[CHNOSZ-commits] r680 - in pkg/CHNOSZ: . R demo inst inst/extdata/OBIGT inst/extdata/adds man man/macros tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jul 9 15:08:55 CEST 2021
Author: jedick
Date: 2021-07-09 15:08:55 +0200 (Fri, 09 Jul 2021)
New Revision: 680
Removed:
pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/demo/E_coli.R
pkg/CHNOSZ/demo/Pourbaix.R
pkg/CHNOSZ/demo/Shh.R
pkg/CHNOSZ/demo/copper.R
pkg/CHNOSZ/demo/glycinate.R
pkg/CHNOSZ/demo/protein.equil.R
pkg/CHNOSZ/demo/sources.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/man/add.OBIGT.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/macros/macros.Rd
pkg/CHNOSZ/tests/testthat/test-add.protein.R
pkg/CHNOSZ/tests/testthat/test-affinity.R
pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
pkg/CHNOSZ/tests/testthat/test-protein.info.R
pkg/CHNOSZ/tests/testthat/test-recalculate.R
pkg/CHNOSZ/tests/testthat/test-revisit.R
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/equilibrium.Rmd
Log:
Remove OBIGT/OldAA.csv
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/DESCRIPTION 2021-07-09 13:08:55 UTC (rev 680)
@@ -1,6 +1,6 @@
-Date: 2021-06-02
+Date: 2021-07-09
Package: CHNOSZ
-Version: 1.4.1-6
+Version: 1.4.1-7
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/R/info.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -259,7 +259,7 @@
}
# if we got here there were no approximate matches
# 20190127 look for the species in optional data files
- for(opt in c("SLOP98", "SUPCRT92", "OldAA", "AkDi")) {
+ for(opt in c("SLOP98", "SUPCRT92", "AkDi")) {
optdat <- read.csv(system.file(paste0("extdata/OBIGT/", opt, ".csv"), package="CHNOSZ"), as.is=TRUE)
if(species %in% optdat$name) {
message('info.approx: ', species, ' is in an optional database; use add.OBIGT("', opt, '", "', species, '") to load it')
Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/R/util.data.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -269,7 +269,6 @@
else if(what=="DEW") tdata <- read.csv(system.file("extdata/OBIGT/DEW.csv", package="CHNOSZ"), as.is=TRUE)
else if(what=="SLOP98") tdata <- read.csv(system.file("extdata/OBIGT/SLOP98.csv", package="CHNOSZ"), as.is=TRUE)
else if(what=="SUPCRT92") tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
- else if(what=="OldAA") tdata <- read.csv(system.file("extdata/OBIGT/OldAA.csv", package="CHNOSZ"), as.is=TRUE)
else if(what=="AS04") tdata <- read.csv(system.file("extdata/OBIGT/AS04.csv", package="CHNOSZ"), as.is=TRUE)
else if(what=="AkDi") tdata <- read.csv(system.file("extdata/OBIGT/AkDi.csv", package="CHNOSZ"), as.is=TRUE)
ntot <- nrow(tdata)
@@ -307,7 +306,6 @@
out <- rbind(out, checkfun("DEW"))
out <- rbind(out, checkfun("SLOP98"))
out <- rbind(out, checkfun("SUPCRT92"))
- out <- rbind(out, checkfun("OldAA"))
# set differences within a tolerance to NA
out$DCp[abs(out$DCp) < 1] <- NA
out$DV[abs(out$DV) < 1] <- NA
Modified: pkg/CHNOSZ/demo/E_coli.R
===================================================================
--- pkg/CHNOSZ/demo/E_coli.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/demo/E_coli.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -44,7 +44,7 @@
# This command loads "old" parameters for [UPBB]
# (Dick et al., 2006; https://doi.org/10.5194/bg-3-311-2006)
# - increases G.P278 by ca. 35-40% (closer to Figure 5 of Amend et al., 2013)
-add.OBIGT("OldAA")
+mod.OBIGT("[UPBB]", G = -21436, H = -45220, S = 1.62)
# Calculate polymerization contribution
# Standard Gibbs energy (J / mol) for AABB -> PBB + H2O
Modified: pkg/CHNOSZ/demo/Pourbaix.R
===================================================================
--- pkg/CHNOSZ/demo/Pourbaix.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/demo/Pourbaix.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -145,3 +145,5 @@
main <- bquote(.(element)*"-O-H at "*.(Texpr)*" and "*.(Pexpr))
title(main = main)
+# Reset OBIGT database to run other demos
+reset()
Modified: pkg/CHNOSZ/demo/Shh.R
===================================================================
--- pkg/CHNOSZ/demo/Shh.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/demo/Shh.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -3,7 +3,8 @@
library(CHNOSZ)
# to reproduce the calculations in the paper, use superseded data for [Gly] and [UPBB] 20190206
-add.OBIGT("OldAA", c("[Gly]", "[UPBB]"))
