[CHNOSZ-commits] r447 - in pkg/CHNOSZ: . demo inst inst/extdata/OBIGT vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Apr 16 08:07:09 CEST 2019 

Author: jedick
Date: 2019-04-16 08:07:08 +0200 (Tue, 16 Apr 2019)
New Revision: 447

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/aluminum.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
OBIGT: use dawsonite Cp coefficients from Tutolo et al., 2014


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-04-16 05:25:57 UTC (rev 446)
+++ pkg/CHNOSZ/DESCRIPTION	2019-04-16 06:07:08 UTC (rev 447)
@@ -1,6 +1,6 @@
 Date: 2019-04-16
 Package: CHNOSZ
-Version: 1.3.1-27
+Version: 1.3.1-28
 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/demo/aluminum.R
===================================================================
--- pkg/CHNOSZ/demo/aluminum.R	2019-04-16 05:25:57 UTC (rev 446)
+++ pkg/CHNOSZ/demo/aluminum.R	2019-04-16 06:07:08 UTC (rev 447)
@@ -66,7 +66,7 @@
 coeffs <- c(-1, -2, 1, 1, 1, 1)
 Daw1 <- subcrt(species, coeffs, T = T)
 # calculation 2: dawsonite with Cp = 0
-mod.obigt("dawsonite", Cp = 0)
+mod.obigt("dawsonite", Cp = 0, a = 0, b = 0, c = 0)
 Daw2 <- subcrt(species, coeffs, T = T)
 ## plot the calculated logKs
 lines(T, Daw1$out$logK, lwd = 1.5)
@@ -76,7 +76,7 @@
 ## add legend and title
 title(main = describe.reaction(Daw1$reaction), cex.main = 0.95)
 legend("bottomright", lty = c(0, 0, 1, 2), pch = c(1, 4, NA, NA), col = c("black", "red", "black", "red"), lwd = c(1, 1, 1.5, 1),
-       bty = "n", cex = 0.9, legend = c("Ben\u00e9z\u00e9th et al., 2007", "SUPCRTBL", "CHNOSZ", 'mod.obigt("dawsonite", Cp = 0)'))
+       bty = "n", cex = 0.9, legend = c("Ben\u00e9z\u00e9th et al., 2007", "SUPCRTBL", "CHNOSZ", 'Cp(dawsonite) = 0'))
 legend("topleft", c("Dawsonite solubility", "After Zimmer et al., 2016 Fig. 2"), bty = "n")
 reset()
 

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-04-16 05:25:57 UTC (rev 446)
+++ pkg/CHNOSZ/inst/NEWS	2019-04-16 06:07:08 UTC (rev 447)
@@ -43,6 +43,8 @@
 - Rename demo/go-IU.R to aluminum.R, and add plots from Tutolo et al.,
   2014.
 
