[CHNOSZ-commits] r261 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Oct 18 18:07:00 CEST 2017 

Author: jedick
Date: 2017-10-18 18:07:00 +0200 (Wed, 18 Oct 2017)
New Revision: 261

Added:
   pkg/CHNOSZ/demo/go-IU.R
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/subcrt.R
   pkg/CHNOSZ/R/util.expression.R
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/demo/00Index
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/man/util.expression.Rd
   pkg/CHNOSZ/vignettes/obigt.Rmd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
add demo/go-IU.R for diagrams using data in SUPCRTBL


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/DESCRIPTION	2017-10-18 16:07:00 UTC (rev 261)
@@ -1,6 +1,6 @@
-Date: 2017-10-17
+Date: 2017-10-18
 Package: CHNOSZ
-Version: 1.1.0-59
+Version: 1.1.0-60
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/R/subcrt.R	2017-10-18 16:07:00 UTC (rev 261)
@@ -118,9 +118,13 @@
     sinfo <- numeric()
     newstate <- character()
     for(i in 1:length(species)) {
-      mysearch <- species[i]
-      if(can.be.numeric(mysearch)) mysearch <- thermo$obigt$name[as.numeric(mysearch)]
-      si <- info.character(mysearch, state[i])
+      # get the species index for a named species
+      if(!can.be.numeric(species[i])) si <- info.character(species[i], state[i])
+      else {
+        # check that a numeric argument is a rownumber of thermo$obigt
+        si <- as.numeric(species[i])
+        if(!si %in% 1:nrow(thermo$obigt)) stop(paste(species[i], "is not a row number of thermo$obigt"))
+      }
       # that could have the side-effect of adding a protein; re-read thermo
       thermo <- get("thermo", "CHNOSZ")
       if(is.na(si[1])) stop('no info found for ',species[i],' ',state[i])

Modified: pkg/CHNOSZ/R/util.expression.R
===================================================================
--- pkg/CHNOSZ/R/util.expression.R	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/R/util.expression.R	2017-10-18 16:07:00 UTC (rev 261)
@@ -2,19 +2,21 @@
 # write descriptions of chemical species, properties, reactions, conditions
 # modified from describe(), axis.label()  20120121 jmd
 
-expr.species <- function(species, state="", log="", value=NULL) {
+expr.species <- function(species, state="", log="", value=NULL, use.makeup=FALSE) {
   # make plotting expressions for chemical formulas
   # that include subscripts, superscripts (if charged)
   # and optionally designations of states +/- loga or logf prefix
   if(length(species) > 1) (stop("more than one species"))
   # convert to character so that "1", "2", etc. don't get converted to chemical formulas via makeup()
   species <- as.character(species)
-  # the counts of elements in the species:
-  # here we don't care too much if an "element" is a real element
-  # (listed in thermo$element), so we suppress warnings
-  elements <- suppressWarnings(try(makeup(species), TRUE))
-  # if `species` can't be parsed as a chemical formula, we don't do the formula formatting
-  if(identical(class(elements), "try-error")) expr <- species
+  if(use.makeup) {
+    # the counts of elements in the species:
+    # here we don't care too much if an "element" is a real element
+    # (listed in thermo$element), so we suppress warnings
+    elements <- suppressWarnings(try(makeup(species), TRUE))
+  } else elements <- split.formula(species)
+  # if species can't be parsed as a chemical formula, we don't do the formula formatting
+  if(identical(class(elements), "try-error") | !is.numeric(elements)) expr <- species
   else {
     # where we'll put the expression
     expr <- ""
@@ -194,15 +196,18 @@
   return(as.expression(desc))
 }
 