+mod.OBIGT("[Gly]", G = -6075, H = -5570, S = 17.31)
+mod.OBIGT("[UPBB]", G = -21436, H = -45220, S = 1.62)
# UniProt names of the proteins
pname <- c("SHH", "OLIG2", "NKX22", "FOXA2", "IRX3", "PAX6", "NKX62", "DBX1",
Modified: pkg/CHNOSZ/demo/copper.R
===================================================================
--- pkg/CHNOSZ/demo/copper.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/demo/copper.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -4,8 +4,8 @@
## solutions. J. Electrochem. Soc., 148, B51-B57. doi:10.1149/1.1344532)
library(CHNOSZ)
-# we need superseded data for Cu-Gly complexes 20190206
-add.OBIGT("OldAA")
+# we need data for Cu-Gly complexes 20190206
+add.OBIGT(system.file("extdata/adds/SK95.csv", package = "CHNOSZ"))
# add some new species to thermo()$OBIGT
m1 <- makeup(info(c("Cu+", "glycinate", "glycinate")), sum=TRUE)
mod.OBIGT(name="Cu(Gly)2-", formula=as.chemical.formula(m1))
Modified: pkg/CHNOSZ/demo/glycinate.R
===================================================================
--- pkg/CHNOSZ/demo/glycinate.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/demo/glycinate.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -28,7 +28,7 @@
# calculate the logKs for divalent metals using data from Shock and Koretsky, 1995
# doi:10.1016/0016-7037(95)00058-8
-add.OBIGT("OldAA")
+add.OBIGT(system.file("extdata/adds/SK95.csv", package = "CHNOSZ"))
logK_di1_SK95 <- logK_di2_SK95 <- list()
for(i in 1:length(di1)) logK_di1_SK95[[i]] <- subcrt(c(di[i], "glycinate", di1[i]), c(-1, -1, 1), T = T)$out$logK
for(i in 1:length(di2)) logK_di2_SK95[[i]] <- subcrt(c(di[i], "glycinate", di2[i]), c(-1, -2, 1), T = T)$out$logK
Modified: pkg/CHNOSZ/demo/protein.equil.R
===================================================================
--- pkg/CHNOSZ/demo/protein.equil.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/demo/protein.equil.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -4,7 +4,9 @@
protein <- pinfo(c("CSG_METVO", "CSG_METJA"))
# use superseded properties of [Met], [Gly], and [UPBB] (Dick et al., 2006)
-add.OBIGT("OldAA")
+mod.OBIGT("[Met]", G = -35245, H = -59310, S = 40.38)
+mod.OBIGT("[Gly]", G = -6075, H = -5570, S = 17.31)
+mod.OBIGT("[UPBB]", G = -21436, H = -45220, S = 1.62)
# set up the basis species to those used in DS11
basis("CHNOS+")
# note this yields logaH2 = -4.657486
Modified: pkg/CHNOSZ/demo/sources.R
===================================================================
--- pkg/CHNOSZ/demo/sources.R 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/demo/sources.R 2021-07-09 13:08:55 UTC (rev 680)
@@ -18,17 +18,14 @@
tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
os5 <- gsub("\ .*", "", tdata$ref1)
os6 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/OldAA.csv", package="CHNOSZ"), as.is=TRUE)
+tdata <- read.csv(system.file("extdata/OBIGT/AS04.csv", package="CHNOSZ"), as.is=TRUE)
os7 <- gsub("\ .*", "", tdata$ref1)
os8 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/AS04.csv", package="CHNOSZ"), as.is=TRUE)
+tdata <- read.csv(system.file("extdata/OBIGT/AkDi.csv", package="CHNOSZ"), as.is=TRUE)
os9 <- gsub("\ .*", "", tdata$ref1)
os10 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/AkDi.csv", package="CHNOSZ"), as.is=TRUE)
-os11 <- gsub("\ .*", "", tdata$ref1)
-os12 <- gsub("\ .*", "", tdata$ref2)
# all of the thermodynamic data sources - some of them might be NA
-OBIGT.source <- unique(c(ps1, ps2, os1, os2, os3, os4, os5, os6, os7, os8, os9, os10, os11, os12))
+OBIGT.source <- unique(c(ps1, ps2, os1, os2, os3, os4, os5, os6, os7, os8, os9, os10))
OBIGT.source <- OBIGT.source[!is.na(OBIGT.source)]
# these all produce character(0) if the sources are all accounted for
print("missing these sources for thermodynamic properties:")
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2021-07-09 13:08:55 UTC (rev 680)
@@ -10,16 +10,29 @@
\newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
\newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
-\section{Changes in CHNOSZ version 1.4.1-5 (2021-05-17)}{
+\section{Changes in CHNOSZ version 1.4.1-7 (2021-07-09)}{
\subsection{OBIGT DATABASE}{
\itemize{
\item Move Ar, Xe, CH\s{4}, and CO\s{2} from organic_aq.csv to inorganic_aq.csv.
+
+ \item Remove OldAA.csv (superseded thermodynamic parameters for amino
+ acids). This file is now available in the JMDplots package.
}
}
+ \subsection{OTHER CHANGES}{
+ \itemize{
+
+ \item \strong{multi-metal.Rmd} now has a link to the paper published in
+ *Applied Computing & Geosciences*
+ (\href{https://doi.org/10.1016/j.acags.2021.100059}{Dick, 2021}).
+
+ }
+ }
+
}
\section{Changes in CHNOSZ version 1.4.1 (2021-04-08)}{
Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv 2021-07-09 13:08:55 UTC (rev 680)
@@ -1,65 +0,0 @@
-name,abbrv,formula,state,ref1,ref2,date,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-alanylglycine,NA,C5H10N2O3,aq,Sho92,NA,1992-02-28,cal,-116730,-186110,50.7,60.3,95.22,14.6503,21.164,12.0751,-3.6538,54.7374,0.7979,-0.4278,0
-leucylglycine,NA,C8H16N2O3,aq,Sho92,NA,2006-08-27,cal,-110620,-202660,72.6,118.8,145.34,21.3967,34.6501,13.1805,-4.2113,98.6389,6.4783,-0.7594,0
-diglycine,NA,C4H8N2O3,aq,Sho92,NA,1992-02-28,cal,-117020,-175640,54.2,38,76.27,12.0393,15.9447,11.6466,-3.4381,36.349,-1.3673,-0.4808,0
-diketopiperazine,NA,C4H6N2O2,aq,Sho92,NA,1992-02-28,cal,-57440,-99300,53.5,17,76.73,12.1058,16.0764,11.6608,-3.4435,19.5904,-3.4064,-0.4702,0
-glycine,Gly,C2H5NO2,aq,AH97b.2,DLH06.1,2006-08-25,cal,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0
-glycinium,Gly+,C2H6NO2+,aq,AH97b.2,DLH06.1,2006-08-25,cal,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0
-methionine,Met,C5H11NO2S,aq,AH97b.2,DLH06.1,2006-08-25,cal,-120120,-178520,62.36,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
-[Gly],NA,H,aq,DLH06.6,NA,2006-08-25,cal,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0
-[Met],NA,C3H7S,aq,DLH06.6,NA,2006-08-25,cal,-35245,-59310,40.38,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0
-[UPBB],NA,C2H2NO,aq,DLH06.6,NA,2006-08-25,cal,-21436,-45220,1.62,-4.496,26.296,8.1,-3.75,-6.73,1.13,11.2,-7.5,0.05,0
-alanate,NA,C3H6NO2-,aq,SK95.1,AH97b.1,2006-09-03,cal,-75360,-121470,30.71,17.8,61.88,10.6281,17.3648,0.6505,-3.4968,12.685,-4.1859,1.17,-1
-glycinate,NA,C2H4NO2-,aq,SK95.1,AH97b.1,2006-09-03,cal,-77610,-114190,30.07,-6.6,43.77,8.1592,11.7696,1.921,-3.2655,12.9389,-4.1859,1.1975,-1
-Ca(Gly)+,NA,Ca(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-211570,-240519,34.375,59.3,32.6,6.2431,7.4595,2.8241,-3.0873,41.4246,9.0464,0.0543,1
-Ca(Gly)2,NA,Ca(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-290215,-351722,77.929,131,89,13.9371,26.2517,-4.5733,-3.8641,82.6597,23.6485,-0.03,0
-Mg(Gly)+,NA,Mg(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-190820,-227064,7.788,64.2,28.7,5.8466,6.4953,3.1944,-3.0474,48.0086,10.0502,0.4555,1
-Mg(Gly)2,NA,Mg(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-272534,-343783,43.136,140.6,84.7,13.3443,24.8034,-4.0028,-3.8043,88.2942,25.6069,-0.03,0
-Sr(Gly)+,NA,Sr(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-213664,-241197,42.515,53.6,33.3,6.3007,7.6019,2.7652,-3.0932,36.9719,7.8914,-0.0684,1
-Sr(Gly)2,NA,Sr(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-291859,-351200,88.581,119.9,89.8,14.0476,26.5176,-4.6704,-3.8751,76.1763,21.395,-0.03,0
-Ba(Gly)+,NA,Ba(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-213671,-237698,55.917,48.6,38.7,6.9656,9.2295,2.1164,-3.1604,32.1389,6.8602,-0.2709,1
-Ba(Gly)2,NA,Ba(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-292479,-347082,106.12,110.1,95.8,14.8647,28.514,-5.4575,-3.9577,70.3874,19.383,-0.03,0
-Mn(Gly)+,NA,Mn(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-137101,-167693,26.59,67,33.7,6.4299,7.9186,2.6372,-3.1063,47.0493,10.6185,0.1739,1
-Mn(Gly)2,NA,Mn(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-218761,-282627,67.741,146.1,90.2,14.1002,26.6481,-4.7253,-3.8805,91.4846,26.7157,-0.03,0
