[CHNOSZ-commits] r309 - in pkg/CHNOSZ: . R data demo inst inst/extdata/Berman/unused inst/extdata/OBIGT man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 27 17:19:33 CEST 2018
Author: jedick
Date: 2018-03-27 17:19:33 +0200 (Tue, 27 Mar 2018)
New Revision: 309
Added:
pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRT92.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/R/cgl.R
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/subcrt.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/R/util.misc.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/DEW.R
pkg/CHNOSZ/demo/activity_ratios.R
pkg/CHNOSZ/demo/go-IU.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/info.Rd
pkg/CHNOSZ/man/util.misc.Rd
pkg/CHNOSZ/tests/testthat/test-basis.R
pkg/CHNOSZ/tests/testthat/test-berman.R
pkg/CHNOSZ/tests/testthat/test-makeup.R
pkg/CHNOSZ/tests/testthat/test-subcrt.R
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
Helgeson minerals are superseded by Berman dataset
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/DESCRIPTION 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,6 +1,6 @@
Date: 2018-03-27
Package: CHNOSZ
-Version: 1.1.3-16
+Version: 1.1.3-17
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/berman.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -49,7 +49,7 @@
# assign values to the variables used below
for(i in 1:ncol(dat)) assign(colnames(dat)[i], dat[irow, i])
# get the entropy of the elements using the chemical formula in thermo$obigt
- if(is.null(thisinfo)) thisinfo <- info(info(name, "cr_Berman", check.it=FALSE))
+ if(is.null(thisinfo)) thisinfo <- info(info(name, "cr", check.it=FALSE))
SPrTr_elements <- convert(entropy(thisinfo$formula), "J")
# check that G in data file is the G of formation from the elements --> Benson-Helgeson convention (DG = DH - T*DS)
if(check.G) {
Modified: pkg/CHNOSZ/R/cgl.R
===================================================================
--- pkg/CHNOSZ/R/cgl.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/cgl.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -14,7 +14,7 @@
for(k in 1:nrow(parameters)) {
# the parameters for *this* species
PAR <- parameters[k, ]
- if(PAR$state=="cr_Berman") {
+ if(all(is.na(PAR[8:20]))) {
# use Berman equations (parameters not in thermo$obigt)
properties <- berman(PAR$name, T=T, P=P, thisinfo=PAR)
iprop <- match(property, colnames(properties))
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/diagram.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -575,14 +575,6 @@
} # end if(nd==2)
} # end if(plot.it)
- # warn if we have a system with both Berman and Helgeson minerals 20180315
- ref1 <- get("thermo")$obigt$ref1
- ref2 <- get("thermo")$obigt$ref2
- ispecies <- eout$species$ispecies
- hasHelgeson <- any(grepl("HDNB78", ref1[ispecies])) | any(grepl("HDNB78", ref2[ispecies]))
- hasBerman <- any(get("thermo")$obigt$state[ispecies]=="cr_Berman")
- if(hasHelgeson & hasBerman) warning("the system has minerals from both the Helgeson and Berman datasets; data may not be internally consistent")
-
out <- c(eout, list(plotvar=plotvar, plotvals=plotvals, names=names, predominant=predominant), out2D)
return(invisible(out))
}
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/info.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -131,11 +131,7 @@
# if a single name matches, use that one (useful for distinguishing pseudo-H4SiO4 and H4SiO4) 20171020
matches.name <- matches.species & thermo$obigt$name==species
if(sum(matches.name)==1) ispecies.out <- which(matches.name)
- else {
- # prefer the Berman minerals?
- if(thermo$opt$Berman & "cr_Berman" %in% thermo$obigt$state[ispecies]) ispecies.out <- ispecies[thermo$obigt$state[ispecies]=="cr_Berman"]
- else ispecies.out <- ispecies[1] # otherwise, return only the first species that matches
- }
+ else ispecies.out <- ispecies[1] # otherwise, return only the first species that matches
# let user know if there is more than one state for this species
mystate <- thermo$obigt$state[ispecies.out]
ispecies.other <- ispecies[!ispecies %in% ispecies.out]
Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/subcrt.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -147,15 +147,6 @@
ton <- thermo$obigt$name
tos <- thermo$obigt$state
- # warn if we're running a reaction with both Berman and Helgeson minerals 20171110
- if(do.reaction) {
- ref1 <- thermo$obigt$ref1
- ref2 <- thermo$obigt$ref2
- hasHelgeson <- any(grepl("HDNB78", ref1[sinfo])) | any(grepl("HDNB78", ref2[sinfo]))
- hasBerman <- any(tos[sinfo]=="cr_Berman")
- if(hasHelgeson & hasBerman) warning("the reaction has minerals from both the Helgeson and Berman datasets; data may not be internally consistent")
- }
-
# stop if species not found
noname <- is.na(sinfo)
if(TRUE %in% noname)
@@ -310,7 +301,7 @@
}
# crystalline, gas, liquid (except water) species
- cglstates <- c("liq", "cr", "gas", "cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9", "cr_Berman")
+ cglstates <- c("liq", "cr", "gas", "cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9")
iscgl <- reaction$state %in% cglstates & reaction$name != "water"
if(TRUE %in% iscgl) {
@@ -330,8 +321,8 @@
# name and state
myname <- reaction$name[i]
mystate <- reaction$state[i]
- # don't proceed if the state is cr_Berman
- if(mystate=="cr_Berman") next
+# # don't proceed if the state is cr_Berman
+# if(mystate=="cr_Berman") next
# if this phase is cr2 or higher, check if we're below the transition temperature
if(!(reaction$state[i] %in% c('liq','cr','gas'))) {
Ttr <- Ttr(inpho[i]-1,P=P,dPdT=dPdTtr(inpho[i]-1))
Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/util.data.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -256,6 +256,7 @@
if(what=="OBIGT") tdata <- get("thermo")$obigt
else if(what=="DEW") tdata <- read.csv(system.file("extdata/OBIGT/DEW_aq.csv", package="CHNOSZ"), as.is=TRUE)
else if(what=="SUPCRTBL") tdata <- read.csv(system.file("extdata/OBIGT/SUPCRTBL.csv", package="CHNOSZ"), as.is=TRUE)
+ else if(what=="SUPCRT92") tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
ntot <- nrow(tdata)
# where to keep the results
DCp <- DV <- DG <- rep(NA,ntot)
@@ -288,6 +289,7 @@
# check optional data
out <- rbind(out, checkfun("DEW"))
out <- rbind(out, checkfun("SUPCRTBL"))
+ out <- rbind(out, checkfun("SUPCRT92"))
# set differences within a tolerance to NA
out$DCp[abs(out$DCp) < 1] <- NA
out$DV[abs(out$DV) < 1] <- NA
@@ -356,15 +358,17 @@
# dump all thermodynamic data in CHNOSZ 20171121
dumpdata <- function(file=NULL) {
# default database (OBIGT)
- Odata <- get("thermo")$obigt
- Odata <- cbind(source="OBIGT", Odata)
+ dat <- get("thermo")$obigt
+ OBIGT <- cbind(source="OBIGT", dat)
# optional data
- Ddata <- read.csv(system.file("extdata/OBIGT/DEW_aq.csv", package="CHNOSZ"), as.is=TRUE)
- Ddata <- cbind(source="DEW", Ddata)
- Sdata <- read.csv(system.file("extdata/OBIGT/SUPCRTBL.csv", package="CHNOSZ"), as.is=TRUE)
- Sdata <- cbind(source="SUPCRTBL", Sdata)
+ dat <- read.csv(system.file("extdata/OBIGT/DEW_aq.csv", package="CHNOSZ"), as.is=TRUE)
+ DEW <- cbind(source="DEW", dat)
+ dat <- read.csv(system.file("extdata/OBIGT/SUPCRTBL.csv", package="CHNOSZ"), as.is=TRUE)
+ SUPCRTBL <- cbind(source="SUPCRTBL", dat)
+ dat <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
+ SUPCRT92 <- cbind(source="SUPCRT92", dat)
# put it all together
- out <- rbind(Odata, Ddata, Sdata)
+ out <- rbind(OBIGT, DEW, SUPCRTBL, SUPCRT92)
# quote columns 2 (name) and 3 (abbrv) because they have commas for some entries
if(!is.null(file)) write.csv(out, file, row.names=FALSE, quote=c(2, 3))
else(return(out))
Modified: pkg/CHNOSZ/R/util.misc.R
===================================================================
--- pkg/CHNOSZ/R/util.misc.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/R/util.misc.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -7,13 +7,13 @@
# (argument is index of the lower-T phase)
thermo <- get("thermo")
pars <- info(c(ispecies, ispecies+1), check.it=FALSE)
- # the special handling for quartz and coesite interferece with this function,
+ # if these aren't the same mineral all we can say is zero
+ # actually, should be infinity ... the volume change is zero
+ if(as.character(pars$name[1]) != as.character(pars$name[2])) return(Inf)
+ # the special handling for quartz and coesite interfere with this function,
# so we convert to uppercase names to prevent cgl() from calling quartz_coesite()
pars$name <- toupper(pars$name)
props <- cgl(c("G", "S", "V"), pars, P=0, T=thermo$obigt$z.T[ispecies])
- # if these aren't the same mineral all we can say is zero
- # actually, should be infinity ... the volume change is zero
- if(as.character(pars$name[1]) != as.character(pars$name[2])) return(Inf)
# we really hope the G's are the same ...
#if(abs(props[[2]]$G - props[[1]]$G) > 0.1) warning('dP.dT: inconsistent values of G for different phases of ',ispecies,call.=FALSE)
dP.dT <- convert( ( props[[2]]$S - props[[1]]$S ) / ( props[[2]]$V - props[[1]]$V ), 'cm3bar' )
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/data/refs.csv 2018-03-27 15:19:33 UTC (rev 309)
@@ -6,12 +6,13 @@
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,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for 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
-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,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","chlorargyrite",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
+RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",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/DEW.R
===================================================================
--- pkg/CHNOSZ/demo/DEW.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/demo/DEW.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -26,9 +26,9 @@
PT20.0 <- data.frame(P=20000, T=seq(200, 800, 10))
PT <- rbind(PT0.5, PT1.0, PT2.0, PT5.0, PT10.0, PT20.0)
# reaction 1: quartz = SiO2(aq) [equivalent to quartz + 3 H2O = Si(OH)4]
-SiO2_logK <- subcrt(c("quartz", "SiO2"), c("cr_Berman", "aq"), c(-1, 1), P=PT$P, T=PT$T)$out$logK
+SiO2_logK <- subcrt(c("quartz", "SiO2"), c("cr", "aq"), c(-1, 1), P=PT$P, T=PT$T)$out$logK
# reaction 2: 2 quartz = Si2O4(aq) [equivalent to 2 quartz + 3 H2O = Si2O(OH)6]
-Si2O4_logK <- subcrt(c("quartz", "Si2O4"), c("cr_Berman", "aq"), c(-2, 1), P=PT$P, T=PT$T)$out$logK
+Si2O4_logK <- subcrt(c("quartz", "Si2O4"), c("cr", "aq"), c(-2, 1), P=PT$P, T=PT$T)$out$logK
# plot the sum of molalities (== activities) for each pressure
plot(c(200, 1000), c(-2.5, 0.5), type="n", xlab=axis.label("T"), ylab="log molality")
for(P in unique(PT$P)) {
@@ -45,8 +45,7 @@
t1 <- quote("Solubility of"~alpha*"-quartz")
t2 <- "after Sverjensky et al., 2014a"
mtitle(as.expression(c(t1, t2)))
-# TODO: lines are a little low at highest P and P ...
-# does the Berman, 1988 quartz data increase high-PT solubilities?
+# TODO: lines are a little low at highest P and T ...
###########
#### plot 2: correlations between non-solvation volume and HKF a1 parameter
@@ -146,10 +145,8 @@
add.obigt("DEW", c(inorganics, organics[-4]))
## set basis species
basis(c("Fe", "SiO2", "CO3-2", "H2O", "oxygen", "H+"))
-## define a QFM buffer using Berman's equations for minerals
-mod.buffer("QFM_Berman", c("quartz", "fayalite", "magnetite"), "cr_Berman", 0)
## calculate logfO2 in QFM buffer
-basis("O2", "QFM_Berman")
+basis("O2", "QFM")
T <- seq(600, 1000, 100)
buf <- affinity(T=T, P=50000, return.buffer=TRUE)
## add species
Modified: pkg/CHNOSZ/demo/activity_ratios.R
===================================================================
--- pkg/CHNOSZ/demo/activity_ratios.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/demo/activity_ratios.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -6,6 +6,13 @@
res <- 200
fill <- "terrain"
+data(thermo)
+## get data for gibbsite from the SUPCRT92 database, without loading minerals that
+## have been superseded by the Berman dataset (the default in CHNOSZ)
+add.obigt("SUPCRT92", "gibbsite")
+## or, get data for gibbsite and Al-bearing aqueous species from the SUPCRTBL database
+#add.obigt("SUPCRTBL")
+
## K2O-Al2O3-SiO2-H2O, 25 degree C, 1 bar
## Steinmann et al., 1994 (http://ccm.geoscienceworld.org/content/42/2/197)
## Garrels and Christ, p. 361 (http://www.worldcat.org/oclc/517586)
@@ -45,7 +52,7 @@
## CaO-Al2O3-MgO-SiO2-H2O at 300 degree C and 500 bar
## Bach and Klein, 2009 (https://doi.org/10.1016/j.lithos.2008.10.022)
basis(c("Ca+2", "Al+3", "Mg+2", "SiO2", "H2O", "O2", "H+"))
-species(c("clinochlore,14a", "clinozoisite", "prehnite", "grossular"))
+species(c("clinochlore", "clinozoisite", "prehnite", "grossular"))
a <- affinity(SiO2 = c(-5, 0, res), `Ca+2` = c(6, 11, res), T = 300, P = 500)
diagram(a, ylab = ratlab("Ca+2"), balance = "Al+3", fill = fill, yline = 1.7)
# (Hmmm... where is clinochlore? it doesn't appear on our diagram)
Modified: pkg/CHNOSZ/demo/go-IU.R
===================================================================
--- pkg/CHNOSZ/demo/go-IU.R 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/demo/go-IU.R 2018-03-27 15:19:33 UTC (rev 309)
@@ -21,18 +21,20 @@
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)
+## first calculation: after SUPCRT92 (SiO2(aq) from SHS89)
+add.obigt("SUPCRT92") # gets 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)
+data(thermo)
+add.obigt("SUPCRT92", "boehmite") # gets only boehmite from HDNB78
+r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), 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)
+r3 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), 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)
+r4 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), 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)
@@ -41,7 +43,7 @@
## add points calculated using the SUPCRTBL package
points(seq(125, 350, 25), -c(3.489, 3.217, 2.967, 2.734, 2.517, 2.314, 2.124, 1.946, 1.781, 1.628), pch=4, col="red")
## add labels, legend, and title
-text(182.5, -3.17, "SUPCRT92\n(CHNOSZ default)", srt=48, cex=0.7, font=2)
+text(182.5, -3.17, "SUPCRT92", srt=48, cex=0.7, font=2)
text(154, -3.04, "circa SUPCRTBL", srt=45, cex=0.7, font=2, col="red")
legend("topleft", lty=c(1, 2, 2, 1, 0), pch=c(NA, NA, NA, NA, 4),
col=c("black", "black", "red", "red", "red"), bty="n", cex=0.9,
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/inst/NEWS 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,8 +1,27 @@
-CHANGES IN CHNOSZ 1.1.3-16 (2018-03-27)
+CHANGES IN CHNOSZ 1.1.3-17 (2018-03-27)
---------------------------------------
-BERMAN EQUATIONS AND DATA
+THERMODYNAMIC DATA
+- The Berman data (Berman, 1988 and later additions) have replaced the
+ SUPCRT92 data (based on Helgeson et al., 1978) for most minerals in
+ the default database (i.e. the one loaded by data(thermo)). Only
+ native elements, sulfides, halides, sulfates, and selected carbonates
+ and oxides from SUPCRT92 that do not duplicate any in the Berman
+ dataset are loaded by default.
+
+- The superseded SUPCRT92 minerals (primarily the silicates and
+ Al-bearing minerals, as well as calcite, dolomite, hematite, and
+ magnetite) are in the file extdata/OBIGT/SUPCRT92.csv, which can be
+ loaded with add.obigt("SUPCRT92"). This is used in some examples for
+ comparing the datasets (see ?berman and demo(go-IU.R)), but should not
+ be needed by most users.
+
+- In thermo$obigt, the minerals using the Berman equations are
+ identified as those having NA values for all thermodynamic properties
+ (columns 8-20). These minerals have the state of "cr" (not "cr_Berman"
+ as before).
+
- berman() now reads data from a user-supplied file berman.csv if it is
present in the working directory.
Modified: pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,21 +1,21 @@
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
-almandine,Alm,Si3Fe3Al2O12,cr_Berman,BA96.1,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-anthophyllite,Ath,Mg7Si8O24H2,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-cordierite,Cd,Mg2Al4Si5O18,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-enstatite,En,MgSiO3,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fayalite,Fa,Fe2SiO4,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ferrosilite,Fsl,SiFeO3,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-forsterite,Fo,Mg2SiO4,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hematite,Hm,Fe2O3,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ilmenite,Ilm,FeTiO3,cr_Berman,Ber88,BA96.4,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-magnetite,Mt,Fe3O4,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pyrope,Py,Mg3Al2Si3O12,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-rutile,Rt,TiO2,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-spinel,Sp,MgAl2O4,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-talc,Tc,Mg3Si4O12H2,cr_Berman,Ber88,BA96.4,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-Fe-cordierite,fCd,Fe2Al4Si5O18,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-geikelite,Gk,MgTiO3,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hercynite,Hc,FeAl2O4,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-iron-a,aFe,Fe,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-iron-g,gFe,Fe,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-orthocorundum,Ok,Al2O3,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+almandine,Alm,Si3Fe3Al2O12,cr,BA96.1,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+enstatite,En,MgSiO3,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fayalite,Fa,Fe2SiO4,cr,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ferrosilite,Fsl,SiFeO3,cr,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+forsterite,Fo,Mg2SiO4,cr,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hematite,Hm,Fe2O3,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ilmenite,Ilm,FeTiO3,cr,Ber88,BA96.4,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+magnetite,Mt,Fe3O4,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pyrope,Py,Mg3Al2Si3O12,cr,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+rutile,Rt,TiO2,cr,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+spinel,Sp,MgAl2O4,cr,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+talc,Tc,Mg3Si4O12H2,cr,Ber88,BA96.4,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Fe-cordierite,fCd,Fe2Al4Si5O18,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+geikelite,Gk,MgTiO3,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hercynite,Hc,FeAl2O4,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-a,aFe,Fe,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-g,gFe,Fe,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+orthocorundum,Ok,Al2O3,cr,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2018-03-27 07:57:23 UTC (rev 308)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2018-03-27 15:19:33 UTC (rev 309)
@@ -1,87 +1,87 @@
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
-akermanite,Ak,Ca2MgSi2O7,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-albite,Ab,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"albite,high",hAb,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"albite,low",lAb,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-almandine,Alm,Si3Fe3Al2O12,cr_Berman,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-andalusite,And,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-anorthite,An,Al2CaSi2O8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-anthophyllite,Ath,Mg7Si8O24H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-antigorite,Atg,Mg48Si34O99H62O48,cr_Berman,Ber88,BDat17.1,09.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-brucite,Br,MgO2H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-Ca-Al-pyroxene,CTs,CaAl2SiO6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-calcite,Cc,CaCO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chrysotile,Chr,Mg3Si2O9H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-clinochlore,Chl,Mg5Al2Si3O18H8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-coesite,Cs,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-cordierite,Cd,Mg2Al4Si5O18,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-corundum,Co,Al2O3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"cristobalite,alpha",aCr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"cristobalite,beta",bCr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-diaspore,Dsp,AlO2H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-diopside,Di,MgCaSi2O6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-dolomite,Do,MgCaC2O6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"enstatite,clino",cEn,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-enstatite,En,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"enstatite,proto",pEn,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fayalite,Fa,Fe2SiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ferrosilite,Fsl,SiFeO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-forsterite,Fo,Mg2SiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-gehlenite,Ge,Al2Ca2SiO7,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-grossular,Gr,Ca3Al2Si3O12,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hematite,Hm,Fe2O3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ilmenite,Ilm,FeTiO3,cr_Berman,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-jadeite,Jd,NaAlSi2O6,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-kaolinite,Kln,Al2Si2O9H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-kyanite,Ky,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-lawsonite,Lw,CaAl2Si2O10H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-lime,Lm,CaO,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-magnesite,Mst,MgCO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-magnetite,Mt,Fe3O4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-margarite,Mrg,CaAl4Si2O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-meionite,Me,Ca4Al6Si6O27C,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-merwinite,Mw,Ca3MgSi2O8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-monticellite,Mo,CaMgSiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-muscovite,Ms,KAl3Si3O12H2,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-paragonite,Pg,NaAl3Si3O12H2,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-periclase,Pe,MgO,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-phlogopite,Phl,KMg3AlSi3O12H2,cr_Berman,Ber88,SHD91.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-K-feldspar,Kfs,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"K-feldspar,high",Sa,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"K-feldspar,low",Mcr,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-prehnite,Prh,Ca2Al2Si3O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pyrope,Py,Mg3Al2Si3O12,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pyrophyllite,Prl,Al2Si4O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-quartz,aQz,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"quartz,beta",bQz,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-rutile,Rt,TiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-sillimanite,Si,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-sphene,Sph,CaTiSiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-spinel,Sp,MgAl2O4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-talc,Tc,Mg3Si4O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-tremolite,Tr,Ca2Mg5Si8O24H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"tridymite,high",hTr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"tridymite,low",lTr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-wollastonite,Wo,CaSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pseudowollastonite,pWo,CaSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-zoisite,Zo,Ca2Al3Si3O13H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-clinozoisite,cZo,Ca2Al3Si3O13H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-annite,Ann,Si3Fe3AlKH2O12,cr_Berman,Ber90,SHD91.2,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluormuscovite,Flms,KAl3Si3O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluorphlogopite,Fphl,KMg3AlSi3O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluorannite,Flan,Si3Fe3AlKO10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluortremolite,Fltr,Ca2Mg5Si8O22F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluorapatite,Flap,Ca5P3O12F,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hydroxyapatite,Hyap,Ca5P3O13H,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chlorapatite,Clap,Ca5P3O12Cl,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fluortalc,Fltc,Mg3Si4O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chlorphlogopite,Cphl,KMg3AlSi3O10Cl2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-chlorannite,Clan,Si3Fe3AlKO10Cl2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-glaucophane,Glc,Na2Al2Mg3Si8O24H2,cr_Berman,Eva90,JUN92,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pumpellyite,Pmp,Ca4Al5MgSi6O28H7,cr_Berman,Eva90,JUN92,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-aragonite,Arg,CaCO3,cr_Berman,FDM+14.1,NA,08.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hedenbergite,Hd,CaFeSi2O6,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-andradite,Adr,Ca3Fe2Si3O12,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ferro-actinolite,Fac,Ca2Fe5Si8O22(OH)2,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-grunerite,Gru,Fe7Si8O22(OH)2,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ilvaite,Ilv,CaFe2FeSi2O7O(OH),cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+akermanite,Ak,Ca2MgSi2O7,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+albite,Ab,NaAlSi3O8,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"albite,high",hAb,NaAlSi3O8,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"albite,low",lAb,NaAlSi3O8,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+almandine,Alm,Si3Fe3Al2O12,cr,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+andalusite,And,Al2SiO5,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anorthite,An,Al2CaSi2O8,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+antigorite,Atg,Mg48Si34O99H62O48,cr,Ber88,BDat17.1,09.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+brucite,Br,MgO2H2,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Ca-Al-pyroxene,CTs,CaAl2SiO6,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+calcite,Cc,CaCO3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+chrysotile,Chr,Mg3Si2O9H4,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+clinochlore,Chl,Mg5Al2Si3O18H8,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+coesite,Cs,SiO2,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+corundum,Co,Al2O3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 309
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