[CHNOSZ-commits] r239 - in pkg/CHNOSZ: . R data demo inst inst/extdata/Berman inst/extdata/OBIGT man tests/testthat vignettes

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2017-10-03 09:35:24 +0200 (Tue, 03 Oct 2017)
New Revision: 239

Added:
   pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/affinity.R
   pkg/CHNOSZ/R/berman.R
   pkg/CHNOSZ/R/info.R
   pkg/CHNOSZ/R/subcrt.R
   pkg/CHNOSZ/R/util.expression.R
   pkg/CHNOSZ/R/util.misc.R
   pkg/CHNOSZ/data/buffer.csv
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/demo/buffer.R
   pkg/CHNOSZ/demo/dehydration.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
   pkg/CHNOSZ/man/basis.Rd
   pkg/CHNOSZ/man/data.Rd
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/man/species.Rd
   pkg/CHNOSZ/man/subcrt.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-subcrt.R
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/obigt.Rmd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
rename "cr1" to "cr" (lowest-T polymorph for minerals with transitions)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/DESCRIPTION	2017-10-03 07:35:24 UTC (rev 239)
@@ -1,6 +1,6 @@
 Date: 2017-10-03
 Package: CHNOSZ
-Version: 1.1.0-37
+Version: 1.1.0-38
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/R/affinity.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -1,6 +1,13 @@
 # CHNOSZ/affinity.R
 # calculate affinities of formation reactions
 
+## if this file is interactively sourced, the following are also needed to provide unexported functions:
+#source("util.affinity.R")
+#source("util.units.R")
+#source("util.character.R")
+#source("util.list.R")
+#source("subcrt.R")
+
 affinity <- function(...,property=NULL,sout=NULL,exceed.Ttr=FALSE,
   return.buffer=FALSE,balance="PBB",iprotein=NULL,loga.protein=-3) {
   # ...: variables over which to calculate

Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/R/berman.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -8,16 +8,20 @@
   # reference temperature and pressure
   Pr <- 1
   Tr <- 298.15
-  # the number of conditions we have
+  # get T and P to be same length
   ncond <- max(length(T), length(P))
+  T <- rep(T, length.out=ncond)
+  P <- rep(P, length.out=ncond)
   # get thermodynamic parameters
   dir <- system.file("extdata/Berman/", package="CHNOSZ")
   Ber88 <- read.csv(paste0(dir, "/Ber88.csv"), as.is=TRUE)
   Ber90 <- read.csv(paste0(dir, "/Ber90.csv"), as.is=TRUE)
   SHD91 <- read.csv(paste0(dir, "/SHD91.csv"), as.is=TRUE)
   ZS92 <- read.csv(paste0(dir, "/ZS92.csv"), as.is=TRUE)
-  # assemble the files and remove duplicates (keep the latest)
-  dat <- rbind(ZS92, SHD91, Ber90, Ber88)
+  JUN92 <- read.csv(paste0(dir, "/JUN92.csv"), as.is=TRUE)
+  # assemble the files in reverse chronological order
+  dat <- rbind(JUN92, ZS92, SHD91, Ber90, Ber88)
+  # remove duplicates (only the first, i.e. latest entry is kept)
   dat <- dat[!duplicated(dat$name), ]
   # remove the multipliers
   multexp <- c(0, 0, 0, 0,          # Ber88 Table 2
@@ -90,6 +94,8 @@
     # the lower integration limit is Tref
     iTtr <- T > Tref
     Ttr <- T[iTtr]
+    Tlambda_P <- Tlambda_P[iTtr]
+    Td <- Td[iTtr]
     # the upper integration limit is Tlambda_P
     Ttr[Ttr >= Tlambda_P] <- Tlambda_P[Ttr >= Tlambda_P]
     # derived variables
@@ -137,12 +143,17 @@
     S <- S + Sds
     V <- V + Vds
     Cp <- Cp + Cpds
+  } else {
+
+    # FIXME: for now, we skip this check if disorder properties are calculated
+
+    ### (for testing) use G = H - TS to check that integrals for H and S are written correctly
+    Ga_fromHminusTS <- Ha - T * S
+    # (fails with with berman("K-feldspar", T=convert(600, "K"), P=10000))
+    if(!isTRUE(all.equal(Ga_fromHminusTS, Ga))) stop(paste0(name, ": incorrect integrals detected using DG = DH - T*S"))
+
   }
 
