkenes,"personal communication", @@ -81,7 +84,7 @@ RG11,"L. Richard and X. Gaona",2011,"organic iodine compounds","Geochim. Cosmochim. Acta 75, 7304-7350",http://dx.doi.org/10.1016/j.gca.2011.07.030 LD12,"D. E. LaRowe and J. M. Dick",2012,"amino acids and protein groups","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 LD12.1,"D. E. LaRowe and J. M. Dick",2012,"methionine and methionine sidechain GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 -DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"phenanthrene and isomers of methylphenanthrene","Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020 +DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"phenanthrene and methylphenanthrene isomers","Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020 CS16,"P. A. Canovas III and E. L. Shock",2016,"citric acid cycle metabolites","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 -CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a1-a4 parameters and corrected Cp and V","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 +CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a1-a4 parameters","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 UniProt,"The UniProt Consortium",2017,,"The UniProt knowledgebase",http://www.uniprot.org/ Modified: pkg/CHNOSZ/data/thermo.R =================================================================== --- pkg/CHNOSZ/data/thermo.R 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/data/thermo.R 2017-03-01 13:12:27 UTC (rev 178) @@ -9,9 +9,9 @@ local({ # create obigt data frame - sources_aq <- paste0(c("H2O", "Shock", "Amend", "Schulte", "LaRowe", "Dick", "Canovas", - "Tardy", "Tremaine", "Marini", "CHNOSZ"), "_aq") - sources_cr <- paste0(c("Helgeson", "Shock", "Richard", "LaRowe", "Other", "CHNOSZ"), "_cr") + sources_aq <- paste0(c("H2O", "Shock", "Amend", "Schulte", "LaRowe", "Dick", + "Tremaine", "Marini", "Canovas", "CHNOSZ"), "_aq") + sources_cr <- paste0(c("Helgeson", "Shock", "Tardy", "Richard", "Majzlan", "LaRowe", "Other"), "_cr") sources_liq <- paste0(c("Richard", "LaRowe"), "_liq") sources_gas <- paste0(c("Wagman", "Shock", "Richard", "Other"), "_gas") OBIGTdir <- system.file("extdata/OBIGT/", package="CHNOSZ") Modified: pkg/CHNOSZ/demo/sources.R =================================================================== --- pkg/CHNOSZ/demo/sources.R 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/demo/sources.R 2017-03-01 13:12:27 UTC (rev 178) @@ -4,8 +4,9 @@ # sources of elemental data element.source <- thermo$element$source # sources in the primary thermodynamic database -os1 <- thermo$obigt$ref1 -os2 <- thermo$obigt$ref2 +# we omit the [S92] in "HDNB78 [S92]" etc. +os1 <- gsub("\ .*", "", thermo$obigt$ref1) +os2 <- gsub("\ .*", "", thermo$obigt$ref2) # all of the thermodynamic data sources - some of them might be NA obigt.source <- unique(c(os1,os2)) obigt.source <- obigt.source[!is.na(obigt.source)] Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/inst/NEWS 2017-03-01 13:12:27 UTC (rev 178) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-67 (2017-02-27) +CHANGES IN CHNOSZ 1.0.8-68 (2017-03-01) --------------------------------------- DOCUMENTATION: @@ -89,6 +89,11 @@ - Add syslab() and ratlab() to make formatted expressions for sets of thermodynamic components and activity ratios. +- Add GHS_Tr() to calculate G, H, and S at Tr (298.15 K) of phases + stable at high temperature, using provided enthalpies of transition + and database values of transition temperatures and heat capacity + parameters, and GHS at Tr of the low-temperature phase. + NEW AND OLD DATA: - Split OBIGT.csv and OBIGT-2.csv into multiple files according to @@ -118,6 +123,9 @@ - Remove other conflicting datasets previously in OBIGT-2.csv (21 sources). +- Replace GHS for iron (c2, c3) calculated in CHNOSZ with values derived + from sprons92.dat. + - extdata: Add fasta/rubisco.fasta and cpetc/*.csv files SS98_Fig5a, SS98_Fig5b, PM90 (all used in anintro.Rmd). Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv 2017-03-01 13:12:27 UTC (rev 178) @@ -1,5 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -Fe,iron,Fe,cr1,RH95.1,CHNOSZ.2,05.Aug.07,0,0,6.475,5.994,7.092,7.162,-6.9682,0,0,1.2294,0,0,1043 -Fe,iron,Fe,cr2,RH95.1,CHNOSZ.2,05.Aug.07,-32284.5,-87223.4,-177.791,NA,7.092,504.577,-807.244,0,0,32.754,0,0,1185 -Fe,iron,Fe,cr3,RH95.1,CHNOSZ.2,05.Aug.07,1348.8,1843.8,8.1352,NA,7.092,5.1938,2.3381,1.5019,0,0,0,0,1667 -Fe,iron,Fe,cr4,RH95.1,CHNOSZ.2,05.Aug.07,3190.2,4835.6,11.994,NA,7.092,-4.033,8.0055,9.5584,0,0,0,0,1809 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-03-01 13:12:27 UTC (rev 178) @@ -1,5 +1,4 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -methionine,Met,C5H11NO2S,aq,LD12.1,DLH06.1,10.Jul.15,-76959.8,-135210.3,62.81,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0 [Ala],NA,CH3,aq,DLH06,NA,25.Aug.06,-3936,-13290,16.85,35.671,26.864,5.43,3.6,4.39,-1.92,27.9,3.6,-0.05,0 [Arg],NA,C4H10N3,aq,DLH06,NA,25.Aug.06,31624,-20730,54.75,74.167,105.825,18.08,13.39,50.81,-10.09,73.2,-1.9,-0.53,0 [Arg+],NA,C4H11N3+,aq,DLH06,NA,25.Aug.06,14943,-35670,60.59,79.677,88.906,22.25,2.08,2.69,-3.38,82.2,1,0.5,0 @@ -18,7 +17,6 @@ [Leu],NA,C4H9,aq,DLH06,NA,25.Aug.06,675,-34390,28.43,97.21,74.2,15.21,9.37,17.16,-6.6,81.1,7.3,-0.14,0 [Lys],NA,C4H10N,aq,DLH06,NA,25.Aug.06,5657,-37650,39.3,65.848,75.048,15.09,10.16,21.66,-7.76,65,-0.3,-0.16,0 [Lys+],NA,C4H11N+,aq,DLH06,NA,25.Aug.06,-8014,-51160,39.84,69.955,73.89,19.15,0.35,1.7,-2.22,73.6,2.6,0.98,0 -[Met],NA,C3H7S,aq,LD12.1,DLH06.1,10.Jul.15,7911.1,-16001.4,40.82,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0 [Phe],NA,C7H7,aq,DLH06,NA,25.Aug.06,35444,10310,34.62,95.834,88.545,18.8,10.66,16.57,-7.61,86.5,4.1,-0.11,0 [Pro],NA,C3H5,aq,DLH06,NA,25.Aug.06,11314,-4890,27.85,45.055,49.049,9.92,6.73,9.11,-3.91,42,1.1,-0.09,0 [Ser],NA,CH3O,aq,DLH06,NA,25.Aug.06,-39054,-53210,25.26,29.794,27.042,6.22,2.59,1.1,-1.72,26.9,1.2,-0.05,0 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv 2017-03-01 13:12:27 UTC (rev 178) @@ -1,4 +1,4 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -water,NA,H2O,liq,NA,NA,25.Oct.06,-56687.711481,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +water,NA,H2O,liq,NA,NA,25.Oct.06,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA e-,NA,Z0-1,aq,NA,NA,28.Oct.06,0,0,15.6166,0,0,0,0,0,0,0,0,0,0 H+,H+,H+,aq,NA,NA,06.Nov.97,0,0,0,0,0,0,0,0,0,0,0,0,0 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-02-27 11:09:54 UTC (rev 177) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-03-01 13:12:27 UTC (rev 178) @@ -1,241 +1,245 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -acanthite,Acn,Ag2S,cr1,HDNB78,NA,5.May.78,-9446,-7550,34.3,NA,34.2,15.63,8.6,0,0,0,0,0,450 -acanthite,Acn,Ag2S,cr2,HDNB78,NA,5.May.78,-9235.197,-7024.866,35.3543,NA,34.2,1.819,53,0,0,0,0,0,620 -acanthite,Acn,Ag2S,cr3,HDNB78,NA,5.May.78,-8227.324,-4960.457,38.898,NA,34.2,21.6,0,0,0,0,0,0,1000 -aegerine,Agt,NaFe(SiO3)2,cr1,HDNB78,NA,5.May.78,NA,NA,36.7,NA,64.37,46.16,19.31,-9.46,0,0,0,0,950 -aegerine,Agt,NaFe(SiO3)2,cr2,HDNB78,NA,5.May.78,-82.386,NA,34.6051,NA,64.37,52.42,10.01,-7.68,0,0,0,0,1050 -aegerine,Agt,NaFe(SiO3)2,cr3,HDNB78,NA,5.May.78,478.346,NA,36.6502,NA,64.37,50.27,10.89,-7.68,0,0,0,0,1400 -akermanite,Ak,Ca2MgSi2O7,cr,HDNB78,SH88.1,15.Mar.90,-879362,-926497,50.03,NA,92.81,60.09,11.4,-11.4,0,0,0,0,1700 -alabandite,Alb,MnS,cr,HDNB78,NA,5.May.78,-52178,-51000,19.2,NA,21.46,11.4,1.8,0,0,0,0,0,1803 -albite,Ab,Na(AlSi3)O8,cr1,HDNB78,NA,5.May.78,-886308,-939680,49.51,NA,100.25,61.7,13.9,-15.01,0,0,0,0,473 -albite,Ab,Na(AlSi3)O8,cr2,HDNB78,NA,5.May.78,-886096.268,NA,53.9193,NA,100.25,81.88,3.554,-50.154,0,0,0,0,1200 -"albite,high",Hi-Ab,NaAlSi3O8,cr1,HDNB78,NA,5.May.78,-884509,-937050,52.3,NA,100.43,61.7,13.9,-15.01,0,0,0,0,623 -"albite,high",Hi-Ab,NaAlSi3O8,cr2,HDNB78,NA,5.May.78,-884768.678,NA,50.4797,NA,100.43,64.17,13.9,-15.01,0,0,0,0,1400 -"albite,low",Lo-Ab,Na(AlSi3)O8,cr,HDNB78,NA,5.May.78,-886308,-939680,49.51,NA,100.07,61.7,13.9,-15.01,0,0,0,0,1400 -"albite,low",Alm,Fe3Al2Si3O12,cr1,HDNB78,NA,5.May.78,NA,NA,75.6,NA,115.28,97.52,33.64,-18.73,0,0,0,0,848 -almandine,Alm,Fe3Al2Si3O12,cr2,HDNB78,NA,5.May.78,-11.741,NA,71.93,NA,115.28,107.09,14.86,-10.63,0,0,0,0,1600 -alunite,Alu,KAl3(OH)6(SO4)2,cr,HDNB78,NA,5.May.78,-1113600,-1235600,78.4,NA,293.6,153.45,0,-54.95,0,0,0,0,650 -"amesite,14a",14A-Am,Mg4Al2(Al2Si2)O10(OH)8,cr1,HDNB78,NA,5.May.78,NA,NA,108.9,NA,205.4,172.59,34.98,-41.67,0,0,0,0,848 -"amesite,14a",14A-Am,Mg4Al2(Al2Si2)O10(OH)8,cr2,HDNB78,NA,5.May.78,3.895,NA,110.1233,NA,205.4,169.4,41.24,-44.37,0,0,0,0,1000 -"amesite,7a",Ams-7A,Mg2Al(AlSi)O5(OH)4,cr,HDNB78,NA,5.May.78,NA,NA,52,NA,103,81.03,24.738,-20.23,0,0,0,0,1000 -"amorphous silica",Amor-Sl,SiO2,cr,HDNB78,NA,5.May.78,-202892,-214568,14.34,NA,29,5.93,47.2,-22.78,0,0,0,0,622 -analcime,Anl,NaAlSi2O6*H2O,cr,HDNB78,NA,5.May.78,-738098,-790193,56,NA,97.1,53.49,24.14,-8.88,0,0,0,0,1000 -"analcime,dehydrated",Dhyd-Anl,NaAlSi2O6,cr,HDNB78,NA,5.May.78,-674989,-714678,41.9,NA,89.1,42.09,24.14,-8.88,0,0,0,0,1000 -andalusite,And,Al2SiO5,cr,HDNB78,NA,5.May.78,-580587,-615866,22.2,NA,51.53,41.310833,6.292556,-12.392063,0,0,0,0,1043 -andradite,Adr,Ca3Fe2Si3O12,cr,HDNB78,SH88.1,15.Mar.90,-1296819,-1380345,70.13,NA,131.85,113.532,15.636,-30.889,0,0,0,0,1100 -anglesite,Ang,PbSO4,cr,HDNB78,NA,5.May.78,-194353,-219870,35.51,NA,47.95,10.96,31,4.2,0,0,0,0,1100 -anhydrite,Anh,CaSO4,cr,HDNB78,NA,5.May.78,-315925,-342760,25.5,NA,45.94,16.78,23.6,0,0,0,0,0,1453 -annite,Ann,KFe3(AlSi3)O10(OH)2,cr,HDNB78,NA,5.May.78,-1147156,-1232195,95.2,NA,154.32,106.43,29.77,-19.31,0,0,0,0,1000 -anorthite,An,Ca(Al2Si2)O8,cr,HDNB78,SH88.1,15.Mar.90,-954078,-1007552,49.1,NA,100.79,63.311,14.794,-15.44,0,0,0,0,1700 -anthophyllite,Ath,Mg7Si8O22(OH)2,cr1,HDNB78,NA,5.May.78,-2715430,-2888749,128.6,NA,264.4,180.682,60.574,-38.462,0,0,0,0,903 -anthophyllite,Ath,Mg7Si8O22(OH)2,cr2,HDNB78,NA,5.May.78,-2718479.297,NA,108.796,NA,264.4,197.542,41.614,-13.342,0,0,0,0,1258 -anthophyllite,Ath,Mg7Si8O22(OH)2,cr3,HDNB78,NA,5.May.78,-2719529.932,NA,105.9454,NA,264.4,199.522,41.614,-13.342,0,0,0,0,1800 -antigorite,Atg,Mg48Si34O85(OH)62,cr1,HDNB78,NA,5.May.78,-15808020,-17070891,861.36,NA,1749.13,1228.45,513.76,-286.68,0,0,0,0,848 -antigorite,Atg,Mg48Si34O85(OH)62,cr2,HDNB78,NA,5.May.78,-15808027.845,NA,858.9133,NA,1749.13,1234.83,501.24,-281.28,0,0,0,0,1000 -aragonite,Arg,CaCO3,cr,HDNB78,PB82,9.Mar.90,-269683,-288531,21.56,NA,34.15,20.13,10.24,-3.34,0,0,0,0,600 -artinite,Art,Mg2(OH)2(CO3)*3H2O,cr,HDNB78,NA,5.May.78,-613915,-698043,55.67,NA,96.9,70.87,27.66,-7.43,0,0,0,0,1000 -azurite,Azr,Cu3(OH)2(CO3)2,cr,HDNB78,NA,5.May.78,-334417,-390100,66.97,NA,91.01,36.88,77.44,-0.92,0,0,0,0,780 -barite,Brt,BaSO4,cr,HDNB78,NA,5.May.78,-325563,-352100,31.6,NA,52.1,33.8,0,-8.43,0,0,0,0,1422 -boehmite,Bhm,AlO(OH),cr,HDNB78,NA,5.May.78,-217250,-235078,11.58,NA,19.535,14.435,4.2,0,0,0,0,0,500 -bornite,Bn,Cu5FeS4,cr1,HDNB78,PK70,5.May.78,-86704,-79922,99.29,NA,98.6,49.76,35.08,-1.35,0,0,0,0,485 -bornite,Bn,Cu5FeS4,cr2,HDNB78,PK70,5.May.78,-86373.231,-78463.256,103.0733,NA,98.6,-34.31,247,0,0,0,0,0,540 -bornite,Bn,Cu5FeS4,cr3,HDNB78,PK70,5.May.78,-86513.642,-80947.917,95.2106,NA,98.6,80.33,-2.04,0,0,0,0,0,1200 -bromellite,Brm,BeO,cr,HDNB78,NA,5.May.78,NA,NA,3.38,NA,8.309,8.45,4,-3.17,0,0,0,0,1200 -brucite,Brc,Mg(OH)2,cr,HDNB78,NA,5.May.78,-199646,-221390,15.09,NA,24.63,24.147,4.0124,-6.11,0,0,0,0,900 -bunsenite,Bsn,NiO,cr1,HDNB78,NA,5.May.78,-50573,-57300,9.08,NA,10.97,-4.99,37.58,3.89,0,0,0,0,525 -bunsenite,Bsn,NiO,cr2,HDNB78,NA,5.May.78,-50581.657,-57508.213,8.4107,NA,10.97,13.88,0,0,0,0,0,0,565 -bunsenite,Bsn,NiO,cr3,HDNB78,NA,5.May.78,-50447.661,-57020.353,9.5976,NA,10.97,11.18,2.02,0,0,0,0,0,2000 -ca-al-pyroxene,Ca-Al-Px,CaAl(AlSi)O6,cr,HDNB78,SH88.1,15.Mar.90,-742067,-783793,35,NA,63.5,54.13,6.42,-14.9,0,0,0,0,1400 -ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr1,HDNB78,NA,5.May.78,NA,NA,166.6,NA,265,145.82,52.67,-19.13,0,0,0,0,848 -ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr2,HDNB78,NA,5.May.78,-3.895,NA,165.3767,NA,265,149.01,46.41,-16.43,0,0,0,0,1000 -calcite,Cal,CaCO3,cr,HDNB78,PB82,9.Mar.90,-269880,-288552,22.15,NA,36.934,24.98,5.24,-6.2,0,0,0,0,1200 -celadonite,Cln,K(MgAl)Si4O10(OH)2,cr,HDNB78,NA,5.May.78,NA,NA,74.9,NA,157.1,80.25,25.3,-18.54,0,0,0,0,1000 -celestite,Cls,SrSO4,cr,HDNB78,NA,5.May.78,-320435,-347300,28,NA,46.25,21.8,13.3,0,0,0,0,0,1500 -cerussite,Cer,PbCO3,cr,HDNB78,NA,5.May.78,-150370,-168000,31.3,NA,40.59,12.39,28.6,0,0,0,0,0,800 -chabazite,Cbz,Ca(Al2Si4)O12*6H2O,cr,HDNB78,NA,5.May.78,NA,NA,152.9,NA,247.76,146,44.47,-16.43,0,0,0,0,1000 -chalcedony,Cha,SiO2,cr,HDNB78,NA,5.May.78,-204276,-217282,9.88,NA,22.688,11.22,8.2,-2.7,0,0,0,0,848 -chalcocite,Cc,Cu2S,cr1,HDNB78,NA,5.May.78,-20626,-19000,28.9,NA,27.48,12.63,18.82,0,0,0,0,0,376 -chalcocite,Cc,Cu2S,cr2,HDNB78,NA,5.May.78,-20479.051,-18494.843,30.1015,NA,27.48,26.78,-7.35,0,0,0,0,0,717 -chalcocite,Cc,Cu2S,cr3,HDNB78,NA,5.May.78,-19940.435,-17064.666,33.0917,NA,27.48,20.32,0,0,0,0,0,0,1400 -chalcopyrite,Ccp,CuFeS2,cr1,HDNB78,PK70,5.May.78,-44900,-44453,31.15,NA,42.83,20.79,12.8,-1.34,0,0,0,0,830 -chalcopyrite,Ccp,CuFeS2,cr2,HDNB78,PK70,5.May.78,-34590.133,-15235.889,94.5651,NA,42.83,-141.4,210,0,0,0,0,0,930 -chalcopyrite,Ccp,CuFeS2,cr3,HDNB78,PK70,5.May.78,-46119.409,-49143.645,19.5073,NA,42.83,41.22,0,0,0,0,0,0,1200 -chloritoid,Cld,FeAl2SiO5(OH)2,cr,HDNB78,NA,5.May.78,NA,NA,42.1,NA,69.8,60.63,17.13,-13.63,0,0,0,0,1000 -chrysotile,Ctl,Mg3Si2O5(OH)4,cr,HDNB78,NA,5.May.78,-964871,-1043123,52.9,NA,108.5,75.82,31.6,-17.58,0,0,0,0,1000 -cinnabar,Cin,HgS,cr,HDNB78,NA,5.May.78,-10940,-12750,19.7,NA,28.416,10.46,3.72,0,0,0,0,0,618 -"clinochlore,14a",14A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr,HDNB78,NA,5.May.78,-1961703,-2116964,111.2,NA,207.11,166.5,42.1,-37.47,0,0,0,0,900 -"clinochlore,7a",7A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr1,HDNB78,NA,5.May.78,-1957101,-2113197,106.5,NA,211.5,162.82,50.62,-40.88,0,0,0,0,848 -"clinochlore,7a",7A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr2,HDNB78,NA,5.May.78,-1957104.895,NA,105.2767,NA,211.5,166.01,44.36,-38.18,0,0,0,0,900 -clinozoisite,Czo,Ca2Al3Si3O12(OH),cr,HDNB78,SH88.1,15.Mar.90,-1549240,-1643781,70.64,NA,136.2,106.118,25.214,-27.145,0,0,0,0,700 -coesite,Cos,SiO2,cr1,HDNB78,NA,5.May.78,-203541,-216614,9.65,NA,20.641,11,8.2,-2.7,0,0,0,0,848 -coesite,Cos,SiO2,cr2,HDNB78,NA,5.May.78,-203544.895,NA,8.4267,NA,20.641,14.19,1.94,0,0,0,0,0,2000 -copper,Cu,Cu,cr,HDNB78,NA,5.May.78,0,0,7.923,NA,7.113,5.41,1.5,0,0,0,0,0,1357 -cordierite,Crd,Mg2Al3(AlSi5)O18,cr,HDNB78,NA,5.May.78,-2061279,-2183199,97.33,NA,233.22,143.83,25.8,-38.6,0,0,0,0,1700 -"cordierite,hydrous",Hyd-Crd,Mg2Al3(AlSi5)O18*H2O,cr,HDNB78,NA,5.May.78,-2121350,-2255676,111.43,NA,241.22,155.23,25.8,-38.6,0,0,0,0,1700 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 178 From noreply at r-forge.r-project.org Thu Mar 2 14:42:26 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 2 Mar 2017 14:42:26 +0100 (CET) Subject: [CHNOSZ-commits] r179 - in pkg/CHNOSZ: . R data inst inst/extdata inst/extdata/OBIGT inst/extdata/supcrt man vignettes Message-ID: <20170302134226.67F9B188458@r-forge.r-project.org> Author: jedick Date: 2017-03-02 14:42:25 +0100 (Thu, 02 Mar 2017) New Revision: 179 Added: pkg/CHNOSZ/inst/extdata/supcrt/ pkg/CHNOSZ/inst/extdata/supcrt/compare.R pkg/CHNOSZ/inst/extdata/supcrt/newnames.csv pkg/CHNOSZ/inst/extdata/supcrt/read.supcrt.R Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/util.misc.R pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_gas.csv pkg/CHNOSZ/man/extdata.Rd pkg/CHNOSZ/vignettes/obigt.Rmd pkg/CHNOSZ/vignettes/obigt.bib Log: obigt.Rmd: document slop98.dat additions Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-03-01 13:12:27 UTC (rev 178) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-02 13:42:25 UTC (rev 179) @@ -1,6 +1,6 @@ -Date: 2017-03-01 +Date: 2017-03-02 Package: CHNOSZ -Version: 1.0.8-68 +Version: 1.0.8-69 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/util.misc.R =================================================================== --- pkg/CHNOSZ/R/util.misc.R 2017-03-01 13:12:27 UTC (rev 178) +++ pkg/CHNOSZ/R/util.misc.R 2017-03-02 13:42:25 UTC (rev 179) @@ -45,6 +45,8 @@ if(thisinfo$state!=thiscr | thisinfo$name!=name) stop(paste("species", thisis, "is not", name, thiscr)) # if we're above cr1, calculate the equivalent GHS at Tr if(i > 1) { + # set the starting GHS to 0 (in case they're NA - we only need the increments over temperature) + thisinfo$G <- thisinfo$H <- thisinfo$S <- 0 # the HS increments from 298.15 to Ttr HSinc <- cgl(c("H", "S"), T=c(298.15, Ttr), ghs=thisinfo, eos=thisinfo) Hf_Tr <- c(Hf_Tr, Hf - diff(HSinc[[1]]$H)) Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-03-01 13:12:27 UTC (rev 178) +++ pkg/CHNOSZ/data/refs.csv 2017-03-02 13:42:25 UTC (rev 179) @@ -1,13 +1,15 @@ key,author,year,note,citation,URL Kel60,"K. K. Kelley",1960,"gases Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 -Kel60.1,"K. K. Kelley",1960,larnite,"U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 -Kel60.2,"K. K. Kelley",1960,"gypsum Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 +Kel60.1,"K. K. Kelley",1960,larnite Cp,"U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 +Kel60.2,"K. K. Kelley",1960,"iron Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 +Kel60.3,"K. K. Kelley",1960,"gypsum Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 Pan70,"L. B. Pankratz",1970,chlorargyrite,"U. S. Bureau of Mines Report of Investigations 7430",http://www.worldcat.org/oclc/14154245 PK70,"L. B. Pankratz and E. G. King",1970,"bornite and chalcopyrite","U. S. Bureau of Mines Report of Investigations 7435",http://www.worldcat.org/oclc/14154292 HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"minerals and phase transitions","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862 HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"litharge S, V, and Cp parameters","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862 RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"chlorargyrite, rutile, and titanite","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"dickite, fluorphlogopite, halloysite, and pyrope","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 +RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"iron","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 PB82,"L. N. Plummer and E. Busenberg",1982,"aragonite and calcite","Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4 WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"gases GHS","J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,manganosite,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 @@ -34,22 +36,32 @@ RH95,"R. A. Robie and B. S. Hemingway",1995,"gypsum GHS","U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131 SK95,"E. L. Shock and C. M. Koretsky",1995,"metal-organic acid complexes","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8 Sho95,"E. L. Shock",1995,"carboxylic acids","Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496 -Gur96,"S. Gurrieri",1996,sulfur,"personal communication", AH97b,"J. P. Amend and H. C. Helgeson",1997,"amino acids GHS","J. Chem. Soc., Faraday Trans. 93, 1927-1941",http://dx.doi.org/10.1039/A608126F DSM+97,"J. D. Dale, E. L. Shock et al.",1997,alkylphenols,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 MS97,"T. M. McCollom and E. L. Shock",1997,"MgSO4, NaSO4-, and HCl","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X +MS97.1,"T. M. McCollom and E. L. Shock",1997,"sulfur","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uranium species","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8 +SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uraninite","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8 SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"metal complexes","Geochim. Cosmochim. Acta 61, 1359-1412",http://dx.doi.org/10.1016/S0016-7037(97)00009-4 -SSW+97,"E. L. Shock, D. C. Sassani et al.",1997,"inorganic ions and hydroxide complexes","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 -SSW+97.1,"E. L. Shock, D. C. Sassani et al.",1997,"zincite and litharge","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 +SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"inorganic ions and hydroxide complexes","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 +SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"zincite and litharge","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"humic acid, microflora, and plants","C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 -HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 RH98,"L. Richard and H. C. Helgeson",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 3591-3636",http://dx.doi.org/10.1016/S0016-7037(97)00345-1 -SLOP98,"E. L. Shock et al.",1998,,"slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.1,"E. L. Shock et al.",1998,"zincite and litharge; "These data were used in @SSW+97, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.1,"E. L. Shock et al.",1998,"zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SLOP98.2,"E. L. Shock et al.",1998,"daphnite; "Gf and Hf from @SS93a TMM"","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 +SLOP98.3,"E. L. Shock et al.",1998,""Corrected values based on data from @SH90 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.4,"E. L. Shock et al.",1998,""Corrected values based on data from @SSH97 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.5,"E. L. Shock et al.",1998,""Corrected values based on data from @SS93 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.6,"E. L. Shock et al.",1998,""Corrected values based on data from @SK93 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.7,"E. L. Shock et al.",1998,""Corrected values based on data from @Sho95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.8,"E. L. Shock et al.",1998,""These data were used in @SK95, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.9,"E. L. Shock et al.",1998,""Corrected values based on data from @SK95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.10,"E. L. Shock et al.",1998,""Corrected values based on data from @HSS95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP98.11,"E. L. Shock et al.",1998,""Data and parameters as used by @MS97. "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group ions and complexes","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 +SS98a.1,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 +HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"metal-dicarboxylate complexes","Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5 SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"jarosite, natroalunite, and natrojarosite","Rev. Mineral. Geochem. 