-Fe(Gly)+,NA,Fe(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-105368,-137141,21.59,58,28,5.6774,6.0837,3.3533,-3.0304,42.4593,8.7852,0.2482,1
-Fe(Gly)2,NA,Fe(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-187369,-252307,61.198,128.5,83.9,13.2339,24.5311,-3.8903,-3.793,81.1932,23.1388,-0.03,0
-Ni(Gly)+,NA,Ni(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-96871,-131179,13.59,49.9,20.4,4.6813,3.6515,4.3097,-2.9299,38.8214,7.1352,0.3686,1
-Ni(Gly)2,NA,Ni(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-181191,-249835,51.18,112.7,75.4,12.0787,21.7107,-2.7819,-3.6764,71.9311,19.9195,-0.03,0
-Cu(Gly)+,NA,Cu(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-73625,-104298,26.59,63.4,25.3,5.2864,5.1238,3.7413,-2.9907,44.9395,9.8852,0.1739,1
-Cu(Gly)2,NA,Cu(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-161137,-225550,66.18,139,80.9,12.8262,23.5338,-3.4944,-3.7518,87.3679,25.285,-0.03,0
-Zn(Gly)+,NA,Zn(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-120148,-153499,19.59,62.1,25.6,5.3677,5.3226,3.6628,-2.9989,45.1185,9.6102,0.2792,1
-Zn(Gly)2,NA,Zn(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-203799,-271188,58.18,136.4,81.3,12.8771,23.6625,-3.5537,-3.7571,85.8243,24.7484,-0.03,0
-Pb(Gly)+,NA,Pb(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-90780,-114202,58.508,47.7,35.3,6.4949,8.079,2.5712,-3.1129,31.2483,6.6769,-0.3103,1
-Pb(Gly)2,NA,Pb(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-173013,-226772,109.51,108.3,92.1,14.355,27.2722,-4.9746,-3.9063,69.3582,19.0253,-0.03,0
-Co(Gly)+,NA,Co(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-97525,-130972,16.59,58.7,25.5,5.3683,5.3273,3.6539,-2.9991,43.5722,8.9227,0.326,1
-Co(Gly)2,NA,Co(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-180617,-247207,58.18,129.8,81.2,12.8601,23.6197,-3.5341,-3.7553,81.9652,23.407,-0.03,0
-Cd(Gly)+,NA,Cd(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-102566,-133978,28.59,68.4,35.3,6.6477,8.4525,2.4231,-3.1283,47.5446,10.8935,0.1417,1
-Cd(Gly)2,NA,Cd(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-185236,-250387,68.18,148.7,92.1,14.355,27.2722,-4.9746,-3.9063,93.0282,27.2523,-0.03,0
-Eu(Gly)+,NA,Eu(C2H4NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-208959,-236026,49.509,89.8,50.3,8.5841,13.176,0.5767,-3.3236,57.1645,15.2476,-0.1738,1
-Eu(Gly)2,NA,Eu(C2H4NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-288477,-346709,97.734,190.4,108.7,16.6314,32.8272,-7.1514,-4.136,117.4699,35.7476,-0.03,0
-Ca(Ala)+,NA,Ca(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-209172,-247643,35.015,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
-Ca(Ala)2,NA,Ca(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-285446,-365834,79.755,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
-Mg(Ala)+,NA,Mg(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-186539,-232305,8.428,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
-Mg(Ala)2,NA,Mg(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-263631,-353761,44.962,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
-Sr(Ala)+,NA,Sr(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-211130,-248184,43.155,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
-Sr(Ala)2,NA,Sr(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-286831,-365053,90.407,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
-Ba(Ala)+,NA,Ba(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-210713,-244263,56.557,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
-Ba(Ala)2,NA,Ba(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-286687,-360171,107.946,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
-Mn(Ala)+,NA,Mn(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-134280,-173740,29.425,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
-Mn(Ala)2,NA,Mn(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-213474,-295365,72.44,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
-Fe(Ala)+,NA,Fe(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-103952,-146326,18.518,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
-Fe(Ala)2,NA,Fe(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-184387,-269655,58.166,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
-Ni(Ala)+,NA,Ni(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-94227,-137691,15.46,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
-Ni(Ala)2,NA,Ni(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-175945,-264092,50.92,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
-Cu(Ala)+,NA,Cu(C3H6NO2)+,aq,SK95.1,OBIGT.2,2019-02-06,cal,-71295,-110530,25.46,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
-Cu(Ala)2,NA,Cu(C3H6NO2)2,aq,SK95.1,OBIGT.2,2019-02-06,cal,-156054,-238480,65.92,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
-Zn(Ala)+,NA,Zn(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-117313,-161024,17.46,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
-Zn(Ala)2,NA,Zn(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-198512,-284509,60.92,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
-Pb(Ala)+,NA,Pb(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-87891,-120835,59.148,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
-Pb(Ala)2,NA,Pb(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-167671,-240311,111.336,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
-Co(Ala)+,NA,Co(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-94799,-136805,20.46,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
-Co(Ala)2,NA,Co(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-175193,-260392,60.92,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
-Cd(Ala)+,NA,Cd(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-100782,-141576,29.698,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
-Cd(Ala)2,NA,Cd(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-181340,-264540,72.797,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
-Eu(Ala)+,NA,Eu(C3H6NO2)+,aq,SK95.1,OBIGT.2,2006-09-03,cal,-206029,-242617,50.149,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
-Eu(Ala)2,NA,Eu(C3H6NO2)2,aq,SK95.1,OBIGT.2,2006-09-03,cal,-282521,-359634,99.56,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2021-07-09 13:08:55 UTC (rev 680)
@@ -45,7 +45,6 @@
JOH92,"J. W. Johnson and E. H. Oelkers and H. C. Helgeson",1992,"Comp. Geosci. 18, 899-947",H<sub>2</sub>O,https://doi.org/10.1016/0098-3004(92)90029-Q
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; not present in slop files after slop98.dat",https://doi.org/10.1016/0016-7037(92)90392-V
Sho92.1,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diketopiperazine GHS",https://doi.org/10.1016/0016-7037(92)90392-V
VGT92,"O. Vidal, B. Goffé and T. Theye",1992,"J. Metamorphic Geol. 10, 603-614",sudoite,https://doi.org/10.1111/j.1525-1314.1992.tb00109.x
ZS92,"C. Zhu and D. A. Sverjensky",1982,"Geochim. Cosmochim. Acta 56, 3435-3467","F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of @ZS92; heat capacity and volume parameters from `berman.dat`.",https://doi.org/10.1016/0016-7037(92)90390-5
@@ -68,12 +67,9 @@
RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","linnaeite V",https://doi.org/10.3133/b2131
SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
-SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes with metals. Values are taken from slop98.dat, which notes corrected values for some species.",https://doi.org/10.1016/0016-7037(95)00058-8
Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,https://doi.org/10.1016/0016-7037(95)00403-3
AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F
-AH97b.1,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","alanate and glycinate GHS",https://doi.org/10.1039/A608126F
-AH97b.2,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","glycine, glycinium, and methionine GHS",https://doi.org/10.1039/A608126F
DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3
DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
@@ -157,7 +153,6 @@
DLH06.3,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","glycine, [Gly], and [UPBB] HKF parameters",https://doi.org/10.5194/bg-3-311-2006
DLH06.4,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","methionine HKF parameters",https://doi.org/10.5194/bg-3-311-2006
DLH06.5,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","triglycine Cp, V, and HKF c<sub>1</sub>, c<sub>2</sub>, ω parameters",https://doi.org/10.5194/bg-3-311-2006
-DLH06.6,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","[Gly], [Met], and [UPBB]",https://doi.org/10.5194/bg-3-311-2006
LEB+06,"W. Liu et al.",2006,"Chem. Geol. 231, 326-349","FeCl<sub>2</sub><sup>+</sup>, FeCl<sub>3</sub>, FeCl<sub>4</sub><sup>-</sup>",https://doi.org/10.1016/j.chemgeo.2006.02.005
LMR06,"D. Langmuir et al.",2006,"Geochim. Cosmochim. Acta 70, 2942-2956","scorodite and amorphous ferric arsenate: G",https://doi.org/10.1016/j.gca.2006.03.006
MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175
@@ -218,7 +213,6 @@
ZZL+16.2,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","Cp parameters listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
ZZL+16.3,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","dawsonite GHS",https://doi.org/10.1016/j.cageo.2016.02.013
OBIGT.1,"J. M. Dick",2017,"OBIGT database in CHNOSZ","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.",http://chnosz.net
-OBIGT.2,"J. M. Dick",2017,"OBIGT database in CHNOSZ","metal-amino acid complexes: GHS were recalculated by adding the differences between values from @SK95 and @AH97b for alanate or glycinate to the properties of the complexes reported by @SK95.",http://chnosz.net
OBIGT.3,"J. M. Dick",2017,"OBIGT database in CHNOSZ","AuCl<sub>4</sub><sup>-</sup> renamed to AuCl<sub>4</sub><sup>-3</sup>",http://chnosz.net
OBIGT.4,"J. M. Dick",2017,"OBIGT database in CHNOSZ","charge of NpO<sub>2</sub>(Oxal), La(Succ)<sup>+</sup>, NH<sub>4</sub>(Succ)<sup>-</sup>, and NpO<sub>2</sub>(Succ) as listed by @PSK99",http://chnosz.net
OBIGT.5,"J. M. Dick",2017,"OBIGT database in CHNOSZ","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH<sub>2</sub>NH<sub>2</sub>] were printed in Table 6 of @DLH06; corrected values are used here.",http://chnosz.net
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2021-06-02 00:41:45 UTC (rev 679)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2021-07-09 13:08:55 UTC (rev 680)
@@ -101,135 +101,135 @@
"OBIGT",702,"Rh(SO4)3-3","aq","cal",,-1.33,
"OBIGT",703,"RhOH+2","aq","cal",,,789
"OBIGT",704,"RhO+","aq","cal",,,-2676
-"OBIGT",705,"CF4","aq","cal",5.9,,-2329
-"OBIGT",712,"AsH3","aq","cal",-2.67,,
-"OBIGT",773,"RuCrO4+2","aq","cal",,,-4659
-"OBIGT",795,"AgCl","aq","cal",,-1.88,
-"OBIGT",796,"AgCl2-","aq","cal",1.65,,
-"OBIGT",797,"AgCl3-2","aq","cal",,,-546
-"OBIGT",801,"CuHS","aq","cal",7.35,-16.2,
-"OBIGT",809,"ZnO2-2","aq","cal",,-1.17,
-"OBIGT",835,"S3-","aq","cal",,,661
-"OBIGT",840,"CoCl2(tet)","aq","cal",2.81,,
-"OBIGT",841,"CoCl4-2","aq","cal",1.33,-1.19,
-"OBIGT",850,"Fe(CO3)2-2","aq","cal",,,-4792
-"OBIGT",851,"Zn(CO3)2-2","aq","cal",,,-4724
-"OBIGT",852,"Cu(CO3)2-2","aq","cal",,,-4929
-"OBIGT",853,"Pb(CO3)2-2","aq","cal",,,-6676
-"OBIGT",855,"KCO3-","aq","cal",,,4996
-"OBIGT",857,"RbCO3-","aq","cal",,,-533
-"OBIGT",860,"MnHCO3+","aq","cal",,,945
-"OBIGT",868,"KHCO3","aq","cal",,,3759
-"OBIGT",873,"NbO3-","aq","cal",-1.51,,
-"OBIGT",875,"TaO3-","aq","cal",-1.61,,
-"OBIGT",879,"HTaO3F-","aq","cal",-1.15,-1.91,
-"OBIGT",880,"CH4","aq","cal",-2.61,,
-"OBIGT",885,"hexane","aq","cal",1.43,3.21,
-"OBIGT",888,"ethylene","aq","cal",6.12,-3.82,
-"OBIGT",912,"propanol","aq","cal",-1.89,,
-"OBIGT",959,"La(Ac)2+","aq","cal",,,-779
-"OBIGT",962,"Sm(Ac)+2","aq","cal",,,-660
-"OBIGT",963,"Sm(Ac)2+","aq","cal",,,-621
-"OBIGT",976,"Ca(Ac)2","aq","cal",,,-1006
-"OBIGT",992,"La(Ac)3","aq","cal",,,-564
-"OBIGT",1012,"Ce(Ac)+2","aq","cal",,,797
-"OBIGT",1013,"Ce(Ac)2+","aq","cal",,,567
-"OBIGT",1041,"urea","aq","cal",-23.26,23.32,
-"OBIGT",1054,"propanoic acid","aq","cal",1.42,,
-"OBIGT",1077,"formate","aq","cal",1.96,,
-"OBIGT",1079,"propanoate","aq","cal",1.68,,
-"OBIGT",1086,"n-decanoate","aq","cal",-1.93,,
-"OBIGT",1102,"oxalate-2","aq","cal",-3.19,,
-"OBIGT",1143,"Fe(For)+","aq","cal",,,587
-"OBIGT",1144,"Fe(For)2","aq","cal",,,639
-"OBIGT",1216,"Mg(But)2","aq","cal",,,-3347811
-"OBIGT",1245,"Yb(But)+2","aq","cal",,,665
-"OBIGT",1264,"Fe(Pent)2","aq","cal",,,532
-"OBIGT",1349,"Ba(HCO3)+","aq","cal",,,-5800
-"OBIGT",1369,"Li(Mal)-","aq","cal",,-3.22,
-"OBIGT",1373,"Pb(Mal)","aq","cal",,1.16,
-"OBIGT",1377,"Pb(Succ)","aq","cal",,1.49,
-"OBIGT",1378,"Na(Oxal)-","aq","cal",,-3.14,
-"OBIGT",1379,"K(Oxal)-","aq","cal",,-2.75,
-"OBIGT",1380,"Fe(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1382,"Na(Mal)-","aq","cal",,-3.11,17018
-"OBIGT",1383,"K(Mal)-","aq","cal",,-2.63,17013
-"OBIGT",1385,"La(Mal)+","aq","cal",,-1.92,
-"OBIGT",1386,"Gd(Mal)+","aq","cal",,-1.73,
-"OBIGT",1387,"Lu(Mal)+","aq","cal",,-2.25,
-"OBIGT",1388,"Yb(Mal)+","aq","cal",,-2.05,
-"OBIGT",1389,"Th(Mal)+2","aq","cal",-1.29,-4.79,
-"OBIGT",1391,"Ce(Mal)+","aq","cal",,-1.75,
-"OBIGT",1392,"Nd(Mal)+","aq","cal",4.52,,
-"OBIGT",1393,"Sm(Mal)+","aq","cal",,-1.77,
-"OBIGT",1394,"Pr(Mal)+","aq","cal",,-1.75,
-"OBIGT",1395,"Eu(Mal)+","aq","cal",,-1.87,
-"OBIGT",1396,"Tb(Mal)+","aq","cal",,-1.92,
-"OBIGT",1397,"Dy(Mal)+","aq","cal",,-1.89,
-"OBIGT",1398,"Tm(Mal)+","aq","cal",,-2.08,
-"OBIGT",1399,"Ho(Mal)+","aq","cal",,-2.08,
-"OBIGT",1400,"Er(Mal)+","aq","cal",,-2.11,
-"OBIGT",1401,"Sc(Mal)+","aq","cal",,-1.97,
-"OBIGT",1402,"Fe(Mal)+","aq","cal",,-1.97,
-"OBIGT",1403,"Na(Succ)-","aq","cal",,-2.82,
-"OBIGT",1404,"K(Succ)-","aq","cal",,-2.39,
-"OBIGT",1410,"Th(Succ)+2","aq","cal",-1.21,-4.47,
-"OBIGT",1415,"NH4(Oxal)-","aq","cal",,-2.62,
-"OBIGT",1420,"Yb(Oxal)+","aq","cal",,-2.02,
-"OBIGT",1421,"Ce(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1422,"Nd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1423,"Eu(Oxal)+","aq","cal",,-1.89,
-"OBIGT",1424,"Gd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1425,"Ru(Oxal)+","aq","cal",,-2.41,
-"OBIGT",1426,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1427,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
-"OBIGT",1428,"U(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1430,"Y(Oxal)+","aq","cal",,-2.11,
-"OBIGT",1435,"La(Oxal)+","aq","cal",,-1.87,
-"OBIGT",1436,"Tb(Oxal)+","aq","cal",,-1.92,
-"OBIGT",1437,"Er(Oxal)+","aq","cal",,-2.05,
-"OBIGT",1438,"Lu(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1439,"Cr(Oxal)+","aq","cal",,-2.58,
-"OBIGT",1440,"Ga(Oxal)+","aq","cal",,-2.66,
-"OBIGT",1441,"Sc(Oxal)+","aq","cal",,-2.13,
-"OBIGT",1442,"In(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1443,"Sm(Oxal)+","aq","cal",,-1.84,
-"OBIGT",1444,"Cs(Mal)-","aq","cal",,-2.39,
-"OBIGT",1445,"NH4(Mal)-","aq","cal",,-2.54,
-"OBIGT",1450,"In(Mal)+","aq","cal",,-2.11,
-"OBIGT",1451,"Y(Mal)+","aq","cal",,-2.02,29999
-"OBIGT",1459,"La(Succ)+","aq","cal",,-1.52,
-"OBIGT",1460,"NH4(Succ)-","aq","cal",,-2.26,
-"OBIGT",1462,"Fe(Succ)+","aq","cal",,-1.92,
-"OBIGT",1463,"Sc(Succ)+","aq","cal",,-1.77,
-"OBIGT",1465,"Sm(Succ)+","aq","cal",,-1.48,
-"OBIGT",1466,"Er(Succ)+","aq","cal",,-1.68,
-"OBIGT",1467,"U(Succ)+2","aq","cal",-1.15,-4.27,
-"OBIGT",1471,"La(Glut)+","aq","cal",,-1.23,
-"OBIGT",1472,"Y(Glut)+","aq","cal",,-1.46,
-"OBIGT",1473,"Sc(Glut)+","aq","cal",,-1.5,
-"OBIGT",1474,"Th(Glut)+2","aq","cal",-1.09,-4.05,
-"OBIGT",1477,"Fe(Glut)+","aq","cal",,-1.05,
-"OBIGT",1478,"Sm(Glut)+","aq","cal",,-1.2,
-"OBIGT",1480,"Er(Glut)+","aq","cal",,-1.4,-4673
-"OBIGT",1482,"Ba(Adip)","aq","cal",,1.19,
-"OBIGT",1489,"Pb(Adip)","aq","cal",,1.25,
-"OBIGT",1490,"Sc(Adip)+","aq","cal",,-1.22,
-"OBIGT",1492,"Th(Adip)+2","aq","cal",-1.02,-3.76,
-"OBIGT",1493,"U(Adip)+2","aq","cal",-1,-3.71,
-"OBIGT",1495,"Li(Oxal)-","aq","cal",,-3.3,
-"OBIGT",1499,"Li(Succ)-","aq","cal",,-2.94,
-"OBIGT",1501,"Na(Glut)-","aq","cal",,-2.34,
-"OBIGT",1502,"K(Glut)-","aq","cal",,-2.05,
-"OBIGT",1503,"Li(Glut)-","aq","cal",,-2.66,
-"OBIGT",1508,"Na(Adip)-","aq","cal",,-2.05,
-"OBIGT",1509,"K(Adip)-","aq","cal",,-1.76,
-"OBIGT",1510,"Li(Adip)-","aq","cal",,-2.38,
-"OBIGT",1516,"cyclohexane","aq","cal",9.35,6.64,
-"OBIGT",1517,"Ar","aq","cal",-1.24,-8.59,
-"OBIGT",1518,"benzene","aq","cal",,-1.14,
-"OBIGT",1519,"CO2","aq","cal",-4.94,,
-"OBIGT",1520,"Xe","aq","cal",2.8,,
+"OBIGT",705,"Ar","aq","cal",-1.24,-8.59,
+"OBIGT",706,"Xe","aq","cal",2.8,,
+"OBIGT",707,"CH4","aq","cal",-2.61,,
+"OBIGT",708,"CO2","aq","cal",-4.94,,
+"OBIGT",709,"CF4","aq","cal",5.9,,-2329
+"OBIGT",716,"AsH3","aq","cal",-2.67,,
+"OBIGT",777,"RuCrO4+2","aq","cal",,,-4659
+"OBIGT",799,"AgCl","aq","cal",,-1.88,
+"OBIGT",800,"AgCl2-","aq","cal",1.65,,
+"OBIGT",801,"AgCl3-2","aq","cal",,,-546
+"OBIGT",805,"CuHS","aq","cal",7.35,-16.2,
+"OBIGT",813,"ZnO2-2","aq","cal",,-1.17,
+"OBIGT",839,"S3-","aq","cal",,,661
+"OBIGT",844,"CoCl2(tet)","aq","cal",2.81,,
+"OBIGT",845,"CoCl4-2","aq","cal",1.33,-1.19,
+"OBIGT",854,"Fe(CO3)2-2","aq","cal",,,-4792
+"OBIGT",855,"Zn(CO3)2-2","aq","cal",,,-4724
+"OBIGT",856,"Cu(CO3)2-2","aq","cal",,,-4929
+"OBIGT",857,"Pb(CO3)2-2","aq","cal",,,-6676
+"OBIGT",859,"KCO3-","aq","cal",,,4996
+"OBIGT",861,"RbCO3-","aq","cal",,,-533
+"OBIGT",864,"MnHCO3+","aq","cal",,,945
+"OBIGT",872,"KHCO3","aq","cal",,,3759
+"OBIGT",877,"NbO3-","aq","cal",-1.51,,
+"OBIGT",879,"TaO3-","aq","cal",-1.61,,
+"OBIGT",883,"HTaO3F-","aq","cal",-1.15,-1.91,
+"OBIGT",888,"hexane","aq","cal",1.43,3.21,
+"OBIGT",891,"ethylene","aq","cal",6.12,-3.82,
+"OBIGT",915,"propanol","aq","cal",-1.89,,
+"OBIGT",962,"La(Ac)2+","aq","cal",,,-779
+"OBIGT",965,"Sm(Ac)+2","aq","cal",,,-660
+"OBIGT",966,"Sm(Ac)2+","aq","cal",,,-621
+"OBIGT",979,"Ca(Ac)2","aq","cal",,,-1006
+"OBIGT",995,"La(Ac)3","aq","cal",,,-564
+"OBIGT",1015,"Ce(Ac)+2","aq","cal",,,797
+"OBIGT",1016,"Ce(Ac)2+","aq","cal",,,567
+"OBIGT",1044,"urea","aq","cal",-23.26,23.32,
+"OBIGT",1057,"propanoic acid","aq","cal",1.42,,
+"OBIGT",1080,"formate","aq","cal",1.96,,
+"OBIGT",1082,"propanoate","aq","cal",1.68,,
+"OBIGT",1089,"n-decanoate","aq","cal",-1.93,,
+"OBIGT",1105,"oxalate-2","aq","cal",-3.19,,
+"OBIGT",1146,"Fe(For)+","aq","cal",,,587
+"OBIGT",1147,"Fe(For)2","aq","cal",,,639
+"OBIGT",1219,"Mg(But)2","aq","cal",,,-3347811
+"OBIGT",1248,"Yb(But)+2","aq","cal",,,665
+"OBIGT",1267,"Fe(Pent)2","aq","cal",,,532
+"OBIGT",1352,"Ba(HCO3)+","aq","cal",,,-5800
+"OBIGT",1372,"Li(Mal)-","aq","cal",,-3.22,
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 680
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