+- OBIGT: use dawsonite Cp coefficients from Tutolo et al., 2014.
+
 CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2019-04-16 05:25:57 UTC (rev 446)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2019-04-16 06:07:08 UTC (rev 447)
@@ -1,4 +1,4 @@
-ý7zXZ  æÖ´F !   t/å£à8mE] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;ù"ß“<²ëbï¨gò;ø¥Kä‡¥Šfœ‘1Æw?oz†ÆCþ­aì]IØŽ¨Ý5i‡* p0n¥z†Çj€„Öz‡—ݺ¬b‘UÊeÇÿÀ=´AC⥸ëO7±ŠkÕJُ£Ñ…fþ¿dβfm³¿Ü?pzh¤øÙè[¦O‹†Z®‹ëôžò¯thHÚïk“¼s²3Ç3jn4L¬ëŠ¸JÄ6FPánzºxþŠŸ@ñÛp•:þàM¦¥§éç$üxÇÞ!V‘QrSîÈk‡ü[7„§oŠCŒÀÁùúî%k<ÇÍššõé§å
+ý7zXZ  æÖ´F !   t/å£à8uO] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;ù"ß“<²ëbï¨gò;ø¥Kä‡¥Šfœ‘1Æw?oz†ÆCþ­aì]IØŽ¨Ý5i‡* p0n¥z†Çj€„Öz‡—ݺ¬b‘UÊeÇÿÀ=´AC⥸ëO7±ŠkÕJُ£Ñ…fþ¿dβfm³¿Ü?pzh¤øÙè[¦O‹†Z®‹ëôžò¯thHÚïk“¼s²3Ç3jn4L¬ëŠ¸JÄ6FPánzºxþŠŸ@ñÛp•:þàM¦¥§éç$üxÇÞ!V‘QrSîÈk‡ü[7„§oŠCŒÀÁùúî%k<ÇÍššõé§å
 Û¤#)á×|¸M­(s6{œÑ%ÃNfîr×éâÅš’ß(û>û›Q¶È»7ä.42&l{Ú3ŠºøaŽéžZñr¬»Xe<ëªü\TzÓŠ\¯ÊâSˆ"»uÌçÀ*í}b
 §ÁÊñïΑÚ#=39xŽ'`Q\1J–äs'Ar2
 ,­
@@ -38,5 +38,5 @@
  g®<p°€.”;ýòXòú!Xƒ Kuc ™Ê¶ÓÉë<ÑÇmåò{tÏ^û¼fÂTû3Рc sҍžÚÚU\}¬x×qC‹úÿü&iÑí.@œñf3ûôÖZ®ú³à¹÷ªSÉR¨ˆEh…¯ølbÒ–ýR“×-x«éó[„;o%ڪؐ¶ý±•BE8t:]:„ÏÉ8›sˆu>QoË(lýN»å¹<$>ɏ3OÜRÚ>-$“Cöÿ½êÙ¼HYëðcƒ¬¬úI³‹9¦HôC‹(Žˆ–T†«¨sß.b(WÂVq:v Vg[7Qq3ƒú¦{§m$xt£ÿ‚:dKfZ…‹RxP%@wÂÝþˆc2©_ÙO^ÙoP$íœDŠQyM3Â	R›]uÊišêø_[ƒF5(X2ŠçÜÈ;@õþ#5;'Z¢#}…,	ŒÄÞãg"fÏ?'§‰ô)¡ V¡Ë‹ÞË”Å*%çæœÙ
 ¥µíX¡â\D–]â¶Tú	i…rPз4Nx
 ¯\V°Mc¦ˆÉ Iïºð)쐏ÁÊe¿¯Ïôâ4‡
-©ËHn¹«mŠå?ã@i”¶Ž¡,E”£‘6i2¬«¿zõq‘è«wb•…V´;F†3-½úR‡É
-VQâ#Î'|¬ÅCË2ô¯Ü§”#‰TL}`¿ZKD#†9„›¿ÂÓv}V²nvmD&öi7<¼¨yp    ê;¥Ó6r á$îp  eË]H±Ägû    YZ
\ No newline at end of file
+©ËHn¹«mŠå?ã@i”®/£fÑêP¬ê¥?~Ý'\aYe
+@¨•¼µœÒ‹s"Ð`¾Ðˆªu€¿‹F¢âP¦:±\_¤¬œòïtóž÷×Á‹,ã’ÞuSÑu·°`þð¦ï™†ÕâŸ6¡ô	¥@$_XV•Î¡C,n{ù¾dµ®ð!  ÿÏá4Ö”‹ ë$öp  s—k|±Ägû    YZ
\ No newline at end of file

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2019-04-16 05:25:57 UTC (rev 446)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2019-04-16 06:07:08 UTC (rev 447)
@@ -5,7 +5,6 @@
 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
-FSR76,"M. J. Ferrante et al.",1976,"U. S. Bureau of Mines Report of Investigations 8129","dawsonite Cp (value at 25 °C as listed by @BPAH07; not present in spronsbl.dat)",http://www.worldcat.org/oclc/932914138
 HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals 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
 HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",http://www.worldcat.org/oclc/13594862
@@ -59,6 +58,7 @@
 PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964
 RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",http://pubs.er.usgs.gov/publication/b2131
 RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",http://pubs.er.usgs.gov/publication/b2131
+RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",http://pubs.er.usgs.gov/publication/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

Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib	2019-04-16 05:25:57 UTC (rev 446)
+++ pkg/CHNOSZ/vignettes/obigt.bib	2019-04-16 06:07:08 UTC (rev 447)
@@ -765,13 +765,13 @@
 }
 
 @Article{Ste01,
-  author        = {Stefánsson, Andri},
-  journal       = {Chemical Geology},
-  title         = {{D}issolution of primary minerals of basalt in natural waters. {I}. {C}alculation of mineral solubilities from 0°{C} to 350°{C}},
-  year          = {2001},
-  volume        = {172},
-  pages         = {225--250},
-  doi           = {10.1016/S0009-2541(00)00263-1},
+  author    = {Stefánsson, Andri},
+  journal   = {Chemical Geology},
+  title     = {{D}issolution of primary minerals of basalt in natural waters. {I}. {C}alculation of mineral solubilities from 0°{C} to 350°{C}},
+  year      = {2001},
+  volume    = {172},
+  pages     = {225--250},
+  doi       = {10.1016/S0009-2541(00)00263-1},
 }
 
 @Incollection{SAJ00,
@@ -1449,6 +1449,21 @@
   source    = {Crossref},
 }
 
+ at Article{TKSS14,
+  author    = {Tutolo, Benjamin M. and Kong, Xiang-Zhao and Seyfried, William E., Jr. and Saar, Martin O.},
+  journal   = {Geochimica et Cosmochimica Acta},
+  title     = {{I}nternal consistency in aqueous geochemical data revisited: {A}pplications to the aluminum system},
+  year      = {2014},
+  volume    = {133},
+  pages     = {216--234},
+  doi       = {10.1016/j.gca.2014.02.036},
+  sn        = {0016-7037; 1872-9533},
+  z8        = {0},
+  z9        = {0},
+  zb        = {0},
+  zs        = {0},
+}
+
 @Article{VGT92,
   author    = {Vidal, O. and Goffé, B. and Theye, T.},
   journal   = {Journal of Metamorphic Geology},

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