40, 453-479",http://dx.doi.org/10.2138/rmg.2000.40.9 AP01,"J. P. Amend and A. V. Plyasunov",2001,carbohydrates,"Geochim. Cosmochim. Acta 65, 3901-3917",http://dx.doi.org/10.1016/S0016-7037(01)00707-4 Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-03-01 13:12:27 UTC (rev 178) +++ pkg/CHNOSZ/inst/NEWS 2017-03-02 13:42:25 UTC (rev 179) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-68 (2017-03-01) +CHANGES IN CHNOSZ 1.0.8-69 (2017-03-02) --------------------------------------- DOCUMENTATION: @@ -94,6 +94,10 @@ and database values of transition temperatures and heat capacity parameters, and GHS at Tr of the low-temperature phase. +- Add extdata/supcrt/ directory with files read.supcrt.R, compare.R, + newnames.csv; used to compare data in SUPCRT and slop files + (http://geopig.asu.edu/?q=tools) to data in thermo$obigt. + NEW AND OLD DATA: - Split OBIGT.csv and OBIGT-2.csv into multiple files according to @@ -129,6 +133,10 @@ - extdata: Add fasta/rubisco.fasta and cpetc/*.csv files SS98_Fig5a, SS98_Fig5b, PM90 (all used in anintro.Rmd). +- Replace data for sulfur (cr) from Gurrieri, 1996, personal + communication with that "as used by" McCollom and Shock, 1997 (from + slop98.dat). + BUG FIXES: - Correct charge (-2) of NAD(red)-2 in LaRowe_aq.csv. Thanks to Peter Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-03-01 13:12:27 UTC (rev 178) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-03-02 13:42:25 UTC (rev 179) @@ -5,7 +5,7 @@ aegerine,Agt,NaFe(SiO3)2,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,36.7,NA,64.37,46.16,19.31,-9.46,0,0,0,0,950 aegerine,Agt,NaFe(SiO3)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-82.386,NA,34.6051,NA,64.37,52.42,10.01,-7.68,0,0,0,0,1050 aegerine,Agt,NaFe(SiO3)2,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,478.346,NA,36.6502,NA,64.37,50.27,10.89,-7.68,0,0,0,0,1400 -akermanite,Ak,Ca2MgSi2O7,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-879362,-926497,50.03,NA,92.81,60.09,11.4,-11.4,0,0,0,0,1700 +akermanite,Ak,Ca2MgSi2O7,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-879362,-926497,50.03,NA,92.81,60.09,11.4,-11.4,0,0,0,0,1700 alabandite,Alb,MnS,cr,"HDNB78 [S92]",NA,5.May.78,-52178,-51000,19.2,NA,21.46,11.4,1.8,0,0,0,0,0,1803 albite,Ab,Na(AlSi3)O8,cr1,"HDNB78 [S92]",NA,5.May.78,-886308,-939680,49.51,NA,100.25,61.7,13.9,-15.01,0,0,0,0,473 albite,Ab,Na(AlSi3)O8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-886096.268,NA,53.9193,NA,100.25,81.88,3.554,-50.154,0,0,0,0,1200 @@ -22,11 +22,11 @@ analcime,Anl,NaAlSi2O6*H2O,cr,"HDNB78 [S92]",NA,5.May.78,-738098,-790193,56,NA,97.1,53.49,24.14,-8.88,0,0,0,0,1000 "analcime,dehydrated",Dhyd-Anl,NaAlSi2O6,cr,"HDNB78 [S92]",NA,5.May.78,-674989,-714678,41.9,NA,89.1,42.09,24.14,-8.88,0,0,0,0,1000 andalusite,And,Al2SiO5,cr,"HDNB78 [S92]",NA,5.May.78,-580587,-615866,22.2,NA,51.53,41.310833,6.292556,-12.392063,0,0,0,0,1043 -andradite,Adr,Ca3Fe2Si3O12,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1296819,-1380345,70.13,NA,131.85,113.532,15.636,-30.889,0,0,0,0,1100 +andradite,Adr,Ca3Fe2Si3O12,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1296819,-1380345,70.13,NA,131.85,113.532,15.636,-30.889,0,0,0,0,1100 anglesite,Ang,PbSO4,cr,"HDNB78 [S92]",NA,5.May.78,-194353,-219870,35.51,NA,47.95,10.96,31,4.2,0,0,0,0,1100 anhydrite,Anh,CaSO4,cr,"HDNB78 [S92]",NA,5.May.78,-315925,-342760,25.5,NA,45.94,16.78,23.6,0,0,0,0,0,1453 annite,Ann,KFe3(AlSi3)O10(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-1147156,-1232195,95.2,NA,154.32,106.43,29.77,-19.31,0,0,0,0,1000 -anorthite,An,Ca(Al2Si2)O8,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-954078,-1007552,49.1,NA,100.79,63.311,14.794,-15.44,0,0,0,0,1700 +anorthite,An,Ca(Al2Si2)O8,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-954078,-1007552,49.1,NA,100.79,63.311,14.794,-15.44,0,0,0,0,1700 anthophyllite,Ath,Mg7Si8O22(OH)2,cr1,"HDNB78 [S92]",NA,5.May.78,-2715430,-2888749,128.6,NA,264.4,180.682,60.574,-38.462,0,0,0,0,903 anthophyllite,Ath,Mg7Si8O22(OH)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-2718479.297,NA,108.796,NA,264.4,197.542,41.614,-13.342,0,0,0,0,1258 anthophyllite,Ath,Mg7Si8O22(OH)2,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-2719529.932,NA,105.9454,NA,264.4,199.522,41.614,-13.342,0,0,0,0,1800 @@ -45,7 +45,7 @@ bunsenite,Bsn,NiO,cr1,"HDNB78 [S92]",NA,5.May.78,-50573,-57300,9.08,NA,10.97,-4.99,37.58,3.89,0,0,0,0,525 bunsenite,Bsn,NiO,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-50581.657,-57508.213,8.4107,NA,10.97,13.88,0,0,0,0,0,0,565 bunsenite,Bsn,NiO,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-50447.661,-57020.353,9.5976,NA,10.97,11.18,2.02,0,0,0,0,0,2000 -ca-al-pyroxene,Ca-Al-Px,CaAl(AlSi)O6,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-742067,-783793,35,NA,63.5,54.13,6.42,-14.9,0,0,0,0,1400 +ca-al-pyroxene,Ca-Al-Px,CaAl(AlSi)O6,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-742067,-783793,35,NA,63.5,54.13,6.42,-14.9,0,0,0,0,1400 ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,166.6,NA,265,145.82,52.67,-19.13,0,0,0,0,848 ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-3.895,NA,165.3767,NA,265,149.01,46.41,-16.43,0,0,0,0,1000 calcite,Cal,CaCO3,cr,"HDNB78 [S92]","PB82 [S92]",9.Mar.90,-269880,-288552,22.15,NA,36.934,24.98,5.24,-6.2,0,0,0,0,1200 @@ -66,7 +66,7 @@ "clinochlore,14a",14A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr,"HDNB78 [S92]",NA,5.May.78,-1961703,-2116964,111.2,NA,207.11,166.5,42.1,-37.47,0,0,0,0,900 "clinochlore,7a",7A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr1,"HDNB78 [S92]",NA,5.May.78,-1957101,-2113197,106.5,NA,211.5,162.82,50.62,-40.88,0,0,0,0,848 "clinochlore,7a",7A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-1957104.895,NA,105.2767,NA,211.5,166.01,44.36,-38.18,0,0,0,0,900 -clinozoisite,Czo,Ca2Al3Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1549240,-1643781,70.64,NA,136.2,106.118,25.214,-27.145,0,0,0,0,700 +clinozoisite,Czo,Ca2Al3Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1549240,-1643781,70.64,NA,136.2,106.118,25.214,-27.145,0,0,0,0,700 coesite,Cos,SiO2,cr1,"HDNB78 [S92]",NA,5.May.78,-203541,-216614,9.65,NA,20.641,11,8.2,-2.7,0,0,0,0,848 coesite,Cos,SiO2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-203544.895,NA,8.4267,NA,20.641,14.19,1.94,0,0,0,0,0,2000 copper,Cu,Cu,cr,"HDNB78 [S92]",NA,5.May.78,0,0,7.923,NA,7.113,5.41,1.5,0,0,0,0,0,1357 @@ -83,22 +83,22 @@ "cronstedtite,7a",7A-Csd,Fe2Fe(FeSi)O5(OH)4,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,957.096,NA,73.4065,NA,110.9,93.01,25,-8.93,0,0,0,0,1500 cummingtonite,Cum,Mg7Si8O22(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,127.5,NA,271.9,185.24,58.61,-44.66,0,0,0,0,800 cuprite,Cpr,Cu2O,cr,"HDNB78 [S92]",NA,5.May.78,-35384,-40830,22.08,NA,23.437,14.08,5.88,-0.76,0,0,0,0,1515 -"daphnite,14a",Dph-14A,Fe5Al(AlSi3)O10(OH)8,cr,"HDNB78 [S92]","SLOP98.2 [S98]",5.May.78,-1550482,-1695426,142.5,NA,213.42,176.21,43.76,-33.82,0,0,0,0,1000 +"daphnite,14a",Dph-14A,Fe5Al(AlSi3)O10(OH)8,cr,"HDNB78 [S92]","SLOP98.2",5.May.78,-1550482,-1695426,142.5,NA,213.42,176.21,43.76,-33.82,0,0,0,0,1000 "daphnite,7a",7A-Dph,Fe5Al(AlSi3)O10(OH)8,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,138.9,NA,221.2,172.53,52.28,-37.23,0,0,0,0,848 "daphnite,7a",7A-Dph,Fe5Al(AlSi3)O10(OH)8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,3.159,NA,137.726,NA,221.2,175.72,46.02,-34.63,0,0,0,0,1000 diaspore,Dsp,AlO(OH),cr,"HDNB78 [S92]",NA,5.May.78,-218402,-237170,8.43,NA,17.76,14.435,4.2,0,0,0,0,0,500 dickite,Dck,Al2Si2O5(OH)4,cr,"HDNB78 [S92]","RHF79.1 [S92]",5.May.78,NA,NA,47.1,NA,99.3,72.77,29.2,-21.52,0,0,0,0,1000 -diopside,Di,CaMg(SiO3)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-723780,-765378,34.2,NA,66.09,52.87,7.84,-15.74,0,0,0,0,1600 -dolomite,Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-517760,-556631,37.09,NA,64.365,41.557,23.952,-9.884,0,0,0,0,1000 -"dolomite,disordered",Dis-Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-515653,-553704,39.84,NA,64.39,44.711,17.779,-10.948,0,0,0,0,1000 -"dolomite,ordered",Ord-Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-517760,-556631,37.09,NA,64.34,44.711,17.779,-10.948,0,0,0,0,1000 +diopside,Di,CaMg(SiO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-723780,-765378,34.2,NA,66.09,52.87,7.84,-15.74,0,0,0,0,1600 +dolomite,Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-517760,-556631,37.09,NA,64.365,41.557,23.952,-9.884,0,0,0,0,1000 +"dolomite,disordered",Dis-Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-515653,-553704,39.84,NA,64.39,44.711,17.779,-10.948,0,0,0,0,1000 +"dolomite,ordered",Ord-Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-517760,-556631,37.09,NA,64.34,44.711,17.779,-10.948,0,0,0,0,1000 edenite,Ed,Na(Ca2Mg5)(AlSi7)O22(OH2),cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,161,NA,271,199.71,48.78,-46.01,0,0,0,0,848 edenite,Ed,Na(Ca2Mg5)(AlSi7)O22(OH2),cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-3.895,NA,159.7767,NA,271,202.9,42.52,-43.31,0,0,0,0,1000 enstatite,En,MgSiO3,cr1,"HDNB78 [S92]",NA,5.May.78,-348930,-369686,16.2,NA,31.276,24.55,4.74,-6.28,0,0,0,0,903 enstatite,En,MgSiO3,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-349581.153,-371758.464,11.4328,NA,31.296,28.765,0,0,0,0,0,0,1258 enstatite,En,MgSiO3,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-349546.21,-371843.59,11.0302,NA,32.386,29.26,0,0,0,0,0,0,1800 -epidote,Ep,Ca2FeAl2Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1450906,-1543992,75.28,NA,139.2,117.622,12.816,-31.864,0,0,0,0,1100 -"epidote,ordered",Ord-Ep,Ca2FeAl2Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1450906,-1544016,75.2,NA,139.2,113.78,14.69,-28.92,0,0,0,0,1100 +epidote,Ep,Ca2FeAl2Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1450906,-1543992,75.28,NA,139.2,117.622,12.816,-31.864,0,0,0,0,1100 +"epidote,ordered",Ord-Ep,Ca2FeAl2Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1450906,-1544016,75.2,NA,139.2,113.78,14.69,-28.92,0,0,0,0,1100 epistilbite,Eps,Ca(Al2Si6)O16*5H2O,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,152.9,NA,267.56,157.04,60.87,-21.83,0,0,0,0,848 epistilbite,Eps,Ca(Al2Si6)O16*5H2O,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-7.845,NA,150.4533,NA,267.56,163.42,48.35,-16.43,0,0,0,0,1000 fayalite,Fa,Fe2SiO4,cr,"HDNB78 [S92]",NA,5.May.78,-330233,-354119,35.45,NA,46.39,36.51,9.36,-6.7,0,0,0,0,1490 @@ -119,20 +119,20 @@ fluortremolite,F-Tr,(Ca2Mg5)Si8O22(F)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,129.4,NA,270.45,183.74,55.25,-43.73,0,0,0,0,800 forsterite,Fo,Mg2SiO4,cr,"HDNB78 [S92]",NA,5.May.78,-491564,-520000,22.75,NA,43.79,35.81,6.54,-8.52,0,0,0,0,1800 galena,Gn,PbS,cr,"HDNB78 [S92]",NA,5.May.78,-23115,-23500,21.8,NA,31.49,11.17,2.2,0,0,0,0,0,1388 -gehlenite,Gh,Ca2(Al2Si)O7,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-903148,-951225,48.1,NA,90.24,63.74,8,-15.12,0,0,0,0,1800 +gehlenite,Gh,Ca2(Al2Si)O7,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-903148,-951225,48.1,NA,90.24,63.74,8,-15.12,0,0,0,0,1800 gibbsite,Gbs,Al(OH)3,cr,"HDNB78 [S92]",NA,5.May.78,-276168,-309065,16.75,NA,31.956,8.65,45.6,0,0,0,0,0,425 glaucophane,Gln,Na2(Mg3Al2)Si8O22(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,130,NA,269.7,190.26,59.36,-50.01,0,0,0,0,800 gold,Au,Au,cr,"HDNB78 [S92]",NA,5.May.78,0,0,11.33,NA,10.215,5.66,1.24,0,0,0,0,0,1336 graphite,Gr,C,cr,"HDNB78 [S92]",NA,5.May.78,0,0,1.372,NA,5.298,4.03,1.14,-2.04,0,0,0,0,2500 greenalite,Grn,Fe3Si2O5(OH)4,cr,"HDNB78 [S92]",NA,5.May.78,-715340,-644110,72.6,NA,115,81.65,32.6,-15.39,0,0,0,0,1000 -grossular,Grs,Ca3Al2Si3O12,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1496307,-1582737,60.87,NA,125.3,104.017,17.013,-27.318,0,0,0,0,1000 +grossular,Grs,Ca3Al2Si3O12,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1496307,-1582737,60.87,NA,125.3,104.017,17.013,-27.318,0,0,0,0,1000 grunerite,Gru,Fe7Si8O22(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,163.3,NA,256.67,198.83,60.93,-39.55,0,0,0,0,800 halite,Hl,NaCl,cr,"HDNB78 [S92]",NA,5.May.78,-91807,-98260,17.24,NA,27.015,10.98,3.9,0,0,0,0,0,1073 halloysite,Hal,Al2Si2O5(OH)4,cr,"HDNB78 [S92]","RHF79.1 [S92]",5.May.78,NA,NA,48.52,NA,99.3,72.77,29.2,-21.52,0,0,0,0,1000 hastingsite,Hs,Na(Ca2Fe4Fe)(Al2Si6)O22(OH)2,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,189.2,NA,280.3,211.57,50.88,-44.88,0,0,0,0,950 hastingsite,Hs,Na(Ca2Fe4Fe)(Al2Si6)O22(OH)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-79.315,NA,187.1167,NA,280.3,217.82,41.58,-43.1,0,0,0,0,1050 hastingsite,Hs,Na(Ca2Fe4Fe)(Al2Si6)O22(OH)2,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,477.644,NA,189.1492,NA,280.3,215.68,42.46,-43.1,0,0,0,0,1500 -hedenbergite,Hd,CaFe(SiO3)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",5.Mar.90,-638998,-678276,40.7,NA,68.27,54.81,8.17,-15.01,0,0,0,0,1600 +hedenbergite,Hd,CaFe(SiO3)2,cr,"HDNB78 [S92]","SPRONS92.2",5.Mar.90,-638998,-678276,40.7,NA,68.27,54.81,8.17,-15.01,0,0,0,0,1600 hematite,Hem,Fe2O3,cr1,"HDNB78 [S92]",NA,5.May.78,-178155,-197720,20.94,NA,30.274,23.49,18.6,-3.55,0,0,0,0,950 hematite,Hem,Fe2O3,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-178206.12,-198965.094,16.9353,NA,30.274,36,0,0,0,0,0,0,1050 hematite,Hem,Fe2O3,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-177088.429,-196631.631,21.0129,NA,30.274,31.71,1.76,0,0,0,0,0,1800 @@ -140,10 +140,10 @@ heulandite,Hul,Ca(Al2Si7)O18*6H2O,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-11.741,NA,178.73,NA,316.37,189.23,50.29,-16.43,0,0,0,0,1000 huntite,Hun,CaMg3(CO3)4,cr,"HDNB78 [S92]",NA,5.May.78,-1004710,-1082600,71.59,NA,122.9,84.17,42.86,-20.44,0,0,0,0,1000 hydromagnesite,Hydro-Mgs,Mg5(OH)2(CO3)4*4H2O,cr,"HDNB78 [S92]",NA,5.May.78,-1401687,-1557090,129.38,NA,208.8,141.46,65.28,-21.67,0,0,0,0,1000 -iron,Fe,Fe,cr1,"RHF79 [S92]","Kel60 [S92]",5.May.78,0,0,6.52,NA,7.092,3.04,7.58,0.6,0,0,0,0,1033 -iron,Fe,Fe,cr2,"RHF79 [S92]",CHNOSZ.1,5.May.78,-618.237,-1768.418,2.662,NA,7.092,11.13,0,0,0,0,0,0,1183 -iron,Fe,Fe,cr3,"RHF79 [S92]",CHNOSZ.1,5.May.78,1293.526,1865.343,8.438,NA,7.092,5.8,1.98,0,0,0,0,0,1673 -iron,Fe,Fe,cr4,"RHF79 [S92]",CHNOSZ.1,5.May.78,979.29,1252.891,7.438,NA,7.092,6.74,1.6,0,0,0,0,0,1812 +iron,Fe,Fe,cr1,"RHF79.2 [S92]","Kel60.2 [S92]",5.May.78,0,0,6.52,NA,7.092,3.04,7.58,0.6,0,0,0,0,1033 +iron,Fe,Fe,cr2,"RHF79.2 [S92]",CHNOSZ.1,5.May.78,-618.237,-1768.418,2.662,NA,7.092,11.13,0,0,0,0,0,0,1183 +iron,Fe,Fe,cr3,"RHF79.2 [S92]",CHNOSZ.1,5.May.78,1293.526,1865.343,8.438,NA,7.092,5.8,1.98,0,0,0,0,0,1673 +iron,Fe,Fe,cr4,"RHF79.2 [S92]",CHNOSZ.1,5.May.78,979.29,1252.891,7.438,NA,7.092,6.74,1.6,0,0,0,0,0,1812 jadeite,Jd,NaAl(SiO3)2,cr,"HDNB78 [S92]",NA,5.May.78,-679445,-722116,31.9,NA,60.4,48.16,11.42,-11.87,0,0,0,0,1400 k-feldspar,K-Fs,K(AlSi3)O8,cr,"HDNB78 [S92]",NA,5.May.78,-895374,-949188,51.13,NA,108.87,76.617,4.311,-29.945,0,0,0,0,1400 k-phillipsite,K-Php,K2(Al2Si5)O14*5H2O,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,172.1,NA,265,152.66,60.24,-18.45,0,0,0,0,848 @@ -155,8 +155,8 @@ larnite,Lrn,Ca2SiO4,cr1,"HDNB78 [S92]","Kel60.1 [S92]",5.May.78,NA,NA,30.5,NA,51.6,34.87,9.74,-6.26,0,0,0,0,970 larnite,Lrn,Ca2SiO4,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,379.765,NA,30.1022,NA,51.6,32.16,11.02,0,0,0,0,0,1710 larnite,Lrn,Ca2SiO4,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-844.027,NA,18.2296,NA,51.6,49,0,0,0,0,0,0,2000 -laumontite,lamt,Ca(Al2Si4)O12*4H2O,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1596823,-1728664,116.1,NA,207.55,123.2,44.47,-16.43,0,0,0,0,1000 -lawsonite,Lws,CaAl2Si2O7(OH)2*H2O,cr1,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1073408,-1158104,55.8,NA,101.32,81.8,23.36,-16.26,0,0,0,0,848 +laumontite,lamt,Ca(Al2Si4)O12*4H2O,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1596823,-1728664,116.1,NA,207.55,123.2,44.47,-16.43,0,0,0,0,1000 +lawsonite,Lws,CaAl2Si2O7(OH)2*H2O,cr1,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1073408,-1158104,55.8,NA,101.32,81.8,23.36,-16.26,0,0,0,0,848 lawsonite,Lws,CaAl2Si2O7(OH)2*H2O,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-1073411.895,NA,54.5767,NA,101.32,84.99,17.1,-13.56,0,0,0,0,1000 leonhardite,Lnr,Ca2(Al4Si8)O24*7H2O,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,220.4,NA,407.86,235,88.94,-32.86,0,0,0,0,1000 lime,Lim,CaO,cr,"HDNB78 [S92]",NA,5.May.78,-144366,-151790,9.5,NA,16.764,11.67,1.08,-1.56,0,0,0,0,2000 @@ -171,9 +171,9 @@ magnetite,Mag,Fe3O4,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-240960.953,NA,34.9818,NA,44.524,48,0,0,0,0,0,0,1800 malachite,Mal,Cu2(OH)2(CO3),cr,"HDNB78 [S92]",NA,5.May.78,-214204,-251900,44.5,NA,54.86,27.76,43.78,-1.34,0,0,0,0,780 manganosite,Mng,MnO,cr,"HDNB78 [S92]","WEP+82.1 [S92]",5.May.78,-86735,-92070,14.27,NA,13.221,11.11,1.94,-0.88,0,0,0,0,1800 -margarite,Mrg,CaAl2(Al2Si2)O10(OH)2,cr1,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1394150,-1485803,63.8,NA,129.4,102.5,16.35,-28.05,0,0,0,0,848 +margarite,Mrg,CaAl2(Al2Si2)O10(OH)2,cr1,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1394150,-1485803,63.8,NA,129.4,102.5,16.35,-28.05,0,0,0,0,848 margarite,Mrg,CaAl2(Al2Si2)O10(OH)2,cr2,"HDNB78 [S92]",CHNOSZ.1,15.Mar.90,-1394146.105,NA,65.0233,NA,129.4,99.31,22.61,-30.75,0,0,0,0,1000 -merwinite,Mer,Ca3Mg(SiO4)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1036526,-1090796,60.5,NA,104.4,72.97,11.96,-14.44,0,0,0,0,1700 +merwinite,Mer,Ca3Mg(SiO4)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1036526,-1090796,60.5,NA,104.4,72.97,11.96,-14.44,0,0,0,0,1700 metacinnabar,Met-Cin,HgS,cr,"HDNB78 [S92]",NA,5.May.78,-10437,-11800,21.2,NA,30.169,10.52,3.63,0,0,0,0,0,1000 "microcline,maximum",Max-Mc,K(AlSi3)O8,cr,"HDNB78 [S92]",NA,5.May.78,-895374,-949188,51.13,NA,108.741,63.83,12.9,-17.05,0,0,0,0,1400 minnesotaite,Mnn,Fe3Si4O10(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,83.5,NA,147.86,88.31,42.61,-11.15,0,0,0,0,800 @@ -189,7 +189,7 @@ nickel,Ni,Ni,cr1,"HDNB78 [S92]",NA,5.May.78,0,0,7.14,NA,6.588,4.06,7.04,0,0,0,0,0,633 nickel,Ni,Ni,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,79.615,167.295,7.434,NA,6.588,6,1.8,0,0,0,0,0,1725 paragonite,Pg,NaAl2(AlSi3)O10(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-1326012,-1416963,66.4,NA,132.53,97.43,24.5,-26.44,0,0,0,0,1000 -pargasite,Prg,Na(Ca2Mg4Al)(Al2Si6)O22(OH)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-2846728,-3016624,160,NA,273.5,205.8,41.66,-50.21,0,0,0,0,1000 +pargasite,Prg,Na(Ca2Mg4Al)(Al2Si6)O22(OH)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-2846728,-3016624,160,NA,273.5,205.8,41.66,-50.21,0,0,0,0,1000 pd-oxyannite,Pd-Oxn,KFe3(AlSi3)O10(OH)O-,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,68.5,NA,143.2,88.34,54.12,-18.06,0,0,0,0,848 pd-oxyannite,Pd-Oxn,KFe3(AlSi3)O10(OH)O-,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-11.741,NA,64.83,NA,143.2,97.91,35.34,-9.96,0,0,0,0,950 pd-oxyannite,Pd-Oxn,KFe3(AlSi3)O10(OH)O-,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-255.019,NA,58.562,NA,143.2,116.68,7.44,-4.63,0,0,0,0,1050 @@ -197,7 +197,7 @@ periclase,Per,MgO,cr,"HDNB78 [S92]",NA,5.May.78,-136086,-143800,6.44,NA,11.248,10.18,1.74,-1.48,0,0,0,0,2100 phlogopite,Phl,KMg3(AlSi3)O10(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-1396187,-1488067,76.1,NA,149.66,100.61,28.78,-21.5,0,0,0,0,1000 "potassium oxide",K-Ox,K2O,cr,"HDNB78 [S92]",NA,5.May.78,-77056,-86800,22.5,NA,40.38,18.51,8.65,-0.88,0,0,0,0,1100 -prehnite,Prh,Ca2Al2Si3O10(OH)2,cr1,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1390097,-1481649,65,NA,140.33,91.6,37.82,-19.6,0,0,0,0,848 +prehnite,Prh,Ca2Al2Si3O10(OH)2,cr1,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1390097,-1481649,65,NA,140.33,91.6,37.82,-19.6,0,0,0,0,848 prehnite,Prh,Ca2Al2Si3O10(OH)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-1390108.741,NA,61.33,NA,140.33,101.17,19.04,-11.5,0,0,0,0,1000 pyrite,Py,FeS2,cr,"HDNB78 [S92]",NA,5.May.78,-38293,-41000,12.65,NA,23.94,17.88,1.32,-3.05,0,0,0,0,1000 pyrope,Prp,Mg3Al2Si3O12,cr1,"HDNB78 [S92]","RHF79.1 [S92]",5.May.78,NA,NA,62.3,NA,113.27,91.69,32.64,-20.92,0,0,0,0,848 @@ -233,11 +233,11 @@ sylvite,Sy,KCl,cr,"HDNB78 [S92]",NA,5.May.78,-97735,-104370,19.73,NA,37.524,9.89,5.2,0.77,0,0,0,0,1043 talc,Tcl,Mg3Si4O10(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-1320188,-1410920,62.34,NA,136.25,82.482,41.614,-13.342,0,0,0,0,800 tenorite,Tn,CuO,cr,"HDNB78 [S92]",NA,5.May.78,-30568,-37200,10.18,NA,12.22,11.53,1.88,-1.76,0,0,0,0,1600 -tremolite,Tr,(Ca2Mg5)Si8O22(OH)2,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-2770245,-2944038,131.19,NA,272.92,188.222,57.294,-44.822,0,0,0,0,800 -wairakite,Wai,Ca(Al2Si4)O12*2H2O,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1477432,-1579333,105.1,NA,186.87,100.4,44.47,-16.43,0,0,0,0,1000 -wollastonite,Wo,CaSiO3,cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-369225,-389590,19.6,NA,39.93,26.64,3.6,-6.52,0,0,0,0,1400 +tremolite,Tr,(Ca2Mg5)Si8O22(OH)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-2770245,-2944038,131.19,NA,272.92,188.222,57.294,-44.822,0,0,0,0,800 +wairakite,Wai,Ca(Al2Si4)O12*2H2O,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1477432,-1579333,105.1,NA,186.87,100.4,44.47,-16.43,0,0,0,0,1000 +wollastonite,Wo,CaSiO3,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-369225,-389590,19.6,NA,39.93,26.64,3.6,-6.52,0,0,0,0,1400 wurtzite,Wur,ZnS,cr,"HDNB78 [S92]",NA,5.May.78,-44810,-45850,14.064,NA,23.846,11.82,1.16,-1.04,0,0,0,0,1300 -zoisite,Zo,Ca2Al3Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2 [S92]",15.Mar.90,-1549179,-1643691,70.74,NA,135.9,106.118,25.214,-27.145,0,0,0,0,700 +zoisite,Zo,Ca2Al3Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1549179,-1643691,70.74,NA,135.9,106.118,25.214,-27.145,0,0,0,0,700 berndtite,Brn,SnS2,cr,"JH85 [S92]",NA,5.May.78,-34750,-36700,20.9,NA,40.96,15.51,4.2,0,0,0,0,0,1000 cassiterite,Cst,SnO2,cr,"JH85 [S92]",NA,5.May.78,-124260,-138800,12.5,NA,21.55,17.246,2.8026,-4.9001,0,0,0,0,1500 romarchite,Sn-Ox,SnO,cr,"JH85 [S92]",NA,5.May.78,-61459,-68340,13.66,NA,20.895,9.55,3.5,0,0,0,0,0,1237 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv 2017-03-01 13:12:27 UTC (rev 178) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv 2017-03-02 13:42:25 UTC (rev 179) @@ -1,13 +1,10 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T chlorargyrite,Crg,AgCl,cr,RHF79 [S92],Pan70 [S92],5.May.78,-26247,-30370,23,NA,25.727,14.33,1.821,-2.43,0,0,0,0,728 rutile,TiO2,TiO2,cr,RHF79 [S92],BH83 [S92],31.Mar.92,-212883,-226101,12.02,NA,18.82,15.01442,2.720501,-2.365364,0,0,0,0,1800 -titanite,Ti-SPHENE,CaTiSiO5,cr,RHF79 [S92],SPRONS92.1 [S92],31.Mar.92,-587349,-621180,30.88,NA,55.65,42.23422,5.703951,-9.525038,0,0,0,0,1800 -sulfur,Sul,S,cr1,Gur96,NA,5.Jul.04,0,0,7.6,,15.511,3.58,6.24,0,0,0,0,0,368.6 -sulfur,NA,S,cr2,Gur96,NA,5.Jul.04,14.792,70.499,7.7868,NA,16.49,3.56,6.96,0,0,0,0,0,392 -sulfur,NA,S,cr3,Gur96,NA,5.Jul.04,99.029,371.29,8.5131,NA,17.627,5.4,5,0,0,0,0,0,717.8 +titanite,Ti-SPHENE,CaTiSiO5,cr,RHF79 [S92],SPRONS92.1,31.Mar.92,-587349,-621180,30.88,NA,55.65,42.23422,5.703951,-9.525038,0,0,0,0,1800 natroalunite,NA,NaAl3(SO4)2(OH)6,cr,SAJ00,NA,13.Apr.09,-1104780.1,-1226570.3,76.74,NA,NA,153.322,-1.881,-55.956,0,0,0,0,NA jarosite,NA,KFe3(SO4)2(OH)6,cr,SAJ00,NA,13.Apr.09,-791061.2,-887930.2,92.949,NA,NA,147.44,23.599,-47.706,0,0,0,0,NA natrojarosite,NA,NaFe3(SO4)2(OH)6,cr,SAJ00,NA,13.Apr.09,-778370,-877892,91.396,NA,NA,147.321,21.8,-48.7,0,0,0,0,NA melanterite,NA,FeSO4*7H2O,cr,PK95,NA,13.Apr.09,-599366.6,-720028.7,97.801,NA,NA,0,0,0,0,0,0,0,NA -gypsum,NA,CaSO4*2H2O,cr,RH95,Kel60.2,22.Nov.15,-429493,-483509,46.32,NA,74.69,21.84,76,0,0,0,0,0,400 +gypsum,NA,CaSO4*2H2O,cr,RH95,Kel60.3,22.Nov.15,-429493,-483509,46.32,NA,74.69,21.84,76,0,0,0,0,0,400 MgSO4,NA,MgSO4,cr,WEP+82.2,NA,24.Nov.15,-279780,-307100,21.89,NA,NA,23.06,0,0,0,0,0,0,NA [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 179 From noreply at r-forge.r-project.org Fri Mar 3 17:50:00 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 3 Mar 2017 17:50:00 +0100 (CET) Subject: [CHNOSZ-commits] r180 - in pkg/CHNOSZ: . data inst inst/extdata/OBIGT inst/extdata/supcrt tests/testthat vignettes Message-ID: <20170303165000.334701884C4@r-forge.r-project.org> Author: jedick Date: 2017-03-03 17:49:59 +0100 (Fri, 03 Mar 2017) New Revision: 180 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Schulte_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_gas.csv pkg/CHNOSZ/inst/extdata/supcrt/compare.R pkg/CHNOSZ/inst/extdata/supcrt/newnames.csv pkg/CHNOSZ/inst/extdata/supcrt/read.supcrt.R pkg/CHNOSZ/tests/testthat/test-info.R pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/eos-regress.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd pkg/CHNOSZ/vignettes/obigt.bib Log: obigt.Rmd: document slop07.dat additions Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-03-02 13:42:25 UTC (rev 179) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-03 16:49:59 UTC (rev 180) @@ -1,6 +1,6 @@ -Date: 2017-03-02 +Date: 2017-03-03 Package: CHNOSZ -Version: 1.0.8-69 +Version: 1.0.8-70 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-03-02 13:42:25 UTC (rev 179) +++ pkg/CHNOSZ/data/refs.csv 2017-03-03 16:49:59 UTC (rev 180) @@ -26,7 +26,7 @@ SPRONS92.1,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", SPRONS92.2,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", Sho92,"E. L. Shock",1992,dipeptides,"Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V -Sho93,"E. L. Shock",1993,ethylacetate,"Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 +Sho93,"E. L. Shock",1993,"ethylacetate and acetamide","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 Sho93.1,"E. L. Shock",1993,"carbon monoxide and ethylene","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 SK93,"E. L. Shock and C. M. Koretsky",1993,"metal-acetate complexes","Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J SM93,"E. L. Shock and W. B. McKinnon",1993,"CO, HCN, urea","Icarus 106, 464-477",http://dx.doi.org/10.1006/icar.1993.1185 @@ -59,17 +59,21 @@ SLOP98.9,"E. L. Shock et al.",1998,""Corrected values based on data from @SK95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SLOP98.10,"E. L. Shock et al.",1998,""Corrected values based on data from @HSS95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SLOP98.11,"E. L. Shock et al.",1998,""Data and parameters as used by @MS97. "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP07.1,"E. L. Shock et al.",2007,"corrected charge of Pu(Oxal)+2","slop07.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP07.2,"E. L. Shock et al.",2007,"high-temperature HKF parameters from @AP01","slop07.dat computer data file",http://geopig.asu.edu/?q=tools SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group ions and complexes","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 SS98a.1,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 +MS99,"W. M. Murphy and E. L. Shock",1999,"actinides","Rev. Mineral. Geochem. 38, 221-253",http://rimg.geoscienceworld.org/content/38/1/221 PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"metal-dicarboxylate complexes","Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5 SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"jarosite, natroalunite, and natrojarosite","Rev. Mineral. Geochem. 40, 453-479",http://dx.doi.org/10.2138/rmg.2000.40.9 AP01,"J. P. Amend and A. V. Plyasunov",2001,carbohydrates,"Geochim. Cosmochim. Acta 65, 3901-3917",http://dx.doi.org/10.1016/S0016-7037(01)00707-4 AS01,"J. P. Amend and E. L. Shock",2001,"NO and N2O","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 +AS01.1,"J. P. Amend and E. L. Shock",2001,"selenium and molybdenite","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"ice polymorphs","Appl. Geochem. 