-  ### (for testing) use G = H - TS to check that integrals for H and S are written correctly
-  Ga_fromHminusTS <- Ha - T * S
-  if(!all.equal(Ga_fromHminusTS, Ga)) stop("incorrect integrals detected using DG = DH - T*S")
-
   ### thermodynamic and unit conventions used in SUPCRT ###
   # use entropy of the elements in calculation of G --> Benson-Helgeson convention (DG = DH - T*DS)
   Gf <- Ga + Tr * SPrTr_elements

Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/R/info.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -129,15 +129,23 @@
   # all of the species that match
   ispecies <- which(matches.species)
   # we return only the first species that matches
-  # unless they are 'cr1' 'cr2' etc. and we requested state 'cr'
-  if(identical(state, "cr")) ispecies.out <- ispecies
-  else ispecies.out <- ispecies[1]
+  ispecies.out <- ispecies[1]
   # let user know if there is more than one state for this species
   if(length(ispecies) > length(ispecies.out)) {
     ispecies.other <- ispecies[!ispecies %in% ispecies.out]
-    othertext <- paste(thermo$obigt$state[ispecies.other], collapse=", ")
-    message("info.character: found ", species, "(", thermo$obigt$state[ispecies.out], 
-      "), also available in ", othertext)
+    otherstates <- thermo$obigt$state[ispecies.other]
+    transtext <- othertext <- ""
+    # we count, but don't show the states for phase transitions (cr2, cr3, etc)
+    istrans <- otherstates %in% c("cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9")
+    ntrans <- sum(istrans)
+    if(ntrans == 1) transtext <- paste(" with", ntrans, "phase transition")
+    else if(ntrans > 1) transtext <- paste(" with", ntrans, "phase transitions")
+    otherstates <- otherstates[!istrans]
+    if(length(otherstates) > 0) othertext <- paste0(", also available in ", paste(otherstates, collapse=", "))
+    if(transtext != "" | othertext != "") {
+      starttext <- paste0("info.character: found ", species, "(", thermo$obigt$state[ispecies.out], ")")
+      message(starttext, transtext, othertext)
+    }
   }
   return(ispecies.out)
 }

Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/R/subcrt.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -116,7 +116,7 @@
     sinfo <- ispecies
   } else {
     # from names, get species indices and states and possibly
-    # keep track of phase species (cr1 cr2 ...)
+    # keep track of phase species (cr,cr2 ...)
     sinfo <- numeric()
     newstate <- character()
     for(i in 1:length(species)) {
@@ -127,7 +127,7 @@
       thermo <- get("thermo", "CHNOSZ")
       if(is.na(si[1])) stop('no info found for ',species[i],' ',state[i])
       if(!is.null(state[i])) is.cr <- state[i]=='cr' else is.cr <- FALSE
-      if(thermo$obigt$state[si[1]]=='cr1' & (is.null(state[i]) | is.cr)) {
+      if(thermo$obigt$state[si[1]]=='cr' & (is.null(state[i]) | is.cr)) {
         newstate <- c(newstate,'cr')
         sinfo <- c(sinfo,si[1])
       } else {
@@ -151,7 +151,7 @@
   state <- as.character(tos[sinfo])
   name <- as.character(ton[sinfo])
   # a counter of all species considered
-  # inpho is longer than sinfo if cr1 cr2 ... phases are present
+  # inpho is longer than sinfo if cr,cr2 ... phases are present
   # sinph shows which of sinfo correspond to inpho
   # pre-20091114: the success of this depends on there not being duplicated aqueous or other
   # non-mineral-phase species (i.e., two entries in obigt for Cu+ screw this up
@@ -160,7 +160,7 @@
   inpho <- sinph <- coeff.new <- numeric()
   for(i in 1:length(sinfo)) {
      if(newstate[i]=='cr') {
-       searchstates <- c('cr','cr1','cr2','cr3','cr4','cr5','cr6','cr7','cr8','cr9') 
+       searchstates <- c('cr','cr2','cr3','cr4','cr5','cr6','cr7','cr8','cr9') 
        tghs <- thermo$obigt[(ton %in% name[i]) & tos %in% searchstates,]
        # we only take one if they are in fact duplicated species and not phase species
        if(all(tghs$state==tghs$state[1])) tghs <- thermo$obigt[sinfo[i],]
@@ -293,11 +293,10 @@
   }
 
