[CHNOSZ-commits] r260 - in pkg/CHNOSZ: . R data inst inst/extdata/OBIGT vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Oct 17 08:44:14 CEST 2017 

Author: jedick
Date: 2017-10-17 08:44:12 +0200 (Tue, 17 Oct 2017)
New Revision: 260

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/info.R
   pkg/CHNOSZ/R/subcrt.R
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
   pkg/CHNOSZ/vignettes/obigt.Rmd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
more SUPCRTBL data (aqueous As species and Al minerals)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/DESCRIPTION	2017-10-17 06:44:12 UTC (rev 260)
@@ -1,6 +1,6 @@
-Date: 2017-10-16
+Date: 2017-10-17
 Package: CHNOSZ
-Version: 1.1.0-58
+Version: 1.1.0-59
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/R/info.R	2017-10-17 06:44:12 UTC (rev 260)
@@ -73,7 +73,7 @@
   return(out)
 }
 
-info.character <- function(species, state=NULL, check.protein=TRUE, grep.state=FALSE) {
+info.character <- function(species, state=NULL, check.protein=TRUE) {
   # returns the rownumbers of thermo$obigt having an exact match of 'species' to
   # thermo$obigt$[species|abbrv|formula] or NA otherwise
   # a match to thermo$obigt$state is also required if 'state' is not NULL
@@ -113,8 +113,7 @@
     # special treatment for H2O: aq retrieves the liq
     if(species %in% c("H2O", "water") & state=="aq") state <- "liq"
     # the matches for both species and state
-    if(grep.state) matches.state <- matches.species & grepl(state, thermo$obigt$state)
-    else matches.state <- matches.species & state == thermo$obigt$state
+    matches.state <- matches.species & state == thermo$obigt$state
     if(!any(matches.state)) {
       # the requested state is not available for this species
       available.states <- thermo$obigt$state[matches.species]

Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/R/subcrt.R	2017-10-17 06:44:12 UTC (rev 260)
@@ -120,7 +120,7 @@
     for(i in 1:length(species)) {
       mysearch <- species[i]
       if(can.be.numeric(mysearch)) mysearch <- thermo$obigt$name[as.numeric(mysearch)]
-      si <- info.character(mysearch, state[i], grep.state=TRUE)
+      si <- info.character(mysearch, state[i])
       # that could have the side-effect of adding a protein; re-read thermo
       thermo <- get("thermo", "CHNOSZ")
       if(is.na(si[1])) stop('no info found for ',species[i],' ',state[i])

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/data/refs.csv	2017-10-17 06:44:12 UTC (rev 260)
@@ -10,6 +10,7 @@
 RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","chlorargyrite, rutile, and titanite",http://pubs.er.usgs.gov/publication/b1452
 RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452
 RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452
+RHF79.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","gibbsite GHS",http://pubs.er.usgs.gov/publication/b1452
 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
@@ -26,6 +27,7 @@
 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
 SH90.1,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","formic acid, formate, and propanoate",https://doi.org/10.1016/0016-7037(90)90429-O
 BN91,"J. W. Ball and D. K. Nordstrom",1991,"User's manual for WATEQ4F, with revised thermodynamic data base and text cases for calculating speciation of major, trace, and redox elements in natural waters. USGS Open-File Report 91-183","arsenopyrite: G",https://pubs.er.usgs.gov/publication/ofr91183
+HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457","bohemite",http://pubs.er.usgs.gov/publication/70016664
 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
@@ -86,7 +88,8 @@
 SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
 TS01,"B. Tagirov and J. Schott",2001,"Geochim. Cosmochim. Acta 65, 3965-3992","aqueous Al species",http://dx.doi.org/10.1016/S0016-7037(01)00705-0
 MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",https://doi.org/10.2138/am-2003-5-614
-NA03,"D. K. Nordstrom and D. G. Archer",2003,"Arsenic thermodynamic data and environmental geochemistry. In Arsenic in Groundwater, eds. Welch and Stollenwerk, Kluwer","As-bearing minerals",
+NA03,"D. K. Nordstrom and D. G. Archer",2003,"Arsenic thermodynamic data and environmental geochemistry. In Arsenic in Groundwater, eds. Welch and Stollenwerk, Kluwer","As oxide and sulfide minerals",
+NA03.1,"D. K. Nordstrom and D. G. Archer",2003,"Arsenic thermodynamic data and environmental geochemistry. In Arsenic in Groundwater, eds. Welch and Stollenwerk, Kluwer","aqueous As oxides and sulfides",
 MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",https://doi.org/10.2138/am-2003-5-613
 AS04,"J. Apps and N. Spycher",2004,"Data qualification for thermodynamic data used to support THC calculations. Bechtel SAIC Company, LLC. ANL-NBS-HS-000043 REV 00 (DOC.20041118.0004)",aqueous SiO<sub>2</sub>,
 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",https://doi.org/10.1007/s00269-004-0405-z
@@ -135,7 +138,9 @@
 CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid cycle metabolites",https://doi.org/10.1016/j.gca.2016.08.028
 CS16.1,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid species HKF a<sub>1</sub>--a<sub>4</sub> parameters",https://doi.org/10.1016/j.gca.2016.08.028
 ZZL+16,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","data listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
-ZZL+16.1,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","As(α): V data listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
+ZZL+16.1,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","As(α): V listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
+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
 CHNOSZ.1,"J. M. Dick",2017,"CHNOSZ package documentation","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
 CHNOSZ.2,"J. M. Dick",2017,"CHNOSZ package documentation","alanate and glycinate: GHS as used by @DLH06",http://chnosz.net
 CHNOSZ.3,"J. M. Dick",2017,"CHNOSZ package documentation","metal-amino acid complexes: GHS were recalculated by adding the differences between values from @AH97b and @DLH06 for alanate or glycinate to the properties of the complexes reported by @SK95.",http://chnosz.net

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/inst/NEWS	2017-10-17 06:44:12 UTC (rev 260)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-58 (2017-10-16)
+CHANGES IN CHNOSZ 1.1.0-59 (2017-10-17)
 ---------------------------------------
 
 MAJOR CHANGES:
@@ -94,11 +94,12 @@
   (May 2017 version). Species with data that do not differ from the
   default database in CHNOSZ are not included. Currently, detailed
   reference keys and descriptions (in thermo$refs) are given for
-  selected species only. [Optional Data; not loaded by data(thermo).]
+  selected species only. [Optional Data; not loaded by data(thermo)]
 
-- Add SUPCRTBL.csv with mineral and aqueous species data from
-  spronsbl.dat (http://www.indiana.edu/~hydrogeo/supcrtbl.html), as
-  described by Zimmer et al., 2016. [Optional Data.]
+- Add SUPCRTBL.csv with mineral and aqueous species data compiled by
+  Zimmer et al., 2016. Data were taken from original references or
+  from spronsbl.dat (http://www.indiana.edu/~hydrogeo/supcrtbl.html).
+  [Optional Data]
 
 - Update HKF parameters of adenine based on experimental heat capacity
   and volume data (Lowe et al., 2017). Add demo/adenine.R comparing

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv	2017-10-17 06:44:12 UTC (rev 260)
@@ -1,4 +1,32 @@
 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
+"arsenic,alpha",NA,As,cr,NA03,ZZL+16.1,16.Oct.17,0,0,8.515774378585085,5.838910133843212,12.96,NA,NA,NA,NA,NA,NA,NA,NA
+arsenolite,NA,As2O3,cr,NA03,NA,16.Oct.17,-137748.56596558317,-157091.3001912046,25.664435946462714,23.154875717017205,NA,NA,NA,NA,NA,NA,NA,NA,NA
+claudetite,NA,As2O3,cr,NA03,NA,16.Oct.17,-137793.97705544933,-156708.8910133843,27.09608030592734,23.178776290630974,NA,NA,NA,NA,NA,NA,NA,NA,NA
+As2O5,NA,As2O5,cr,NA03,NA,16.Oct.17,-185172.08413001912,-219309.27342256214,25.20076481835564,27.70076481835564,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"realgar,alpha",NA,AsS,cr,NA03,NA,16.Oct.17,-7480.879541108986,-7600.38240917782,15.033460803059272,11.233269598470363,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"realgar,beta",NA,AsS,cr,NA03,NA,16.Oct.17,-7385.277246653919,-7409.177820267686,15.176864244741873,11.233269598470363,NA,NA,NA,NA,NA,NA,NA,NA,NA
+orpiment,NA,As2S3,cr,NA03,NA,16.Oct.17,-20291.586998087954,-20506.692160611852,39.14913957934991,38.95793499043977,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"orpiment,amorphous",NA,As2S3,cr,NA03,NA,16.Oct.17,-18355.640535372848,-15989.483747609942,47.801147227533455,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+arsenopyrite,NA,FeAsS,cr,BN91,ZZL+16,16.Oct.17,-33843.21223709369,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+scorodite,NA,FeAsO4.2H2O,cr,LMR06,ZZL+16,16.Oct.17,-307619.5028680688,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"ferric arsenate,amorphous",NA,FeAsO4.2H2O,cr,LMR06,ZZL+16,16.Oct.17,-303771.51051625237,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"barium arsenate",NA,Ba3(AsO4)2,cr,ZZX+05,ZZL+16,16.Oct.17,-739749.0439770555,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"barium hydrogen arsenate",NA,BaHAsO4.H2O,cr,ZZX+05,ZZL+16,16.Oct.17,-367746.1759082218,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+boehmite,NA,AlO2H,cr,HRA91,ZZL+16.2,17.Oct.17,-219502.86806883363,-238145.3154875717,8.888623326959847,12.97634,19.535,40.48757170172084,-4.1108986615678775,0.6962476099426387,-467.3996175908221,0,0,0,NA
+gibbsite,NA,Al(OH)3,cr,RHF79.3,ZZL+16.2,17.Oct.17,-276025.1,-309065,16.35755,21.72251,31.956,22.179732313575524,45.276768642447415,0.3199569789674952,-247.20363288718926,0,0,0,NA
+dawsonite,NA,NaAlCO3(OH)2,cr,ZZL+16.3,NA,17.Oct.17,-425979.9,-463456,32.91109,NA,NA,0,0,0,0,0,0,0,NA
+H3AsO4,NA,H3AsO4,aq,NA03.1,NA,17.Oct.17,-183257.6481835564,-215929.7323135755,43.75478011472275,NA,NA,NA,NA,NA,NA,NA,NA,NA,0
+H2AsO4-,NA,H2AsO4-,aq,NA03.1,NA,17.Oct.17,-180126.67304015296,-217834.60803059273,26.85946462715105,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
+HAsO4-2,NA,HAsO4-2,aq,NA03.1,NA,17.Oct.17,-170585.56405353727,-217115.20076481835,-2.7294455066921604,NA,NA,NA,NA,NA,NA,NA,NA,NA,-2
+AsO4-3,NA,AsO4-3,aq,NA03.1,NA,17.Oct.17,-154483.74760994263,-212765.2963671128,-42.13910133843212,NA,NA,NA,NA,NA,NA,NA,NA,NA,-3
+H3AsO3,NA,H3AsO3,aq,NA03.1,NA,17.Oct.17,-152970.8413001912,-177428.29827915868,46.80449330783939,NA,NA,NA,NA,NA,NA,NA,NA,NA,0
+H2AsO3-,NA,H2AsO3-,aq,NA03.1,NA,17.Oct.17,-140454.11089866157,-170826.9598470363,26.957456978967496,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
+HAsO3-2,NA,HAsO3-2,aq,NA03.1,NA,17.Oct.17,-121271.51051625238,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-2
+AsO3-3,NA,AsO3-3,aq,NA03.1,NA,17.Oct.17,-100812.61950286807,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-3
+As3S4(HS)2-,NA,As3S4(HS)2-,aq,NA03.1,NA,17.Oct.17,-30019.12045889101,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
+AsS(OH)SH-,NA,AsS(OH)SH-,aq,NA03.1,NA,17.Oct.17,-58413.00191204589,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
+SiO2,NA,SiO2,aq,AS04,ZZL+16,16.Oct.17,-199539.9,-212179,11.12811,NA,NA,1.9,1.7,20,-2.7,32.22,-25.29001,0.3427103,0
+H4SiO4,NA,H4SiO4,aq,Ste01,NA,31.Aug.06,-312919.933078394,-348676.147227533,45.1003824091778,15.0095602294455,52.3,18.7299235181644,-21.2600382409178,18.6199808795411,-1.20004780114723,58.0305927342256,-20.789913957935,0.0869024856596558,0
 Al+3,NA,Al+3,aq,TS01,NA,25.Aug.06,-116510,NA,-81.203,-28.56,-45.3,-3.3984,-16.0789,12.0699,-2.1143,14.4295,-8.8523,2.7403,3
 Al(OH)4-,NA,Al(OH)4-,aq,TS01,NA,25.Aug.06,-312087,NA,24.748,23.06,46.3,8.4938,12.9576,0.657,-3.3147,55.7265,-11.4047,1.0403,-1
 AlOH+2,NA,AlOH+2,aq,TS01,NA,25.Aug.06,-166425,NA,-43.29,-8.97,-20.6,-0.4532,-8.8878,9.2434,-2.4116,15.4131,-4.8618,1.5897,2
@@ -16,18 +44,55 @@
 NaAl(OH)2F2,NA,NaAl(OH)2F2,aq,TS01,NA,25.Aug.06,-403511,NA,128.933,24.2,42.4,7.567,10.6947,1.5464,-3.2211,20.3493,1.8949,0,0
 NaAl(OH)4,NA,NaAl(OH)4,aq,TS01,DPS+96,25.Aug.06,-374611,-413601,48.8,32.2,53.6,9.1267,14.3411,0.1121,-3.3719,60.7157,-14.0523,0,0
 AlH3SiO4+2,NA,AlH3SiO4+2,aq,TS01,NA,25.Aug.06,-425860,NA,13.57,-71.9,-13.93,0.16,-7.23,8.61,-2.48,37.07,-49.66,0.88,2
-H4SiO4,NA,H4SiO4,aq,Ste01,NA,31.Aug.06,-312919.933078394,-348676.147227533,45.1003824091778,15.0095602294455,52.3,18.7299235181644,-21.2600382409178,18.6199808795411,-1.20004780114723,58.0305927342256,-20.789913957935,0.0869024856596558,0
-SiO2,NA,SiO2,aq,AS04,ZZL+16,16.Oct.17,-199539.9,-212179,11.12811,NA,NA,1.9,1.7,20,-2.7,32.22,-25.29001,0.3427103,0
-"arsenic,alpha",NA,As,cr,NA03,ZZL+16.1,16.Oct.17,0,0,8.515774378585085,5.838910133843212,12.96,NA,NA,NA,NA,NA,NA,NA,NA
-arsenolite,NA,As2O3,cr,NA03,NA,16.Oct.17,-137748.56596558317,-157091.3001912046,25.664435946462714,23.154875717017205,NA,NA,NA,NA,NA,NA,NA,NA,NA
-claudetite,NA,As2O3,cr,NA03,NA,16.Oct.17,-137793.97705544933,-156708.8910133843,27.09608030592734,23.178776290630974,NA,NA,NA,NA,NA,NA,NA,NA,NA
-As2O5,NA,As2O5,cr,NA03,NA,16.Oct.17,-185172.08413001912,-219309.27342256214,25.20076481835564,27.70076481835564,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"realgar,alpha",NA,AsS,cr,NA03,NA,16.Oct.17,-7480.879541108986,-7600.38240917782,15.033460803059272,11.233269598470363,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"realgar,beta",NA,AsS,cr,NA03,NA,16.Oct.17,-7385.277246653919,-7409.177820267686,15.176864244741873,11.233269598470363,NA,NA,NA,NA,NA,NA,NA,NA,NA
-orpiment,NA,As2S3,cr,NA03,NA,16.Oct.17,-20291.586998087954,-20506.692160611852,39.14913957934991,38.95793499043977,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"orpiment,amorphous",NA,As2S3,cr,NA03,NA,16.Oct.17,-18355.640535372848,-15989.483747609942,47.801147227533455,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-arsenopyrite,NA,FeAsS,cr,BN91,ZZL+16,16.Oct.17,-33843.21223709369,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-scorodite,NA,FeAsO4.2H2O,cr,LMR06,ZZL+16,16.Oct.17,-307619.5028680688,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"ferric arsenate,amorphous",NA,FeAsO4.2H2O,cr,LMR06,ZZL+16,16.Oct.17,-303771.51051625237,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"barium arsenate",NA,Ba3(AsO4)2,cr,ZZX+05,ZZL+16,16.Oct.17,-739749.0439770555,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-"barium hydrogen arsenate",NA,BaHAsO4.H2O,cr,ZZX+05,ZZL+16,16.Oct.17,-367746.1759082218,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+NaH2AsO4,NA,NaH2AsO4,aq,MA07,MA10,12.Sep.07,-240179,-272608,41.2,37.8,41.1,7.3772,10.2352,1.1421,-3.2022,27.9202,4.6622,-0.038,0
+KH2AsO4,NA,KH2AsO4,aq,MA07,MA10,12.Sep.07,-244935,-274352,54.5,21.9,52.4,8.9277,14.0226,-0.484,-3.3587,18.6125,1.4173,-0.038,0
+MgH2AsO4+,NA,MgH2AsO4+,aq,MA07,MA10,12.Sep.07,-290910,-332717,-10.4,50.7,18.3,4.5105,3.2335,4.1483,-2.9127,42.265,7.2899,0.7009,1
+CaH2AsO4+,NA,CaH2AsO4+,aq,MA07,MA10,12.Sep.07,-314170,-348007,18.5,45.8,22.2,4.8949,4.1724,3.7452,-2.9515,35.3597,6.2862,0.2639,1
+SrH2AsO4+,NA,SrH2AsO4+,aq,MA07,MA10,12.Sep.07,-315896,-347841,27.3,40.1,22.9,4.9488,4.3041,3.6887,-2.957,30.8142,5.1312,0.1301,1
+MnH2AsO4+,NA,MnH2AsO4+,aq,MA07,MA10,12.Sep.07,-236482,-270828,14.5,53.5,23.3,5.0617,4.5799,3.5702,-2.9684,40.4264,7.8583,0.3244,1
+FeH2AsO4+,NA,FeH2AsO4+,aq,MA07,MA10,12.Sep.07,-205693,-243719,1,44.9,17.6,4.3531,2.849,4.3134,-2.8968,37.3097,6.1166,0.5283,1
+CoH2AsO4+,NA,CoH2AsO4+,aq,MA07,MA10,12.Sep.07,-193388,-232357,-1.5,45.2,13.9,3.8628,1.6516,4.8275,-2.8473,37.7921,6.1625,0.5664,1
+NiH2AsO4+,NA,NiH2AsO4+,aq,MA07,MA10,12.Sep.07,-193146,-233785,-7.1,36.4,10,3.358,0.4185,5.3569,-2.7963,33.4496,4.375,0.6516,1
+CuH2AsO4+,NA,CuH2AsO4+,aq,MA07,MA10,12.Sep.07,-166866,-204382,4.1,49.9,14.9,3.9712,1.9164,4.7138,-2.8583,39.7683,7.1249,0.4813,1
+ZnH2AsO4+,NA,ZnH2AsO4+,aq,MA07,MA10,12.Sep.07,-215927,-255372,-0.3,50.7,15.3,4.0397,2.0836,4.642,-2.8652,40.8741,7.2945,0.5485,1
+PbH2AsO4+,NA,PbH2AsO4+,aq,MA07,MA10,12.Sep.07,-187896,-215577,44.7,34.1,25,5.1359,4.7611,3.4924,-2.9759,24.9084,3.9167,-0.1328,1
+AlH2AsO4+2,NA,AlH2AsO4+2,aq,MA07,MA10,12.Sep.07,-299978,-350717,-57,34.9,-7.1,1.4491,-4.244,7.3587,-2.6036,44.5413,4.0694,1.9508,2
+FeH2AsO4+2,NA,FeH2AsO4+2,aq,MA07,MA10,12.Sep.07,-189949,-235535,-39.9,66.2,1.1,2.4901,-1.7013,6.267,-2.7087,60.4374,10.4402,1.6927,2
+NaHAsO4-,NA,NaHAsO4-,aq,MA07,MA10,12.Sep.07,-234025,-272938,19.4,11,16.4,4.464,3.12,4.197,-2.908,24.8601,-0.79,1.3274,-1
+KHAsO4-,NA,KHAsO4-,aq,MA07,MA10,12.Sep.07,-238754,-275247,30.7,3.9,26.1,5.7282,6.2078,2.8713,-3.0357,19.1455,-2.2322,1.1561,-1
+MgHAsO4,NA,MgHAsO4,aq,MA07,MA10,12.Sep.07,-282655,-326456,-17.1,-3.4,-0.5,1.6885,-3.6591,7.1076,-2.6278,3.8675,-3.7233,-0.038,0
+CaHAsO4,NA,CaHAsO4,aq,MA07,MA10,12.Sep.07,-306038,-344341,3.5,-5.6,2,2.0228,-2.8426,6.757,-2.6615,2.5879,-4.1694,-0.038,0
+SrHAsO4,NA,SrHAsO4,aq,MA07,MA10,12.Sep.07,-307750,-344917,9.8,-8.1,2.4,2.0851,-2.6905,6.6917,-2.6678,1.1155,-4.6827,-0.038,0
+MnHAsO4,NA,MnHAsO4,aq,MA07,MA10,12.Sep.07,-229564,-268033,0.7,-2.1,2.7,2.1148,-2.618,6.6606,-2.6708,4.592,-3.4707,-0.038,0
+FeHAsO4,NA,FeHAsO4,aq,MA07,MA10,12.Sep.07,-196961,-237958,-8.9,-5.9,-0.9,1.6263,-3.8112,7.1729,-2.6215,2.3717,-4.2448,-0.038,0
+CoHAsO4,NA,CoHAsO4,aq,MA07,MA10,12.Sep.07,-187516,-229240,-10.7,-5.8,-3.2,1.3102,-4.5832,7.5044,-2.5896,2.4302,-4.2244,-0.038,0
+NiHAsO4,NA,NiHAsO4,aq,MA07,MA10,12.Sep.07,-185083,-227995,-14.7,-9.7,-5.7,0.9749,-5.4021,7.8559,-2.5557,0.1514,-5.0188,-0.038,0
+CuHAsO4,NA,CuHAsO4,aq,MA07,MA10,12.Sep.07,-160044,-200797,-6.7,-3.7,-2.6,1.3964,-4.3727,7.414,-2.5983,3.6572,-3.7966,-0.038,0
+ZnHAsO4,NA,ZnHAsO4,aq,MA07,MA10,12.Sep.07,-209827,-252128,-9.9,-3.4,-2.4,1.4251,-4.3025,7.3838,-2.6012,3.8733,-3.7213,-0.038,0
+PbHAsO4,NA,PbHAsO4,aq,MA07,MA10,12.Sep.07,-180119,-214509,22.2,-10.7,3.7,2.2585,-2.267,6.5099,-2.6853,-0.4328,-5.2225,-0.038,0
+AlHAsO4+,NA,AlHAsO4+,aq,MA07,MA10,12.Sep.07,-295884,-343378,-46.1,-37.3,-8.2,1.0572,-5.2011,7.7697,-2.564,-4.1613,-10.6336,1.242,1
+FeHAsO4+,NA,FeHAsO4+,aq,MA07,MA10,12.Sep.07,-188188,-232211,-34.7,-23.4,-4.9,1.4545,-4.2306,7.353,-2.6042,2.37,-7.8022,1.0694,1
+NaAsO4-2,NA,NaAsO4-2,aq,MA07,MA10,12.Sep.07,-223700,-253943,48.5,-38.4,-17,0.2824,-7.0935,8.5822,-2.4858,6.8433,-10.8648,2.5085,-2
+KAsO4-2,NA,KAsO4-2,aq,MA07,MA10,12.Sep.07,-228428,-249049,84,-45.5,-9.64,1.1121,-5.0669,7.712,-2.5696,-2.2416,-12.307,1.9714,-2
+MgAsO4-,NA,MgAsO4-,aq,MA07,MA10,12.Sep.07,-271474,-307316,9.64,-55,-25.98,-1.3284,-11.0278,10.2713,-2.3232,-12.33,-14.2311,1.3662,-1
+CaAsO4-,NA,CaAsO4-,aq,MA07,MA10,12.Sep.07,-294913,-323114,37.4,-57.2,-25.5,-1.3685,-11.1259,10.3134,-2.3191,-17.4821,-14.6772,1.0531,-1
+SrAsO4-,NA,SrAsO4-,aq,MA07,MA10,12.Sep.07,-296243,-323239,43.9,-59.7,-25.41,-1.3889,-11.1758,10.3349,-2.317,-19.8655,-15.1905,0.9562,-1
+MnAsO4-,NA,MnAsO4-,aq,MA07,MA10,12.Sep.07,-218289,-247805,30.7,-53.7,-25.37,-1.2541,-10.8464,10.1934,-2.3307,-14.5434,-13.9785,1.339,-1
+FeAsO4-,NA,FeAsO4-,aq,MA07,MA10,12.Sep.07,-186668,-218541,21.7,-57.5,-26.07,-1.3653,-11.1181,10.3101,-2.3194,-15.504,-14.7525,1.2932,-1
+CoAsO4-,NA,CoAsO4-,aq,MA07,MA10,12.Sep.07,-177190,-210481,17.6,-57.4,-26.53,-1.4073,-11.2205,10.3541,-2.3152,-14.8722,-14.7322,1.3555,-1
+NiAsO4-,NA,NiAsO4-,aq,MA07,MA10,12.Sep.07,-176304,-211320,11.8,-61.3,-27.01,-1.4432,-11.3083,10.3918,-2.3116,-16.3404,-15.5266,1.4434,-1
+CuAsO4-,NA,CuAsO4-,aq,MA07,MA10,12.Sep.07,-151743,-183607,23.1,-55.3,-26.4,-1.4178,-11.2463,10.3651,-2.3141,-14.418,-14.3044,1.2716,-1
+ZnAsO4-,NA,ZnAsO4-,aq,MA07,MA10,12.Sep.07,-200121,-233853,18.9,-55,-26.36,-1.3907,-11.1799,10.3366,-2.3169,-13.6104,-14.229,1.3358,-1
+PbAsO4-,NA,PbAsO4-,aq,MA07,MA10,12.Sep.07,-169793,-194437,54.9,-62.3,-25.16,-1.4108,-11.2291,10.3577,-2.3148,-22.9414,-15.7303,0.7904,-1
+AlAsO4,NA,AlAsO4,aq,MA07,MA10,12.Sep.07,-285558,-330011,-35.9,-60.2,-9.75,0.418,-6.7624,8.44,-2.4995,-29.3427,-15.3014,-0.038,0
+FeAsO4,NA,FeAsO4,aq,MA07,MA10,12.Sep.07,-177862,-218546,-23.5,-84.8,-13.09,-0.0391,-7.8787,8.9193,-2.4533,-43.7161,-20.3124,-0.038,0
+NaH2AsO3,NA,NaH2AsO3,aq,MA07,MA10,12.Sep.07,-203270,-228832,39.7,28.4,32.7,6.2236,7.4178,2.3518,-3.0857,22.4338,2.7495,-0.038,0
+AgH2AsO3,NA,AgH2AsO3,aq,MA07,MA10,12.Sep.07,-123526,-147071,44.3,25.8,33,6.2709,7.5332,2.3022,-3.0905,20.9088,2.2178,-0.038,0
+MgH2AsO3+,NA,MgH2AsO3+,aq,MA07,MA10,12.Sep.07,-251410,-286183,-11.3,41.3,9.9,3.3617,0.4276,5.353,-2.7967,36.9078,5.3772,0.7149,1
+CaH2AsO3+,NA,CaH2AsO3+,aq,MA07,MA10,12.Sep.07,-274922,-301872,17.1,36.4,13.8,3.7486,1.3726,4.9473,-2.8358,30.0706,4.3735,0.2853,1
+SrH2AsO3+,NA,SrH2AsO3+,aq,MA07,MA10,12.Sep.07,-275601,-300702,25.8,30.7,14.5,3.8032,1.506,4.89,-2.8413,25.5459,3.2185,0.1538,1
+BaH2AsO3+,NA,BaH2AsO3+,aq,MA07,MA10,12.Sep.07,-276315,-297936,40.1,25.6,19.9,4.4634,3.1185,4.1977,-2.908,20.5926,2.1872,-0.0628,1
+CuH2AsO3+,NA,CuH2AsO3+,aq,MA07,MA10,12.Sep.07,-134368,-164924,3,40.5,6.5,2.8237,-0.8865,5.9172,-2.7424,34.4453,5.2122,0.499,1
+PbH2AsO3+,NA,PbH2AsO3+,aq,MA07,MA10,12.Sep.07,-153138,-174063,42.8,24.7,16.5,3.9918,1.9667,4.6922,-2.8603,19.6811,2.0039,-0.1047,1
+AlH2AsO3+2,NA,AlH2AsO3+2,aq,MA07,MA10,12.Sep.07,-266611,-309612,-55.5,25.5,-15.6,0.2882,-7.0795,8.5761,-2.4864,38.8545,2.1567,1.929,2
+FeH2AsO3+2,NA,FeH2AsO3+2,aq,MA07,MA10,12.Sep.07,-154392,-192413,-39.1,56.8,-7.3,1.3321,-4.5295,7.4813,-2.5918,54.8314,8.5274,1.6797,2

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2017-10-17 06:44:12 UTC (rev 260)
@@ -1,4 +1,4 @@
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\ No newline at end of file

Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd	2017-10-16 14:30:48 UTC (rev 259)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd	2017-10-17 06:44:12 UTC (rev 260)
@@ -107,7 +107,7 @@
 ```
 
 This [vignette](index.html), produced on `r Sys.Date()`, documents the sources of thermodynamic data in CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
-Running `data(thermo)` creates the default database, which is present in the R session as `thermo$obigt`.
+Running `data(thermo)` creates the default database (`thermo$obigt`) in the R session.
 
 The sections below correspond to CSV data files that are stored in the `extdata/OBIGT` package directory and read by `data(thermo)` (except for Optional Data).
 In each section, the primary references (`ref1` in `thermo$obigt`) are listed in chronological order.
@@ -236,9 +236,10 @@
 
 ### `r setfile("SUPCRTBL.csv")`
 ```{r SUPCRTBL, results="asis", echo=FALSE}
-cat("<a href=http://www.indiana.edu/~hydrogeo/supcrtbl.html>SUPCRTBL</a> is a modification and data update for the SUPCRT92 package ([Zimmer et al., 2016](https://doi.org/10.1016/j.cageo.2016.02.013)). Data for SiO<sub>2(*aq*)</sub> were updated to reflect the higher observed solubility of quartz compared to the SUPCRT92 dataset, and other aqueous species and minerals relevant to environmental geochemistry were added.\n\n")
-cat("NOTE 1: The SUPCRTBL modifications apply the [Holland and Powell (2011)](https://doi.org/10.1111/j.1525-1314.2010.00923.x) equations and dataset for minerals, which are not available in CHNOSZ. As an alternative to the default dataset of [Helgeson et al. (1978)](http://www.worldcat.org/oclc/13594862), CHNOSZ offers the [Berman (1988)](https://doi.org/10.1093/petrology/29.2.445) formulation (see the **Solids** / **Berman** section of this vignette).\n")
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 260

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