16, 161-181",http://dx.doi.org/10.1016/S0883-2927(00)00025-1 -PS01,"A. V. Plyasunov and E. L. Shock",2001,cyclohexane,"Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0 +PS01,"A. V. Plyasunov and E. L. Shock",2001,"CO2, argon, benzene, cyclohexane, and xenon","Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0 Ric01,"L. Richard",2001,"organic sulfur compounds","Geochim. Cosmochim. Acta 65, 3827-3877",http://dx.doi.org/10.1016/S0016-7037(01)00761-X -SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"nonelectrolytes HKF heat capacity parameters","Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7 +SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6","Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7 MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"goethite, lepidocrocite, and maghemite GHS","Am. Mineral. 88, 855-859",http://dx.doi.org/10.2138/am-2003-5-614 MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"goethite, lepidocrocite, and maghemite Cp","Am. Mineral. 88, 846-854",http://dx.doi.org/10.2138/am-2003-5-613 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"hydronium jarosite","Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z @@ -85,6 +89,9 @@ CHNOSZ.1,"J. M. Dick",2017,"GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.","CHNOSZ package documentation",http://chnosz.net CHNOSZ.2,"J. M. Dick",2017,"The standard molal Gibbs energies and enthalpies of formation from the elements and entropies at 25 °C and 1 bar of aqueous metal-amino acid (alanate or glycinate) complexes reported by @SK95 were recalculated by adding the differences between values reported by @AH97b and @DLH06 for alanate or glycinate.","CHNOSZ package documentation",http://chnosz.net CHNOSZ.3,"J. M. Dick",2017,pseudo-H4SiO4,"CHNOSZ package documentation",http://chnosz.net +CHNOSZ.4,"J. M. Dick",2017,"AuCl4- renamed to AuCl4-3","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.5,"J. M. Dick",2017,"leucylglycine not in slop98.dat","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.6,"J. M. Dick",2017,"charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99","CHNOSZ package documentation",http://chnosz.net Dic07,"J. M. Dick",2007,"glutathione, cystine, and cystine sidechain","Ph.D. Dissertation, U.C. Berkeley", MA07,"L. Marini and M. Accornero",2007,"metal-arsenate and metal-arsenite complexes","Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5 Ric08,"L. Richard",2008,alkenes,"personal communication", Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-03-02 13:42:25 UTC (rev 179) +++ pkg/CHNOSZ/inst/NEWS 2017-03-03 16:49:59 UTC (rev 180) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-69 (2017-03-02) +CHANGES IN CHNOSZ 1.0.8-70 (2017-03-03) --------------------------------------- DOCUMENTATION: Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-03-02 13:42:25 UTC (rev 179) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-03-03 16:49:59 UTC (rev 180) @@ -1,40 +1,40 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -alanine,Ala,C3H7NO2,aq,AH97b,DLH06.1,25.Aug.06,-88810,-132500,38.83,33.6,60.4,14.9,1.74,7.16,-3.69,49.5,-7,0.18,0 -arginine,Arg,C6H14N4O2,aq,AH97b,DLH06.1,25.Aug.06,-57360,-143060,80.06,67.4,123.9,28.83,8.21,7.2,-5.95,94.8,-12.5,0.22,0 -argininium,Arg+,C6H15N4O2+,aq,AH97b,DLH06.1,25.Aug.06,-69930,-154880,82.57,77.6,122.5,31.72,0.22,5.46,-5.15,103.8,-9.6,0.73,0 -argininate,Arg-,C6H13N4O2-,aq,AH97b,DLH06.1,25.Aug.06,-40340,-129420,68.72,81.1,143,31.28,13.76,32.12,-9.94,141.9,-19.6,2.3,0 -asparagine,Asn,C4H8N2O3,aq,AH97b,DLH06.1,25.Aug.06,-125490,-182700,57.88,30.8,77.4,19.83,2.37,3.76,-4.81,56.5,-11.7,0.21,0 -"aspartic acid",Asp,C4H7NO4,aq,AH97b,DLH06.1,25.Aug.06,-172510,-226340,55.22,32.4,74.7,18.96,3.05,-6.62,-2.23,58.1,-11.9,0.17,0 -aspartate,Asp-,C4H6NO4-,aq,AH97b,DLH06.1,25.Aug.06,-167170,-224540,43.34,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,0 -cysteine,Cys,C3H7NO2S,aq,AH97b,DLH06.1,25.Aug.06,-80330,-124070,46.32,47.1,73.5,18.14,2.4,9.31,-4.97,59.8,-5.6,0.15,0 -cysteinate,Cys-,C3H6NO2S-,aq,AH97b,DLH06.1,25.Aug.06,-68920,-115440,37.01,19.1,60.6,14.43,5.11,12.35,-3.71,61,-9.5,2.48,0 -glutamine,Gln,C5H10N2O3,aq,AH97b,DLH06.1,25.Aug.06,-126280,-191860,62.41,43.8,93.7,23.22,3.58,5.44,-5.23,68.6,-11.4,0.18,0 -"glutamic acid",Glu,C5H9NO4,aq,AH97b,DLH06.1,25.Aug.06,-173050,-234820,61.2,43.5,90.2,22.3,4.23,6.55,-5.84,65.2,-10,0.15,0 -glutamate,Glu-,C5H8NO4-,aq,AH97b,DLH06.1,25.Aug.06,-167210,-234150,43.86,7.6,80,20.49,6.96,10.86,-7.02,47.6,-7.8,2.65,0 -glycine,Gly,C2H5NO2,aq,AH97b,DLH06.1,25.Aug.06,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0 -glycinium,Gly+,C2H6NO2+,aq,AH97b,DLH06.1,25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0 -histidine,His,C6H9N3O2,aq,AH97b,DLH06.1,25.Aug.06,-48420,-108200,66,56.2,99.3,24.32,4.8,7.52,-6.05,81.6,-11.3,0.27,0 -histidinium,His+,C6H10N3O2+,aq,AH97b,DLH06.1,25.Aug.06,-56700,-115250,70.13,59.1,97,26.64,-3.4,-0.88,-3.07,88,-12,0.5,0 -isoleucine,Ile,C6H13NO2,aq,AH97b,DLH06.1,25.Aug.06,-81990,-151600,49.7,91.6,105.8,24.49,6.55,18.16,-7.76,99.7,-3.6,0.09,0 -leucine,Leu,C6H13NO2,aq,AH97b,DLH06.1,25.Aug.06,-84200,-153600,50.41,95.2,107.8,24.68,7.51,19.93,-8.37,102.7,-3.3,0.09,0 -lysine,Lys,C6H14N2O2,aq,AH97b,DLH06.1,25.Aug.06,-80680,-159330,57.91,63.8,108.6,24.56,8.3,24.43,-9.53,86.6,-10.9,0.07,0 -lysinium,Lys+,C6H15N2O2+,aq,AH97b,DLH06.1,25.Aug.06,-92890,-170370,61.82,67.9,107.5,28.62,-1.51,4.47,-3.99,95.2,-8,1.21,0 -lysinate,Lys-,C6H13N2O2-,aq,AH97b,DLH06.1,25.Aug.06,-66310,-146340,53.27,72.8,112.2,28.29,10.53,2.97,-7.61,133.7,-18,2.67,0 -phenylalanine,Phe,C9H11NO2,aq,AH97b,DLH06.1,25.Aug.06,-49430,-108900,56.6,93.8,122.1,28.27,8.8,19.34,-9.38,108.1,-6.5,0.12,0 -proline,Pro,C5H9NO2,aq,AH97b,DLH06.1,25.Aug.06,-73560,-124100,49.83,43,82.6,19.39,4.87,11.88,-5.68,63.6,-9.5,0.14,0 -serine,Ser,C3H7NO3,aq,AH97b,DLH06.1,25.Aug.06,-123930,-172420,47.24,27.8,60.6,15.69,0.73,3.87,-3.49,48.5,-9.4,0.18,0 -threonine,Thr,C4H9NO3,aq,AH97b,DLH06.1,25.Aug.06,-119830,-178940,44.23,50.1,77.6,18.94,2.83,8.87,-4.87,65.5,-7.1,0.11,0 -tryptophan,Trp,C11H12N2O2,aq,AH97b,DLH06.1,25.Aug.06,-26820,-97590,59.96,99.6,143.6,33.91,9.21,14.78,-9.36,116.8,-7.8,0.15,0 -tyrosine,Tyr,C9H11NO3,aq,AH97b,DLH06.1,25.Aug.06,-91800,-157740,59.41,80.2,124.5,30.06,8.49,8.36,-8.58,106.2,-12.4,0.09,0 -tyrosinate,Tyr-,C9H10NO3-,aq,AH97b,DLH06.1,25.Aug.06,-79380,-149420,45.66,51.2,111.8,26.34,10.49,16.42,-7.59,109,-16,2.78,0 -valine,Val,C5H11NO2,aq,AH97b,DLH06.1,25.Aug.06,-85330,-146420,45.68,74,90.9,21.35,4.48,14.58,-6.12,83.8,-4.3,0.12,0 -xylose,xylose,C5H10O5,aq,AP01,NA,24.Aug.06,-179371.414913958,-249937.858508604,48.7332695984704,65.9655831739962,95.7,22.5860420650096,0.90822179732314,4.78011472275335,-2.77246653919694,90.9177820267686,-17.5908221797323,-1.31453154875717,0 -arabinose,arabinose,C5H10O5,aq,AP01,NA,24.Aug.06,-177397.227533461,-249471.797323136,43.6663479923518,67.1606118546845,93.3,22.538240917782,0.81261950286807,3.99139579349904,-3.48948374760994,93.7619502868069,-18.4034416826004,-1.31453154875717,0 -lyxose,lyxose,C5H10O5,aq,AP01,NA,24.Aug.06,-179048.757170172,-250164.913957935,47.0841300191205,67.3996175908222,94.2,22.6577437858509,1.2906309751434,1.7925430210325,-3.10707456978967,93.9292543021032,-18.4034416826004,-1.31453154875717,0 -xylulose,xylulose,C5H10O5,aq,AP01,NA,24.Aug.06,-178334.13001912,-246092.256214149,58.1500956022945,76.2428298279159,94.7,22.3231357552581,1.91204588910134,5.32982791586998,-3.58508604206501,102.772466539197,-18.4034416826004,-1.31453154875717,0 -ribulose,ribulose,C5H10O5,aq,AP01,NA,24.Aug.06,-175893.881453155,-244507.648183556,55.2820267686424,76.2428298279159,94.7,22.3231357552581,1.91204588910134,5.32982791586998,-3.58508604206501,102.772466539197,-18.4034416826004,-1.31453154875717,0 -glucose,glucose,C6H12O6,aq,AP01,NA,24.Aug.06,-218905.353728489,-301670.650095602,64.8900573613767,86.7590822179732,112.2,25.5258126195029,3.10707456978967,12.3804971319312,-4.87571701720841,89.7227533460803,-7.88718929254302,-1.5774378585086,0 -mannose,mannose,C6H12O6,aq,AP01,NA,24.Aug.06,-217731.835564054,-300826.959847036,63.7906309751434,81.2619502868069,111.9,26.84034416826,0.47801147227534,1.7208413001912,-2.74856596558317,91.3240917782027,-11.3049713193117,-1.5774378585086,0 -galactose,galactose,C6H12O6,aq,AP01,NA,24.Aug.06,-217239.48374761,-300000,64.9139579349904,90.5831739961759,110.7,26.7208413001912,-0.1434034416826,2.67686424474187,-2.96367112810707,99.7131931166348,-11.1376673040153,-1.5774378585086,0 -fructose,fructose,C6H12O6,aq,AP01,NA,24.Aug.06,-218812.141491396,-300999.043977055,66.8260038240918,84.1300191204589,111,25.8604206500956,4.51720841300191,8.98661567877629,-6.04684512428298,107.433078393881,-17.9015296367113,-1.5774378585086,0 -sorbose,sorbose,C6H12O6,aq,AP01,NA,24.Aug.06,-217961.281070746,-301935.946462715,60.8508604206501,84.1300191204589,111,25.8604206500956,4.51720841300191,8.98661567877629,-6.04684512428298,107.433078393881,-17.9015296367113,-1.5774378585086,0 +alanine,Ala,C3H7NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-88810,-132500,38.83,33.6,60.4,14.9,1.74,7.16,-3.69,49.5,-7,0.18,0 +arginine,Arg,C6H14N4O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-57360,-143060,80.06,67.4,123.9,28.83,8.21,7.2,-5.95,94.8,-12.5,0.22,0 +argininium,Arg+,C6H15N4O2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-69930,-154880,82.57,77.6,122.5,31.72,0.22,5.46,-5.15,103.8,-9.6,0.73,0 +argininate,Arg-,C6H13N4O2-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-40340,-129420,68.72,81.1,143,31.28,13.76,32.12,-9.94,141.9,-19.6,2.3,0 +asparagine,Asn,C4H8N2O3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-125490,-182700,57.88,30.8,77.4,19.83,2.37,3.76,-4.81,56.5,-11.7,0.21,0 +"aspartic acid",Asp,C4H7NO4,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-172510,-226340,55.22,32.4,74.7,18.96,3.05,-6.62,-2.23,58.1,-11.9,0.17,0 +aspartate,Asp-,C4H6NO4-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-167170,-224540,43.34,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,0 +cysteine,Cys,C3H7NO2S,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-80330,-124070,46.32,47.1,73.5,18.14,2.4,9.31,-4.97,59.8,-5.6,0.15,0 +cysteinate,Cys-,C3H6NO2S-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-68920,-115440,37.01,19.1,60.6,14.43,5.11,12.35,-3.71,61,-9.5,2.48,0 +glutamine,Gln,C5H10N2O3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-126280,-191860,62.41,43.8,93.7,23.22,3.58,5.44,-5.23,68.6,-11.4,0.18,0 +"glutamic acid",Glu,C5H9NO4,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-173050,-234820,61.2,43.5,90.2,22.3,4.23,6.55,-5.84,65.2,-10,0.15,0 +glutamate,Glu-,C5H8NO4-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-167210,-234150,43.86,7.6,80,20.49,6.96,10.86,-7.02,47.6,-7.8,2.65,0 +glycine,Gly,C2H5NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0 +glycinium,Gly+,C2H6NO2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0 +histidine,His,C6H9N3O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-48420,-108200,66,56.2,99.3,24.32,4.8,7.52,-6.05,81.6,-11.3,0.27,0 +histidinium,His+,C6H10N3O2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-56700,-115250,70.13,59.1,97,26.64,-3.4,-0.88,-3.07,88,-12,0.5,0 +isoleucine,Ile,C6H13NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-81990,-151600,49.7,91.6,105.8,24.49,6.55,18.16,-7.76,99.7,-3.6,0.09,0 +leucine,Leu,C6H13NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-84200,-153600,50.41,95.2,107.8,24.68,7.51,19.93,-8.37,102.7,-3.3,0.09,0 +lysine,Lys,C6H14N2O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-80680,-159330,57.91,63.8,108.6,24.56,8.3,24.43,-9.53,86.6,-10.9,0.07,0 +lysinium,Lys+,C6H15N2O2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-92890,-170370,61.82,67.9,107.5,28.62,-1.51,4.47,-3.99,95.2,-8,1.21,0 +lysinate,Lys-,C6H13N2O2-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-66310,-146340,53.27,72.8,112.2,28.29,10.53,2.97,-7.61,133.7,-18,2.67,0 +phenylalanine,Phe,C9H11NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-49430,-108900,56.6,93.8,122.1,28.27,8.8,19.34,-9.38,108.1,-6.5,0.12,0 +proline,Pro,C5H9NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-73560,-124100,49.83,43,82.6,19.39,4.87,11.88,-5.68,63.6,-9.5,0.14,0 +serine,Ser,C3H7NO3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-123930,-172420,47.24,27.8,60.6,15.69,0.73,3.87,-3.49,48.5,-9.4,0.18,0 +threonine,Thr,C4H9NO3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-119830,-178940,44.23,50.1,77.6,18.94,2.83,8.87,-4.87,65.5,-7.1,0.11,0 +tryptophan,Trp,C11H12N2O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-26820,-97590,59.96,99.6,143.6,33.91,9.21,14.78,-9.36,116.8,-7.8,0.15,0 +tyrosine,Tyr,C9H11NO3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-91800,-157740,59.41,80.2,124.5,30.06,8.49,8.36,-8.58,106.2,-12.4,0.09,0 +tyrosinate,Tyr-,C9H10NO3-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-79380,-149420,45.66,51.2,111.8,26.34,10.49,16.42,-7.59,109,-16,2.78,0 +valine,Val,C5H11NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-85330,-146420,45.68,74,90.9,21.35,4.48,14.58,-6.12,83.8,-4.3,0.12,0 +xylose,xylose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-179252,-249771,48.7,65.97,95.7,22.5,5.016,7.715,-4.681,107.74,-19.896,0.1672,0 +arabinose,arabinose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-177279,-249305,43.64,67.16,93.3,22.48,4.92,6.903,-5.398,110.75,-20.78,0.1672,0 +lyxose,lyxose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-178929,-249998,47.05,67.4,94.2,22.64,5.493,4.419,-5.064,110.97,-20.78,0.1672,0 +xylulose,xylulose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-178215,-245928,58.11,76.24,94.7,22.33,5.971,7.715,-5.493,119.81,-20.78,0.1672,0 +ribulose,ribulose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-175776,-244344,55.25,76.24,94.7,22.33,5.971,7.715,-5.493,119.81,-20.78,0.1672,0 +glucose,glucose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-218759,-301469,64.85,86.76,112.2,26.3,6.831,10.485,-6.306,115.89,-12.826,0.215,0 +mannose,mannose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-217586,-300626,63.75,81.26,111.9,26.56,5.446,6.712,-5.064,111.78,-14.14,0.215,0 +galactose,galactose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-217094,-299800,64.87,90.58,110.7,27.25,4.825,2.508,-5.279,128.07,-17.77,0.215,0 +fructose,fructose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-218666,-300798,66.78,84.13,111,26.23,7.5,9.554,-6.998,127.95,-20.756,0.215,0 +sorbose,sorbose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-217816,-301734,60.81,84.13,111,26.23,7.5,9.554,-6.998,127.95,-20.756,0.215,0 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv 2017-03-02 13:42:25 UTC (rev 179) +++ pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv 2017-03-03 16:49:59 UTC (rev 180) @@ -1,177 +1,177 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -adenine,NA,C5H5N5,aq,LH06a,NA,3.Feb.03,74770,31235,53.41,56.24,89.59,21.5046,8.501,-2.6632,-5.3561,97.68,-20.1,0.065,0 -guanine,NA,C5H5N5O,aq,LH06a,NA,3.Feb.03,16702,-34803,51.19,60.06,97.9,23.298,7.4602,-5.4837,-3.4136,103,-20.1,0.23,0 -cytosine,NA,C4H5N3O,aq,LH06a,NA,3.Feb.03,-8411,-46915,47.64,41.81,73.35,17.3106,5.8612,6.6034,-5.2201,70.51,-13.36,0.17,0 -thymine,NA,C5H6N2O2,aq,LH06a,NA,3.Feb.03,-61315,-104969,48.96,56.93,88.04,21.2655,7.2705,-1.0309,-5.0944,83.2,-12.39,0.12,0 -uracil,NA,C4H4N2O2,aq,LH06a,NA,3.Feb.03,-59734,-94587,45.88,36.19,71.55,17.5038,5.9312,-1.6074,-4.3091,56.57,-9.4,0.14,0 -ribose,NA,C5H10O5,aq,LH06a,NA,3.Feb.03,-179739,-247132,59.53,66.46,95.71,22.6455,7.293,-5.3875,-3.4054,134.7,-32.82,0.17,0 -deoxyribose,NA,C5H10O4,aq,LH06a,NA,3.Feb.03,-144433,-205037,57.82,56.16,94.65,22.537,7.2652,-5.3715,-3.404,124.4,-32.82,0.17,0 -adenosine,NA,C10H13N5O4,aq,LH06a,NA,3.Feb.03,-46499,-148490,87.19,120.3,170.7,39.5452,12.9013,8.9651,-8.8169,163.2,-20.1,0.23,0 -cytidine,NA,C9H13N3O5,aq,LH06a,NA,3.Feb.03,-130179,-226640,83.09,96.38,153.3,36.3116,7.996,7.5934,-6.5938,132.6,-16.3,0.34,0 -guanosine,NA,C10H13N5O5,aq,LH06a,NA,3.Feb.03,-105568,-214528,88.33,124.9,174.2,42.2627,8.3757,-2.4562,-5.8937,169.3,-20.1,0.39,0 -thymidine,NA,C10H14N2O6,aq,LH06a,NA,3.Feb.03,-183083,-284694,84.42,110.5,167.4,38.1602,10.9585,12.3953,-7.1879,143.4,-14.9,0.29,0 -uridine,NA,C9H12N2O6,aq,LH06a,NA,3.Feb.03,-181502,-274312,81.34,95.14,151.8,36.1528,7.091,5.1259,-5.6836,131.8,-16.65,0.31,0 -deoxyadenosine,NA,C10H13N5O3,aq,LH06a,NA,3.Feb.03,-11193,-106386,85.48,111.2,170,38.0314,16.957,15.1636,-10.834,154.2,-20.1,0.23,0 -deoxycytidine,NA,C9H13N3O4,aq,LH06a,NA,24.Sep.06,-96652,-184534,87.35,87.28,154,35.8171,9.7174,7.4022,-6.5327,123.5,-16.3,0.34,0 -deoxyguanosine,NA,C10H13N5O4,aq,LH06a,NA,3.Feb.03,-71539,-176273,77.99,115.8,173.2,39.4526,15.4982,14.2847,-10.5692,160.3,-20.1,0.39,0 -deoxythymidine,NA,C10H14N2O5,aq,LH06a,NA,3.Feb.03,-149556,-242588,88.68,101.4,167.5,38.8728,11.4509,-7.7797,-3.6098,134.4,-14.9,0.29,0 -deoxyuridine,NA,C9H12N2O5,aq,LH06a,NA,3.Feb.03,-147975,-232206,85.59,86.04,151.2,35.5945,9.6188,3.5015,-6.2803,122.8,-16.65,0.31,0 -AMP-2,NA,C10H12N5O7P-2,aq,LH06a,NA,3.Feb.03,-247417,-389148,52.89,61.68,161.03,2.3198,108.8148,-18.734,-1.7194,130.2,-19.82,3.1,-2 -HAMP-,NA,C10H13N5O7P-,aq,LH06a,NA,3.Feb.03,-255617,-388308,83.21,114.39,187.55,2.4065,126.2531,-19.139,-2.4403,187.95,-22.3,3.1,-1 -H2AMP,NA,C10H14N5O7P,aq,LH06a,NA,3.Feb.03,-260817,-392608,86.23,120.01,187.02,2.3993,124.8091,-19.105,-2.3806,181.6,-19.1,2.5,0 -CMP-2,NA,C9H12N3O8P-2,aq,LH06a,NA,3.Feb.03,-331097,-467460,48.24,37.71,142.39,2.2606,96.923,-18.459,-1.2278,101.1,-16.4,3.3,-2 -HCMP-,NA,C9H13N3O8P1-,aq,LH06a,NA,3.Feb.03,-340147,-466110,83.09,90.6,168.91,2.3474,114.3613,-18.863,-1.9487,158.79,-18.76,3.3,-1 -H2CMP,NA,C9H14N3O8P,aq,LH06a,NA,3.Feb.03,-345343,-470410,86.18,96.06,168.37,2.3411,113.0988,-18.834,-1.8965,154.1,-16.01,2.8,0 -GMP-2,NA,C10H12N5O8P-2,aq,LH06a,NA,3.Feb.03,-306486,-455676,52.39,65.81,159.8,2.3194,108.7392,-18.733,-1.7163,140.8,-21.21,3.5,-2 -HGMP-,NA,C10H13N5O8P-,aq,LH06a,NA,3.Feb.03,-315586,-454226,87.77,118.45,186.32,2.4062,126.1775,-19.137,-2.4372,198.5,-23.7,3.5,-1 -H2GMP,NA,C10H14N5O8P,aq,LH06a,NA,3.Feb.03,-320786,-458526,90.79,123.82,185.79,2.399,124.7309,-19.104,-2.3774,192.3,-20.7,2.9,0 -TMP-2,NA,C10H13N2O9P-2,aq,LH06a,NA,3.Feb.03,-384001,-525514,49.58,51.85,155.97,2.3042,105.675,-18.662,-1.5896,111,-14.76,3.2,-2 -HTMP-,NA,C10H14N2O9P-,aq,LH06a,NA,3.Feb.03,-393021,-524279,83.97,104.8,182.49,2.3909,123.1133,-19.066,-2.3105,168.7,-17.1,3.2,-1 -H2TMP,NA,C10H15N2O9P,aq,LH06a,NA,3.Feb.03,-398221,-528579,86.99,110.62,181.97,2.3838,121.6733,-19.033,-2.251,162.27,-13.76,2.6,0 -UMP-2,NA,C9H11N2O9P-2,aq,LH06a,NA,3.Feb.03,-382420,-515132,46.49,36.19,141.33,2.2572,96.226,-18.442,-1.199,101.1,-17.15,3.3,-2 -HUMP-,NA,C9H12N2O9P-,aq,LH06a,NA,3.Feb.03,-391470,-514012,80.6,89.05,167.85,2.3439,113.6643,-18.847,-1.9199,158.78,-19.52,3.3,-1 -H2UMP,NA,C9H13N2O9P,aq,LH06a,NA,3.Feb.03,-396670,-518312,83.62,94.7,167.31,2.3367,112.2177,-18.813,-1.8601,152.46,-16.32,2.7,0 -dAMP-2,NA,C10H12N5O6P-2,aq,LH06a,NA,3.Feb.03,-212111,-347206,50.63,53.02,160.05,2.3166,108.1737,-18.72,-1.6929,121.5,-19.8,3.1,-2 -dHAMP-,NA,C10H13N5O6P-,aq,LH06a,NA,3.Feb.03,-221205,-346166,84.61,105.7,186.57,2.4033,125.612,-19.124,-2.4138,179.3,-22.32,3.1,-1 -dH2AMP,NA,C10H14N5O6P,aq,LH06a,NA,3.Feb.03,-226401,-350466,87.62,111.28,186.05,2.3962,124.172,-19.091,-2.3543,172.91,-19.12,2.5,0 -dCMP-2,NA,C9H12N3O7P-2,aq,LH06a,NA,3.Feb.03,-297270,-425354,52.5,28.13,144.34,2.2679,98.3893,-18.493,-1.2884,94.34,-17.34,3.4,-2 -dHCMP-,NA,C9H13N3O7P-,aq,LH06a,NA,3.Feb.03,-306660,-424314,86.48,80.1,170.8,2.3547,115.8276,-18.987,-2.0093,152.04,-19.74,3.4,-1 -dH2CMP,NA,C9H14N3O7P,aq,LH06a,NA,3.Feb.03,-311860,-428614,89.5,86.59,170.32,2.3475,114.381,-18.864,-1.9495,145.71,-16.54,2.8,0 -dGMP-2,NA,C10H12N5O7P-2,aq,LH06a,NA,3.Feb.03,-272457,-417092,43.15,56.41,158.23,2.3143,107.7069,-18.709,-1.6736,131.4,-21.21,3.5,-2 -dHGMP-,NA,C10H13N5O7P-,aq,LH06a,NA,3.Feb.03,-281547,-416052,77.13,109.06,184.75,2.401,125.1452,-19.113,-2.3945,189.11,-23.7,3.5,-1 -dH2GMP,NA,C10H14N5O7P,aq,LH06a,NA,3.Feb.03,-286747,-420352,80.14,114.46,184.22,2.3938,123.6985,-19.08,-2.3347,182.88,-20.67,2.9,0 -dTMP-2,NA,C10H13N2O8P-2,aq,LH06a,NA,3.Feb.03,-350474,-483408,53.83,43.05,156.72,2.3066,106.1682,-18.673,-1.61,102.2,-14.76,3.2,-2 -dHTMP-,NA,C10H14N2O8P-,aq,LH06a,NA,3.Feb.03,-359564,-482368,87.81,96,183.24,2.3934,123.6065,-19.078,-2.3309,159.9,-17.1,3.2,-1 -dH2TMP,NA,C10H15N2O8P,aq,LH06a,NA,3.Feb.03,-364764,-486668,90.83,101.82,183.72,2.3862,122.1664,-19.044,-2.2714,153.47,-13.76,2.6,0 -dUMP-2,NA,C9H11N2O8P-2,aq,LH06a,NA,3.Feb.03,-348893,-473026,50.75,27.36,140.78,2.2549,95.7723,-18.432,-1.118,92.27,-17.15,3.3,-2 -dHUMP-,NA,C9H12N2O8P-,aq,LH06a,NA,3.Feb.03,-357983,-471986,84.73,78.34,167.16,2.3417,113.2106,-18.836,-1.9011,149.97,-19.55,3.3,-1 -dH2UMP,NA,C9H13N2O8P,aq,LH06a,NA,3.Feb.03,-363183,-476286,87.74,85.83,166.62,2.3345,111.764,-18.803,-1.8413,143.65,-16.35,2.7,0 -ADP-3,NA,C10H12N5O10P2-3,aq,LH06a,NA,3.Feb.03,-452649,-624106,52.17,41.54,191.72,2.4286,130.6804,-19.242,-2.6233,128.7,-24.87,4.02,-3 -HADP-2,NA,C10H13N5O10P2-2,aq,LH06a,NA,3.Feb.03,-462549,-623266,88.2,107.59,202.95,2.4633,137.657,-19.403,-2.9117,186.2,-21.65,3.8,-2 -H2ADP-,NA,C10H14N5O10P2-,aq,LH06a,NA,3.Feb.03,-468249,-627666,92.56,136.4,202.41,2.4533,135.6647,-19.357,-2.8294,193.1,-14.9,2.9,-1 -H3ADP,NA,C10H15N5O10P2,aq,LH06a,NA,3.Feb.03,-470749,-625106,109.53,169.36,207.55,2.4543,135.8481,-19.361,-2.837,204,-11.89,1.15,0 -CDP-3,NA,C9H12N3O11P2-3,aq,LH06a,NA,3.Feb.03,-536329,-702338,47.8,18.49,173.36,2.3692,118.7524,-18.965,-2.1302,99.37,-21.42,4.1,-3 -HCDP-2,NA,C9H13N3O11P2-2,aq,LH06a,NA,3.Feb.03,-546119,-700998,85.13,83.59,184.3,2.4041,125.7619,-19.128,-2.42,157.12,-18.25,4,-2 -H2CDP-,NA,C9H14N3O11P2-,aq,LH06a,NA,3.Feb.03,-551819,-705398,89.49,112.41,183.77,2.3942,123.7696,-19.081,-2.3376,163.98,-11.48,3.1,-1 -H3CDP,NA,C9H15N3O11P2,aq,LH06a,NA,3.Feb.03,-554319,-702838,106.64,145.32,188.96,2.3951,123.9596,-19.086,-2.3255,174.98,-8.545,1.35,0 -GDP-3,NA,C10H12N5O11P2-3,aq,LH06a,NA,3.Feb.03,-511718,-690384,52.51,45.87,190.49,2.4273,130.4371,-19.236,-2.6133,137.7,-25.78,4.33,-3 -HGDP-2,NA,C10H13N5O11P2-2,aq,LH06a,NA,3.Feb.03,-521518,-688904,90.34,111.91,201.71,2.4619,137.394,-19.397,-2.9009,194.96,-22.49,4.1,-2 -H2GDP-,NA,C10H14N5O11P2-,aq,LH06a,NA,3.Feb.03,-527218,-693304,94.7,140.73,201.18,2.452,135.4017,-19.351,-2.8185,201.79,-15.7,3.2,-1 -H3GDP,NA,C10H15N5O11P2,aq,LH06a,NA,3.Feb.03,-529718,-690744,111.68,173.68,206.33,2.4525,135.4996,-19.353,-2.8226,212.04,-12.6,1.4,0 -TDP-3,NA,C10H13N2O12P2-3,aq,LH06a,NA,3.Feb.03,-589233,-760392,49.13,31.84,186.68,2.4128,127.511,-19.168,-2.4923,109.16,-19.67,4.1,-3 -HTDP-2,NA,C10H14N2O12P2-2,aq,LH06a,NA,3.Feb.03,-599033,-759182,86.06,97.83,197.9,2.4477,134.5205,-19.331,-2.7821,166.97,-16.54,3.9,-2 -H2TDP-,NA,C10H15N2O12P2-,aq,LH06a,NA,3.Feb.03,-604733,-763582,90.42,126.65,197.37,2.4377,132.5282,-19.284,-2.6997,173.85,-9.78,3,-1 -H3TDP,NA,C10H16N2O12P2,aq,LH06a,NA,3.Feb.03,-607233,-761022,107.39,159.63,202.5,2.4382,132.6196,-19.287,-2.7035,183.98,-6.602,1.2,0 -UDP-3,NA,C9H11N2O12P2-3,aq,LH06a,NA,3.Feb.03,-587652,-750010,46.04,16.08,172.03,2.3658,118.0554,-18.949,-2.1014,99.37,-22.16,4.2,-3 -HUDP-2,NA,C9H12N2O12P2-2,aq,LH06a,NA,3.Feb.03,-597432,-748930,82.47,82.09,183.24,2.4006,125.0649,-19.111,-2.3912,157.12,-18.99,4,-2 -H2UDP-,NA,C9H13N2O12P2-,aq,LH06a,NA,3.Feb.03,-603132,-753330,86.83,110.91,182.71,2.3907,123.0725,-19.065,-2.3088,163.98,-12.22,3.1,-1 -H3UDP,NA,C9H14N2O12P2,aq,LH06a,NA,3.Feb.03,-605632,-750770,103.8,143.87,187.85,2.3912,123.1705,-19.067,-2.3129,174.16,-9.078,1.3,0 -dADP-3,NA,C10H12N5O9P2-3,aq,LH06a,NA,3.Feb.03,-417343,-582164,49.91,32.91,190.75,2.4254,130.0426,-19.227,-2.597,120.03,-24.85,4.02,-3 -dHADP-2,NA,C10H13N5O9P2-2,aq,LH06a,NA,3.Feb.03,-427243,-581324,85.94,98.91,201.98,2.4601,137.0192,-19.389,-2.8854,177.46,-21.62,3.8,-2 -dH2ADP-,NA,C10H14N5O9P2-,aq,LH06a,NA,3.Feb.03,-432943,-585742,90.3,127.72,201.44,2.4502,135.0269,-19.342,-2.803,184.36,-14.87,2.9,-1 -dH3ADP,NA,C10H15N5O9P2,aq,LH06a,NA,3.Feb.03,-435443,-583164,107.27,160.66,206.58,2.4511,135.2103,-19.347,-2.8106,195.24,-11.86,1.15,0 -dCDP-3,NA,C9H12N3O10P2-3,aq,LH06a,NA,3.Feb.03,-502802,-660232,52.05,10.69,175.45,2.3761,120.1267,-18.997,-2.187,91.57,-21.42,4.1,-3 -dHCDP-2,NA,C9H13N3O10P2-2,aq,LH06a,NA,3.Feb.03,-512592,-658892,89.39,74.99,186.25,2.4105,127.0442,-19.157,-2.473,148.52,-18.25,4,-2 -dH2CDP-,NA,C9H14N3O10P2-,aq,LH06a,NA,3.Feb.03,-518292,-663292,93.75,103.81,185.72,2.4006,125.0518,-19.11,-2.3906,155.38,-11.48,3.1,-1 -dH3CDP,NA,C9H15N3O10P2,aq,LH06a,NA,3.Feb.03,-520792,-660732,110.72,135.91,190.73,2.401,125.1498,-19.113,-2.3947,165.57,-8.545,1.35,0 -dGDP-3,NA,C10H12N5O10P2-3,aq,LH06a,NA,3.Feb.03,-477689,-651800,43.27,36.48,188.92,2.4222,129.4048,-19.212,-2.5706,128.31,-25.78,4.33,-3 -dHGDP-2,NA,C10H13N5O10P2-2,aq,LH06a,NA,3.Feb.03,-487489,-650320,81.11,102.51,200.14,2.4568,136.3617,-19.373,-2.8582,185.56,-22.49,4.1,-2 -dH2GDP-,NA,C10H14N5O10P2-,aq,LH06a,NA,3.Feb.03,-493189,-654720,85.47,131.33,199.61,2.4469,134.3693,-19.327,-2.7758,192.39,-15.7,3.2,-1 -dH3GDP,NA,C10H15N5O10P2,aq,LH06a,NA,3.Feb.03,-495689,-652160,102.44,164.28,204.76,2.4474,134.4673,-19.329,-2.7799,202.64,-12.6,1.4,0 -dTDP-3,NA,C10H13N2O11P2-3,aq,LH06a,NA,3.Feb.03,-555706,-718286,53.39,22.98,187.42,2.4152,127.9976,-19.179,-2.5124,100.36,-19.7,4.1,-3 -dHTDP-2,NA,C10H14N2O11P2-2,aq,LH06a,NA,3.Feb.03,-565506,-717076,90.31,88.99,198.65,2.4501,135.0137,-19.342,-2.8025,158.13,-16.54,3.9,-2 -dH2TDP-,NA,C10H15N2O11P2-1,aq,LH06a,NA,3.Feb.03,-571206,-721476,94.67,117.81,198.12,2.4402,133.0213,-19.296,-2.7201,165.01,-9.78,3,-1 -dH3TDP,NA,C10H16N2O11P2,aq,LH06a,NA,3.Feb.03,-573706,-718916,111.65,150.79,203.25,2.4406,133.1127,-19.298,-2.7239,175.14,-6.602,1.2,0 -dUDP-3,NA,C9H11N2O11P2-3,aq,LH06a,NA,3.Feb.03,-554125,-707904,50.3,7.25,171.34,2.3635,117.6017,-18.938,-2.0827,90.54,-22.16,4.2,-3 -dHUDP-2,NA,C9H12N2O11P2-2,aq,LH06a,NA,3.Feb.03,-563905,-706842,86.73,73.26,182.55,2.3984,124.6112,-19.101,-2.3724,148.29,-18.99,4,-2 -dH2UDP-,NA,C9H13N2O11P2-,aq,LH06a,NA,3.Feb.03,-569605,-711224,91.09,102.08,182.02,2.3885,122.6188,-19.055,-2.2901,155.15,-12.22,3.1,-1 -dH3UDP,NA,C9H14N2O11P2,aq,LH06a,NA,3.Feb.03,-572105,-708664,108.06,135.04,187.16,2.3889,122.7168,-19.057,-2.2941,165.33,-9.078,1.3,0 -ATP-4,NA,C10H12N5O13P3-4,aq,LH06a,NA,4.Feb.03,-657038,-859264,47.96,21.34,196.77,2.454,135.7876,-19.36,-2.8345,131.94,-31.94,5,-4 -HATP-3,NA,C10H13N5O13P3-3,aq,LH06a,NA,4.Feb.03,-667538,-857864,87.87,92.83,212.26,2.5037,145.789,-19.592,-3.2479,199.18,-30.37,4.9,-3 -H2ATP-2,NA,C10H14N5O13P3-2,aq,LH06a,NA,4.Feb.03,-673738,-861764,95.59,133.39,211.73,2.5002,145.0789,-19.576,-3.2186,239.28,-31.04,4.7,-2 -H3ATP-,NA,C10H15N5O13P3-,aq,LH06a,NA,4.Feb.03,-676438,-860264,109.67,194.02,222.95,2.535,152.0884,-19.738,-3.5083,296.43,-30.22,4.5,-1 -H4ATP,NA,C10H16N5O13P3,aq,LH06a,NA,4.Feb.03,-678500,-858553,122.33,250.04,228.09,2.5509,155.2834,-19.812,-3.6404,351.9,-30.4,4.4,0 -CTP-4,NA,C9H12N3O14P3-4,aq,LH06a,NA,4.Feb.03,-740718,-937496,43.58,-2.79,178.13,2.3948,123.8925,-19.084,-2.3427,99.59,-27.07,5.2,-4 -HCTP-3,NA,C9H13N3O14P3-3,aq,LH06a,NA,4.Feb.03,-751148,-935746,84.44,67.84,193.62,2.4446,133.9005,-19.316,-2.7564,171.02,-27.91,5.1,-3 -H2CTP-2,NA,C9H14N3O14P3-2,aq,LH06a,NA,4.Feb.03,-757348,-939646,92.15,108.54,193.09,2.441,133.1837,-19.3,-2.7268,211.07,-28.49,4.9,-2 -H3CTP-,NA,C9H15N3O14P3-,aq,LH06a,NA,4.Feb.03,-760048,-938146,106.24,169.34,204.31,2.4759,140.1998,-19.462,-3.0169,268.1,-27.53,4.7,-1 -H4CTP,NA,C9H16N3O14P3,aq,LH06a,NA,4.Feb.03,-762090,-936314,119.23,225,209.45,2.4918,143.3949,-19.536,-3.1489,323.3,-27.75,4.6,0 -GTP-4,NA,C10H12N5O14P3-4,aq,LH06a,NA,4.Feb.03,-716107,-925542,48.3,25.36,195.54,2.4522,135.4326,-19.352,-2.8198,136.09,-30.73,5.3,-4 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 180 From noreply at r-forge.r-project.org Sat Mar 4 08:24:48 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 4 Mar 2017 08:24:48 +0100 (CET) Subject: [CHNOSZ-commits] r181 - in pkg/CHNOSZ: . R data inst inst/extdata/OBIGT inst/extdata/supcrt man vignettes Message-ID: <20170304072448.2871F186959@r-forge.r-project.org> Author: jedick Date: 2017-03-04 08:24:47 +0100 (Sat, 04 Mar 2017) New Revision: 181 Removed: pkg/CHNOSZ/inst/extdata/OBIGT/Canovas_aq.