-describe.property <- function(property=NULL, value=NULL, digits=1, oneline=FALSE, ret.val=FALSE) {
+describe.property <- function(property=NULL, value=NULL, digits=0, oneline=FALSE, ret.val=FALSE) {
   # make expressions for pressure, temperature, other conditions
   if(is.null(property) | is.null(value)) stop("property or value is NULL")
   propexpr <- valexpr <- character()
   for(i in 1:length(property)) {
     propexpr <- c(propexpr, expr.property(property[i]))
-    thisvalue <- format(round(value[i], digits), nsmall=digits)
-    thisunits <- expr.units(property[i])
-    thisvalexpr <- substitute(a~b, list(a=thisvalue, b=thisunits))
+    if(value[i]=="Psat") thisvalexpr <- quote(italic(P)[sat])
+    else {
+      thisvalue <- format(round(as.numeric(value[i]), digits), nsmall=digits)
+      thisunits <- expr.units(property[i])
+      thisvalexpr <- substitute(a~b, list(a=thisvalue, b=thisunits))
+    }
     valexpr <- c(valexpr, as.expression(thisvalexpr))
   } 
   # with ret.val=TRUE, return just the value with the units (e.g. 55 degC)
@@ -280,3 +285,54 @@
   }
   lab
 }
+
+### unexported function ###
+
+split.formula <- function(formula) {
+  ## like makeup(), but split apart the formula based on
+  ## numbers (subscripts); don't scan for elemental symbols 20171018
+  # if there are no numbers or charge, return the formula as-is
+  if(! (grepl("[0-9]", formula) | grepl("\\+[0-9]?$", formula) | grepl("-[0-9]?$", formula))) return(formula)
+  # first split off charge
+  # (assume that no subscripts are signed)
+  Z <- 0
+  hascharge <- grepl("\\+[0-9]?$", formula) | grepl("-[0-9]?$", formula)
+  if(hascharge) {
+    # for charge, we match + or - followed by zero or more numbers at the end of the string
+    if(grepl("\\+[0-9]?$", formula)) {
+      fsplit <- strsplit(formula, "+", fixed=TRUE)[[1]]
+      if(is.na(fsplit[2])) Z <- 1 else Z <- as.numeric(fsplit[2])
+    }
+    if(grepl("-[0-9]?$", formula)) {
+      fsplit <- strsplit(formula, "-")[[1]]
+      if(is.na(fsplit[2])) Z <- -1 else Z <- -as.numeric(fsplit[2])
+    }
+    formula <- fsplit[1]
+  }
+  # to get strings, replace all numbers with placeholder (#), then split on that symbol
+  # the outer gsub is to replace multiple #'s with one
+  numhash <- gsub("#+", "#", gsub("[0-9]", "#", formula))
+  strings <- strsplit(numhash, "#")[[1]]
+  # to get coefficients, replace all characters (non-numbers) with placeholder, then split
+  charhash <- gsub("#+", "#", gsub("[^0-9]", "#", formula))
+  coeffs <- strsplit(charhash, "#")[[1]]
+  # if the first coefficient is empty, remove it
+  if(coeffs[1]=="") coeffs <- tail(coeffs, -1) else {
+    # if the first string is empty, treat the first coefficient as a leading string (e.g. in 2-octanone)
+    if(strings[1]=="") {
+      strings[2] <- paste0(coeffs[1], strings[2])
+      coeffs <- tail(coeffs, -1)
+      strings <- tail(strings, -1)
+    }
+  }
+  # if we're left with no coefficients, just return the string
+  if(length(coeffs)==0 & Z==0) return(strings)
+  # if we're missing a coefficient, append one
+  if(length(coeffs) < length(strings)) coeffs <- c(coeffs, 1)
+  # use strings as names for the numeric coefficients
+  coeffs <- as.numeric(coeffs)
+  names(coeffs) <- strings
+  # include charge if it is not 0
+  if(Z!=0) coeffs <- c(coeffs, Z=Z)
+  return(coeffs)
+}

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/data/refs.csv	2017-10-18 16:07:00 UTC (rev 261)
@@ -5,12 +5,13 @@
 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
+FSR76,"M. J. Ferrante et al.",1976,"U. S. Bureau of Mines Report of Investigations 8129","dawsonite Cp (value at 25 °C as listed by @BPAH07; not present in spronsbl.dat)",http://www.worldcat.org/oclc/932914138
 HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals (n = 167) 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
-RHF79.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","gibbsite GHS",http://pubs.er.usgs.gov/publication/b1452
+RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","chlorargyrite, rutile, and titanite",http://pubs.er.usgs.gov/publication/b1452
+RHF78.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452
+RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452
+RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",http://pubs.er.usgs.gov/publication/b1452
 PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
 WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
 WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",manganosite,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf

Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/demo/00Index	2017-10-18 16:07:00 UTC (rev 261)
@@ -20,5 +20,6 @@
 activity_ratios Mineral stability plots with activity ratios on the axes
 adenine         HKF parameters regressed from heat capacity and volume of aqueous adenine
 DEW             Deep Earth Water (DEW) model for high pressures
-lambda          Effects of lambda transtion on thermodynamic properties of quartz
-TCA             Standard Gibbs energies of steps of the tricarboxylic acid cycle
+lambda          Thermodynamic properties of lambda transition in quartz
+TCA             Standard Gibbs energies of steps of the citric acid cycle
+go-IU           Diagrams using thermodynamic data in the SUPCRTBL compilation

Added: pkg/CHNOSZ/demo/go-IU.R
===================================================================
--- pkg/CHNOSZ/demo/go-IU.R	                        (rev 0)
+++ pkg/CHNOSZ/demo/go-IU.R	2017-10-18 16:07:00 UTC (rev 261)
@@ -0,0 +1,140 @@
+# CHNOSZ/demo/go-IU.R  20171018
+# diagrams using data from the SUPCRTBL compilation
+# (BL = Bloomington campus of Indiana University)
+
+## set up plotting area
+par(mfrow=c(2, 2))
+
+## start with default database
+data(thermo)
+
+###########
+### plot 1: boehmite - kaolinite equilibrium
+###########
+## experimental data from Table 1 of Hemley et al., 1980
+# doi:10.2113/gsecongeo.75.2.210
+xT <- c(200, 200, 200, 200, 250, 250, 300, 300, 300, 300)
+xlogaSiO2 <- -c(2.54, 2.59, 2.65, 2.77, 2.21, 2.32, 1.90, 1.95, 1.94, 1.90)
+## set up basis species so that axis.label shows activity of SiO2
+basis(c("Al2O3","SiO2", "H2O", "O2"))
+T <- 125:350
+thermo.plot.new(xlim=range(T), ylim=c(-3.5, -1.5), xlab = axis.label("T"), ylab=axis.label("SiO2"))
+points(xT, xlogaSiO2)
+basis(delete=TRUE)
+## first calculation: CHNOSZ default (SiO2 from SHS89, kaolinite and boehmite from HDNB78)
+r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T=T, P=1000, exceed.Ttr = TRUE) 
+# we need exceed.Ttr = TRUE because the T limit for boehmite is 500 K (Helgeson et al., 1978)
+## second calculation: kaolinite from Berman, 1988
+Kln_Berman <- info("kaolinite", "cr_Berman")
+r2 <- subcrt(c("boehmite", "H2O", "SiO2", Kln_Berman), c(-1, -0.5, -1, 0.5), T=T, P=1000, exceed.Ttr = TRUE) 
+## third calculation: boehmite from Hemingway et al., 1991
+add.obigt("SUPCRTBL", "boehmite")
+r3 <- subcrt(c("boehmite", "H2O", "SiO2", Kln_Berman), c(-1, -0.5, -1, 0.5), T=T, P=1000) 
+## fourth calculation: SiO2 from Apps and Spycher, 2004