   # crystalline, gas, liquid (except water) species
-  cglstates <- c("liq", "cr", "gas", "cr1", "cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9", "cr_Berman")
+  cglstates <- c("liq", "cr", "gas", "cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9", "cr_Berman")
   iscgl <- reaction$state %in% cglstates & reaction$name != "water"
 
   if(TRUE %in% iscgl) {
-    #si <- info(inpho[iscgl],quiet=TRUE)
     si <- obigt2eos(thermo$obigt[inpho[iscgl],], "cgl", fixGHS = TRUE)
     p.cgl <- cgl(eosprop, parameters = si, T = T, P = P)
     # replace Gibbs energies with NA where the
@@ -316,8 +315,8 @@
         mystate <- reaction$state[i]
         # don't proceed if the state is cr_Berman
         if(mystate=="cr_Berman") next
-        # check if we're below the transition temperature
-        if(!(reaction$state[i] %in% c('cr1','liq','cr','gas'))) {
+        # if this phase is cr2 or higher, check if we're below the transition temperature
+        if(!(reaction$state[i] %in% c('liq','cr','gas'))) {
           Ttr <- Ttr(inpho[i]-1,P=P,dPdT=dPdTtr(inpho[i]-1))
           if(all(is.na(Ttr))) next
           if(any(T < Ttr)) {
@@ -327,14 +326,20 @@
               p.cgl[[ncgl[i]]]$G[T<Ttr] <- NA
               status.Ttr <- "(using NA for G)"
             } 
-            message(paste('subcrt: some points below transition temperature for',myname, mystate, status.Ttr))
+            #message(paste('subcrt: some points below transition temperature for',myname, mystate, status.Ttr))
           }
         }
-        # check if we're above the transition temperature
-        if(!(reaction$state[i] %in% c('cr','liq','gas')))
-          Ttr <- Ttr(inpho[i],P=P,dPdT=dPdTtr(inpho[i]))
-        else {
-          Ttr <- thermo$obigt$z.T[inpho[i]]
+        # check if we're above the temperature limit or transition temperature
+        # T limit (or Ttr) from the database
+        warn.above <- TRUE
+        Ttr <- thermo$obigt$z.T[inpho[i]]
+        # calculate Ttr at higher P if a phase transition is present
+        if(i < nrow(reaction)) {
+          # if the next one is cr2, cr3, etc we have a transition
+          if(reaction$state[i+1] %in% c("cr1", "cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9"))
+            Ttr <- Ttr(inpho[i],P=P,dPdT=dPdTtr(inpho[i]))
+          # we don't warn here about the transition
+          warn.above <- FALSE
         }
         if(all(is.na(Ttr))) next
         if(!all(Ttr==0) & any(T >= Ttr)) {
@@ -343,7 +348,7 @@
             p.cgl[[ncgl[i]]]$G[T>=Ttr] <- NA
             status.Ttr <- "(using NA for G)"
           }
-          message(paste('subcrt: some points above transition temperature for',myname, mystate, status.Ttr))
+          if(warn.above) message(paste('subcrt: some points above temperature limit for',myname, mystate, status.Ttr))
         }
       }
     }
@@ -380,7 +385,7 @@
   for(i in 1:length(is))  v[[i]] <- out[[match(ns[i],is)]]
   out <- v
 