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/EOSregress.R pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/data/thermo.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Majzlan_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Other_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/Richard_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/Tardy_cr.csv pkg/CHNOSZ/inst/extdata/supcrt/compare.R pkg/CHNOSZ/inst/extdata/supcrt/newnames.csv pkg/CHNOSZ/man/EOSregress.Rd pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/eos-regress.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd pkg/CHNOSZ/vignettes/obigt.bib pkg/CHNOSZ/vignettes/vig.bib Log: obigt.Rmd: document slop15.dat additions Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-04 07:24:47 UTC (rev 181) @@ -1,6 +1,6 @@ -Date: 2017-03-03 +Date: 2017-03-04 Package: CHNOSZ -Version: 1.0.8-70 +Version: 1.0.8-71 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/EOSregress.R =================================================================== --- pkg/CHNOSZ/R/EOSregress.R 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/R/EOSregress.R 2017-03-04 07:24:47 UTC (rev 181) @@ -128,7 +128,8 @@ } EOSplot <- function(exptdata, var=NULL, T.max=9999, T.plot=NULL, - fun.legend="topleft", coefficients=NULL, add=FALSE, lty=1, ...) { + fun.legend="topleft", coefficients=NULL, add=FALSE, + lty=par("lty"), col=par("col"), ...) { # plot experimental and modelled volumes and heat capacities # first figure out the property (Cp or V) from the exptdata prop <- colnames(exptdata)[3] @@ -170,7 +171,7 @@ message("EOSplot: plotting line for P=", P, " bar") xs <- seq(xlim[1], xlim[2], length.out=200) calc.X <- EOScalc(coefficients, xs, P, ...) - lines(xs, calc.X, lty=lty) + lines(xs, calc.X, lty=lty, col=col) # make legend if(!is.null(fun.legend) & !add) { # 20161101: negate QBorn and V_s_var Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/data/refs.csv 2017-03-04 07:24:47 UTC (rev 181) @@ -25,7 +25,8 @@ Joh92a,"J. W. Johnson",1992,"steam, Cp represented by Maier-Kelley equation","personal communication", SPRONS92.1,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", SPRONS92.2,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", -Sho92,"E. L. Shock",1992,dipeptides,"Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V +SPRONS92.3,"H. C. Helgeson et al.",1992,""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)."","slop98.dat computer data file", +Sho92,"E. L. Shock",1992,"diglycine, alanylglycine, leucylglycine, and diketopiperazine","Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V Sho93,"E. L. Shock",1993,"ethylacetate and acetamide","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 Sho93.1,"E. L. Shock",1993,"carbon monoxide and ethylene","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 SK93,"E. L. Shock and C. M. Koretsky",1993,"metal-acetate complexes","Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J @@ -35,6 +36,7 @@ PK95,"V. B. Parker and I. L. Khodakovskii",1995,melanterite,"J. Phys. Chem. Ref. Data 24, 1699-1745",http://dx.doi.org/10.1063/1.555964 RH95,"R. A. Robie and B. S. Hemingway",1995,"gypsum GHS","U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131 SK95,"E. L. Shock and C. M. Koretsky",1995,"metal-organic acid complexes","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8 +SK95.1,"E. L. Shock and C. M. Koretsky",1995,"alanate, glycinate and their complexes not included in later slop files.","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8 Sho95,"E. L. Shock",1995,"carboxylic acids","Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496 AH97b,"J. P. Amend and H. C. Helgeson",1997,"amino acids GHS","J. Chem. Soc., Faraday Trans. 93, 1927-1941",http://dx.doi.org/10.1039/A608126F DSM+97,"J. D. Dale, E. L. Shock et al.",1997,alkylphenols,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 @@ -47,6 +49,7 @@ SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"zincite and litharge","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"humic acid, microflora, and plants","C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 +HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"amino acids","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 RH98,"L. Richard and H. C. Helgeson",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 3591-3636",http://dx.doi.org/10.1016/S0016-7037(97)00345-1 SLOP98.1,"E. L. Shock et al.",1998,"zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SLOP98.2,"E. L. Shock et al.",1998,"daphnite; "Gf and Hf from @SS93a TMM"","slop98.dat computer data file",http://geopig.asu.edu/?q=tools @@ -59,8 +62,6 @@ SLOP98.9,"E. L. Shock et al.",1998,""Corrected values based on data from @SK95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SLOP98.10,"E. L. Shock et al.",1998,""Corrected values based on data from @HSS95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SLOP98.11,"E. L. Shock et al.",1998,""Data and parameters as used by @MS97. "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP07.1,"E. L. Shock et al.",2007,"corrected charge of Pu(Oxal)+2","slop07.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP07.2,"E. L. Shock et al.",2007,"high-temperature HKF parameters from @AP01","slop07.dat computer data file",http://geopig.asu.edu/?q=tools SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group ions and complexes","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 SS98a.1,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 @@ -71,29 +72,26 @@ AS01,"J. P. Amend and E. L. Shock",2001,"NO and N2O","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 AS01.1,"J. P. Amend and E. L. Shock",2001,"selenium and molybdenite","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"ice polymorphs","Appl. Geochem. 16, 161-181",http://dx.doi.org/10.1016/S0883-2927(00)00025-1 -PS01,"A. V. Plyasunov and E. L. Shock",2001,"CO2, argon, benzene, cyclohexane, and xenon","Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0 +PS01,"A. V. Plyasunov and E. L. Shock",2001,"aqueous nonelectrolytes","Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0 Ric01,"L. Richard",2001,"organic sulfur compounds","Geochim. Cosmochim. Acta 65, 3827-3877",http://dx.doi.org/10.1016/S0016-7037(01)00761-X SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6","Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7 MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"goethite, lepidocrocite, and maghemite GHS","Am. Mineral. 88, 855-859",http://dx.doi.org/10.2138/am-2003-5-614 MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"goethite, lepidocrocite, and maghemite Cp","Am. Mineral. 88, 846-854",http://dx.doi.org/10.2138/am-2003-5-613 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"hydronium jarosite","Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z SR04,"M. D. Schulte and K. L. Rogers",2004,"alkane thiols","Geochim. Cosmochim. Acta 68, 1087-1097",http://dx.doi.org/10.1016/j.gca.2003.06.001 -DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acid, protein, and organic groups","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 -DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acids HKF parameters","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 -DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Gly-X-Gly tripeptides","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"methyldiethanolamine and methyldiethanolammonium chloride","J. Chem. Thermodynamics 38, 988-1007",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013 LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"nucleic-acid bases, nucleosides, and nucleotides","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010 +LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"citric acid and citrate","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010 LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Mg-complexed adenosine nucleotides (ATP), NAD, and NADP","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008 LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"pyridine and piperidine","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008 +DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acid, protein, and organic groups","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 +DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acids HKF parameters","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 +DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Gly-X-Gly tripeptides","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"coquimbite, ferricopiapite, rhomboclase","Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175 -CHNOSZ.1,"J. M. Dick",2017,"GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.2,"J. M. Dick",2017,"The standard molal Gibbs energies and enthalpies of formation from the elements and entropies at 25 °C and 1 bar of aqueous metal-amino acid (alanate or glycinate) complexes reported by @SK95 were recalculated by adding the differences between values reported by @AH97b and @DLH06 for alanate or glycinate.","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.3,"J. M. Dick",2017,pseudo-H4SiO4,"CHNOSZ package documentation",http://chnosz.net -CHNOSZ.4,"J. M. Dick",2017,"AuCl4- renamed to AuCl4-3","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.5,"J. M. Dick",2017,"leucylglycine not in slop98.dat","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.6,"J. M. Dick",2017,"charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99","CHNOSZ package documentation",http://chnosz.net Dic07,"J. M. Dick",2007,"glutathione, cystine, and cystine sidechain","Ph.D. Dissertation, U.C. Berkeley", MA07,"L. Marini and M. Accornero",2007,"metal-arsenate and metal-arsenite complexes","Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5 +SLOP07.1,"E. L. Shock et al.",2007,"corrected charge of Pu(Oxal)+2","slop07.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP07.2,"E. L. Shock et al.",2007,"high-temperature HKF parameters from @AP01","slop07.dat computer data file",http://geopig.asu.edu/?q=tools Ric08,"L. Richard",2008,alkenes,"personal communication", GM09,"K.-D. Grevel and J. Majzlan",2009,"kieserite, starkeyite, hexahydrite, and epsomite","Geochim. Cosmochim. Acta 73, 6805 - 6815",http://dx.doi.org/10.1016/j.gca.2009.08.005 HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,kerogens,"Geochim. Cosmochim. Acta 73, 594-695",http://dx.doi.org/10.1016/j.gca.2008.03.004 @@ -101,9 +99,21 @@ MA10,"L. Marini and M. Accornero",2010,"corrected values","Environ. Earth Sci. 59, 1601-1606",http://dx.doi.org/10.1007/s12665-009-0369-x Sch10,"M. Schulte",2010,"organic sulfides","Aquat. Geochem. 16, 621-637",http://dx.doi.org/10.1007/s10498-010-9102-3 RG11,"L. Richard and X. Gaona",2011,"organic iodine compounds","Geochim. Cosmochim. Acta 75, 7304-7350",http://dx.doi.org/10.1016/j.gca.2011.07.030 -LD12,"D. E. LaRowe and J. M. Dick",2012,"amino acids and protein groups","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 -LD12.1,"D. E. LaRowe and J. M. Dick",2012,"methionine and methionine sidechain GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 +LD12,"D. E. LaRowe and J. M. Dick",2012,"4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 +LD12.1,"D. E. LaRowe and J. M. Dick",2012,"updated and corrected parameters for cysteine, glycine, leucine, and methionine","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 +LD12.2,"D. E. LaRowe and J. M. Dick",2012,"methionine GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 +LD12.3,"D. E. LaRowe and J. M. Dick",2012,"methionine sidechain GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"phenanthrene and methylphenanthrene isomers","Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020 +SLOP15.1,"E. L. Shock et al.",2015,""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP15.2,"E. L. Shock et al.",2015,""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools CS16,"P. A. Canovas III and E. L. Shock",2016,"citric acid cycle metabolites","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 -CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a1-a4 parameters","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 +CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a1--a4 parameters","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 UniProt,"The UniProt Consortium",2017,,"The UniProt knowledgebase",http://www.uniprot.org/ +CHNOSZ.1,"J. M. Dick",2017,"GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.2,"J. M. Dick",2017,"alanate and glycinate: GHS as used by @DLH06","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.3,"J. M. Dick",2017,"metal-amino acid complexes: GHS were recalculated by adding the differences between values from @AH97b and @DLH06 for alanate or glycinate to the properties of the complexes reported by @SK95.","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.4,"J. M. Dick",2017,pseudo-H4SiO4,"CHNOSZ package documentation",http://chnosz.net +CHNOSZ.5,"J. M. Dick",2017,"AuCl4- renamed to AuCl4-3","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.6,"J. M. Dick",2017,"dipeptides not included in slop files after slop98.dat","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.7,"J. M. Dick",2017,"charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.8,"J. M. Dick",2017,"Incorrect values of HKF *a*1--*a*4 parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here","CHNOSZ package documentation",http://chnosz.net Modified: pkg/CHNOSZ/data/thermo.R =================================================================== --- pkg/CHNOSZ/data/thermo.R 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/data/thermo.R 2017-03-04 07:24:47 UTC (rev 181) @@ -10,7 +10,7 @@ local({ # create obigt data frame sources_aq <- paste0(c("H2O", "Shock", "Amend", "Schulte", "LaRowe", "Dick", - "Tremaine", "Marini", "Canovas", "CHNOSZ"), "_aq") + "Tremaine", "Marini", "CHNOSZ"), "_aq") sources_cr <- paste0(c("Helgeson", "Shock", "Tardy", "Richard", "Majzlan", "LaRowe", "Other"), "_cr") sources_liq <- paste0(c("Richard", "LaRowe"), "_liq") sources_gas <- paste0(c("Wagman", "Shock", "Richard", "Other"), "_gas") Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/inst/NEWS 2017-03-04 07:24:47 UTC (rev 181) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-70 (2017-03-03) +CHANGES IN CHNOSZ 1.0.8-71 (2017-03-04) --------------------------------------- DOCUMENTATION: @@ -101,8 +101,13 @@ NEW AND OLD DATA: - Split OBIGT.csv and OBIGT-2.csv into multiple files according to - author names. All files are now under extdata/OBIGT/. + author names. All files are now under extdata/OBIGT/. Conflicting data + from OBIGT-2.csv were removed (see below). +- Citations in OBIGT now have a suffix (e.g. [S92] or [S98]) if the data + were first present in sprons92.dat from SUPCRT, slop98.dat, or later + versions of the slop data files (http://geopig.asu.edu/?q=tools). + - Canovas_aq.csv: Add data for citric acid cycle metabolites from Canovas and Shock, 2016. @@ -124,19 +129,23 @@ used in tests, examples, or vignettes, from OBIGT-2.csv to extdata/thermo (Ste01.csv and BZA10.csv). -- Remove other conflicting datasets previously in OBIGT-2.csv (21 - sources). +- Remove other conflicting datasets (i.e. that provide different data + for a species already in the database) previously listed in + OBIGT-2.csv (21 sources). - Replace GHS for iron (c2, c3) calculated in CHNOSZ with values derived from sprons92.dat. -- extdata: Add fasta/rubisco.fasta and cpetc/*.csv files SS98_Fig5a, - SS98_Fig5b, PM90 (all used in anintro.Rmd). - - Replace data for sulfur (cr) from Gurrieri, 1996, personal communication with that "as used by" McCollom and Shock, 1997 (from slop98.dat). +- Update selected nonelectrolytes with data from Plyasunov and Shock, + 2001, as listed in slop07.dat (http://geopig.asu.edu/?q=tools). + +- extdata: Add fasta/rubisco.fasta and cpetc/*.csv files SS98_Fig5a, + SS98_Fig5b, PM90 (all used in anintro.Rmd). + BUG FIXES: - Correct charge (-2) of NAD(red)-2 in LaRowe_aq.csv. Thanks to Peter Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-03-04 07:24:47 UTC (rev 181) @@ -7,7 +7,7 @@ "aspartic acid",Asp,C4H7NO4,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-172510,-226340,55.22,32.4,74.7,18.96,3.05,-6.62,-2.23,58.1,-11.9,0.17,0 aspartate,Asp-,C4H6NO4-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-167170,-224540,43.34,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,0 cysteine,Cys,C3H7NO2S,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-80330,-124070,46.32,47.1,73.5,18.14,2.4,9.31,-4.97,59.8,-5.6,0.15,0 -cysteinate,Cys-,C3H6NO2S-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-68920,-115440,37.01,19.1,60.6,14.43,5.11,12.35,-3.71,61,-9.5,2.48,0 +cysteinate,Cys-,C3H6NO2S-,aq,"AH97b [S07]","DLH06.1 [S07]",28.Nov.06,-68920,-115440,37.01,19.1,60.6,14.44,5.08,12.24,-3.68,61,-9.5,2.59,0 glutamine,Gln,C5H10N2O3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-126280,-191860,62.41,43.8,93.7,23.22,3.58,5.44,-5.23,68.6,-11.4,0.18,0 "glutamic acid",Glu,C5H9NO4,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-173050,-234820,61.2,43.5,90.2,22.3,4.23,6.55,-5.84,65.2,-10,0.15,0 glutamate,Glu-,C5H8NO4-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-167210,-234150,43.86,7.6,80,20.49,6.96,10.86,-7.02,47.6,-7.8,2.65,0 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv 2017-03-04 07:24:47 UTC (rev 181) @@ -1,2 +1,2 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -pseudo-H4SiO4,NA,H4SiO4,aq,CHNOSZ.3,NA,18.Feb.17,-312565,-346409,51.4246,-40.0964,52.1998,89.2031,-176.5071,-452.1431,101.36051,67.0854,-52.0776,0.1215745,0 +pseudo-H4SiO4,NA,H4SiO4,aq,CHNOSZ.4,NA,18.Feb.17,-312565,-346409,51.4246,-40.0964,52.1998,89.2031,-176.5071,-452.1431,101.36051,67.0854,-52.0776,0.1215745,0 Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/Canovas_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Canovas_aq.csv 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Canovas_aq.csv 2017-03-04 07:24:47 UTC (rev 181) @@ -1,25 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -"cis-aconitic acid",NA,C6H6O6,aq,CS16,NA,21.Dec.16,-236200,-291400,63.9,64,108.7,16.5766,30.8449,-2.4072,-4.0541,59.7379,1.3622,-0.164,0 -H2-cis-aconitate,NA,C6H5O6-,aq,CS16,NA,21.Dec.16,-233600,-290480,58.2,37.6,98.2,15.4873,28.376,-1.8452,-3.9521,51.8298,-3.6503,0.7477,-1 -H-cis-aconitate-2,NA,C6H4O6-2,aq,CS16,NA,21.Dec.16,-227700,-289900,40.4,-1.7,86.8,14.6306,26.4342,-1.4046,-3.8718,30.3757,-4.1266,2.601,-2 -cis-aconitate-3,NA,C6H3O6-3,aq,CS16,NA,21.Dec.16,-218970,-290700,8.4,-52.6,69.8,13.0954,22.9544,-0.6139,-3.7279,-0.2807,-4.7435,4.6843,-3 -"isocitric acid",NA,C6H8O7,aq,CS16,NA,21.Dec.16,-295880,-363960,76.4,74.5,114.3,17.3743,32.653,-2.817,-4.1289,68.8768,2.3996,-0.082,0 -H2-isocitrate,NA,C6H7O7-,aq,CS16,NA,21.Dec.16,-291390,-362960,64.7,48.1,103.8,16.2126,30.0199,-2.2197,-4.02,61.1741,-3.523,0.6493,-1 -H-isocitrate-2,NA,C6H6O7-2,aq,CS16,NA,21.Dec.16,-284960,-362380,45.1,8.8,92.4,15.3672,28.1034,-1.783,-3.9408,39.977,-3.9993,2.5298,-2 -isocitrate-3,NA,C6H5O7-3,aq,CS16,NA,21.Dec.16,-276230,-363180,13.1,-42.1,75.4,13.8316,24.623,-0.9928,-3.7969,9.3108,-4.6163,4.6132,-3 -"a-ketoglutaric acid",NA,C5H6O5,aq,CS16,NA,21.Dec.16,-201800,-245700,76.1,39.9,95.7,14.8287,26.8831,-1.5061,-3.8903,41.2055,-1.0189,-0.084,0 -H-a-ketoglutarate,NA,C5H5O5-,aq,CS16,NA,21.Dec.16,-198800,-242300,77.1,2.9,88.9,14.1054,25.2437,-1.1337,-3.8226,15.3765,-4.0709,0.4615,-1 -a-ketoglutarate-2,NA,C5H4O5-2,aq,CS16,NA,21.Dec.16,-191800,-240400,60.1,-49.9,82.7,13.9562,24.9058,-1.057,-3.8086,-19.3472,-4.7108,2.3026,-2 -H-succinate,NA,C4H5O4-,aq,CS16,NA,21.Dec.16,-172060,-217350,45.2,9.3,69.99,11.6617,19.7057,0.1226,-3.5935,26.1173,-3.9932,0.9446,-1 -succinate-2,NA,C4H4O4-2,aq,CS16,NA,21.Dec.16,-164380,-217350,19.5,-50.5,56.32,10.4577,15.8622,3.5716,-3.4346,-14.0383,-4.718,2.917,-2 -"fumaric acid",NA,C4H4O4,aq,CS16,NA,21.Dec.16,-154820,-186260,60.62,47,77.9,12.3542,21.2748,-0.2318,-3.6585,45.951,-0.3174,-0.186,0 -H-fumarate,NA,C4H3O4-,aq,CS16,NA,21.Dec.16,-150600,-186150,46.83,10,65.4,11.0637,18.3498,0.4327,-3.5376,26.4785,-3.9848,0.9199,-1 -fumarate-2,NA,C4H2O4-2,aq,CS16,NA,21.Dec.16,-144320,-186830,23.48,-42.8,51.7,9.9248,15.7683,1.0191,-3.4309,-7.3722,-4.6247,2.8572,-2 -"malic acid",NA,C4H6O5,aq,CS16,NA,21.Dec.16,-213530,-259310,68.21,56.43,82.22,12.9644,22.6577,-0.5461,-3.7157,53.9427,0.6143,-0.136,0 -H-malate,NA,C4H5O5-,aq,CS16,NA,21.Dec.16,-208810,-258610,54.75,19.4,75.4,12.3867,21.3482,-0.249,-3.6615,34.5541,-3.8709,0.8,-1 -malate-2,NA,C4H4O5-2,aq,CS16,NA,21.Dec.16,-201860,-258890,30.48,-33.4,69.19,12.2779,21.1017,-0.1928,-3.6513,0.8264,-4.5108,2.7512,-2 -"oxaloacetic acid",NA,C4H4O5,aq,CS16,NA,21.Dec.16,-200000,-235100,72.9,29.1,79.1,12.5492,21.7168,-0.3324,-3.6768,32.3818,-2.0859,-0.105,0 -H-oxaloacetate,NA,C4H3O5-,aq,CS16,NA,21.Dec.16,-196600,-231300,74,-7.9,72.3,11.8516,20.1357,0.0269,-3.6114,5.2703,-4.2017,0.5084,-1 -oxaloacetate-2,NA,C4H2O5-2,aq,CS16,NA,21.Dec.16,-190600,-230300,57.2,-60.7,66.1,11.7014,19.7949,0.1041,-3.5973,-29.4812,-4.8417,2.3465,-2 -"pyruvic acid",NA,CH3COCOOH,aq,CS16,NA,21.Dec.16,-117000,-140300,62.1,36.3,64.6,10.5381,17.1584,0.7032,-3.4883,37.4903,-1.3746,-0.176,0 -pyruvate,NA,CH3COCOO-,aq,CS16,NA,21.Dec.16,-113600,-137400,60.4,-3.7,51.5,9.0836,13.862,1.4526,-3.3521,11.2428,-4.1508,0.7144,-1 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-03-03 16:49:59 UTC (rev 180) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-03-04 07:24:47 UTC (rev 181) @@ -1,43 +1,45 @@ name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -[Ala],NA,CH3,aq,DLH06,NA,25.Aug.06,-3936,-13290,16.85,35.671,26.864,5.43,3.6,4.39,-1.92,27.9,3.6,-0.05,0 -[Arg],NA,C4H10N3,aq,DLH06,NA,25.Aug.06,31624,-20730,54.75,74.167,105.825,18.08,13.39,50.81,-10.09,73.2,-1.9,-0.53,0 -[Arg+],NA,C4H11N3+,aq,DLH06,NA,25.Aug.06,14943,-35670,60.59,79.677,88.906,22.25,2.08,2.69,-3.38,82.2,1,0.5,0 -[Asn],NA,C2H4NO,aq,DLH06,NA,25.Aug.06,-40615,-63490,35.9,32.847,43.826,10.36,4.23,0.99,-3.04,34.9,-1.1,-0.02,0 -[Asp],NA,C2H3O2,aq,DLH06,NA,25.Aug.06,-87635,-107130,33.24,34.405,41.116,9.49,4.91,-9.39,-0.46,36.5,-1.3,-0.06,0 -[Asp-],NA,C2H2O2-,aq,DLH06,NA,25.Aug.06,-82293,-105330,21.36,4.742,31.224,7.49,7.63,7.34,-4.6,34.7,-4.7,2.24,0 -[Cys],NA,CH3S,aq,DLH06,NA,25.Aug.06,4545,-4860,24.34,49.089,39.913,8.67,4.26,6.54,-3.2,38.2,5,-0.08,0 -[Cys-],NA,CH2S-,aq,DLH06,NA,25.Aug.06,15950,3770,15.03,21.137,26.985,4.96,6.97,9.58,-1.94,39.4,1.1,2.25,0 -[Gln],NA,C3H6NO,aq,DLH06,NA,25.Aug.06,-41404,-72650,40.43,45.83,60.078,13.75,5.44,2.67,-3.46,47,-0.8,-0.05,0 -[Glu],NA,C3H5O2,aq,DLH06,NA,25.Aug.06,-88177,-115610,39.22,45.548,56.621,12.83,6.09,3.78,-4.07,43.6,0.6,-0.08,0 -[Glu-],NA,C3H4O2-,aq,DLH06,NA,25.Aug.06,-82337,-114940,21.88,9.643,46.365,11.02,8.82,8.09,-5.25,26,2.8,2.42,0 -[Gly],NA,H,aq,DLH06,NA,25.Aug.06,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0 -[His],NA,C4H5N2,aq,DLH06,NA,25.Aug.06,36456,11010,44.02,58.213,65.753,14.85,6.66,4.75,-4.28,60,-0.7,0.04,0 -[His+],NA,C4H6N2+,aq,DLH06,NA,25.Aug.06,28175,3960,48.15,61.095,63.454,17.17,-1.54,-3.65,-1.3,66.4,-1.4,0.27,0 -[Ile],NA,C4H9,aq,DLH06,NA,25.Aug.06,2886,-32390,27.72,93.6,72.204,15.02,8.41,15.39,-5.99,78.1,7,-0.14,0 -[Leu],NA,C4H9,aq,DLH06,NA,25.Aug.06,675,-34390,28.43,97.21,74.2,15.21,9.37,17.16,-6.6,81.1,7.3,-0.14,0 -[Lys],NA,C4H10N,aq,DLH06,NA,25.Aug.06,5657,-37650,39.3,65.848,75.048,15.09,10.16,21.66,-7.76,65,-0.3,-0.16,0 -[Lys+],NA,C4H11N+,aq,DLH06,NA,25.Aug.06,-8014,-51160,39.84,69.955,73.89,19.15,0.35,1.7,-2.22,73.6,2.6,0.98,0 -[Phe],NA,C7H7,aq,DLH06,NA,25.Aug.06,35444,10310,34.62,95.834,88.545,18.8,10.66,16.57,-7.61,86.5,4.1,-0.11,0 -[Pro],NA,C3H5,aq,DLH06,NA,25.Aug.06,11314,-4890,27.85,45.055,49.049,9.92,6.73,9.11,-3.91,42,1.1,-0.09,0 -[Ser],NA,CH3O,aq,DLH06,NA,25.Aug.06,-39054,-53210,25.26,29.794,27.042,6.22,2.59,1.1,-1.72,26.9,1.2,-0.05,0 -[Thr],NA,C2H5O,aq,DLH06,NA,25.Aug.06,-34956,-59730,22.25,52.106,44.03,9.47,4.69,6.1,-3.1,43.9,3.5,-0.12,0 -[Trp],NA,C9H8N,aq,DLH06,NA,25.Aug.06,58053,21620,37.98,101.619,110.045,24.44,11.07,12.01,-7.59,95.2,2.8,-0.08,0 -[Tyr],NA,C7H7O,aq,DLH06,NA,25.Aug.06,-6924,-38530,37.43,82.218,90.904,20.59,10.35,5.59,-6.81,84.6,-1.8,-0.14,0 -[Tyr-],NA,C7H6O-,aq,DLH06,NA,25.Aug.06,5495,-30210,23.68,53.196,78.168,16.87,12.35,13.65,-5.82,87.4,-5.4,2.55,0 -[Val],NA,C3H7,aq,DLH06,NA,25.Aug.06,-456,-27210,23.7,76.004,57.279,11.88,6.34,11.81,-4.35,62.2,6.3,-0.11,0 -[AABB],NA,C2H4NO2,aq,DLH06,NA,25.Aug.06,-84875,-119210,21.98,-2.036,33.585,9.47,-1.86,2.77,-1.77,21.6,-10.6,0.23,0 -[AABB+],NA,C2H5NO2+,aq,DLH06,NA,25.Aug.06,-88003,-119580,31.23,28.596,36.219,11.5,-4.58,-13.96,2.37,42.1,-4,0.59,0 -[AABB-],NA,C2H3NO2-,aq,DLH06,NA,25.Aug.06,-71967,-108690,13.97,6.95,37.165,13.2,0.37,-18.69,0.15,68.7,-17.7,2.83,0 -[UPBB],NA,C2H2NO,aq,DLH06,NA,25.Aug.06,-21436,-45220,1.62,-4.496,26.296,8.1,-3.75,-6.73,1.13,11.2,-7.5,0.05,0 -[-CH2-],NA,CH2,aq,DLH06,NA,25.Aug.06,2240,-5670,6.07,20.7,16,3.49,2.15,3.09,-1.7,16,2.3,0,0 -[-CH3],NA,CH3,aq,DLH06,NA,25.Aug.06,-2190,-12460,13.78,35.8,27.1,5.55,3.6,3.96,-1.92,31.5,1.9,-0.05,0 -[-CHCH3-],NA,C2H4,aq,DLH06,NA,25.Aug.06,3470,-12480,11.71,39.9,31.2,6.2,3.62,10.12,-2.98,30.1,4.4,-0.09,0 -[-CH2NH2],NA,CH4N,aq,DLH06,NA,31.Aug.06,7040,-12430,21.44,22.6,29.3,5.55,3.71,9.49,-2.66,25.9,-2.5,-0.19,0 -[-CH2OH],NA,CH3O,aq,DLH06,NA,25.Aug.06,-41530,-56790,21.57,28.5,26.7,5.86,2.59,3.03,-1.72,26.2,0.9,-0.05,0 -[-CONH2],NA,CH2NO,aq,DLH06,NA,25.Aug.06,-46550,-61420,30.14,5,28.2,7.02,1.14,-5.03,-0.06,14.5,-4.9,-0.05,0 -[-COOH],NA,CHO2,aq,DLH06,NA,25.Aug.06,-92570,-104380,26.41,5.3,24.5,5.82,1.79,-2.4,-0.67,12.9,-4.1,-0.08,0 -[-C6H5],NA,C6H5,aq,DLH06,NA,25.Aug.06,31660,15170,31.02,75.1,72.6,15.33,8.51,13.47,-5.91,70.4,1.8,-0.11,0 -[di.corr],NA,C0,aq,DLH06,NA,25.Aug.06,0,0,0,-13.5,3.2,0.06,-1.48,-0.05,2.32,-0.1,-6.7,-0.02,0 +methionine,Met,C5H11NO2S,aq,DLH06.1 [S07],LD12.2 [S15],10.Jul.15,-76959.8,-135210.3,62.81,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0 +[Ala],NA,CH3,aq,DLH06 [S15],NA,25.Aug.06,-3936,-13290,16.85,35.671,26.864,5.43,3.6,4.39,-1.92,27.9,3.6,-0.05,0 +[Arg],NA,C4H10N3,aq,DLH06 [S15],NA,25.Aug.06,31624,-20730,54.75,74.167,105.825,18.08,13.39,50.81,-10.09,73.2,-1.9,-0.53,0 +[Arg+],NA,C4H11N3+,aq,DLH06 [S15],NA,25.Aug.06,14943,-35670,60.59,79.677,88.906,22.25,2.08,2.69,-3.38,82.2,1,0.5,0 +[Asn],NA,C2H4NO,aq,DLH06 [S15],NA,25.Aug.06,-40615,-63490,35.9,32.847,43.826,10.36,4.23,0.99,-3.04,34.9,-1.1,-0.02,0 +[Asp],NA,C2H3O2,aq,DLH06 [S15],NA,25.Aug.06,-87635,-107130,33.24,34.405,41.116,9.49,4.91,-9.39,-0.46,36.5,-1.3,-0.06,0 +[Asp-],NA,C2H2O2-,aq,DLH06 [S15],NA,25.Aug.06,-82293,-105330,21.36,4.742,31.224,7.49,7.63,7.34,-4.6,34.7,-4.7,2.24,0 +[Cys],NA,CH3S,aq,DLH06 [S15],NA,25.Aug.06,4545,-4860,24.34,49.089,39.913,8.67,4.26,6.54,-3.2,38.2,5,-0.08,0 +[Cys-],NA,CH2S-,aq,DLH06 [S15],NA,25.Aug.06,15950,3770,15.03,21.137,26.985,4.96,6.97,9.58,-1.94,39.4,1.1,2.25,0 +[Gln],NA,C3H6NO,aq,DLH06 [S15],NA,25.Aug.06,-41404,-72650,40.43,45.83,60.078,13.75,5.44,2.67,-3.46,47,-0.8,-0.05,0 +[Glu],NA,C3H5O2,aq,DLH06 [S15],NA,25.Aug.06,-88177,-115610,39.22,45.548,56.621,12.83,6.09,3.78,-4.07,43.6,0.6,-0.08,0 +[Glu-],NA,C3H4O2-,aq,DLH06 [S15],NA,25.Aug.06,-82337,-114940,21.88,9.643,46.365,11.02,8.82,8.09,-5.25,26,2.8,2.42,0 +[Gly],NA,H,aq,DLH06 [S15],NA,25.Aug.06,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0 +[His],NA,C4H5N2,aq,DLH06 [S15],NA,25.Aug.06,36456,11010,44.02,58.213,65.753,14.85,6.66,4.75,-4.28,60,-0.7,0.04,0 +[His+],NA,C4H6N2+,aq,DLH06 [S15],NA,25.Aug.06,28175,3960,48.15,61.095,63.454,17.17,-1.54,-3.65,-1.3,66.4,-1.4,0.27,0 +[Ile],NA,C4H9,aq,DLH06 [S15],NA,25.Aug.06,2886,-32390,27.72,93.6,72.204,15.02,8.41,15.39,-5.99,78.1,7,-0.14,0 +[Leu],NA,C4H9,aq,DLH06 [S15],NA,25.Aug.06,675,-34390,28.43,97.21,74.2,15.21,9.37,17.16,-6.6,81.1,7.3,-0.14,0 +[Lys],NA,C4H10N,aq,DLH06 [S15],NA,25.Aug.06,5657,-37650,39.3,65.848,75.048,15.09,10.16,21.66,-7.76,65,-0.3,-0.16,0 +[Lys+],NA,C4H11N+,aq,DLH06 [S15],NA,25.Aug.06,-8014,-51160,39.84,69.955,73.89,19.15,0.35,1.7,-2.22,73.6,2.6,0.98,0 +[Met],NA,C3H7S,aq,DLH06 [S15],LD12.3,10.Jul.15,7911.1,-16001.4,40.82,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0 +[Phe],NA,C7H7,aq,DLH06 [S15],NA,25.Aug.06,35444,10310,34.62,95.834,88.545,18.8,10.66,16.57,-7.61,86.5,4.1,-0.11,0 +[Pro],NA,C3H5,aq,DLH06 [S15],NA,25.Aug.06,11314,-4890,27.85,45.055,49.049,9.92,6.73,9.11,-3.91,42,1.1,-0.09,0 +[Ser],NA,CH3O,aq,DLH06 [S15],NA,25.Aug.06,-39054,-53210,25.26,29.794,27.042,6.22,2.59,1.1,-1.72,26.9,1.2,-0.05,0 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 181 From noreply at r-forge.r-project.org Wed Mar 8 15:25:12 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 8 Mar 2017 15:25:12 +0100 (CET) Subject: [CHNOSZ-commits] r182 - in pkg/CHNOSZ: . data inst inst/extdata/OBIGT inst/extdata/supcrt vignettes Message-ID: <20170308142512.72E8B1889C4@r-forge.r-project.org> Author: jedick Date: 2017-03-08 15:25:11 +0100 (Wed, 08 Mar 2017) New Revision: 182 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_gas.csv pkg/CHNOSZ/inst/extdata/supcrt/compare.R pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd Log: some data updates Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-03-04 07:24:47 UTC (rev 181) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-08 14:25:11 UTC (rev 182) @@ -1,20 +1,22 @@ -Date: 2017-03-04 +Date: 2017-03-08 Package: CHNOSZ -Version: 1.0.8-71 +Version: 1.0.8-72 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Depends: R (>= 3.1.0) Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice Imports: grDevices, graphics, stats, utils, colorspace -Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry - and low-temperature geochemistry. The features include calculation of the standard molal - thermodynamic properties and chemical affinities of reactions involving minerals and/or - biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous - species; amino acid group additivity for the standard molal thermodynamic properties of - neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state - for aqueous species; construction of equilibrium activity diagrams as a function of - temperature, pressure, and chemical activities or fugacities of basis species. +Description: Tools for thermodynamic calculations in compositional biology and + low-temperature geochemistry. Thermodynamic properties are taken from a database + including aqueous species, minerals, and 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. Functions + are provided to define a system using basis species, automatically balance reactions, + calculate the chemical affinities of reactions for selected species, and plot the + results on potential diagrams or equilibrium activity diagrams. Experimental functions + calculate activity coefficients for aqueous species or optimize multiple thermodynamic + variables using an objective function for chemical activities. License: GPL (>= 2) BuildResaveData: no ZipData: no Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-03-04 07:24:47 UTC (rev 181) +++ pkg/CHNOSZ/data/refs.csv 2017-03-08 14:25:11 UTC (rev 182) @@ -13,7 +13,7 @@ PB82,"L. N. Plummer and E. Busenberg",1982,"aragonite and calcite","Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4 WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"gases GHS","J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,manganosite,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 -WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,MgSO4,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 +WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,MgSO4,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 BH83,"T. S. Bowers and H. C. Helgeson",1983,rutile,"Geochim. Cosmochim. Acta 47, 1247-1275",http://dx.doi.org/10.1016/0016-7037(83)90066-2 Hel85,"H. C. Helgeson",1985,"ferrosilite and siderite","Am. J. Sci. 285, 845-855",http://dx.doi.org/10.2475/ajs.285.9.845 JH85,"K. J. Jackson and H. C. Helgeson",1985,"Sn minerals","Econ. Geol. 80, 1365-1378",http://dx.doi.org/10.2113/gsecongeo.80.5.1365 @@ -23,7 +23,7 @@ SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"inorganic neutral species","Geochim. Cosmochim. Acta 53, 2157-2183",http://dx.doi.org/10.1016/0016-7037(89)90341-4 SH90,"E. L. Shock and H. C. Helgeson",1990,"organic species","Geochim. Cosmochim. Acta 54, 915-945",http://dx.doi.org/10.1016/0016-7037(90)90429-O Joh92a,"J. W. Johnson",1992,"steam, Cp represented by Maier-Kelley equation","personal communication", -SPRONS92.1,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", +SPRONS92.1,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", SPRONS92.2,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", SPRONS92.3,"H. C. Helgeson et al.",1992,""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)."","slop98.dat computer data file", Sho92,"E. L. Shock",1992,"diglycine, alanylglycine, leucylglycine, and diketopiperazine","Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V @@ -40,6 +40,8 @@ Sho95,"E. L. Shock",1995,"carboxylic acids","Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496 AH97b,"J. P. Amend and H. C. Helgeson",1997,"amino acids GHS","J. Chem. Soc., Faraday Trans. 93, 1927-1941",http://dx.doi.org/10.1039/A608126F DSM+97,"J. D. Dale, E. L. Shock et al.",1997,alkylphenols,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 +DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"phenol, and cresol isomers","Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 +DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"dimethylphenol isomers","Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 MS97,"T. M. McCollom and E. L. Shock",1997,"MgSO4, NaSO4-, and HCl","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X MS97.1,"T. M. McCollom and E. L. Shock",1997,"sulfur","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uranium species","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8 @@ -64,6 +66,7 @@ SLOP98.11,"E. L. Shock et al.",1998,""Data and parameters as used by @MS97. "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group ions and complexes","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 SS98a.1,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 +SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Rh+3","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 MS99,"W. M. Murphy and E. L. Shock",1999,"actinides","Rev. Mineral. Geochem. 38, 221-253",http://rimg.geoscienceworld.org/content/38/1/221 PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"metal-dicarboxylate complexes","Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5 @@ -79,7 +82,7 @@ MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"goethite, lepidocrocite, and maghemite Cp","Am. Mineral. 88, 846-854",http://dx.doi.org/10.2138/am-2003-5-613 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"hydronium jarosite","Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z SR04,"M. D. Schulte and K. L. Rogers",2004,"alkane thiols","Geochim. Cosmochim. Acta 68, 1087-1097",http://dx.doi.org/10.1016/j.gca.2003.06.001 -HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"methyldiethanolamine and methyldiethanolammonium chloride","J. Chem. Thermodynamics 38, 988-1007",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013 +HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"methyldiethanolamine and methyldiethanolammonium chloride HKF parameters","J. Chem. Thermodynamics 38, 988-1007",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013 LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"nucleic-acid bases, nucleosides, and nucleotides","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010 LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"citric acid and citrate","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010 LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Mg-complexed adenosine nucleotides (ATP), NAD, and NADP","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008 @@ -87,7 +90,7 @@ DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acid, protein, and organic groups","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acids HKF parameters","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Gly-X-Gly tripeptides","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 -MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"coquimbite, ferricopiapite, rhomboclase","Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175 +MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"coquimbite, ferricopiapite, and rhomboclase","Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175 Dic07,"J. M. Dick",2007,"glutathione, cystine, and cystine sidechain","Ph.D. Dissertation, U.C. Berkeley", MA07,"L. Marini and M. Accornero",2007,"metal-arsenate and metal-arsenite complexes","Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5 SLOP07.1,"E. L. Shock et al.",2007,"corrected charge of Pu(Oxal)+2","slop07.dat computer data file",http://geopig.asu.edu/?q=tools @@ -105,7 +108,12 @@ LD12.3,"D. E. LaRowe and J. M. Dick",2012,"methionine sidechain GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"phenanthrene and methylphenanthrene isomers","Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020 SLOP15.1,"E. L. Shock et al.",2015,""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP15.2,"E. L. Shock et al.",2015,""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP15.2,"E. L. Shock et al.",2015,"Zn(Ac)3-: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP15.3,"E. L. Shock et al.",2015,"formaldehyde: "Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of @SS93."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP15.4,"E. L. Shock et al.",2015,"adipic acid and n-dodecanoate: "Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of @Sho95."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP15.5,"E. L. Shock et al.",2015,"n-octanoate: "Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of @Sho95."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP15.6,"E. L. Shock et al.",2015,""Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools +SLOP15.7,"E. L. Shock et al.",2015,"heptanol, hexanol, and octanol: "Minor differences in Gibbs energy, entropy, omega, a1, a2, a3, a4 and c1 values compared to @SH90."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools CS16,"P. A. Canovas III and E. L. Shock",2016,"citric acid cycle metabolites","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a1--a4 parameters","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 UniProt,"The UniProt Consortium",2017,,"The UniProt knowledgebase",http://www.uniprot.org/ @@ -116,4 +124,4 @@ CHNOSZ.5,"J. M. Dick",2017,"AuCl4- renamed to AuCl4-3","CHNOSZ package documentation",http://chnosz.net CHNOSZ.6,"J. M. Dick",2017,"dipeptides not included in slop files after slop98.dat","CHNOSZ package documentation",http://chnosz.net CHNOSZ.7,"J. M. Dick",2017,"charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.8,"J. M. Dick",2017,"Incorrect values of HKF *a*1--*a*4 parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here","CHNOSZ package documentation",http://chnosz.net +CHNOSZ.8,"J. M. Dick",2017,"Incorrect values of HKF a1--a4 parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here.","CHNOSZ package documentation",http://chnosz.net Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-03-04 07:24:47 UTC (rev 181) +++ pkg/CHNOSZ/inst/NEWS 2017-03-08 14:25:11 UTC (rev 182) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-71 (2017-03-04) +CHANGES IN CHNOSZ 1.0.8-72 (2017-03-08) --------------------------------------- DOCUMENTATION: Modified: pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv 2017-03-04 07:24:47 UTC (rev 181) +++ pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv 2017-03-08 14:25:11 UTC (rev 182) @@ -6,170 +6,170 @@ uracil,NA,C4H4N2O2,aq,"LH06a [S07]",NA,3.Feb.03,-59734,-94587,45.88,36.19,71.55,17.5038,5.9312,-1.6074,-4.3091,56.57,-9.4,0.14,0 ribose,NA,C5H10O5,aq,"LH06a [S07]",NA,3.Feb.03,-179739,-247132,59.53,66.46,95.71,22.6455,7.293,-5.3875,-3.4054,134.7,-32.82,0.17,0 deoxyribose,NA,C5H10O4,aq,"LH06a [S07]",NA,3.Feb.03,-144433,-205037,57.82,56.16,94.65,22.537,7.2652,-5.3715,-3.404,124.4,-32.82,0.17,0 -adenosine,NA,C10H13N5O4,aq,"LH06a [S07]",NA,3.Feb.03,-46499,-148490,87.19,120.3,170.7,39.5452,12.9013,8.9651,-8.8169,163.2,-20.1,0.23,0 +adenosine,NA,C10H13N5O4,aq,"LH06a [S07]",NA,3.Feb.03,-46499,-148490,87.19,120.3,170.7,39.5452,12.901,8.9651,-8.8169,163.2,-20.1,0.23,0 cytidine,NA,C9H13N3O5,aq,"LH06a [S07]",NA,3.Feb.03,-130179,-226640,83.09,96.38,153.3,36.3116,7.996,7.5934,-6.5938,132.6,-16.3,0.34,0 guanosine,NA,C10H13N5O5,aq,"LH06a [S07]",NA,3.Feb.03,-105568,-214528,88.33,124.9,174.2,42.2627,8.3757,-2.4562,-5.8937,169.3,-20.1,0.39,0 -thymidine,NA,C10H14N2O6,aq,"LH06a [S07]",NA,3.Feb.03,-183083,-284694,84.42,110.5,167.4,38.1602,10.9585,12.3953,-7.1879,143.4,-14.9,0.29,0 +thymidine,NA,C10H14N2O6,aq,"LH06a [S07]",NA,3.Feb.03,-183083,-284694,84.42,110.5,167.4,38.1602,10.959,12.395,-7.1879,143.4,-14.9,0.29,0 uridine,NA,C9H12N2O6,aq,"LH06a [S07]",NA,3.Feb.03,-181502,-274312,81.34,95.14,151.8,36.1528,7.091,5.1259,-5.6836,131.8,-16.65,0.31,0 deoxyadenosine,NA,C10H13N5O3,aq,"LH06a [S07]",NA,3.Feb.03,-11193,-106386,85.48,111.2,170,38.0314,16.957,15.1636,-10.834,154.2,-20.1,0.23,0 deoxycytidine,NA,C9H13N3O4,aq,"LH06a [S07]",NA,24.Sep.06,-96652,-184534,87.35,87.28,154,35.8171,9.7174,7.4022,-6.5327,123.5,-16.3,0.34,0 -deoxyguanosine,NA,C10H13N5O4,aq,"LH06a [S07]",NA,3.Feb.03,-71539,-176273,77.99,115.8,173.2,39.4526,15.4982,14.2847,-10.5692,160.3,-20.1,0.39,0 -deoxythymidine,NA,C10H14N2O5,aq,"LH06a [S07]",NA,3.Feb.03,-149556,-242588,88.68,101.4,167.5,38.8728,11.4509,-7.7797,-3.6098,134.4,-14.9,0.29,0 +deoxyguanosine,NA,C10H13N5O4,aq,"LH06a [S07]",NA,3.Feb.03,-71539,-176273,77.99,115.8,173.2,39.4526,15.498,14.2847,-10.569,160.3,-20.1,0.39,0 +deoxythymidine,NA,C10H14N2O5,aq,"LH06a [S07]",NA,3.Feb.03,-149556,-242588,88.68,101.4,167.5,38.8728,11.451,-7.7797,-3.6098,134.4,-14.9,0.29,0 deoxyuridine,NA,C9H12N2O5,aq,"LH06a [S07]",NA,3.Feb.03,-147975,-232206,85.59,86.04,151.2,35.5945,9.6188,3.5015,-6.2803,122.8,-16.65,0.31,0 -AMP-2,NA,C10H12N5O7P-2,aq,"LH06a [S07]",NA,3.Feb.03,-247417,-389148,52.89,61.68,161.03,2.3198,108.8148,-18.734,-1.7194,130.2,-19.82,3.1,-2 -HAMP-,NA,C10H13N5O7P-,aq,"LH06a [S07]",NA,3.Feb.03,-255617,-388308,83.21,114.39,187.55,2.4065,126.2531,-19.139,-2.4403,187.95,-22.3,3.1,-1 -H2AMP,NA,C10H14N5O7P,aq,"LH06a [S07]",NA,3.Feb.03,-260817,-392608,86.23,120.01,187.02,2.3993,124.8091,-19.105,-2.3806,181.6,-19.1,2.5,0 -CMP-2,NA,C9H12N3O8P-2,aq,"LH06a [S07]",NA,3.Feb.03,-331097,-467460,48.24,37.71,142.39,2.2606,96.923,-18.459,-1.2278,101.1,-16.4,3.3,-2 -HCMP-,NA,C9H13N3O8P1-,aq,"LH06a [S07]",NA,3.Feb.03,-340147,-466110,83.09,90.6,168.91,2.3474,114.3613,-18.863,-1.9487,158.79,-18.76,3.3,-1 -H2CMP,NA,C9H14N3O8P,aq,"LH06a [S07]",NA,3.Feb.03,-345343,-470410,86.18,96.06,168.37,2.3411,113.0988,-18.834,-1.8965,154.1,-16.01,2.8,0 -GMP-2,NA,C10H12N5O8P-2,aq,"LH06a [S07]",NA,3.Feb.03,-306486,-455676,52.39,65.81,159.8,2.3194,108.7392,-18.733,-1.7163,140.8,-21.21,3.5,-2 -HGMP-,NA,C10H13N5O8P-,aq,"LH06a [S07]",NA,3.Feb.03,-315586,-454226,87.77,118.45,186.32,2.4062,126.1775,-19.137,-2.4372,198.5,-23.7,3.5,-1 -H2GMP,NA,C10H14N5O8P,aq,"LH06a [S07]",NA,3.Feb.03,-320786,-458526,90.79,123.82,185.79,2.399,124.7309,-19.104,-2.3774,192.3,-20.7,2.9,0 -TMP-2,NA,C10H13N2O9P-2,aq,"LH06a [S07]",NA,3.Feb.03,-384001,-525514,49.58,51.85,155.97,2.3042,105.675,-18.662,-1.5896,111,-14.76,3.2,-2 -HTMP-,NA,C10H14N2O9P-,aq,"LH06a [S07]",NA,3.Feb.03,-393021,-524279,83.97,104.8,182.49,2.3909,123.1133,-19.066,-2.3105,168.7,-17.1,3.2,-1 -H2TMP,NA,C10H15N2O9P,aq,"LH06a [S07]",NA,3.Feb.03,-398221,-528579,86.99,110.62,181.97,2.3838,121.6733,-19.033,-2.251,162.27,-13.76,2.6,0 -UMP-2,NA,C9H11N2O9P-2,aq,"LH06a [S07]",NA,3.Feb.03,-382420,-515132,46.49,36.19,141.33,2.2572,96.226,-18.442,-1.199,101.1,-17.15,3.3,-2 -HUMP-,NA,C9H12N2O9P-,aq,"LH06a [S07]",NA,3.Feb.03,-391470,-514012,80.6,89.05,167.85,2.3439,113.6643,-18.847,-1.9199,158.78,-19.52,3.3,-1 -H2UMP,NA,C9H13N2O9P,aq,"LH06a [S07]",NA,3.Feb.03,-396670,-518312,83.62,94.7,167.31,2.3367,112.2177,-18.813,-1.8601,152.46,-16.32,2.7,0 -dAMP-2,NA,C10H12N5O6P-2,aq,"LH06a [S07]",NA,3.Feb.03,-212111,-347206,50.63,53.02,160.05,2.3166,108.1737,-18.72,-1.6929,121.5,-19.8,3.1,-2 -dHAMP-,NA,C10H13N5O6P-,aq,"LH06a [S07]",NA,3.Feb.03,-221205,-346166,84.61,105.7,186.57,2.4033,125.612,-19.124,-2.4138,179.3,-22.32,3.1,-1 -dH2AMP,NA,C10H14N5O6P,aq,"LH06a [S07]",NA,3.Feb.03,-226401,-350466,87.62,111.28,186.05,2.3962,124.172,-19.091,-2.3543,172.91,-19.12,2.5,0 -dCMP-2,NA,C9H12N3O7P-2,aq,"LH06a [S07]",NA,3.Feb.03,-297270,-425354,52.5,28.13,144.34,2.2679,98.3893,-18.493,-1.2884,94.34,-17.34,3.4,-2 -dHCMP-,NA,C9H13N3O7P-,aq,"LH06a [S07]",NA,3.Feb.03,-306660,-424314,86.48,80.1,170.8,2.3547,115.8276,-18.987,-2.0093,152.04,-19.74,3.4,-1 -dH2CMP,NA,C9H14N3O7P,aq,"LH06a [S07]",NA,3.Feb.03,-311860,-428614,89.5,86.59,170.32,2.3475,114.381,-18.864,-1.9495,145.71,-16.54,2.8,0 -dGMP-2,NA,C10H12N5O7P-2,aq,"LH06a [S07]",NA,3.Feb.03,-272457,-417092,43.15,56.41,158.23,2.3143,107.7069,-18.709,-1.6736,131.4,-21.21,3.5,-2 -dHGMP-,NA,C10H13N5O7P-,aq,"LH06a [S07]",NA,3.Feb.03,-281547,-416052,77.13,109.06,184.75,2.401,125.1452,-19.113,-2.3945,189.11,-23.7,3.5,-1 -dH2GMP,NA,C10H14N5O7P,aq,"LH06a [S07]",NA,3.Feb.03,-286747,-420352,80.14,114.46,184.22,2.3938,123.6985,-19.08,-2.3347,182.88,-20.67,2.9,0 -dTMP-2,NA,C10H13N2O8P-2,aq,"LH06a [S07]",NA,3.Feb.03,-350474,-483408,53.83,43.05,156.72,2.3066,106.1682,-18.673,-1.61,102.2,-14.76,3.2,-2 -dHTMP-,NA,C10H14N2O8P-,aq,"LH06a [S07]",NA,3.Feb.03,-359564,-482368,87.81,96,183.24,2.3934,123.6065,-19.078,-2.3309,159.9,-17.1,3.2,-1 -dH2TMP,NA,C10H15N2O8P,aq,"LH06a [S07]",NA,3.Feb.03,-364764,-486668,90.83,101.82,183.72,2.3862,122.1664,-19.044,-2.2714,153.47,-13.76,2.6,0 -dUMP-2,NA,C9H11N2O8P-2,aq,"LH06a [S07]",NA,3.Feb.03,-348893,-473026,50.75,27.36,140.78,2.2549,95.7723,-18.432,-1.118,92.27,-17.15,3.3,-2 -dHUMP-,NA,C9H12N2O8P-,aq,"LH06a [S07]",NA,03.Mar.17,-357983,-471986,84.73,78.34,167.16,2.3417,113.2106,-18.836,-1.9011,145,-19.55,3.3,-1 -dH2UMP,NA,C9H13N2O8P,aq,"LH06a [S07]",NA,3.Feb.03,-363183,-476286,87.74,85.83,166.62,2.3345,111.764,-18.803,-1.8413,143.65,-16.35,2.7,0 -ADP-3,NA,C10H12N5O10P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-452649,-624106,52.17,41.54,191.72,2.4286,130.6804,-19.242,-2.6233,128.7,-24.87,4.02,-3 -HADP-2,NA,C10H13N5O10P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-462549,-623266,88.2,107.59,202.95,2.4633,137.657,-19.403,-2.9117,186.2,-21.65,3.8,-2 -H2ADP-,NA,C10H14N5O10P2-,aq,"LH06a [S07]",NA,3.Feb.03,-468249,-627666,92.56,136.4,202.41,2.4533,135.6647,-19.357,-2.8294,193.1,-14.9,2.9,-1 -H3ADP,NA,C10H15N5O10P2,aq,"LH06a [S07]",NA,3.Feb.03,-470749,-625106,109.53,169.36,207.55,2.4543,135.8481,-19.361,-2.837,204,-11.89,1.15,0 -CDP-3,NA,C9H12N3O11P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-536329,-702338,47.8,18.49,173.36,2.3692,118.7524,-18.965,-2.1302,99.37,-21.42,4.1,-3 -HCDP-2,NA,C9H13N3O11P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-546119,-700998,85.13,83.59,184.3,2.4041,125.7619,-19.128,-2.42,157.12,-18.25,4,-2 -H2CDP-,NA,C9H14N3O11P2-,aq,"LH06a [S07]",NA,3.Feb.03,-551819,-705398,89.49,112.41,183.77,2.3942,123.7696,-19.081,-2.3376,163.98,-11.48,3.1,-1 -H3CDP,NA,C9H15N3O11P2,aq,"LH06a [S07]",NA,3.Feb.03,-554319,-702838,106.64,145.32,188.96,2.3951,123.9596,-19.086,-2.3255,174.98,-8.545,1.35,0 -GDP-3,NA,C10H12N5O11P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-511718,-690384,52.51,45.87,190.49,2.4273,130.4371,-19.236,-2.6133,137.7,-25.78,4.33,-3 -HGDP-2,NA,C10H13N5O11P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-521518,-688904,90.34,111.91,201.71,2.4619,137.394,-19.397,-2.9009,194.96,-22.49,4.1,-2 -H2GDP-,NA,C10H14N5O11P2-,aq,"LH06a [S07]",NA,3.Feb.03,-527218,-693304,94.7,140.73,201.18,2.452,135.4017,-19.351,-2.8185,201.79,-15.7,3.2,-1 -H3GDP,NA,C10H15N5O11P2,aq,"LH06a [S07]",NA,3.Feb.03,-529718,-690744,111.68,173.68,206.33,2.4525,135.4996,-19.353,-2.8226,212.04,-12.6,1.4,0 -TDP-3,NA,C10H13N2O12P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-589233,-760392,49.13,31.84,186.68,2.4128,127.511,-19.168,-2.4923,109.16,-19.67,4.1,-3 -HTDP-2,NA,C10H14N2O12P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-599033,-759182,86.06,97.83,197.9,2.4477,134.5205,-19.331,-2.7821,166.97,-16.54,3.9,-2 -H2TDP-,NA,C10H15N2O12P2-,aq,"LH06a [S07]",NA,3.Feb.03,-604733,-763582,90.42,126.65,197.37,2.4377,132.5282,-19.284,-2.6997,173.85,-9.78,3,-1 -H3TDP,NA,C10H16N2O12P2,aq,"LH06a [S07]",NA,3.Feb.03,-607233,-761022,107.39,159.63,202.5,2.4382,132.6196,-19.287,-2.7035,183.98,-6.602,1.2,0 -UDP-3,NA,C9H11N2O12P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-587652,-750010,46.04,16.08,172.03,2.3658,118.0554,-18.949,-2.1014,99.37,-22.16,4.2,-3 -HUDP-2,NA,C9H12N2O12P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-597432,-748930,82.47,82.09,183.24,2.4006,125.0649,-19.111,-2.3912,157.12,-18.99,4,-2 -H2UDP-,NA,C9H13N2O12P2-,aq,"LH06a [S07]",NA,3.Feb.03,-603132,-753330,86.83,110.91,182.71,2.3907,123.0725,-19.065,-2.3088,163.98,-12.22,3.1,-1 -H3UDP,NA,C9H14N2O12P2,aq,"LH06a [S07]",NA,3.Feb.03,-605632,-750770,103.8,143.87,187.85,2.3912,123.1705,-19.067,-2.3129,174.16,-9.078,1.3,0 -dADP-3,NA,C10H12N5O9P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-417343,-582164,49.91,32.91,190.75,2.4254,130.0426,-19.227,-2.597,120.03,-24.85,4.02,-3 -dHADP-2,NA,C10H13N5O9P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-427243,-581324,85.94,98.91,201.98,2.4601,137.0192,-19.389,-2.8854,177.46,-21.62,3.8,-2 -dH2ADP-,NA,C10H14N5O9P2-,aq,"LH06a [S07]",NA,3.Feb.03,-432943,-585742,90.3,127.72,201.44,2.4502,135.0269,-19.342,-2.803,184.36,-14.87,2.9,-1 -dH3ADP,NA,C10H15N5O9P2,aq,"LH06a [S07]",NA,3.Feb.03,-435443,-583164,107.27,160.66,206.58,2.4511,135.2103,-19.347,-2.8106,195.24,-11.86,1.15,0 -dCDP-3,NA,C9H12N3O10P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-502802,-660232,52.05,10.69,175.45,2.3761,120.1267,-18.997,-2.187,91.57,-21.42,4.1,-3 -dHCDP-2,NA,C9H13N3O10P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-512592,-658892,89.39,74.99,186.25,2.4105,127.0442,-19.157,-2.473,148.52,-18.25,4,-2 -dH2CDP-,NA,C9H14N3O10P2-,aq,"LH06a [S07]",NA,3.Feb.03,-518292,-663292,93.75,103.81,185.72,2.4006,125.0518,-19.11,-2.3906,155.38,-11.48,3.1,-1 -dH3CDP,NA,C9H15N3O10P2,aq,"LH06a [S07]",NA,3.Feb.03,-520792,-660732,110.72,135.91,190.73,2.401,125.1498,-19.113,-2.3947,165.57,-8.545,1.35,0 -dGDP-3,NA,C10H12N5O10P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-477689,-651800,43.27,36.48,188.92,2.4222,129.4048,-19.212,-2.5706,128.31,-25.78,4.33,-3 -dHGDP-2,NA,C10H13N5O10P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-487489,-650320,81.11,102.51,200.14,2.4568,136.3617,-19.373,-2.8582,185.56,-22.49,4.1,-2 -dH2GDP-,NA,C10H14N5O10P2-,aq,"LH06a [S07]",NA,3.Feb.03,-493189,-654720,85.47,131.33,199.61,2.4469,134.3693,-19.327,-2.7758,192.39,-15.7,3.2,-1 -dH3GDP,NA,C10H15N5O10P2,aq,"LH06a [S07]",NA,3.Feb.03,-495689,-652160,102.44,164.28,204.76,2.4474,134.4673,-19.329,-2.7799,202.64,-12.6,1.4,0 -dTDP-3,NA,C10H13N2O11P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-555706,-718286,53.39,22.98,187.42,2.4152,127.9976,-19.179,-2.5124,100.36,-19.7,4.1,-3 -dHTDP-2,NA,C10H14N2O11P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-565506,-717076,90.31,88.99,198.65,2.4501,135.0137,-19.342,-2.8025,158.13,-16.54,3.9,-2 -dH2TDP-,NA,C10H15N2O11P2-1,aq,"LH06a [S07]",NA,3.Feb.03,-571206,-721476,94.67,117.81,198.12,2.4402,133.0213,-19.296,-2.7201,165.01,-9.78,3,-1 -dH3TDP,NA,C10H16N2O11P2,aq,"LH06a [S07]",NA,3.Feb.03,-573706,-718916,111.65,150.79,203.25,2.4406,133.1127,-19.298,-2.7239,175.14,-6.602,1.2,0 -dUDP-3,NA,C9H11N2O11P2-3,aq,"LH06a [S07]",NA,3.Feb.03,-554125,-707904,50.3,7.25,171.34,2.3635,117.6017,-18.938,-2.0827,90.54,-22.16,4.2,-3 -dHUDP-2,NA,C9H12N2O11P2-2,aq,"LH06a [S07]",NA,3.Feb.03,-563905,-706842,86.73,73.26,182.55,2.3984,124.6112,-19.101,-2.3724,148.29,-18.99,4,-2 -dH2UDP-,NA,C9H13N2O11P2-,aq,"LH06a [S07]",NA,3.Feb.03,-569605,-711224,91.09,102.08,182.02,2.3885,122.6188,-19.055,-2.2901,155.15,-12.22,3.1,-1 -dH3UDP,NA,C9H14N2O11P2,aq,"LH06a [S07]",NA,3.Feb.03,-572105,-708664,108.06,135.04,187.16,2.3889,122.7168,-19.057,-2.2941,165.33,-9.078,1.3,0 -ATP-4,NA,C10H12N5O13P3-4,aq,"LH06a [S07]",NA,03.Mar.17,-657038,-859264,47.96,21.34,196.77,2.454,135.7876,-19.36,-2.8345,128.4,-30.27,5,-4 -HATP-3,NA,C10H13N5O13P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-667538,-857864,87.87,92.83,212.26,2.5037,145.789,-19.592,-3.2479,199.18,-30.37,4.9,-3 -H2ATP-2,NA,C10H14N5O13P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-673738,-861764,95.59,133.39,211.73,2.5002,145.0789,-19.576,-3.2186,239.28,-31.04,4.7,-2 -H3ATP-,NA,C10H15N5O13P3-,aq,"LH06a [S07]",NA,4.Feb.03,-676438,-860264,109.67,194.02,222.95,2.535,152.0884,-19.738,-3.5083,296.43,-30.22,4.5,-1 -H4ATP,NA,C10H16N5O13P3,aq,"LH06a [S07]",NA,4.Feb.03,-678500,-858553,122.33,250.04,228.09,2.5509,155.2834,-19.812,-3.6404,351.9,-30.4,4.4,0 -CTP-4,NA,C9H12N3O14P3-4,aq,"LH06a [S07]",NA,4.Feb.03,-740718,-937496,43.58,-2.79,178.13,2.3948,123.8925,-19.084,-2.3427,99.59,-27.07,5.2,-4 -HCTP-3,NA,C9H13N3O14P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-751148,-935746,84.44,67.84,193.62,2.4446,133.9005,-19.316,-2.7564,171.02,-27.91,5.1,-3 -H2CTP-2,NA,C9H14N3O14P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-757348,-939646,92.15,108.54,193.09,2.441,133.1837,-19.3,-2.7268,211.07,-28.49,4.9,-2 -H3CTP-,NA,C9H15N3O14P3-,aq,"LH06a [S07]",NA,4.Feb.03,-760048,-938146,106.24,169.34,204.31,2.4759,140.1998,-19.462,-3.0169,268.1,-27.53,4.7,-1 -H4CTP,NA,C9H16N3O14P3,aq,"LH06a [S07]",NA,4.Feb.03,-762090,-936314,119.23,225,209.45,2.4918,143.3949,-19.536,-3.1489,323.3,-27.75,4.6,0 -GTP-4,NA,C10H12N5O14P3-4,aq,"LH06a [S07]",NA,4.Feb.03,-716107,-925542,48.3,25.36,195.54,2.4522,135.4326,-19.352,-2.8198,136.09,-30.73,5.3,-4 -HGTP-3,NA,C10H13N5O14P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-726537,-923792,89.15,95.5,211.03,2.5028,145.6181,-19.588,-3.2409,209.18,-32.18,5.3,-3 -H2GTP-2,NA,C10H14N5O14P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-732737,-927692,96.86,135.94,210.5,2.4993,144.9079,-19.572,-3.2115,249.3,-32.92,5.1,-2 -H3GTP-,NA,C10H15N5O14P3-,aq,"LH06a [S07]",NA,4.Feb.03,-735437,-926192,110.95,196.82,221.72,2.5346,152.0095,-19.736,-3.5051,307.16,-32.33,4.9,-1 -H4GTP,NA,C10H16N5O14P3,aq,"LH06a [S07]",NA,4.Feb.03,-737480,-924362,123.94,252.16,226.86,2.5505,155.2045,-19.81,-3.6372,361,-32.04,4.8,0 -TTP-4,NA,C10H13N2O15P3-4,aq,"LH06a [S07]",NA,4.Feb.03,-793622,-995550,44.92,11.48,191.72,2.4384,132.6511,-19.287,-2.7048,109.37,-25.31,5.1,-4 -HTTP-3,NA,C10H14N2O15P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-803972,-993530,86.4,81.89,207.21,2.489,142.8366,-19.524,-3.1259,182.41,-26.6,5.1,-3 -H2TTP-2,NA,C10H15N2O15P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-810172,-997430,94.12,122.61,206.68,2.4854,142.1199,-19.507,-3.0962,222.48,-27.18,4.9,-2 -H3TTP-,NA,C10H16N2O15P3-,aq,"LH06a [S07]",NA,24.Oct.06,-812872,-995930,108.21,183.15,218.18,2.5221,149.4976,-19.678,-3.4012,281.12,-26.69,4.8,-1 -H4TTP,NA,C10H17N2O15P3,aq,"LH06a [S07]",NA,4.Feb.03,-815000,-994118,121.42,237.83,223.04,2.5372,152.5151,-19.748,-3.526,334.4,-26.45,4.7,0 -UTP-4,NA,C9H11N2O15P3-4,aq,"LH06a [S07]",NA,4.Feb.03,-792041,-985168,41.83,-4.51,177.08,2.3909,123.11,-19.066,-2.3104,98.4,-27.33,5.2,-4 -HUTP-3,NA,C9H12N2O15P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-802441,-983278,83.05,65.83,192.57,2.4416,133.2955,-19.302,-2.7314,171.44,-28.66,5.2,-3 -H2UTP-2,NA,C9H13N2O15P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-808641,-987178,90.77,106.77,192.03,2.4385,132.6708,-19.288,-2.7056,212.31,-29.52,5,-2 -H3UTP-,NA,C9H14N2O15P3-,aq,"LH06a [S07]",NA,24.Oct.06,-811341,-985678,104.85,167.22,203.25,2.4742,139.8645,-19.455,-3.003,270.93,-29.07,4.9,-1 -H4UTP,NA,C9H15N2O15P3,aq,"LH06a [S07]",NA,4.Feb.03,-813380,-983806,117.97,222.65,208.39,2.4901,143.0595,-19.529,-3.1351,324.6,-28.65,4.8,0 -dATP-4,NA,C10H12N5O12P3-4,aq,"LH06a [S07]",NA,4.Feb.03,-621732,-817322,45.7,12.6,195.8,2.4508,135.1498,-19.345,-2.8081,119.66,-30.27,5,-4 -dHATP-3,NA,C10H13N5O12P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-632233,-815922,85.61,84.15,211.29,2.5014,145.3353,-19.581,-3.2292,190.5,-30.37,4.9,-3 -dH2ATP-2,NA,C10H14N5O12P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-638432,-819822,93.33,124.71,210.76,2.4988,144.8027,-19.569,-3.2071,230.6,-31.04,4.7,-2 -dH3ATP-,NA,C10H15N5O12P3-,aq,"LH06a [S07]",NA,4.Feb.03,-641132,-818322,107.42,185.29,221.98,2.5346,151.9963,-19.736,-3.5045,287.7,-30.22,4.5,-1 -dH4ATP,NA,C10H16N5O12P3,aq,"LH06a [S07]",NA,4.Feb.03,-643200,-816614,120.08,241.34,227.12,2.5505,155.1979,-19.81,-3.6369,343.2,-30.4,4.4,0 -dCTP-4,NA,C9H12N3O13P3-4,aq,"LH06a [S07]",NA,4.Feb.03,-707191,-895390,47.84,-12,180.08,2.4012,125.1747,-19.114,-2.3957,90.63,-27.07,5.2,-4 -dHCTP-3,NA,C9H13N3O13P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-717621,-893640,88.69,58.82,195.57,2.4518,135.3602,-19.35,-2.8168,162,-27.91,5.1,-3 -dH2CTP-2,NA,C9H14N3O13P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-723821,-897540,96.41,99.57,195.04,2.4492,134.8342,-19.338,-2.795,202.1,-28.49,4.9,-2 -dH3CTP-,NA,C9H15N3O13P3-,aq,"LH06a [S07]",NA,4.Feb.03,-726521,-896040,110.49,160.34,206.26,2.485,142.0278,-19.505,-3.0924,259.1,-27.53,4.7,-1 -dH4CTP,NA,C9H16N3O13P3,aq,"LH06a [S07]",NA,4.Feb.03,-728570,-894253,123.36,216,211.4,2.5009,145.2229,-19.579,-3.2245,314.3,-27.75,4.6,0 -dGTP-4,NA,C10H12N5O13P3-4,aq,"LH06a [S07]",NA,4.Feb.03,-682078,-886958,39.06,16.2,193.97,2.4475,134.4923,-19.33,-2.7809,127.87,-30.73,5.3,-4 -dHGTP-3,NA,C10H13N5O13P3-3,aq,"LH06a [S07]",NA,4.Feb.03,-692508,-885208,79.91,87.27,209.46,2.4982,144.6778,-19.566,-3.202,200.95,-32.18,5.3,-3 -dH2GTP-2,NA,C10H14N5O13P3-2,aq,"LH06a [S07]",NA,4.Feb.03,-698708,-889108,87.63,127.74,208.93,2.4955,144.1451,-19.554,-3.18,241.1,-32.92,5,-2 -dH3GTP-,NA,C10H15N5O13P3-,aq,"LH06a [S07]",NA,4.Feb.03,-701408,-887608,101.71,188.66,220.15,2.5313,151.3453,-19.721,-3.4776,299,-32.33,4.9,-1 -dH4GTP,NA,C10H16N5O13P3,aq,"LH06a [S07]",NA,4.Feb.03,-703450,-885778,114.7,243.96,225.29,2.5472,154.5404,-19.795,-3.6097,352.8,-32.04,4.8,0 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 182 From noreply at r-forge.r-project.org Wed Mar 8 16:20:10 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 8 Mar 2017 16:20:10 +0100 (CET) Subject: [CHNOSZ-commits] r183 - pkg/CHNOSZ/vignettes Message-ID: <20170308152010.37DA11883B9@r-forge.r-project.org> Author: jedick Date: 2017-03-08 16:20:09 +0100 (Wed, 08 Mar 2017) New Revision: 183 Modified: pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd Log: vignettes: comment csl lines for building on R-Forge Modified: pkg/CHNOSZ/vignettes/anintro.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-03-08 14:25:11 UTC (rev 182) +++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-03-08 15:20:09 UTC (rev 183) @@ -22,7 +22,7 @@ link-citations: yes # The custom CSL file gives a build error on R-Forge (20170212): # pandoc-citeproc: error while parsing the XML string -csl: elementa.csl +#csl: elementa.csl --- ```{r options, include=FALSE} Modified: pkg/CHNOSZ/vignettes/obigt.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/obigt.Rmd 2017-03-08 14:25:11 UTC (rev 182) +++ pkg/CHNOSZ/vignettes/obigt.Rmd 2017-03-08 15:20:09 UTC (rev 183) @@ -17,7 +17,7 @@ @SPRONS92, @SLOP98, @SLOP07, @SLOP15, @CHNOSZ # 20170212: comment the csl line to build package on R-Forge, to avoid # getting an error there (pandoc-citeproc: error while parsing the XML string) -csl: elementa.csl +#csl: elementa.csl --- From noreply at r-forge.r-project.org Thu Mar 9 16:05:14 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 9 Mar 2017 16:05:14 +0100 (CET) Subject: [CHNOSZ-commits] r184 - in pkg/CHNOSZ: . data inst inst/extdata/OBIGT tests/testthat vignettes Message-ID: <20170309150514.78FF21885A1@r-forge.r-project.org> Author: jedick Date: 2017-03-09 16:05:13 +0100 (Thu, 09 Mar 2017) New Revision: 184 Added: pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/organic_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/organic_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/organic_liq.csv Removed: pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_liq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Majzlan_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Marini_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Other_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/Richard_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Richard_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/Richard_liq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Schulte_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Shock_gas.csv pkg/CHNOSZ/inst/extdata/OBIGT/Tardy_cr.csv pkg/CHNOSZ/inst/extdata/OBIGT/Tremaine_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/Wagman_gas.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/data/thermo.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/tests/testthat/test-info.R pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd Log: OBIGT: name datafiles inorganic, organic, biotic Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-03-08 15:20:09 UTC (rev 183) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-09 15:05:13 UTC (rev 184) @@ -1,6 +1,6 @@ -Date: 2017-03-08 +Date: 2017-03-09 Package: CHNOSZ -Version: 1.0.8-72 +Version: 1.0.8-73 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/data/thermo.R =================================================================== --- pkg/CHNOSZ/data/thermo.R 2017-03-08 15:20:09 UTC (rev 183) +++ pkg/CHNOSZ/data/thermo.R 2017-03-09 15:05:13 UTC (rev 184) @@ -9,11 +9,10 @@ local({ # create obigt data frame - sources_aq <- paste0(c("H2O", "Shock", "Amend", "Schulte", "LaRowe", "Dick", - "Tremaine", "Marini", "CHNOSZ"), "_aq") - sources_cr <- paste0(c("Helgeson", "Shock", "Tardy", "Richard", "Majzlan", "LaRowe", "Other"), "_cr") - sources_liq <- paste0(c("Richard", "LaRowe"), "_liq") - sources_gas <- paste0(c("Wagman", "Shock", "Richard", "Other"), "_gas") + sources_aq <- paste0(c("H2O", "inorganic", "organic", "biotic", "CHNOSZ"), "_aq") + sources_cr <- paste0(c("inorganic", "organic"), "_cr") + sources_liq <- paste0(c("organic"), "_liq") + sources_gas <- paste0(c("inorganic", "organic"), "_gas") OBIGTdir <- system.file("extdata/OBIGT/", package="CHNOSZ") # need explicit "/" for Windows sourcefiles <- paste0(OBIGTdir, "/", c(sources_aq, sources_cr, sources_liq, sources_gas), ".csv") Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-03-08 15:20:09 UTC (rev 183) +++ pkg/CHNOSZ/inst/NEWS 2017-03-09 15:05:13 UTC (rev 184) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-72 (2017-03-08) +CHANGES IN CHNOSZ 1.0.8-73 (2017-03-09) --------------------------------------- DOCUMENTATION: @@ -100,19 +100,20 @@ NEW AND OLD DATA: -- Split OBIGT.csv and OBIGT-2.csv into multiple files according to - author names. All files are now under extdata/OBIGT/. Conflicting data - from OBIGT-2.csv were removed (see below). +- Split OBIGT.csv and OBIGT-2.csv into multiple files according to type + of substance (inorganic, organic, or biotic). All files are now under + extdata/OBIGT/. Conflicting data from OBIGT-2.csv were removed (see + below). - Citations in OBIGT now have a suffix (e.g. [S92] or [S98]) if the data were first present in sprons92.dat from SUPCRT, slop98.dat, or later versions of the slop data files (http://geopig.asu.edu/?q=tools). -- Canovas_aq.csv: Add data for citric acid cycle metabolites from Canovas and - Shock, 2016. +- Canovas_aq.csv: Add data for citric acid cycle metabolites from + Canovas and Shock, 2016. -- CHNOSZ_aq.csv: Add H4SiO4 pseudospecies (pseudo-H4SiO4); see calculations - in eos-regress.Rmd. +- CHNOSZ_aq.csv: Add H4SiO4 pseudospecies (pseudo-H4SiO4); see + calculations in eos-regress.Rmd. - Dick_aq.csv: Add data for aqueous phenanthrene and methylphenanthrene from Dick et al., 2013. @@ -162,8 +163,8 @@ OTHER CHANGES: - Remove msgout(), and replace previous calls to that function with - message() from base R. As a result, the messages don't appear in Sweave - vignettes, but can be turned on or off in knitr vignettes. + message() from base R. As a result, the messages don't appear in + Sweave vignettes, but can be turned on or off in knitr vignettes. - Remove HTCC1062.faa.xz. Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-03-08 15:20:09 UTC (rev 183) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-03-09 15:05:13 UTC (rev 184) @@ -1,40 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -alanine,Ala,C3H7NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-88810,-132500,38.83,33.6,60.4,14.9,1.74,7.16,-3.69,49.5,-7,0.18,0 -arginine,Arg,C6H14N4O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-57360,-143060,80.06,67.4,123.9,28.83,8.21,7.2,-5.95,94.8,-12.5,0.22,0 -argininium,Arg+,C6H15N4O2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-69930,-154880,82.57,77.6,122.5,31.72,0.22,5.46,-5.15,103.8,-9.6,0.73,0 -argininate,Arg-,C6H13N4O2-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-40340,-129420,68.72,81.1,143,31.28,13.76,32.12,-9.94,141.9,-19.6,2.3,0 -asparagine,Asn,C4H8N2O3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-125490,-182700,57.88,30.8,77.4,19.83,2.37,3.76,-4.81,56.5,-11.7,0.21,0 -"aspartic acid",Asp,C4H7NO4,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-172510,-226340,55.22,32.4,74.7,18.96,3.05,-6.62,-2.23,58.1,-11.9,0.17,0 -aspartate,Asp-,C4H6NO4-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-167170,-224540,43.34,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,0 -cysteine,Cys,C3H7NO2S,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-80330,-124070,46.32,47.1,73.5,18.14,2.4,9.31,-4.97,59.8,-5.6,0.15,0 -cysteinate,Cys-,C3H6NO2S-,aq,"AH97b [S07]","DLH06.1 [S07]",28.Nov.06,-68920,-115440,37.01,19.1,60.6,14.44,5.08,12.24,-3.68,61,-9.5,2.59,0 -glutamine,Gln,C5H10N2O3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-126280,-191860,62.41,43.8,93.7,23.22,3.58,5.44,-5.23,68.6,-11.4,0.18,0 -"glutamic acid",Glu,C5H9NO4,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-173050,-234820,61.2,43.5,90.2,22.3,4.23,6.55,-5.84,65.2,-10,0.15,0 -glutamate,Glu-,C5H8NO4-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-167210,-234150,43.86,7.6,80,20.49,6.96,10.86,-7.02,47.6,-7.8,2.65,0 -glycine,Gly,C2H5NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0 -glycinium,Gly+,C2H6NO2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0 -histidine,His,C6H9N3O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-48420,-108200,66,56.2,99.3,24.32,4.8,7.52,-6.05,81.6,-11.3,0.27,0 -histidinium,His+,C6H10N3O2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-56700,-115250,70.13,59.1,97,26.64,-3.4,-0.88,-3.07,88,-12,0.5,0 -isoleucine,Ile,C6H13NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-81990,-151600,49.7,91.6,105.8,24.49,6.55,18.16,-7.76,99.7,-3.6,0.09,0 -leucine,Leu,C6H13NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-84200,-153600,50.41,95.2,107.8,24.68,7.51,19.93,-8.37,102.7,-3.3,0.09,0 -lysine,Lys,C6H14N2O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-80680,-159330,57.91,63.8,108.6,24.56,8.3,24.43,-9.53,86.6,-10.9,0.07,0 -lysinium,Lys+,C6H15N2O2+,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-92890,-170370,61.82,67.9,107.5,28.62,-1.51,4.47,-3.99,95.2,-8,1.21,0 -lysinate,Lys-,C6H13N2O2-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-66310,-146340,53.27,72.8,112.2,28.29,10.53,2.97,-7.61,133.7,-18,2.67,0 -phenylalanine,Phe,C9H11NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-49430,-108900,56.6,93.8,122.1,28.27,8.8,19.34,-9.38,108.1,-6.5,0.12,0 -proline,Pro,C5H9NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-73560,-124100,49.83,43,82.6,19.39,4.87,11.88,-5.68,63.6,-9.5,0.14,0 -serine,Ser,C3H7NO3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-123930,-172420,47.24,27.8,60.6,15.69,0.73,3.87,-3.49,48.5,-9.4,0.18,0 -threonine,Thr,C4H9NO3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-119830,-178940,44.23,50.1,77.6,18.94,2.83,8.87,-4.87,65.5,-7.1,0.11,0 -tryptophan,Trp,C11H12N2O2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-26820,-97590,59.96,99.6,143.6,33.91,9.21,14.78,-9.36,116.8,-7.8,0.15,0 -tyrosine,Tyr,C9H11NO3,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-91800,-157740,59.41,80.2,124.5,30.06,8.49,8.36,-8.58,106.2,-12.4,0.09,0 -tyrosinate,Tyr-,C9H10NO3-,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-79380,-149420,45.66,51.2,111.8,26.34,10.49,16.42,-7.59,109,-16,2.78,0 -valine,Val,C5H11NO2,aq,"AH97b [S07]","DLH06.1 [S07]",25.Aug.06,-85330,-146420,45.68,74,90.9,21.35,4.48,14.58,-6.12,83.8,-4.3,0.12,0 -xylose,xylose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-179252,-249771,48.7,65.97,95.7,22.5,5.016,7.715,-4.681,107.74,-19.896,0.1672,0 -arabinose,arabinose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-177279,-249305,43.64,67.16,93.3,22.48,4.92,6.903,-5.398,110.75,-20.78,0.1672,0 -lyxose,lyxose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-178929,-249998,47.05,67.4,94.2,22.64,5.493,4.419,-5.064,110.97,-20.78,0.1672,0 -xylulose,xylulose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-178215,-245928,58.11,76.24,94.7,22.33,5.971,7.715,-5.493,119.81,-20.78,0.1672,0 -ribulose,ribulose,C5H10O5,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-175776,-244344,55.25,76.24,94.7,22.33,5.971,7.715,-5.493,119.81,-20.78,0.1672,0 -glucose,glucose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-218759,-301469,64.85,86.76,112.2,26.3,6.831,10.485,-6.306,115.89,-12.826,0.215,0 -mannose,mannose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-217586,-300626,63.75,81.26,111.9,26.56,5.446,6.712,-5.064,111.78,-14.14,0.215,0 -galactose,galactose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-217094,-299800,64.87,90.58,110.7,27.25,4.825,2.508,-5.279,128.07,-17.77,0.215,0 -fructose,fructose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-218666,-300798,66.78,84.13,111,26.23,7.5,9.554,-6.998,127.95,-20.756,0.215,0 -sorbose,sorbose,C6H12O6,aq,"AP01 [S07]",SLOP07.2,13.Nov.07,-217816,-301734,60.81,84.13,111,26.23,7.5,9.554,-6.998,127.95,-20.756,0.215,0 Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-03-08 15:20:09 UTC (rev 183) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-03-09 15:05:13 UTC (rev 184) @@ -1,72 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -methionine,Met,C5H11NO2S,aq,DLH06.1 [S07],LD12.2 [S15],10.Jul.15,-76959.8,-135210.3,62.81,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0 -[Ala],NA,CH3,aq,DLH06 [S15],NA,25.Aug.06,-3936,-13290,16.85,35.671,26.864,5.43,3.6,4.39,-1.92,27.9,3.6,-0.05,0 -[Arg],NA,C4H10N3,aq,DLH06 [S15],NA,25.Aug.06,31624,-20730,54.75,74.167,105.825,18.08,13.39,50.81,-10.09,73.2,-1.9,-0.53,0 -[Arg+],NA,C4H11N3+,aq,DLH06 [S15],NA,25.Aug.06,14943,-35670,60.59,79.677,88.906,22.25,2.08,2.69,-3.38,82.2,1,0.5,0 -[Asn],NA,C2H4NO,aq,DLH06 [S15],NA,25.Aug.06,-40615,-63490,35.9,32.847,43.826,10.36,4.23,0.99,-3.04,34.9,-1.1,-0.02,0 -[Asp],NA,C2H3O2,aq,DLH06 [S15],NA,25.Aug.06,-87635,-107130,33.24,34.405,41.116,9.49,4.91,-9.39,-0.46,36.5,-1.3,-0.06,0 -[Asp-],NA,C2H2O2-,aq,DLH06 [S15],NA,25.Aug.06,-82293,-105330,21.36,4.742,31.224,7.49,7.63,7.34,-4.6,34.7,-4.7,2.24,0 -[Cys],NA,CH3S,aq,DLH06 [S15],NA,25.Aug.06,4545,-4860,24.34,49.089,39.913,8.67,4.26,6.54,-3.2,38.2,5,-0.08,0 -[Cys-],NA,CH2S-,aq,DLH06 [S15],NA,25.Aug.06,15950,3770,15.03,21.137,26.985,4.96,6.97,9.58,-1.94,39.4,1.1,2.25,0 -[Gln],NA,C3H6NO,aq,DLH06 [S15],NA,25.Aug.06,-41404,-72650,40.43,45.83,60.078,13.75,5.44,2.67,-3.46,47,-0.8,-0.05,0 -[Glu],NA,C3H5O2,aq,DLH06 [S15],NA,25.Aug.06,-88177,-115610,39.22,45.548,56.621,12.83,6.09,3.78,-4.07,43.6,0.6,-0.08,0 -[Glu-],NA,C3H4O2-,aq,DLH06 [S15],NA,25.Aug.06,-82337,-114940,21.88,9.643,46.365,11.02,8.82,8.09,-5.25,26,2.8,2.42,0 -[Gly],NA,H,aq,DLH06 [S15],NA,25.Aug.06,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0 -[His],NA,C4H5N2,aq,DLH06 [S15],NA,25.Aug.06,36456,11010,44.02,58.213,65.753,14.85,6.66,4.75,-4.28,60,-0.7,0.04,0 -[His+],NA,C4H6N2+,aq,DLH06 [S15],NA,25.Aug.06,28175,3960,48.15,61.095,63.454,17.17,-1.54,-3.65,-1.3,66.4,-1.4,0.27,0 -[Ile],NA,C4H9,aq,DLH06 [S15],NA,25.Aug.06,2886,-32390,27.72,93.6,72.204,15.02,8.41,15.39,-5.99,78.1,7,-0.14,0 -[Leu],NA,C4H9,aq,DLH06 [S15],NA,25.Aug.06,675,-34390,28.43,97.21,74.2,15.21,9.37,17.16,-6.6,81.1,7.3,-0.14,0 -[Lys],NA,C4H10N,aq,DLH06 [S15],NA,25.Aug.06,5657,-37650,39.3,65.848,75.048,15.09,10.16,21.66,-7.76,65,-0.3,-0.16,0 -[Lys+],NA,C4H11N+,aq,DLH06 [S15],NA,25.Aug.06,-8014,-51160,39.84,69.955,73.89,19.15,0.35,1.7,-2.22,73.6,2.6,0.98,0 -[Met],NA,C3H7S,aq,DLH06 [S15],LD12.3,10.Jul.15,7911.1,-16001.4,40.82,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0 -[Phe],NA,C7H7,aq,DLH06 [S15],NA,25.Aug.06,35444,10310,34.62,95.834,88.545,18.8,10.66,16.57,-7.61,86.5,4.1,-0.11,0 -[Pro],NA,C3H5,aq,DLH06 [S15],NA,25.Aug.06,11314,-4890,27.85,45.055,49.049,9.92,6.73,9.11,-3.91,42,1.1,-0.09,0 -[Ser],NA,CH3O,aq,DLH06 [S15],NA,25.Aug.06,-39054,-53210,25.26,29.794,27.042,6.22,2.59,1.1,-1.72,26.9,1.2,-0.05,0 -[Thr],NA,C2H5O,aq,DLH06 [S15],NA,25.Aug.06,-34956,-59730,22.25,52.106,44.03,9.47,4.69,6.1,-3.1,43.9,3.5,-0.12,0 -[Trp],NA,C9H8N,aq,DLH06 [S15],NA,25.Aug.06,58053,21620,37.98,101.619,110.045,24.44,11.07,12.01,-7.59,95.2,2.8,-0.08,0 -[Tyr],NA,C7H7O,aq,DLH06 [S15],NA,25.Aug.06,-6924,-38530,37.43,82.218,90.904,20.59,10.35,5.59,-6.81,84.6,-1.8,-0.14,0 -[Tyr-],NA,C7H6O-,aq,DLH06 [S15],NA,25.Aug.06,5495,-30210,23.68,53.196,78.168,16.87,12.35,13.65,-5.82,87.4,-5.4,2.55,0 -[Val],NA,C3H7,aq,DLH06 [S15],NA,25.Aug.06,-456,-27210,23.7,76.004,57.279,11.88,6.34,11.81,-4.35,62.2,6.3,-0.11,0 -[AABB],NA,C2H4NO2,aq,DLH06 [S15],NA,25.Aug.06,-84875,-119210,21.98,-2.036,33.585,9.47,-1.86,2.77,-1.77,21.6,-10.6,0.23,0 -[AABB+],NA,C2H5NO2+,aq,DLH06 [S15],NA,25.Aug.06,-88003,-119580,31.23,28.596,36.219,11.5,-4.58,-13.96,2.37,42.1,-4,0.59,0 -[AABB-],NA,C2H3NO2-,aq,DLH06 [S15],NA,25.Aug.06,-71967,-108690,13.97,6.95,37.165,13.2,0.37,-18.69,0.15,68.7,-17.7,2.83,0 -[UPBB],NA,C2H2NO,aq,DLH06 [S15],NA,25.Aug.06,-21436,-45220,1.62,-4.496,26.296,8.1,-3.75,-6.73,1.13,11.2,-7.5,0.05,0 -[-CH2-],NA,CH2,aq,DLH06 [S15],NA,25.Aug.06,2240,-5670,6.07,20.7,16,3.49,2.15,3.09,-1.7,16,2.3,0,0 -[-CH3],NA,CH3,aq,DLH06 [S15],NA,25.Aug.06,-2190,-12460,13.78,35.8,27.1,5.55,3.6,3.96,-1.92,31.5,1.9,-0.05,0 -[-CHCH3-],NA,C2H4,aq,DLH06 [S15],NA,25.Aug.06,3470,-12480,11.71,39.9,31.2,6.2,3.62,10.12,-2.98,30.1,4.4,-0.09,0 -[-CH2NH2],NA,CH4N,aq,DLH06 [S15],CHNOSZ.8 [S15],31.Aug.06,7040,-12430,21.44,22.6,29.3,5.55,3.71,9.49,-2.66,25.9,-2.5,-0.19,0 -[-CH2OH],NA,CH3O,aq,DLH06 [S15],NA,25.Aug.06,-41530,-56790,21.57,28.5,26.7,5.86,2.59,3.03,-1.72,26.2,0.9,-0.05,0 -[-CONH2],NA,CH2NO,aq,DLH06 [S15],NA,25.Aug.06,-46550,-61420,30.14,5,28.2,7.02,1.14,-5.03,-0.06,14.5,-4.9,-0.05,0 -[-COOH],NA,CHO2,aq,DLH06 [S15],NA,25.Aug.06,-92570,-104380,26.41,5.3,24.5,5.82,1.79,-2.4,-0.67,12.9,-4.1,-0.08,0 -[-C6H5],NA,C6H5,aq,DLH06 [S15],NA,25.Aug.06,31660,15170,31.02,75.1,72.6,15.33,8.51,13.47,-5.91,70.4,1.8,-0.11,0 -[di.corr],NA,C0,aq,DLH06 [S15],NA,25.Aug.06,0,0,0,-13.5,3.2,0.06,-1.48,-0.05,2.32,-0.1,-6.7,-0.02,0 -glutathione,GSH,C10H17N3O6S,aq,Dic07,NA,25.Feb.07,-217454,-335690,106.09,115.9,193.6,49.3,3.56,0.85,-8.05,153.5,-17.8,0.17,0 -"glutathione,ox",GSSG,C20H32N6O12S2,aq,Dic07,NA,25.Feb.07,-428031,-661380,NA,201.6,365,94.48,4.22,-0.04,-15.66,276,-34.8,0.44,0 -cystine,NA,C6H12N2O4S2,aq,Dic07,NA,25.Feb.07,-150781,-238140,NA,64,124.8,32.16,1.9,16.88,-9.5,88.6,-10.4,0.4,0 -[CysS],NA,CH2S,aq,Dic07,NA,25.Feb.07,9484.5,140,NA,33.84,28.75,6.61,2.81,5.67,-2.98,22.7,5.4,-0.03,0 -Gly-Ala-Gly,GAG,C7H13N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,68.2,130.5,0,0,0,0,85.8,-15.8,-1.59,0 -Gly-Arg+-Gly,GRG+,C10H21N6O4+,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,84.8,184.9,0,0,0,0,116,-20,-1.04,1 -Gly-Asn-Gly,GNG,C8H14N4O5,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,66.6,150.1,0,0,0,0,89,-18,-1.56,0 -Gly-Asp-Gly,GDG,C8H13N3O6,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,65.4,143.6,0,0,0,0,78.9,-13.8,-1.6,0 -Gly-Cys-Gly,GCG,C7H13N3O4S,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,79.8,143.7,0,0,0,0,89,-11.8,-1.62,0 -Gly-Gln-Gly,GQG,C9H16N4O5,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,76.8,162.5,0,0,0,0,100.5,-18.8,-1.59,0 -Gly-Glu-Gly,GEG,C9H15N3O6,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,77.9,159.9,0,0,0,0,94.6,-15.5,-1.62,0 -Gly-Gly-Gly,GGG,C6H11N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,44.2,112.1,0,0,0,0,63.9,-16.6,-1.54,0 -Gly-His-Gly,GHG,C10H15N5O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,92.2,172,0,0,0,0,151.9,-36.1,-1.5,0 -Gly-Ile-Gly,GIG,C10H19N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,124.1,176.9,0,0,0,0,122.6,-6.8,-1.68,0 -Gly-Leu-Gly,GLG,C10H19N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,125.2,176.4,0,0,0,0,129.4,-9.6,-1.68,0 -Gly-Lys+-Gly,GKG+,C10H21N4O4+,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,112,177,0,0,0,0,180,-36,-0.56,1 -Gly-Met-Gly,GMG,C9H17N3O4S,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,101.7,177,0,0,0,0,105.9,-9.4,-1.64,0 -Gly-Phe-Gly,GFG,C13H17N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,120.5,193.1,0,0,0,0,128.4,-11.3,-1.65,0 -Gly-Pro-Gly,GPG,C9H15N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,70.2,145.2,0,0,0,0,91.5,-17.8,-1.63,0 -Gly-Ser-Gly,GSG,C7H13N3O5,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,60.1,130.2,0,0,0,0,77.5,-15.7,-1.59,0 -Gly-Thr-Gly,GTG,C8H15N3O5,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,80.9,145.8,0,0,0,0,99.3,-16.5,-1.66,0 -Gly-Tyr-Gly,GYG,C13H17N3O5,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,107.2,194.9,0,0,0,0,126.8,-17.2,-1.68,0 -Gly-Val-Gly,GVG,C9H17N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,104.9,160.3,0,0,0,0,111.8,-10.8,-1.65,0 -[GXGBB],NA,C6H10N3O4,aq,DLH06.2,NA,10.Sep.11,NA,NA,NA,30.9,103.2,0,0,0,0,52.6,-17.6,-1.54,0 -phenanthrene,NA,C14H10,aq,DEH+13,NA,13.Dec.12,300730,155570,246.9,447.3,161.6,NA,NA,NA,NA,NA,NA,NA,0 -1-methylphenanthrene,NA,C15H12,aq,DEH+13,NA,13.Dec.12,299310,128600,297.6,549.4,165.6,NA,NA,NA,NA,NA,NA,NA,0 -2-methylphenanthrene,NA,C15H12,aq,DEH+13,NA,13.Dec.12,293740,120150,287.9,539.8,171.1,NA,NA,NA,NA,NA,NA,NA,0 -3-methylphenanthrene,NA,C15H12,aq,DEH+13,NA,13.Dec.12,294290,120610,287.7,539.8,171.1,NA,NA,NA,NA,NA,NA,NA,0 -4-methylphenanthrene,NA,C15H12,aq,DEH+13,NA,13.Dec.12,330230,152660,274.6,569.2,177.6,NA,NA,NA,NA,NA,NA,NA,0 -9-methylphenanthrene,NA,C15H12,aq,DEH+13,NA,13.Dec.12,298090,126760,295.5,549.4,165.6,NA,NA,NA,NA,NA,NA,NA,0 Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-03-08 15:20:09 UTC (rev 183) +++ pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-03-09 15:05:13 UTC (rev 184) @@ -1,245 +0,0 @@ -name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T -acanthite,Acn,Ag2S,cr1,"HDNB78 [S92]",NA,5.May.78,-9446,-7550,34.3,NA,34.2,15.63,8.6,0,0,0,0,0,450 -acanthite,Acn,Ag2S,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-9235.197,-7024.866,35.3543,NA,34.2,1.819,53,0,0,0,0,0,620 -acanthite,Acn,Ag2S,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-8227.324,-4960.457,38.898,NA,34.2,21.6,0,0,0,0,0,0,1000 -aegerine,Agt,NaFe(SiO3)2,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,36.7,NA,64.37,46.16,19.31,-9.46,0,0,0,0,950 -aegerine,Agt,NaFe(SiO3)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-82.386,NA,34.6051,NA,64.37,52.42,10.01,-7.68,0,0,0,0,1050 -aegerine,Agt,NaFe(SiO3)2,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,478.346,NA,36.6502,NA,64.37,50.27,10.89,-7.68,0,0,0,0,1400 -akermanite,Ak,Ca2MgSi2O7,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-879362,-926497,50.03,NA,92.81,60.09,11.4,-11.4,0,0,0,0,1700 -alabandite,Alb,MnS,cr,"HDNB78 [S92]",NA,5.May.78,-52178,-51000,19.2,NA,21.46,11.4,1.8,0,0,0,0,0,1803 -albite,Ab,Na(AlSi3)O8,cr1,"HDNB78 [S92]",NA,5.May.78,-886308,-939680,49.51,NA,100.25,61.7,13.9,-15.01,0,0,0,0,473 -albite,Ab,Na(AlSi3)O8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-886096.268,NA,53.9193,NA,100.25,81.88,3.554,-50.154,0,0,0,0,1200 -"albite,high",Hi-Ab,NaAlSi3O8,cr1,"HDNB78 [S92]",NA,5.May.78,-884509,-937050,52.3,NA,100.43,61.7,13.9,-15.01,0,0,0,0,623 -"albite,high",Hi-Ab,NaAlSi3O8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-884768.678,NA,50.4797,NA,100.43,64.17,13.9,-15.01,0,0,0,0,1400 -"albite,low",Lo-Ab,Na(AlSi3)O8,cr,"HDNB78 [S92]",NA,5.May.78,-886308,-939680,49.51,NA,100.07,61.7,13.9,-15.01,0,0,0,0,1400 -almandine,Alm,Fe3Al2Si3O12,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,75.6,NA,115.28,97.52,33.64,-18.73,0,0,0,0,848 -almandine,Alm,Fe3Al2Si3O12,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-11.741,NA,71.93,NA,115.28,107.09,14.86,-10.63,0,0,0,0,1600 -alunite,Alu,KAl3(OH)6(SO4)2,cr,"HDNB78 [S92]",NA,5.May.78,-1113600,-1235600,78.4,NA,293.6,153.45,0,-54.95,0,0,0,0,650 -"amesite,14a",14A-Am,Mg4Al2(Al2Si2)O10(OH)8,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,108.9,NA,205.4,172.59,34.98,-41.67,0,0,0,0,848 -"amesite,14a",14A-Am,Mg4Al2(Al2Si2)O10(OH)8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,3.895,NA,110.1233,NA,205.4,169.4,41.24,-44.37,0,0,0,0,1000 -"amesite,7a",Ams-7A,Mg2Al(AlSi)O5(OH)4,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,52,NA,103,81.03,24.738,-20.23,0,0,0,0,1000 -"amorphous silica",Amor-Sl,SiO2,cr,"HDNB78 [S92]",NA,5.May.78,-202892,-214568,14.34,NA,29,5.93,47.2,-22.78,0,0,0,0,622 -analcime,Anl,NaAlSi2O6*H2O,cr,"HDNB78 [S92]",NA,5.May.78,-738098,-790193,56,NA,97.1,53.49,24.14,-8.88,0,0,0,0,1000 -"analcime,dehydrated",Dhyd-Anl,NaAlSi2O6,cr,"HDNB78 [S92]",NA,5.May.78,-674989,-714678,41.9,NA,89.1,42.09,24.14,-8.88,0,0,0,0,1000 -andalusite,And,Al2SiO5,cr,"HDNB78 [S92]",NA,5.May.78,-580587,-615866,22.2,NA,51.53,41.310833,6.292556,-12.392063,0,0,0,0,1043 -andradite,Adr,Ca3Fe2Si3O12,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1296819,-1380345,70.13,NA,131.85,113.532,15.636,-30.889,0,0,0,0,1100 -anglesite,Ang,PbSO4,cr,"HDNB78 [S92]",NA,5.May.78,-194353,-219870,35.51,NA,47.95,10.96,31,4.2,0,0,0,0,1100 -anhydrite,Anh,CaSO4,cr,"HDNB78 [S92]",NA,5.May.78,-315925,-342760,25.5,NA,45.94,16.78,23.6,0,0,0,0,0,1453 -annite,Ann,KFe3(AlSi3)O10(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-1147156,-1232195,95.2,NA,154.32,106.43,29.77,-19.31,0,0,0,0,1000 -anorthite,An,Ca(Al2Si2)O8,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-954078,-1007552,49.1,NA,100.79,63.311,14.794,-15.44,0,0,0,0,1700 -anthophyllite,Ath,Mg7Si8O22(OH)2,cr1,"HDNB78 [S92]",NA,5.May.78,-2715430,-2888749,128.6,NA,264.4,180.682,60.574,-38.462,0,0,0,0,903 -anthophyllite,Ath,Mg7Si8O22(OH)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-2718479.297,NA,108.796,NA,264.4,197.542,41.614,-13.342,0,0,0,0,1258 -anthophyllite,Ath,Mg7Si8O22(OH)2,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-2719529.932,NA,105.9454,NA,264.4,199.522,41.614,-13.342,0,0,0,0,1800 -antigorite,Atg,Mg48Si34O85(OH)62,cr1,"HDNB78 [S92]",NA,5.May.78,-15808020,-17070891,861.36,NA,1749.13,1228.45,513.76,-286.68,0,0,0,0,848 -antigorite,Atg,Mg48Si34O85(OH)62,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-15808027.845,NA,858.9133,NA,1749.13,1234.83,501.24,-281.28,0,0,0,0,1000 -aragonite,Arg,CaCO3,cr,"HDNB78 [S92]","PB82 [S92]",9.Mar.90,-269683,-288531,21.56,NA,34.15,20.13,10.24,-3.34,0,0,0,0,600 -artinite,Art,Mg2(OH)2(CO3)*3H2O,cr,"HDNB78 [S92]",NA,5.May.78,-613915,-698043,55.67,NA,96.9,70.87,27.66,-7.43,0,0,0,0,1000 -azurite,Azr,Cu3(OH)2(CO3)2,cr,"HDNB78 [S92]",NA,5.May.78,-334417,-390100,66.97,NA,91.01,36.88,77.44,-0.92,0,0,0,0,780 -barite,Brt,BaSO4,cr,"HDNB78 [S92]",NA,5.May.78,-325563,-352100,31.6,NA,52.1,33.8,0,-8.43,0,0,0,0,1422 -boehmite,Bhm,AlO(OH),cr,"HDNB78 [S92]",NA,5.May.78,-217250,-235078,11.58,NA,19.535,14.435,4.2,0,0,0,0,0,500 -bornite,Bn,Cu5FeS4,cr1,"HDNB78 [S92]","PK70 [S92]",5.May.78,-86704,-79922,99.29,NA,98.6,49.76,35.08,-1.35,0,0,0,0,485 -bornite,Bn,Cu5FeS4,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-86373.231,-78463.256,103.0733,NA,98.6,-34.31,247,0,0,0,0,0,540 -bornite,Bn,Cu5FeS4,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-86513.642,-80947.917,95.2106,NA,98.6,80.33,-2.04,0,0,0,0,0,1200 -bromellite,Brm,BeO,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,3.38,NA,8.309,8.45,4,-3.17,0,0,0,0,1200 -brucite,Brc,Mg(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-199646,-221390,15.09,NA,24.63,24.147,4.0124,-6.11,0,0,0,0,900 -bunsenite,Bsn,NiO,cr1,"HDNB78 [S92]",NA,5.May.78,-50573,-57300,9.08,NA,10.97,-4.99,37.58,3.89,0,0,0,0,525 -bunsenite,Bsn,NiO,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-50581.657,-57508.213,8.4107,NA,10.97,13.88,0,0,0,0,0,0,565 -bunsenite,Bsn,NiO,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-50447.661,-57020.353,9.5976,NA,10.97,11.18,2.02,0,0,0,0,0,2000 -ca-al-pyroxene,Ca-Al-Px,CaAl(AlSi)O6,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-742067,-783793,35,NA,63.5,54.13,6.42,-14.9,0,0,0,0,1400 -ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,166.6,NA,265,145.82,52.67,-19.13,0,0,0,0,848 -ca-phillipsite,Ca-Php,Ca(Al2Si5)O14*5H2O,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-3.895,NA,165.3767,NA,265,149.01,46.41,-16.43,0,0,0,0,1000 -calcite,Cal,CaCO3,cr,"HDNB78 [S92]","PB82 [S92]",9.Mar.90,-269880,-288552,22.15,NA,36.934,24.98,5.24,-6.2,0,0,0,0,1200 -celadonite,Cln,K(MgAl)Si4O10(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,74.9,NA,157.1,80.25,25.3,-18.54,0,0,0,0,1000 -celestite,Cls,SrSO4,cr,"HDNB78 [S92]",NA,5.May.78,-320435,-347300,28,NA,46.25,21.8,13.3,0,0,0,0,0,1500 -cerussite,Cer,PbCO3,cr,"HDNB78 [S92]",NA,5.May.78,-150370,-168000,31.3,NA,40.59,12.39,28.6,0,0,0,0,0,800 -chabazite,Cbz,Ca(Al2Si4)O12*6H2O,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,152.9,NA,247.76,146,44.47,-16.43,0,0,0,0,1000 -chalcedony,Cha,SiO2,cr,"HDNB78 [S92]",NA,5.May.78,-204276,-217282,9.88,NA,22.688,11.22,8.2,-2.7,0,0,0,0,848 -chalcocite,Cc,Cu2S,cr1,"HDNB78 [S92]",NA,5.May.78,-20626,-19000,28.9,NA,27.48,12.63,18.82,0,0,0,0,0,376 -chalcocite,Cc,Cu2S,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-20479.051,-18494.843,30.1015,NA,27.48,26.78,-7.35,0,0,0,0,0,717 -chalcocite,Cc,Cu2S,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-19940.435,-17064.666,33.0917,NA,27.48,20.32,0,0,0,0,0,0,1400 -chalcopyrite,Ccp,CuFeS2,cr1,"HDNB78 [S92]","PK70 [S92]",5.May.78,-44900,-44453,31.15,NA,42.83,20.79,12.8,-1.34,0,0,0,0,830 -chalcopyrite,Ccp,CuFeS2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-34590.133,-15235.889,94.5651,NA,42.83,-141.4,210,0,0,0,0,0,930 -chalcopyrite,Ccp,CuFeS2,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-46119.409,-49143.645,19.5073,NA,42.83,41.22,0,0,0,0,0,0,1200 -chloritoid,Cld,FeAl2SiO5(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,42.1,NA,69.8,60.63,17.13,-13.63,0,0,0,0,1000 -chrysotile,Ctl,Mg3Si2O5(OH)4,cr,"HDNB78 [S92]",NA,5.May.78,-964871,-1043123,52.9,NA,108.5,75.82,31.6,-17.58,0,0,0,0,1000 -cinnabar,Cin,HgS,cr,"HDNB78 [S92]",NA,5.May.78,-10940,-12750,19.7,NA,28.416,10.46,3.72,0,0,0,0,0,618 -"clinochlore,14a",14A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr,"HDNB78 [S92]",NA,5.May.78,-1961703,-2116964,111.2,NA,207.11,166.5,42.1,-37.47,0,0,0,0,900 -"clinochlore,7a",7A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr1,"HDNB78 [S92]",NA,5.May.78,-1957101,-2113197,106.5,NA,211.5,162.82,50.62,-40.88,0,0,0,0,848 -"clinochlore,7a",7A-Cnc,Mg5Al(AlSi3)O10(OH)8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-1957104.895,NA,105.2767,NA,211.5,166.01,44.36,-38.18,0,0,0,0,900 -clinozoisite,Czo,Ca2Al3Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1549240,-1643781,70.64,NA,136.2,106.118,25.214,-27.145,0,0,0,0,700 -coesite,Cos,SiO2,cr1,"HDNB78 [S92]",NA,5.May.78,-203541,-216614,9.65,NA,20.641,11,8.2,-2.7,0,0,0,0,848 -coesite,Cos,SiO2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-203544.895,NA,8.4267,NA,20.641,14.19,1.94,0,0,0,0,0,2000 -copper,Cu,Cu,cr,"HDNB78 [S92]",NA,5.May.78,0,0,7.923,NA,7.113,5.41,1.5,0,0,0,0,0,1357 -cordierite,Crd,Mg2Al3(AlSi5)O18,cr,"HDNB78 [S92]",NA,5.May.78,-2061279,-2183199,97.33,NA,233.22,143.83,25.8,-38.6,0,0,0,0,1700 -"cordierite,hydrous",Hyd-Crd,Mg2Al3(AlSi5)O18*H2O,cr,"HDNB78 [S92]",NA,5.May.78,-2121350,-2255676,111.43,NA,241.22,155.23,25.8,-38.6,0,0,0,0,1700 -corundum,Crn,Al2O3,cr,"HDNB78 [S92]",NA,5.May.78,-374824,-397145,12.18,NA,25.575,27.49,2.82,-8.38,0,0,0,0,1800 -covellite,Cv,CuS,cr,"HDNB78 [S92]",NA,5.May.78,-12612,-12500,15.9,NA,20.42,10.6,2.64,0,0,0,0,0,1273 -cristobalite,Crs,SiO2,cr1,"HDNB78 [S92]",NA,5.May.78,-203895,-216755,10.372,NA,25.74,13.98,3.34,-3.81,0,0,0,0,543 -cristobalite,Crs,SiO2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-203677.53,-216037.379,12.0495,NA,25.74,17.39,0.31,-9.89,0,0,0,0,2000 -"cristobalite,alpha",A-Crs,SiO2,cr,"HDNB78 [S92]",NA,5.May.78,-203895,-216755,10.372,NA,25.74,13.98,3.34,-3.81,0,0,0,0,1000 -"cristobalite,beta",B-Crs,SiO2,cr,"HDNB78 [S92]",NA,5.May.78,-203290,-215675,11.963,NA,27.38,17.39,0.31,-9.89,0,0,0,0,2000 -"cronstedtite,7a",7A-Csd,Fe2Fe(FeSi)O5(OH)4,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,73.5,NA,110.9,84.79,41.84,-12.476,0,0,0,0,950 -"cronstedtite,7a",7A-Csd,Fe2Fe(FeSi)O5(OH)4,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-160.595,NA,69.3289,NA,110.9,97.3,23.24,-8.93,0,0,0,0,1050 -"cronstedtite,7a",7A-Csd,Fe2Fe(FeSi)O5(OH)4,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,957.096,NA,73.4065,NA,110.9,93.01,25,-8.93,0,0,0,0,1500 -cummingtonite,Cum,Mg7Si8O22(OH)2,cr,"HDNB78 [S92]",NA,16.Aug.15,NA,NA,127.5,NA,271.9,185.24,58.61,-41.66,0,0,0,0,800 -cuprite,Cpr,Cu2O,cr,"HDNB78 [S92]",NA,5.May.78,-35384,-40830,22.08,NA,23.437,14.08,5.88,-0.76,0,0,0,0,1515 -"daphnite,14a",Dph-14A,Fe5Al(AlSi3)O10(OH)8,cr,"HDNB78 [S92]","SLOP98.2",5.May.78,-1550482,-1695426,142.5,NA,213.42,176.21,43.76,-33.82,0,0,0,0,1000 -"daphnite,7a",7A-Dph,Fe5Al(AlSi3)O10(OH)8,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,138.9,NA,221.2,172.53,52.28,-37.23,0,0,0,0,848 -"daphnite,7a",7A-Dph,Fe5Al(AlSi3)O10(OH)8,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,3.159,NA,137.726,NA,221.2,175.72,46.02,-34.63,0,0,0,0,1000 -diaspore,Dsp,AlO(OH),cr,"HDNB78 [S92]",NA,5.May.78,-218402,-237170,8.43,NA,17.76,14.435,4.2,0,0,0,0,0,500 -dickite,Dck,Al2Si2O5(OH)4,cr,"HDNB78 [S92]","RHF79.1 [S92]",5.May.78,NA,NA,47.1,NA,99.3,72.77,29.2,-21.52,0,0,0,0,1000 -diopside,Di,CaMg(SiO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-723780,-765378,34.2,NA,66.09,52.87,7.84,-15.74,0,0,0,0,1600 -dolomite,Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-517760,-556631,37.09,NA,64.365,41.557,23.952,-9.884,0,0,0,0,1000 -"dolomite,disordered",Dis-Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-515653,-553704,39.84,NA,64.39,44.711,17.779,-10.948,0,0,0,0,1000 -"dolomite,ordered",Ord-Dol,CaMg(CO3)2,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-517760,-556631,37.09,NA,64.34,44.711,17.779,-10.948,0,0,0,0,1000 -edenite,Ed,Na(Ca2Mg5)(AlSi7)O22(OH2),cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,161,NA,271,199.71,48.78,-46.01,0,0,0,0,848 -edenite,Ed,Na(Ca2Mg5)(AlSi7)O22(OH2),cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-3.895,NA,159.7767,NA,271,202.9,42.52,-43.31,0,0,0,0,1000 -enstatite,En,MgSiO3,cr1,"HDNB78 [S92]",NA,5.May.78,-348930,-369686,16.2,NA,31.276,24.55,4.74,-6.28,0,0,0,0,903 -enstatite,En,MgSiO3,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-349581.153,-371758.464,11.4328,NA,31.296,28.765,0,0,0,0,0,0,1258 -enstatite,En,MgSiO3,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-349546.21,-371843.59,11.0302,NA,32.386,29.26,0,0,0,0,0,0,1800 -epidote,Ep,Ca2FeAl2Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1450906,-1543992,75.28,NA,139.2,117.622,12.816,-31.864,0,0,0,0,1100 -"epidote,ordered",Ord-Ep,Ca2FeAl2Si3O12(OH),cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-1450906,-1544016,75.2,NA,139.2,113.78,14.69,-28.92,0,0,0,0,1100 -epistilbite,Eps,Ca(Al2Si6)O16*5H2O,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,152.9,NA,267.56,157.04,60.87,-21.83,0,0,0,0,848 -epistilbite,Eps,Ca(Al2Si6)O16*5H2O,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-7.845,NA,150.4533,NA,267.56,163.42,48.35,-16.43,0,0,0,0,1000 -fayalite,Fa,Fe2SiO4,cr,"HDNB78 [S92]",NA,5.May.78,-330233,-354119,35.45,NA,46.39,36.51,9.36,-6.7,0,0,0,0,1490 -ferroedenite,Fe-Ed,Na(Ca2Fe5)(AlSi7)O22(OH)2,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,193.7,NA,280.9,209.42,50.44,-42.36,0,0,0,0,848 -ferroedenite,Fe-Ed,Na(Ca2Fe5)(AlSi7)O22(OH)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-3.895,NA,192.4767,NA,280.9,212.61,44.18,-39.66,0,0,0,0,1000 -ferrogedrite,Fe-Ged,(Fe5Al2)(Al2Si6)O22(OH)2,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,153.5,NA,265.9,196.27,58.39,-39.01,0,0,0,0,903 -ferrogedrite,Fe-Ged,(Fe5Al2)(Al2Si6)O22(OH)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-1524.649,NA,143.598,NA,265.9,204.7,48.91,-26.45,0,0,0,0,1258 -ferrogedrite,Fe-Ged,(Fe5Al2)(Al2Si6)O22(OH)2,cr3,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-2049.966,NA,142.1727,NA,265.9,205.69,48.91,-26.45,0,0,0,0,1500 -ferropargasite,Fe-Prg,Na(Ca2Fe4Al)(Al2Si6)O22(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-2526187,-2686900,185.5,NA,279.89,213.57,42.99,-47.29,0,0,0,0,1000 -ferrosilite,Fs,FeSiO3,cr1,"HDNB78 [S92]","Hel85 [S92]",5.May.78,-267588,-285658,21.63,NA,32.952,26.49,5.07,-5.55,0,0,0,0,413 -ferrosilite,Fs,FeSiO3,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-267566.749,-285550.307,21.9199,NA,33.008,23.865,8.78,-4.7,0,0,0,0,1400 -ferrotremolite,Fe-Tr,(Ca2Fe5)Si8O22(OH)2,cr,"HDNB78 [S92]",NA,5.May.78,-2349100,-2511300,163.5,NA,282.8,197.93,58.95,-41.17,0,0,0,0,800 -ferrous-oxide,Frs-Ox,FeO,cr,"HDNB78 [S92]",NA,5.May.78,-60097,-65020,14.52,NA,12,12.122,2.072,-0.75,0,0,0,0,1600 -fluoredenite,Fl-Ed,Na(Ca2Mg5)(AlSi7)O22(F)2,cr1,"HDNB78 [S92]",NA,5.May.78,NA,NA,146.7,NA,272.5,195.23,46.74,-44.92,0,0,0,0,848 -fluoredenite,Fl-Ed,Na(Ca2Mg5)(AlSi7)O22(F)2,cr2,"HDNB78 [S92]",CHNOSZ.1,5.May.78,-3.895,NA,145.4767,NA,272.5,198.42,40.48,-42.22,0,0,0,0,1000 -fluorite,Fl,CaF2,cr,"HDNB78 [S92]",NA,5.May.78,-280493,-293000,16.39,NA,24.542,14.3,7.28,0.47,0,0,0,0,1424 -fluorphlogopite,F-Phl,KMg3(AlSi3)O10(F)2,cr,"HDNB78 [S92]","RHF79.1 [S92]",5.May.78,NA,NA,80.38,NA,146.37,96.13,26.74,-20.41,0,0,0,0,1000 -fluortremolite,F-Tr,(Ca2Mg5)Si8O22(F)2,cr,"HDNB78 [S92]",NA,5.May.78,NA,NA,129.4,NA,270.45,183.74,55.25,-43.73,0,0,0,0,800 -forsterite,Fo,Mg2SiO4,cr,"HDNB78 [S92]",NA,5.May.78,-491564,-520000,22.75,NA,43.79,35.81,6.54,-8.52,0,0,0,0,1800 -galena,Gn,PbS,cr,"HDNB78 [S92]",NA,5.May.78,-23115,-23500,21.8,NA,31.49,11.17,2.2,0,0,0,0,0,1388 -gehlenite,Gh,Ca2(Al2Si)O7,cr,"HDNB78 [S92]","SPRONS92.2",15.Mar.90,-903148,-951225,48.1,NA,90.24,63.74,8,-15.12,0,0,0,0,1800 -gibbsite,Gbs,Al(OH)3,cr,"HDNB78 [S92]",NA,5.May.78,-276168,-309065,16.75,NA,31.956,8.65,45.6,0,0,0,0,0,425 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 184 From noreply at r-forge.r-project.org Fri Mar 17 12:54:22 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 17 Mar 2017 12:54:22 +0100 (CET) Subject: [CHNOSZ-commits] r185 - in pkg/CHNOSZ: . R data demo inst inst/extdata man vignettes Message-ID: <20170317115422.D94CF188404@r-forge.r-project.org> Author: jedick Date: 2017-03-17 12:54:22 +0100 (Fri, 17 Mar 2017) New Revision: 185 Removed: pkg/CHNOSZ/inst/extdata/js/ Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/util.data.R pkg/CHNOSZ/data/protein.csv pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/demo/sources.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/data.Rd pkg/CHNOSZ/vignettes/obigt.Rmd pkg/CHNOSZ/vignettes/obigt.bib Log: remove sorttable.js Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-03-09 15:05:13 UTC (rev 184) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-17 11:54:22 UTC (rev 185) @@ -1,6 +1,6 @@ -Date: 2017-03-09 +Date: 2017-03-17 Package: CHNOSZ -Version: 1.0.8-73 +Version: 1.0.8-74 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/util.data.R =================================================================== --- pkg/CHNOSZ/R/util.data.R 2017-03-09 15:05:13 UTC (rev 184) +++ pkg/CHNOSZ/R/util.data.R 2017-03-17 11:54:22 UTC (rev 185) @@ -171,7 +171,7 @@ # list: the output of subcrt() ## first retrieve the sources table thermo <- get("thermo") - x <- thermo$refs + x <- thermo$refs[order(thermo$refs$note), ] ## show a table in the browser if 'key' is NULL if(is.null(key)) { # create the html links @@ -181,49 +181,95 @@ x$citation[notlinked] <- cite[notlinked] # remove the last (URL) component #x$URL <- NULL - x <- x[1:4] - # count the times each source is listed in OBIGT.csv - ns1 <- sapply(x$key, function(x) length(which(thermo$obigt$ref1==x)) ) - ns1.2 <- sapply(x$key, function(x) length(which(thermo$obigt$ref2==x)) ) - ns1 <- ns1 + ns1.2 - ns1[ns1==0] <- "" - # count the times each source is listed in protein.csv - npr <- sapply(x$key, function(x) length(which(thermo$protein$ref==x)) ) - npr[npr==0] <- "" + x <- x[1:5] + # count the number of times each source is cited in thermo$obigt + # e.g. if key is "Kel60" we match "Kel60 [S92]" but not "Kel60.1 [S92]" + # http://stackoverflow.com/questions/6713310/how-to-specify-space-or-end-of-string-and-space-or-start-of-string + # we also have to escape keys with "+" signs + ns1 <- sapply(x$key, function(x) sum(grepl(gsub("+", "\\+", paste0(x, "($|\\s)"), fixed=TRUE), thermo$obigt$ref1)) ) + ns2 <- sapply(x$key, function(x) sum(grepl(gsub("+", "\\+", paste0(x, "($|\\s)"), fixed=TRUE), thermo$obigt$ref2)) ) + number <- ns1 + ns2 + number[number==0] <- "" + # now that we're using the sortTable() from w3schools.com, numbers are sorted like text + # add leading zeros to make the numbers sortable 20170317 + # (the zeros disappear somewhere in the rendering of the page) + number <- formatC(number, width = 3, format = "d", flag = "0") # append the counts to the table to be shown - x <- c(x,list(ns1=ns1,npr=npr)) + x <- c(list(number=number), x) # title to display for web page title <- "Sources of Thermodynamic Data in CHNOSZ" ### the following is adapted from print.findFn in package 'sos' f0 <- tempfile() File <- paste(f0, ".html", sep="") - Dir <- dirname(File) - js <- system.file("extdata/js", "sorttable.js", package = "CHNOSZ") - file.copy(js, Dir) + #Dir <- dirname(File) + #js <- system.file("extdata/js", "sorttable.js", package = "CHNOSZ") + #file.copy(js, Dir) ## Sundar's original construction: con <- file(File, "wt") on.exit(close(con)) .cat <- function(...) cat(..., "\n", sep = "", file = con, append = TRUE) ## start - cat("", file = con) + cat('\n', file = con) + .cat("") .cat("") .cat("", title, "") - .cat("") + # sorttable.js is "Blocked for security reasons" in Gmail 20170317 + #.cat("") + # https://www.w3schools.com/howto/howto_js_sort_table.asp + .cat('') .cat("") ### boilerplate text + .cat("") .cat("