+add.obigt("SUPCRTBL", "SiO2")
+r4 <- subcrt(c("boehmite", "H2O", "SiO2", Kln_Berman), c(-1, -0.5, -1, 0.5), T=T, P=1000) 
+## log activity of SiO2 is -ve logK
+lines(T, -r1$out$logK)
+lines(T, -r2$out$logK, lty=2)
+lines(T, -r3$out$logK, lty=2, col="red")
+lines(T, -r4$out$logK, col="red")
+## add labels, legend, and title
+text(182.5, -3.17, "SUPCRT92\n(CHNOSZ default)", srt=48, cex=0.7, font=2)
+text(147, -3.1, "SUPCRTBL", srt=45.5, cex=0.7, font=2, col="red")
+legend("topleft", lty=c(1, 2, 2, 1), col=c("black", "black", "red", "red"), bty="n", cex=0.9,
+       legend=c("Kln,Bhm:HDNB78; SiO2:SHS89", "Kln:Ber88", "+ Bhm:HRA91", "+ SiO2:AS04"))
+legend("bottomright", pch=1, legend="Hemley et al., 1980", bty="n", cex=0.9)
+mtitle(c("Kaolinite - Boehmite", "After Zhu and Lu, 2009 Fig. A1"), cex=0.95)
+# doi:10.1016/j.gca.2009.03.015
+
+###########
+### plot 2: dawsonite solubility
+###########
+## experimental data from Benezeth et al., 2007 Table 5
+# doi:10.1016/j.gca.2007.07.003
+# (averages for each temperature in a single run)
+T <- c(100.1, 100.1, 150.1, 100.1, 150.1, 99.8, 99.8, 200.7, 99.8, 50.1, 75.1, 100.3, 150.1)
+logK <- -c(14.825, 14.735, 13.625, 14.79, 13.665, 14.725, 14.1775, 12.74, 14.4925, 16.8625, 15.61, 14.51, 13.455)
+plot(T, logK, xlim=c(25, 250), ylim=c(-18, -10), xlab=axis.label("T"), ylab=axis.label("logK"))
+# this gets us dawsonite and Al(OH)4-
+add.obigt("SUPCRTBL")
+T <- 0:250
+# calculation 1: dawsonite with non-zero Cp
+species <- c("dawsonite", "H2O", "Al(OH)4-", "HCO3-", "Na+", "H+")
+coeffs <- c(-1, -2, 1, 1, 1, 1)
+Daw1 <- subcrt(species, coeffs, T=T)
+# calculation 2: dawsonite with 0 Cp
+mod.obigt("dawsonite", Cp=0)
+Daw2 <- subcrt(species, coeffs, T=T)
+## plot the calculated logKs
+lines(T, Daw1$out$logK, col="red")
+lines(T, Daw2$out$logK, col="red", lty=2)
+## add labels, legend, and title
+text(182.5, -3.17, "SUPCRT92\n(CHNOSZ default)", srt=43, cex=0.7, font=2)
+text(145, -3.1, "SUPCRTBL", srt=41.5, cex=0.7, font=2, col="red")
+legend("topleft", lty=1:2, col="red", bty="n", cex=0.9,
+       legend=c("Daw Cp != 0", "Daw Cp = 0"))
+legend("bottomright", pch=1, legend="Ben\u00e9z\u00e9th et al., 2007", bty="n", cex=0.9)
+mtitle(c("Dawsonite - aqueous species", "After Zimmer et al., 2016 Fig. 2"), cex=0.95)
+# doi:10.1016/j.cageo.2016.02.013
+
+###########
+### plot 3: Eh-pH diagram for As-O-H-S
+###########
+add.obigt("SUPCRTBL")
+#basis(c("Fe", "As", "H2O", "H2S", "H+", "e-"))
+#basis(c("Fe", "H2S"), c(-6, -3))