-  # deal with phases (cr1 cr2) here
+  # deal with phases (cr,cr2) here
   # we have to eliminate rows from out, 
   # reaction and values from isaq, iscgl, isH2O
   out.new <- list()
@@ -390,10 +395,12 @@
   isH2O.new <- logical()
   for(i in 1:length(sinfo)) {
     iphases <- which(sinfo[i]==sinph)
-    # deal with repeated species here ... divide iphases 
-    # by the number of duplicates
+    # deal with repeated species here
     if(TRUE %in% duplicated(inpho[iphases])) {
-      iphases <- iphases[length(which(sinfo==sinfo[i]))]
+      # only take the first, not the duplicates
+      ndups <- length(which(sinfo==sinfo[i]))
+      nphases <- length(iphases) / ndups
+      iphases <- iphases[1:nphases]
     }
     if(length(iphases)>1) {
       message(paste('subcrt:',length(iphases),'phases for',thermo$obigt$name[sinfo[i]],'... '), appendLF=FALSE)

Modified: pkg/CHNOSZ/R/util.expression.R
===================================================================
--- pkg/CHNOSZ/R/util.expression.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/R/util.expression.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -53,7 +53,7 @@
   }
   # write logarithm of activity or fugacity
   if(log != "") {
-    if(log %in% c("aq", "cr", "liq", "cr1", "cr2", "cr3", "cr4")) acity <- "a"
+    if(log %in% c("aq", "cr", "liq", "cr2", "cr3", "cr4")) acity <- "a"
     else if(log %in% c("g", "gas")) acity <- "f"
     else stop(paste("'", log, "' is not a recognized state", sep=""))
     logacity <- substitute(log~italic(a), list(a=acity))

Modified: pkg/CHNOSZ/R/util.misc.R
===================================================================
--- pkg/CHNOSZ/R/util.misc.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/R/util.misc.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -31,7 +31,7 @@
 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
+  # ispecies: the species index for cr (the lowest-T phase)
   thisinfo <- info(ispecies)
   name <- thisinfo$name
   # start from Tr (T=298.15 K)
@@ -43,10 +43,10 @@
   # where to store the calculated GHS at Tr
   Gf_Tr <- Hf_Tr <- S_Tr <- numeric()
   for(i in 1:(length(Htr)+1)) {
-    # check that we have the correct one of cr1, cr2, ...
-    thiscr <- paste0("cr", i)
+    # check that we have the correct one of cr, cr2, cr3, ...
+    if(i==1) thiscr <- "cr" else thiscr <- paste0("cr", i)
     if(thisinfo$state!=thiscr | thisinfo$name!=name) stop(paste("species", thisis, "is not", name, thiscr))
-    # if we're above cr1, calculate the equivalent GHS at Tr
+    # if we're above cr (lowest-T), calculate the equivalent GHS at Tr
     if(i > 1) {
       # set the starting GHS to 0 (in case they're NA - we only need the increments over temperature)
       thisinfo$G <- thisinfo$H <- thisinfo$S <- 0

Modified: pkg/CHNOSZ/data/buffer.csv
===================================================================
--- pkg/CHNOSZ/data/buffer.csv	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/data/buffer.csv	2017-10-03 07:35:24 UTC (rev 239)
@@ -12,9 +12,9 @@
 CYSTINE,cystine,aq,-3
 ETHANOL,ethanol,aq,-3
 MAMINE,methanamine,aq,-3
-HM,hematite,cr1,0
-HM,magnetite,cr1,0
-FeFeO,iron,cr1,0
+HM,hematite,cr,0
+HM,magnetite,cr,0
+FeFeO,iron,cr,0
 FeFeO,FeO,cr,0
 CO2-AC,CO2,aq,-3
 CO2-AC,"acetic acid",aq,-3
@@ -30,11 +30,11 @@
 GSH-GSSG,GSSG,aq,-9
 NADred-NADox,HNAD(red)-,aq,-3
 NADred-NADox,NAD(ox)-,aq,-3
-QFM,quartz,cr1,0
+QFM,quartz,cr,0
 QFM,fayalite,cr,0
-QFM,magnetite,cr1,0
+QFM,magnetite,cr,0
 PPM,pyrite,cr,0
-PPM,pyrrhotite,cr1,0
-PPM,magnetite,cr1,0
+PPM,pyrrhotite,cr,0
+PPM,magnetite,cr,0
 water,water,liq,0
-quartz,quartz,cr1,0
+quartz,quartz,cr,0