Listing of all entries in thermo$refs

") - .cat("

Click on hyperlinked references to open URL in new window

") - .cat("

Click on column headers to sort

") - .cat("

Columns 'n..' give number of times each reference appears in data tables:

") - .cat("ns1: 'ref1' and 'ref2' in data/OBIGT.csv
") - .cat("npr: 'ref' in data/protein.csv

") + .cat("

Click on hyperlinked references to open URL in new window.

") + .cat("

Click on column headers to sort.

") + .cat("

Column 'number' gives number of times each reference appears in thermo$obigt.

") ### start table and headers - .cat("\n") + .cat("
") .cat("") - .cat(sprintf(" \n", - paste(names(x), collapse = "\n ") + #.cat(sprintf(" \n", + # paste(names(x), collapse = "\n ', i-1, names(x)[i])) + .cat("") ### now preparing the body of the table paste.list <- c(lapply(x, as.character), sep = "\n
%s
"))) - .cat("\n
%s
"))) + for(i in 1:length(x)) .cat(sprintf(' %s
") tbody.list <- do.call("paste", paste.list) @@ -231,7 +277,7 @@ tbody <- sub("
") + .cat("") ### end adaptation from print.findFn # show table in browser browseURL(File) Modified: pkg/CHNOSZ/data/protein.csv =================================================================== --- pkg/CHNOSZ/data/protein.csv 2017-03-09 15:05:13 UTC (rev 184) +++ pkg/CHNOSZ/data/protein.csv 2017-03-17 11:54:22 UTC (rev 185) @@ -144,7 +144,6 @@ TPX,AQUAE,UniProt,O66780,1,11,2,10,16,6,12,0,11,14,11,5,7,8,5,6,4,10,27,0,4 TPX,ECOLI,UniProt,P0A862,1,22,3,10,7,10,10,1,10,7,15,0,10,6,9,5,10,12,18,0,2 H-NS,PHOPR,UniProt,Q6LT83,1,14,0,9,19,2,5,1,2,14,19,3,2,4,4,9,8,7,5,1,3 -cell,ECOLI,Nei86,NA,1,488,87,229,250,176,582,90,276,326,428,146,229,210,250,281,205,241,402,54,131 PPB,ECOLI,UniProt,P00634,1,64,4,28,24,8,45,10,16,28,39,8,20,21,22,14,22,40,23,3,11 SPTA2.SH3,CHICK,UniProt,P07751,1,3,0,5,4,1,3,0,1,8,7,1,3,3,2,2,2,4,6,2,3 BARS,BACAM,UniProt,P11540,1,6,2,4,11,2,5,1,6,6,12,0,3,2,6,3,5,4,5,3,3 Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-03-09 15:05:13 UTC (rev 184) +++ pkg/CHNOSZ/data/refs.csv 2017-03-17 11:54:22 UTC (rev 185) @@ -1,127 +1,118 @@ -key,author,year,note,citation,URL -Kel60,"K. K. Kelley",1960,"gases Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 -Kel60.1,"K. K. Kelley",1960,larnite Cp,"U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 -Kel60.2,"K. K. Kelley",1960,"iron Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 -Kel60.3,"K. K. Kelley",1960,"gypsum Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901 -Pan70,"L. B. Pankratz",1970,chlorargyrite,"U. S. Bureau of Mines Report of Investigations 7430",http://www.worldcat.org/oclc/14154245 -PK70,"L. B. Pankratz and E. G. King",1970,"bornite and chalcopyrite","U. S. Bureau of Mines Report of Investigations 7435",http://www.worldcat.org/oclc/14154292 -HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"minerals and phase transitions","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862 -HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"litharge S, V, and Cp parameters","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862 -RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"chlorargyrite, rutile, and titanite","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 -RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"dickite, fluorphlogopite, halloysite, and pyrope","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 -RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"iron","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452 -PB82,"L. N. Plummer and E. Busenberg",1982,"aragonite and calcite","Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4 -WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"gases GHS","J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 -WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,manganosite,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 -WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,MgSO4,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661 -BH83,"T. S. Bowers and H. C. Helgeson",1983,rutile,"Geochim. Cosmochim. Acta 47, 1247-1275",http://dx.doi.org/10.1016/0016-7037(83)90066-2 -Hel85,"H. C. Helgeson",1985,"ferrosilite and siderite","Am. J. Sci. 285, 845-855",http://dx.doi.org/10.2475/ajs.285.9.845 -JH85,"K. J. Jackson and H. C. Helgeson",1985,"Sn minerals","Econ. Geol. 80, 1365-1378",http://dx.doi.org/10.2113/gsecongeo.80.5.1365 -Nei86,"F. C. Neidhardt",1986,,"Escherichia coli and Salmonella typhimurium, 3-5",http://www.worldcat.org/oclc/15280827 -SH88,"E. L. Shock and H. C. Helgeson",1988,"ionic species","Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0 -CWM89,"J. D. Cox, D. D. Wagman and V. A. Medvedev, eds.",1989,,"CODATA Key Values for Thermodynamics",http://www.worldcat.org/oclc/18559968 -SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"inorganic neutral species","Geochim. Cosmochim. Acta 53, 2157-2183",http://dx.doi.org/10.1016/0016-7037(89)90341-4 -SH90,"E. L. Shock and H. C. Helgeson",1990,"organic species","Geochim. Cosmochim. Acta 54, 915-945",http://dx.doi.org/10.1016/0016-7037(90)90429-O -Joh92a,"J. W. Johnson",1992,"steam, Cp represented by Maier-Kelley equation","personal communication", -SPRONS92.1,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", -SPRONS92.2,"H. C. Helgeson et al.",1992,"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 "","slop98.dat computer data file", -SPRONS92.3,"H. C. Helgeson et al.",1992,""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)."","slop98.dat computer data file", -Sho92,"E. L. Shock",1992,"diglycine, alanylglycine, leucylglycine, and diketopiperazine","Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V -Sho93,"E. L. Shock",1993,"ethylacetate and acetamide","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 -Sho93.1,"E. L. Shock",1993,"carbon monoxide and ethylene","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5 -SK93,"E. L. Shock and C. M. Koretsky",1993,"metal-acetate complexes","Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J -SM93,"E. L. Shock and W. B. McKinnon",1993,"CO, HCN, urea","Icarus 106, 464-477",http://dx.doi.org/10.1006/icar.1993.1185 -SS93,"M. D. Schulte and E. L. Shock",1993,aldehydes,"Geochim. Cosmochim. Acta 57, 3835-3846",http://dx.doi.org/10.1016/0016-7037(93)90337-V -HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"complexes of rare earth elements","Geochim. Cosmochim. Acta 59, 4329-4350",http://dx.doi.org/10.1016/0016-7037(95)00314-P -PK95,"V. B. Parker and I. L. Khodakovskii",1995,melanterite,"J. Phys. Chem. Ref. Data 24, 1699-1745",http://dx.doi.org/10.1063/1.555964 -RH95,"R. A. Robie and B. S. Hemingway",1995,"gypsum GHS","U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131 -SK95,"E. L. Shock and C. M. Koretsky",1995,"metal-organic acid complexes","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8 -SK95.1,"E. L. Shock and C. M. Koretsky",1995,"alanate, glycinate and their complexes not included in later slop files.","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8 -Sho95,"E. L. Shock",1995,"carboxylic acids","Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496 -AH97b,"J. P. Amend and H. C. Helgeson",1997,"amino acids GHS","J. Chem. Soc., Faraday Trans. 93, 1927-1941",http://dx.doi.org/10.1039/A608126F -DSM+97,"J. D. Dale, E. L. Shock et al.",1997,alkylphenols,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 -DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"phenol, and cresol isomers","Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 -DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"dimethylphenol isomers","Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 -MS97,"T. M. McCollom and E. L. Shock",1997,"MgSO4, NaSO4-, and HCl","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X -MS97.1,"T. M. McCollom and E. L. Shock",1997,"sulfur","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X -SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uranium species","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8 -SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uraninite","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8 -SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"metal complexes","Geochim. Cosmochim. Acta 61, 1359-1412",http://dx.doi.org/10.1016/S0016-7037(97)00009-4 -SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"inorganic ions and hydroxide complexes","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 -SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"zincite and litharge","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 -TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"humic acid, microflora, and plants","C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X -HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 -HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"amino acids","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 -RH98,"L. Richard and H. C. Helgeson",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 3591-3636",http://dx.doi.org/10.1016/S0016-7037(97)00345-1 -SLOP98.1,"E. L. Shock et al.",1998,"zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.2,"E. L. Shock et al.",1998,"daphnite; "Gf and Hf from @SS93a TMM"","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.3,"E. L. Shock et al.",1998,""Corrected values based on data from @SH90 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.4,"E. L. Shock et al.",1998,""Corrected values based on data from @SSH97 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.5,"E. L. Shock et al.",1998,""Corrected values based on data from @SS93 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.6,"E. L. Shock et al.",1998,""Corrected values based on data from @SK93 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.7,"E. L. Shock et al.",1998,""Corrected values based on data from @Sho95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.8,"E. L. Shock et al.",1998,""These data were used in @SK95, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.9,"E. L. Shock et al.",1998,""Corrected values based on data from @SK95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.10,"E. L. Shock et al.",1998,""Corrected values based on data from @HSS95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP98.11,"E. L. Shock et al.",1998,""Data and parameters as used by @MS97. "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools -SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group ions and complexes","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 -SS98a.1,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 -SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Rh+3","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 -HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 -MS99,"W. M. Murphy and E. L. Shock",1999,"actinides","Rev. Mineral. Geochem. 38, 221-253",http://rimg.geoscienceworld.org/content/38/1/221 -PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"metal-dicarboxylate complexes","Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5 -SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"jarosite, natroalunite, and natrojarosite","Rev. Mineral. Geochem. 40, 453-479",http://dx.doi.org/10.2138/rmg.2000.40.9 -AP01,"J. P. Amend and A. V. Plyasunov",2001,carbohydrates,"Geochim. Cosmochim. Acta 65, 3901-3917",http://dx.doi.org/10.1016/S0016-7037(01)00707-4 -AS01,"J. P. Amend and E. L. Shock",2001,"NO and N2O","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 -AS01.1,"J. P. Amend and E. L. Shock",2001,"selenium and molybdenite","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 -MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"ice polymorphs","Appl. Geochem. 16, 161-181",http://dx.doi.org/10.1016/S0883-2927(00)00025-1 -PS01,"A. V. Plyasunov and E. L. Shock",2001,"aqueous nonelectrolytes","Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0 -Ric01,"L. Richard",2001,"organic sulfur compounds","Geochim. Cosmochim. Acta 65, 3827-3877",http://dx.doi.org/10.1016/S0016-7037(01)00761-X -SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6","Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7 -MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"goethite, lepidocrocite, and maghemite GHS","Am. Mineral. 88, 855-859",http://dx.doi.org/10.2138/am-2003-5-614 -MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"goethite, lepidocrocite, and maghemite Cp","Am. Mineral. 88, 846-854",http://dx.doi.org/10.2138/am-2003-5-613 -MSB+04,"J. Majzlan, R. Stevens et al.",2004,"hydronium jarosite","Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z -SR04,"M. D. Schulte and K. L. Rogers",2004,"alkane thiols","Geochim. Cosmochim. Acta 68, 1087-1097",http://dx.doi.org/10.1016/j.gca.2003.06.001 -HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"methyldiethanolamine and methyldiethanolammonium chloride HKF parameters","J. Chem. Thermodynamics 38, 988-1007",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013 -LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"nucleic-acid bases, nucleosides, and nucleotides","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010 -LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"citric acid and citrate","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010 -LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Mg-complexed adenosine nucleotides (ATP), NAD, and NADP","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008 -LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"pyridine and piperidine","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008 -DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acid, protein, and organic groups","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 -DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acids HKF parameters","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 -DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Gly-X-Gly tripeptides","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006 -MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"coquimbite, ferricopiapite, and rhomboclase","Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175 -Dic07,"J. M. Dick",2007,"glutathione, cystine, and cystine sidechain","Ph.D. Dissertation, U.C. Berkeley", -MA07,"L. Marini and M. Accornero",2007,"metal-arsenate and metal-arsenite complexes","Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5 -SLOP07.1,"E. L. Shock et al.",2007,"corrected charge of Pu(Oxal)+2","slop07.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP07.2,"E. L. Shock et al.",2007,"high-temperature HKF parameters from @AP01","slop07.dat computer data file",http://geopig.asu.edu/?q=tools -Ric08,"L. Richard",2008,alkenes,"personal communication", -GM09,"K.-D. Grevel and J. Majzlan",2009,"kieserite, starkeyite, hexahydrite, and epsomite","Geochim. Cosmochim. Acta 73, 6805 - 6815",http://dx.doi.org/10.1016/j.gca.2009.08.005 -HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,kerogens,"Geochim. Cosmochim. Acta 73, 594-695",http://dx.doi.org/10.1016/j.gca.2008.03.004 -AML10,"M. Accornero, L. Marini and M. Lelli",2010,"metal-chromate complexes","Appl. Geochem. 25, 242-260",http://dx.doi.org/10.1016/j.apgeochem.2009.11.010 -MA10,"L. Marini and M. Accornero",2010,"corrected values","Environ. Earth Sci. 59, 1601-1606",http://dx.doi.org/10.1007/s12665-009-0369-x -Sch10,"M. Schulte",2010,"organic sulfides","Aquat. Geochem. 16, 621-637",http://dx.doi.org/10.1007/s10498-010-9102-3 -RG11,"L. Richard and X. Gaona",2011,"organic iodine compounds","Geochim. Cosmochim. Acta 75, 7304-7350",http://dx.doi.org/10.1016/j.gca.2011.07.030 -LD12,"D. E. LaRowe and J. M. Dick",2012,"4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 -LD12.1,"D. E. LaRowe and J. M. Dick",2012,"updated and corrected parameters for cysteine, glycine, leucine, and methionine","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 -LD12.2,"D. E. LaRowe and J. M. Dick",2012,"methionine GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 -LD12.3,"D. E. LaRowe and J. M. Dick",2012,"methionine sidechain GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041 -DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"phenanthrene and methylphenanthrene isomers","Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020 -SLOP15.1,"E. L. Shock et al.",2015,""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP15.2,"E. L. Shock et al.",2015,"Zn(Ac)3-: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP15.3,"E. L. Shock et al.",2015,"formaldehyde: "Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of @SS93."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP15.4,"E. L. Shock et al.",2015,"adipic acid and n-dodecanoate: "Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of @Sho95."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP15.5,"E. L. Shock et al.",2015,"n-octanoate: "Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of @Sho95."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP15.6,"E. L. Shock et al.",2015,""Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -SLOP15.7,"E. L. Shock et al.",2015,"heptanol, hexanol, and octanol: "Minor differences in Gibbs energy, entropy, omega, a1, a2, a3, a4 and c1 values compared to @SH90."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools -CS16,"P. A. Canovas III and E. L. Shock",2016,"citric acid cycle metabolites","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 -CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a1--a4 parameters","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028 -UniProt,"The UniProt Consortium",2017,,"The UniProt knowledgebase",http://www.uniprot.org/ -CHNOSZ.1,"J. M. Dick",2017,"GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.2,"J. M. Dick",2017,"alanate and glycinate: GHS as used by @DLH06","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.3,"J. M. Dick",2017,"metal-amino acid complexes: GHS were recalculated by adding the differences between values from @AH97b and @DLH06 for alanate or glycinate to the properties of the complexes reported by @SK95.","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.4,"J. M. Dick",2017,pseudo-H4SiO4,"CHNOSZ package documentation",http://chnosz.net -CHNOSZ.5,"J. M. Dick",2017,"AuCl4- renamed to AuCl4-3","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.6,"J. M. Dick",2017,"dipeptides not included in slop files after slop98.dat","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.7,"J. M. Dick",2017,"charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99","CHNOSZ package documentation",http://chnosz.net -CHNOSZ.8,"J. M. Dick",2017,"Incorrect values of HKF a1--a4 parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here.","CHNOSZ package documentation",http://chnosz.net +key,author,year,citation,note,URL +Kel60,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gases Cp",http://www.worldcat.org/oclc/693388901 +Kel60.1,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","larnite Cp",http://www.worldcat.org/oclc/693388901 +Kel60.2,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","iron Cp",http://www.worldcat.org/oclc/693388901 +Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",http://www.worldcat.org/oclc/693388901 +Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,http://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",http://www.worldcat.org/oclc/14154292 +HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","minerals and phase transitions",http://www.worldcat.org/oclc/13594862 +HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","litharge S, V, and Cp parameters",http://www.worldcat.org/oclc/13594862 +RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","chlorargyrite, rutile, and titanite",http://pubs.er.usgs.gov/publication/b1452 +RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452 +RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452 +PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",http://dx.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, 1-392","gases GHS",http://dx.doi.org/10.1063/1.555661 +WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",manganosite,http://dx.doi.org/10.1063/1.555661 +WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",MgSO4,http://dx.doi.org/10.1063/1.555661 +BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,http://dx.doi.org/10.1016/0016-7037(83)90066-2 +Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",http://dx.doi.org/10.2475/ajs.285.9.845 +JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",http://dx.doi.org/10.2113/gsecongeo.80.5.1365 +SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",http://dx.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",http://dx.doi.org/10.1016/0016-7037(89)90341-4 +SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",http://dx.doi.org/10.1016/0016-7037(90)90429-O +Joh92a,"J. W. Johnson",1992,"personal communication","steam, Cp represented by the Maier-Kelley equation", +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 "", +SPRONS92.3,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file",""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)."", +Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",http://dx.doi.org/10.1016/0016-7037(92)90392-V +Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",http://dx.doi.org/10.1016/0016-7037(93)90542-5 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 185 From noreply at r-forge.r-project.org Mon Mar 20 13:46:58 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 20 Mar 2017 13:46:58 +0100 (CET) Subject: [CHNOSZ-commits] r186 - in pkg/CHNOSZ: . R data inst Message-ID: <20170320124659.0C21F188972@r-forge.r-project.org> Author: jedick Date: 2017-03-20 13:46:58 +0100 (Mon, 20 Mar 2017) New Revision: 186 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/util.data.R pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/inst/NEWS Log: some fixes for data/refs.csv Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-03-17 11:54:22 UTC (rev 185) +++ pkg/CHNOSZ/DESCRIPTION 2017-03-20 12:46:58 UTC (rev 186) @@ -1,6 +1,6 @@ -Date: 2017-03-17 +Date: 2017-03-20 Package: CHNOSZ -Version: 1.0.8-74 +Version: 1.0.8-75 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/util.data.R =================================================================== --- pkg/CHNOSZ/R/util.data.R 2017-03-17 11:54:22 UTC (rev 185) +++ pkg/CHNOSZ/R/util.data.R 2017-03-20 12:46:58 UTC (rev 186) @@ -197,7 +197,7 @@ # append the counts to the table to be shown x <- c(list(number=number), x) # title to display for web page - title <- "Sources of Thermodynamic Data in CHNOSZ" + title <- "References for thermodynamic data in CHNOSZ" ### the following is adapted from print.findFn in package 'sos' f0 <- tempfile() File <- paste(f0, ".html", sep="") @@ -259,10 +259,10 @@ .cat("") ### boilerplate text .cat("") - .cat("

Listing of all entries in thermo$refs

") - .cat("

Click on hyperlinked references to open URL in new window.

") - .cat("

Click on column headers to sort.

") - .cat("

Column 'number' gives number of times each reference appears in thermo$obigt.

") + .cat('

References for thermodynamic data in CHNOSZ

') + .cat("

Click on a column header to sort, or on a citation to open the URL in new window.

") + .cat("

Column 'number' gives the number of times each reference appears in thermo$obigt.

") + .cat('

See also the vignette Thermodynamic data in CHNOSZ.

') ### start table and headers .cat("") .cat("") Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-03-17 11:54:22 UTC (rev 185) +++ pkg/CHNOSZ/data/refs.csv 2017-03-20 12:46:58 UTC (rev 186) @@ -11,9 +11,9 @@ RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452 RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452 PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",http://dx.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, 1-392","gases GHS",http://dx.doi.org/10.1063/1.555661 -WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",manganosite,http://dx.doi.org/10.1063/1.555661 -WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",MgSO4,http://dx.doi.org/10.1063/1.555661 +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",manganosite,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf +WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",MgSO4,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,http://dx.doi.org/10.1016/0016-7037(83)90066-2 Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",http://dx.doi.org/10.2475/ajs.285.9.845 JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",http://dx.doi.org/10.2113/gsecongeo.80.5.1365 @@ -64,8 +64,8 @@ PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",http://dx.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",http://dx.doi.org/10.2138/rmg.2000.40.9 AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,http://dx.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",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 -AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",http://dx.doi.org/10.1016/S0168-6445(00)00062-0 +AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N2O",http://dx.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",http://dx.doi.org/10.1111/j.1574-6976.2001.tb00576.x MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","ice polymorphs",http://dx.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",http://dx.doi.org/10.1016/S0016-7037(01)00678-0 Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",http://dx.doi.org/10.1016/S0016-7037(01)00761-X @@ -74,7 +74,7 @@ MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",http://dx.doi.org/10.2138/am-2003-5-613 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",http://dx.doi.org/10.1007/s00269-004-0405-z SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",http://dx.doi.org/10.1016/j.gca.2003.06.001 -HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013 +HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",http://dx.doi.org/10.1016/j.jct.2005.10.013 LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",http://dx.doi.org/10.1016/j.gca.2006.04.010 LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",http://dx.doi.org/10.1016/j.gca.2006.04.010 LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",http://dx.doi.org/10.1016/j.tca.2006.06.008 @@ -94,10 +94,10 @@ MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",http://dx.doi.org/10.1007/s12665-009-0369-x Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",http://dx.doi.org/10.1007/s10498-010-9102-3 RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",http://dx.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",http://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",http://10.1016/j.gca.2011.11.041 -LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",http://10.1016/j.gca.2011.11.041 -LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",http://10.1016/j.gca.2011.11.041 +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",http://dx.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",http://dx.doi.org/10.1016/j.gca.2011.11.041 +LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041 +LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041 DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",http://dx.doi.org/10.1016/j.gca.2013.08.020 SLOP15.1,"E. L. Shock et al.",2015,"slop15.dat computer data file",""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."",http://geopig.asu.edu/?q=tools SLOP15.2,"E. L. Shock et al.",2015,"slop15.dat computer data file","Zn(Ac)3-: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."",http://geopig.asu.edu/?q=tools Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-03-17 11:54:22 UTC (rev 185) +++ pkg/CHNOSZ/inst/NEWS 2017-03-20 12:46:58 UTC (rev 186) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-74 (2017-03-17) +CHANGES IN CHNOSZ 1.0.8-75 (2017-03-20) --------------------------------------- DOCUMENTATION: