[CHNOSZ-commits] r208 - in pkg/CHNOSZ: . data inst inst/extdata/OBIGT man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Sep 23 11:50:08 CEST 2017 

Author: jedick
Date: 2017-09-23 11:50:07 +0200 (Sat, 23 Sep 2017)
New Revision: 208

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv.xz
   pkg/CHNOSZ/man/subcrt.Rd
   pkg/CHNOSZ/man/water.Rd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
remove H2O,gas (metastable steam)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-09-23 03:35:48 UTC (rev 207)
+++ pkg/CHNOSZ/DESCRIPTION	2017-09-23 09:50:07 UTC (rev 208)
@@ -1,6 +1,6 @@
 Date: 2017-09-23
 Package: CHNOSZ
-Version: 1.1.0-6
+Version: 1.1.0-7
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2017-09-23 03:35:48 UTC (rev 207)
+++ pkg/CHNOSZ/data/refs.csv	2017-09-23 09:50:07 UTC (rev 208)
@@ -20,10 +20,8 @@
 SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",https://doi.org/10.1016/0016-7037(88)90181-0
 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
 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
-Joh92a,"J. W. Johnson",1992,"personal communication","steam, Cp represented by the Maier-Kelley equation",
 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 "",
-SPRONS92.3,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file",""Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."",
 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
 Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",https://doi.org/10.1016/0016-7037(93)90542-5
 Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",https://doi.org/10.1016/0016-7037(93)90542-5

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-09-23 03:35:48 UTC (rev 207)
+++ pkg/CHNOSZ/inst/NEWS	2017-09-23 09:50:07 UTC (rev 208)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-5 (2017-08-29)
+CHANGES IN CHNOSZ 1.1.0-7 (2017-09-23)
 --------------------------------------
 
 - water.lines() now works for diagrams of Eh, pe, logfO2, logaO2,
@@ -17,6 +17,10 @@
 - Add 'tol' argument to equil.reaction() (convergence tolerance for
   uniroot).
 
+- Remove H2O(gas) from the database (taken from SUPCRT92), as it gives
+  inconsistent results for metastable steam (Zavarin et al., 2016,
+  LLNL-TR-701407, doi: 10.2172/1325873).
+
 CHANGES IN CHNOSZ 1.1.0 (2017-05-04)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv.xz	2017-09-23 03:35:48 UTC (rev 207)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv.xz	2017-09-23 09:50:07 UTC (rev 208)
@@ -1,6 +1,5 @@
-ý7zXZ  æÖ´F !   t/å£àªÂ] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;ù"ß“<²ëbï¨gò;ø¥Kä‡¥Šfœ‘1Æw?oz†ÆCþ­aì]IØŽ¨Ý5i‡*s@/¦L¶ŸeßEJd1
+ý7zXZ  æÖ´F !   t/å£à.}] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;ù"ß“<²ëbï¨gò;ø¥Kä‡¥Šfœ‘1Æw?oz†ÆCþ­aì]IØŽ¨Ý5i‡*s@/¦L¶ŸeßEJd1
 ~HtÙ«ëˆpÃ<¤¬×ŒüzG–ÕÛ?ÄŸÌžÞ¡e©½X¼ÐÓE¡agÐQ–9ÊÇW=Bã
 ZPî¬
-Æès¬ôŠVN÷I,ÆœçËsÍź3¥\\Þ6’Ž^ï*6û›_NÜ`øËaî>¥ÌÇ!ïáÀ{îßQ,ì0ªuY­˜Ô dý¼Þ…×Ö…f¶²ù¼ì°Y¤©	fÈbQ£‹ÑÍ*ДvtP‹t°ŽÝ?‘Ž¥âÀÚ7ÅA+ø‹a0"c1›ÛÍ<êEâ²9ªEú<騅,£3â“UšÆ0†ƒ_pYp'ð›SÆö·”ô—Rf¤«Ž†WŽ<ìÞ:Vâçá'äSg4ˆ‘—n¿rž' ½ÝAOü¸‹Il+ž—q¥DÒ,‘–âÐwÎöæ¥Ñ§Å’Né3ãÍeöÿ&cãÊ7‡Ç u|Xå-_£—:´H$=øœäμcäc+r÷&§,Ø[Šî|ijE‚Ôpó›è°ÍÞ¶…Y)‰Ço-Ü Ê;Î\}qž¥zb¹¥«¥~£ö^)1žÍ=3ù¥WðÜO”Ùû	 ÀQ" ÀÝÿ’¨x(Rô1x¿YÕy…ÌìvIÒjÏçŠÉ¦¼fR_º ¼˜Ç2Ûb#IKgzA£žð‚*³´©Ûµ.¢"/
-¬€ì%¨“w
-ÒuQTDeø&MùÂð?-â9*¸<n‹«2ølÜI|C¨Î»lYŸÑQìto…ÜjÂ$Ê?*¸úë+8ˤ$f&µ⌙Ù÷cLÐÄöC:¹=Ô@   €Ð¬k"òv Þ«  Ëÿ·²±Ägû    YZ
\ No newline at end of file
+Æès¬ôŠVN÷I,ÆœçËsÍź3¥\\Þ6’Ž^ï*6û›_NÜ`øËaî>¥ÌÇ!ïáÀ{îßQ,ì0ªuY­˜Ô dý¼Þ…×Ö…f¶²ù¼ì°Y¤©	fÈbQ£‹ÑÍ*ДvtP‹t°ŽÝ?‘Ž¥âÀÚ7ÅA+ø‹a0"c1›ÛÍ<êEâ²9ªEú<騅,£3â“UšÆ0†ƒ_pYp'ð›SÆö·”ô—Rf¤«Ž†WŽ<ìÞ:Vâçá'äSg4ˆ‘—n¿rž' ½ÝAOü¸‹Il+ž—q¥DÒ,‘–âÐwÎöæ¥Ñ§Å’Né3ãÍeöÿ&cãÊ7‡Ç u|Xå-_£—:´H$=øœäμcäc+r÷&§,Ø[Šî|ijE‚Ôpó›è°ÍÞ¶…Y)‰Ço-Ü Ê;Î\}qž¥zb¹¥«¥~£ö^)1žÍ=3ù¥WðÜQå‰ÌÚ”®@V×ÎÆ"ÓN§ï÷U?ª`ÞA•1ÂàÀÉDîÕbecŸ¯~Xñcn±ÕŽ
+8¿.©xD'°n;ûe{-Ù¨‹. ݍuäw1Ø3§ø\—ø     )kqÀýÞ#X ™¯  8J.±Ägû    YZ
\ No newline at end of file

Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd	2017-09-23 03:35:48 UTC (rev 207)
+++ pkg/CHNOSZ/man/subcrt.Rd	2017-09-23 09:50:07 UTC (rev 208)
@@ -147,17 +147,17 @@
 # to initiate an infinite loop
 basis(c("H2O", "H2S", "O2", "H+"))
 subcrt(c("HS-", "SO4-2"), c(-1, 1))
-# note the next one is a non-reaction
-# (products same as reactants)
-subcrt("H2O", 1)
+# because O2,aq is in the basis, this is a non-reaction
+# (O2,aq to O2,aq)
+subcrt("O2", 1, "aq")
 # but this one auto-balances into a reaction
-# (water to steam)
-subcrt("H2O", 1, "gas")
+# (O2,aq to O2,gas)
+subcrt("O2", 1, "gas")
 # properties of a species and a formation 
 # reaction for that species
 subcrt("C2H5OH")    # species
 basis("CHNOS")
-subcrt("C2H5OH",1)  # reaction
+subcrt("C2H5OH", 1) # reaction
 
 ## properties of mineral phases
 # properties of phase species

Modified: pkg/CHNOSZ/man/water.Rd
===================================================================
--- pkg/CHNOSZ/man/water.Rd	2017-09-23 03:35:48 UTC (rev 207)
+++ pkg/CHNOSZ/man/water.Rd	2017-09-23 09:50:07 UTC (rev 208)
@@ -80,7 +80,6 @@
 These calculations are based on data and equations of Levelt-Sengers et al., 1983, Haar et al., 1984, and Johnson and Norton, 1991, among others (see Johnson et al., 1992).
 A value of \code{P} set to \samp{Psat} refers to one bar below 100 \eqn{^{\circ}}{°}C, otherwise to the vapor-liquid saturation pressure at temperatures below the critical point (\samp{Psat} is not available at temperatures above the critical point).
 \code{water.SUPCRT92} provides a limited interface to the FORTRAN subroutine; some functions provided there are not made available here (e.g., using variable density instead of pressure, or calculating the properties of steam).
-The properties of steam in CHNOSZ, as in \acronym{SUPCRT92}, are calculated using general equations for crystalline, gaseous and liquid species (\code{\link{cgl}}).
 
 The stated temperature limits of validity of calculations in \code{water.SUPCRT92} are from the greater of 0 \eqn{^{\circ}}{°}C or the melting temperature at pressure, to 2250 \eqn{^{\circ}}{°}C (Johnson et al., 1992).
 Valid pressures are from the greater of zero bar or the melting pressure at temperature to 30000 bar.

Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib	2017-09-23 03:35:48 UTC (rev 207)
+++ pkg/CHNOSZ/vignettes/obigt.bib	2017-09-23 09:50:07 UTC (rev 208)
@@ -197,13 +197,6 @@
   doi           = {10.2113/gsecongeo.80.5.1365},
 }
 
- at TechReport{Joh92a,
-  author        = {Johnson, J. W.},
-  title         = {{P}ersonal calculation},
-  institution   = {Earth Sciences Dept., Lawrence Livermore National Lab, Livermore, CA},
-  year          = {1992},
-}
-
 @Article{JOH92,
   author        = {Johnson, James W. and Oelkers, Eric H. and Helgeson, Harold C.},
   journal       = {Computers \& Geosciences},

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