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/data/refs.csv	2017-10-03 07:35:24 UTC (rev 239)
@@ -5,7 +5,7 @@
 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,"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
@@ -22,10 +22,12 @@
 SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4
 Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344","annite",http://ammin.geoscienceworld.org/content/75/3-4/328
 Ber90.1,"R. G. Berman",1990,"Am. Mineral. 75, 328-344","almandine and ilmenite: modified H and/or S",http://ammin.geoscienceworld.org/content/75/3-4/328
+Eva90,"B. W. Evans",1990,"Lithos 25, 3-23","glaucophane and pumpellyite",https://doi.org/10.1016/0024-4937(90)90003-J
 SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O
 SHD91,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","G and H revisions for K- and Al-bearing silicates",https://doi.org/10.1016/0016-7037(89)90341-4
 SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
 SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
+JUN92,"C. de Capitani",1992,"JUN92.bs database supplied with Theriak/Domino software","data as listed in JUN92.bs database",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html
 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 Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@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 Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
 Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",https://doi.org/10.1016/0016-7037(92)90392-V
@@ -73,7 +75,7 @@
 AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,https://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 N<sub>2</sub>O",https://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",https://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",https://doi.org/10.1016/S0883-2927(00)00025-1
+MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","polymorphs of ice",https://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",https://doi.org/10.1016/S0016-7037(01)00678-0
 PS01.1,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","acetic acid and methane",https://doi.org/10.1016/S0016-7037(01)00678-0
 Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",https://doi.org/10.1016/S0016-7037(01)00761-X

Modified: pkg/CHNOSZ/demo/buffer.R
===================================================================
--- pkg/CHNOSZ/demo/buffer.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/demo/buffer.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -3,7 +3,7 @@
 # reproduces Figure 6 of Schulte and Shock, 1995 (doi:10.1007/BF01581580)
 
 b.species <- c("Fe", "CO2", "H2O", "N2", "H2", "H2S", "SiO2")
-b.state <- c("cr1", "gas", "liq", "gas", "gas", "aq", "aq")
+b.state <- c("cr", "gas", "liq", "gas", "gas", "aq", "aq")
 b.logact <- c(0, 1, 0, 0, 0, 0, 0)
 basis(b.species, b.state, b.logact)
 xlim <- c(0, 350)

Modified: pkg/CHNOSZ/demo/dehydration.R
===================================================================
--- pkg/CHNOSZ/demo/dehydration.R	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/demo/dehydration.R	2017-10-03 07:35:24 UTC (rev 239)
@@ -17,7 +17,7 @@
 reactants <- c("[AABB]", "[AABB]", "malate-2", "goethite", "gypsum", "epsomite", "ethanol")
 products <- c("[UPBB]", "[PBB]", "fumarate-2", "hematite", "anhydrite", "hexahydrite", "ethylene")
 rstate <- c("aq", "cr", "aq", "cr", "cr", "cr", "aq")
-pstate <- c("aq", "cr", "aq", "cr1", "cr", "cr", "gas")
+pstate <- c("aq", "cr", "aq", "cr", "cr", "cr", "gas")
 rcoeff <- c(-1, -1, -1, -2, -0.5, -1, -1)
 pcoeff <- c(1, 1, 1, 1, 0.5, 1, 1)
 # position and rotation of the names

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/inst/NEWS	2017-10-03 07:35:24 UTC (rev 239)
@@ -1,12 +1,12 @@
-CHANGES IN CHNOSZ 1.1.0-37 (2017-10-03)
+CHANGES IN CHNOSZ 1.1.0-38 (2017-10-03)
 ---------------------------------------
 
 MAJOR CHANGES:
 
 - Add functions implementing the Deep Earth Water (DEW) model
-  (Sverjensky et al., 2014): calculateDensity(),
-  calculateGibbsofWater(), calculateEpsilon(), calculateQ(), and
-  water.DEW().
+  (Sverjensky et al., 2014): water.DEW() and its supporting functions
+  calculateDensity(), calculateGibbsofWater(), calculateEpsilon(),
+  calculateQ().
 
 - The computational setting for water (thermo$opt$par) can now be
   set using water("DEW"), water("IAPWS"), etc.
@@ -19,14 +19,27 @@
 - Calculations related to Berman's (1988) Figs. 1 and 2 for the lambda
   transition of quartz are presented in the new demo lambda.R.
 
+COMPUTATIONAL IMPROVEMENTS:
+
+- For minerals with phase transitions (states 'cr2' 'cr3' etc.) in
+  thermo$obigt (i.e. the Helgeson minerals), it is now possible to use
+  the minerals in basis(), species(), affinity() with proper accounting
+  for transition effects. Just set the state to 'cr' or omit it,
+  e.g. species("quartz").
+
 - Implement SUPCRT92's handling of variable volume for quartz and
   coesite. Calculations for other minerals still assume constant
   volume of each phase.
 
+- calculations of the g function are now enabled for DEW (with
+  pressure derivative) and IAPWS-95 (no derivatives included).
+
 - water.lines() now works for diagrams of Eh, pe, logfO2, logaO2,
   logfH2, or logaH2 vs pH, T, or P. It is possible to have T or P on
   either the x- or y-axis.
 
+DATABASE UPDATES:
+
 - Add data(OBIGT) and data(CHNOSZ) commands to reset only the
   thermodynamic database (OBIGT) or system settings (CHNOSZ: basis and
   species) to their defaults. data(thermo) is still used to reset
@@ -38,8 +51,6 @@
 
 - add.obigt() gets new argument 'species' for selecting species to add.
 
-DATABASE UPDATES:
-
 - Add DEW_aq.csv with aqueous species data from the DEW spreadsheet
   (May 2017 version). Species with data unchanged from the default
   database in CHNOSZ are not included. For the time being, only
@@ -79,14 +90,11 @@
 
 - In water.* functions, rename the "diel" variable to "epsilon".
 
-- calculations of the g function (but not its derivatives) are now
-  enabled for DEW and IAPWS-95.
+CLEANUP:
 
 - To save space, taxid_names.csv has been trimmed to hold only those
   taxids listed in extdata/bison/gi.taxid.txt.
 
-CLEANUP:
-
 - Remove Eco.csv.xz and rename more.aa() to yeast.aa().
 
 - Remove transfer() and associated functions draw.transfer(), apc(), and

Added: pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv	2017-10-03 07:35:24 UTC (rev 239)
@@ -0,0 +1,3 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+glaucophane,-11225858,-11960500,535,26.05,1717.5,-192.72,70.5,0,-1.16,2.9,22,88,,,,,,,,,,,,,,
+pumpellyite,-13448936,-14402300,584,29.55,1576,-106.038,-283.042,383.8351,-0.51516,1.288,34.67,0,,,,,,,,,,,,,,

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

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2017-10-03 02:31:15 UTC (rev 238)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2017-10-03 07:35:24 UTC (rev 239)
@@ -1,58 +1,81 @@
-ý7zXZ  æÖ´F !
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¨Ý5i‡* p0n¥z†Çj€„Öz‡—Ý»ÖpUÊhÄÛñlrO`©Æû´Y!hA‡Üµ‹îð!¨©n»äü¡¢ì˜JqÆíTHÞ1Êí!Ù(@¬EÉåR(ß±i¡0DíÎò›hŸÏ9rQAee1¾½rƬ$£Ÿ(6/¼ËP†:¢	ð´»Jbtp,B1iúK‚\ê]€ô2}·ïSƒ«éî0w³”ý!Š³
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~R³iÜ õoŽ	ó!Õ—wO0<D–Ê„°aAÏbÿŠæô€±ì…‹]’ZYœxúúÆCåZñ(vÁ¦Öo±Â¶)NÅÆÃdZÖÿÊnWd‡&©˜‡÷Lìå[jm]¨	Îr͆¯:a	¢bþ0ÍëZΏþ$ĝêOlÄö1N +à²7ã9NçZšî’p¬]e”ªÄk)–sf­XA	‚BeX—&#C]Ç Æþ‹Åk]^*e~úšX0¥‚ϔPon/­P½€J*zƒum3žrÙ‚äâ¼Ô¢ÛchTyR€¼V[™*Vì¥Æ|Z²ª»(&FÓ}ñ”¼Ò'ØÕbÙßÓ¢ÃñVY¸TsPöY3wWÁ<öÛSIbÀ椚…§"ëN2 ï
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 239