[CHNOSZ-commits] r178 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 1 14:12:28 CET 2017
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 <j3ffdick at gmail.com>
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 Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@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 Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@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; "G<sub>f</sub> and H<sub>f</sub> 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-H<sub>4</sub>SiO<sub>4</sub>,"CHNOSZ package documentation",http://chnosz.net
+CHNOSZ.1,"J. M. Dick",2017,"GHS (T<sub>r</sub>) of the phase that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) 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-H<sub>4</sub>SiO<sub>4</sub>,"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 a<sub>1</sub>-a<sub>4</sub> 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
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