+basis(c("As", "H2O", "H2S", "H+", "e-"))
+basis(c("H2S"), c(-3))
+As_aq <- c("H3AsO4", "H2AsO4-", "HAsO4-2", "AsO4-3", "H3AsO3", "H2AsO3-", "HAsO3-2", "AsO3-3")
+AsS_aq <- c("AsS(OH)HS-", "As3S4(HS)2-")
+As_cr <- "As"
+AsS_cr <- c("realgar,alpha", "realgar,beta", "orpiment", "orpiment,amorphous")
+FeAs_cr <- c("arsenopyrite", "scorodite", "ferric arsenate,amorphous")
+#species(c(As_aq, AsS_aq, As_cr, AsS_cr, FeAs_cr))
+species(c(As_aq, AsS_aq, As_cr, AsS_cr))
+species(c(As_aq, AsS_aq), -5)
+## a simple diagram, but using only H2S at all pH
+#a <- affinity(pH=c(0, 14), Eh=c(-1, 1.5))
+#diagram(a)
+# the S basis species depends on pH
+bases <- c("H2S", "HS-", "HSO4-", "SO4-2")
+# calculate affinties of formation reactions using the speciated S basis species
+res <- 300
+# we "blend" the transitions with pH, unlike LZ11's diagram where
+# it appears the S-basis species are switched in an on/off fashion
+m <- mosaic(bases, pH=c(2, 14, res), Eh=c(-0.6, 0.8, res), blend=TRUE)
+# adjust colors and names
+fill <- rev(heat.colors(nrow(species())))
+fill[11:15] <- "darkgrey"
+m$A.species$species$name <- gsub(",alpha", "", m$A.species$species$name)
+diagram(m$A.species, fill=fill)
+dprop <- describe.property(c("T", "P"), c(25, 1))
+legend("topright", legend=dprop, bty="n")
+t1 <- quote("As-O-H-S, "~list(sum(S)==10^-3*M, sum(As)==10^-5*M))
+t2 <- "After Lu and Zhu, 2011 Fig. 2b"
+mtitle(as.expression(c(t1, t2)), cex=0.95)
+# doi:10.1007/s12665-010-0652-x
+
+###########
+### plot 4: aqueous Al species
+###########
+add.obigt("SUPCRTBL")
+basis(c("Al+3", "F-", "H+", "O2", "H2O"))
+Al <- "Al+3"
+AlOH <- c("Al(OH)4-", "AlOH+2", "Al(OH)2+", "Al(OH)3")
+AlF <- c("AlF+2", "AlF2+", "AlF3", "AlF4-")
+AlOHF <- c("Al(OH)2F2-", "Al(OH)2F", "AlOHF2")
+species(c(Al, AlOH, AlF, AlOHF), "aq")
+a <- affinity(pH=c(0, 10), `F-`=c(-1, -9), T=200)
+diagram(a, fill=cm.colors(nrow(species())))
+dprop <- describe.property(c("T", "P"), c(200, "Psat"))
+legend("topright", legend=dprop, bty="n")
+mtitle(c("Aqueous aluminum species",
+         "After Tagirov and Schott, 2001 Fig. 4d"), cex=0.95)
+# doi:10.1016/S0016-7037(01)00705-0
+
+###########
+### clean up: restore thermodynamic database to default
+###########
+data(thermo)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/inst/NEWS	2017-10-18 16:07:00 UTC (rev 261)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-59 (2017-10-17)
+CHANGES IN CHNOSZ 1.1.0-60 (2017-10-18)
 ---------------------------------------
 
 MAJOR CHANGES:
@@ -23,7 +23,7 @@
 
 - In equilibrate(), it is now possible to combine affinity calculations
   with variable activity of the balancing basis species (loga.balance).
-  For example, in the last plot of the DEW demo, the affinity transect
+  For example, in the last plot of the DEW demo, the calculation
   involves simultaneously varying temperature and logfO2 (given as
   arguments to affinity()) as well as total concentration of carbon
   (given by the loga.balance argument in equilibrate()).
@@ -99,7 +99,7 @@
 - Add SUPCRTBL.csv with mineral and aqueous species data compiled by
   Zimmer et al., 2016. Data were taken from original references or
   from spronsbl.dat (http://www.indiana.edu/~hydrogeo/supcrtbl.html).
-  [Optional Data]
+  The new demo/go-IU.R uses these data. [Optional Data]
 
 - Update HKF parameters of adenine based on experimental heat capacity
   and volume data (Lowe et al., 2017). Add demo/adenine.R comparing

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
===================================================================
(Binary files differ)

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv	2017-10-18 16:07:00 UTC (rev 261)
@@ -12,9 +12,9 @@
 "ferric arsenate,amorphous",NA,FeAsO4.2H2O,cr,LMR06,ZZL+16,16.Oct.17,-303771.51051625237,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 "barium arsenate",NA,Ba3(AsO4)2,cr,ZZX+05,ZZL+16,16.Oct.17,-739749.0439770555,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 "barium hydrogen arsenate",NA,BaHAsO4.H2O,cr,ZZX+05,ZZL+16,16.Oct.17,-367746.1759082218,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-boehmite,NA,AlO2H,cr,HRA91,ZZL+16.2,17.Oct.17,-219502.86806883363,-238145.3154875717,8.888623326959847,12.97634,19.535,40.48757170172084,-4.1108986615678775,0.6962476099426387,-467.3996175908221,0,0,0,NA
-gibbsite,NA,Al(OH)3,cr,RHF79.3,ZZL+16.2,17.Oct.17,-276025.1,-309065,16.35755,21.72251,31.956,22.179732313575524,45.276768642447415,0.3199569789674952,-247.20363288718926,0,0,0,NA
-dawsonite,NA,NaAlCO3(OH)2,cr,ZZL+16.3,NA,17.Oct.17,-425979.9,-463456,32.91109,NA,NA,0,0,0,0,0,0,0,NA
+boehmite,NA,AlO(OH),cr,HRA91,ZZL+16.2,17.Oct.17,-219502.86806883363,-238145.3154875717,8.888623326959847,12.97634,19.535,40.48757170172084,-4.1108986615678775,0.6962476099426387,-467.3996175908221,0,0,0,NA
+gibbsite,NA,Al(OH)3,cr,RHF78.3,ZZL+16.2,17.Oct.17,-276025.1,-309065,16.35755,21.72251,31.956,22.179732313575524,45.276768642447415,0.3199569789674952,-247.20363288718926,0,0,0,NA
+dawsonite,NA,NaAlCO3(OH)2,cr,ZZL+16.3,FSR76,17.Oct.17,-425979.9,-463456,32.91109,34.08222,NA,NA,NA,NA,NA,NA,NA,NA,NA
 H3AsO4,NA,H3AsO4,aq,NA03.1,NA,17.Oct.17,-183257.6481835564,-215929.7323135755,43.75478011472275,NA,NA,NA,NA,NA,NA,NA,NA,NA,0
 H2AsO4-,NA,H2AsO4-,aq,NA03.1,NA,17.Oct.17,-180126.67304015296,-217834.60803059273,26.85946462715105,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
 HAsO4-2,NA,HAsO4-2,aq,NA03.1,NA,17.Oct.17,-170585.56405353727,-217115.20076481835,-2.7294455066921604,NA,NA,NA,NA,NA,NA,NA,NA,NA,-2
@@ -24,7 +24,7 @@
 HAsO3-2,NA,HAsO3-2,aq,NA03.1,NA,17.Oct.17,-121271.51051625238,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-2
 AsO3-3,NA,AsO3-3,aq,NA03.1,NA,17.Oct.17,-100812.61950286807,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-3
 As3S4(HS)2-,NA,As3S4(HS)2-,aq,NA03.1,NA,17.Oct.17,-30019.12045889101,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
-AsS(OH)SH-,NA,AsS(OH)SH-,aq,NA03.1,NA,17.Oct.17,-58413.00191204589,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
+AsS(OH)HS-,NA,AsS(OH)HS-,aq,NA03.1,NA,17.Oct.17,-58413.00191204589,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
 SiO2,NA,SiO2,aq,AS04,ZZL+16,16.Oct.17,-199539.9,-212179,11.12811,NA,NA,1.9,1.7,20,-2.7,32.22,-25.29001,0.3427103,0
 H4SiO4,NA,H4SiO4,aq,Ste01,NA,31.Aug.06,-312919.933078394,-348676.147227533,45.1003824091778,15.0095602294455,52.3,18.7299235181644,-21.2600382409178,18.6199808795411,-1.20004780114723,58.0305927342256,-20.789913957935,0.0869024856596558,0
 Al+3,NA,Al+3,aq,TS01,NA,25.Aug.06,-116510,NA,-81.203,-28.56,-45.3,-3.3984,-16.0789,12.0699,-2.1143,14.4295,-8.8523,2.7403,3

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2017-10-17 06:44:12 UTC (rev 260)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2017-10-18 16:07:00 UTC (rev 261)
@@ -1,4 +1,4 @@
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  A
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 261

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