[CHNOSZ-commits] r532 - in pkg/CHNOSZ: inst inst/extdata/OBIGT inst/extdata/thermo vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Jun 27 02:51:15 CEST 2020 

Author: jedick
Date: 2020-06-27 02:51:15 +0200 (Sat, 27 Jun 2020)
New Revision: 532

Modified:
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
OBIGT: correct formulas for some As-bearing minerals; add references for H2O, e-, H+


Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2020-06-20 02:59:49 UTC (rev 531)
+++ pkg/CHNOSZ/inst/NEWS	2020-06-27 00:51:15 UTC (rev 532)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.6-9 (2020-06-20)
+CHANGES IN CHNOSZ 1.3.6-9 (2020-06-21)
 --------------------------------------
 
 - OBIGT/organic_aq.csv, AkDi.csv, DEW_aq.csv: Remove "methane" as the
@@ -19,12 +19,23 @@
 - OBIGT/inorganic_aq.csv: Update arsenopyrite with data from Naumov et
   al., 1974 (via Unitherm).
 
+- OBIGT/inorganic_cr.csv: Correct formula for number of H2O in some
+  As-bearing minerals.
+
 - Install bibtex file (docs/obigt.bib) for use in logKcalc package.
 
-- TODO: thermo.refs(): add date, write 'thermo()$obigt'.
+- TODO: thermo.refs(): add current date, write 'thermo()$obigt'.
 
 - TODO: use degree sign in messages from subcrt().
 
+- TODO: rename obigt.Rmd to OBIGT.Rmd.
+
+- TODO: fix error in expr.species("AsO4---")
+
+- TODO: describe default logact in basis.Rd
+
+- TODO: change references for water for different models (IAPWS, DEW)
+
 CHANGES IN CHNOSZ 1.3.6 (2020-03-16)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv.xz	2020-06-20 02:59:49 UTC (rev 531)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv.xz	2020-06-27 00:51:15 UTC (rev 532)
@@ -1,3 +1 @@
-ý7zXZ  æÖ´F !   t/å£à2 °] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;õJT&ŸÝ´V±ë\‚Œ¦Øº7š[JÍ“û5Aç±^iKde³/ñQWs™Ì8 f3s´}OÅ×z¥Rí“Þ]Iƒ|¬kŒ“vÒÉñ•s‚ìÎ}.g™>±¿2
-õ`þ† ÙL“BÌ‘d8jŽ
-à‰è³$ YˆrçþìD•kž¼êôP®?ìÀ èVow¢ ̳  ¸\”±Ägû    YZ
\ No newline at end of file
+ý7zXZ  æÖ´F !   t/å£àB É] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;õJT&ŸÝ´V±ë\‚Œ¦Øº7š[JÍ“û5Aç±^iKde³/ñQWs™Ì8 f3s´}OÅ×z¥Rí“Þ]Iƒ|¬k¢âó8ç½2Ýô€™ ºú50(~ƒW\:ƒ\R.™ ß4_ô:ÉÂýba¬€Š”×ØZÛ#„§ÿ6$Ó¹‹ëž,„,Qæâ ›€&83;vµ ‡/òß»–ÍÀ    Ruí(®Ñ åà  ÚâÀß±Ägû    YZ
\ No newline at end of file

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2020-06-20 02:59:49 UTC (rev 531)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2020-06-27 00:51:15 UTC (rev 532)
@@ -1,4 +1,4 @@
-ý7zXZ  æÖ´F !   t/å£à;ÂÀ] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;õJT&ŸÝ´V±ë\‚Œ¦Øº7š[JÍ“û5Aç±^iKde³/ñQWs™Ì8 f3s´}OÅÕÐ×Wh 1è@,O՝ÄØñ4̪ÙI¸”
+ý7zXZ  æÖ´F !   t/å£à;¾] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;õJT&ŸÝ´V±ë\‚Œ¦Øº7š[JÍ“û5Aç±^iKde³/ñQWs™Ì8 f3s´}OÅÕÐ×Wh 1è@,O՝ÄØñ4̪ÙI¸”
 k×&ªßóƒ™Ôi×øtÍsiÛ¢©¯óóª]1û¹ËÿÔC)9$~6Ӎd‡VìGêÐèp1®¹ Ãw\â,Ðþ0×<§wý¹á,ÑË|ñƒ3H€AÃXvÔŒÿÞ?g²øÐD•'b¹ªbØè)BÐw 1E¨È T—!®„JuqM†dk¿¢.I¾óÒOKZ"c‘)…9©1c*7hö?d€Ì_Òì`¹}-bgÊ‹aË©+Z«€…Gç†0P'¿¬YÚ×ö"¾aZ·ù4Uaf(LjÚSÞ‡òÔ&áIyۍí|ûQ Uˆ:,lêH¾!ÉÓa#õsÍ¥]q«ìNå…ÜÚ<¥ò™<Ô½³X
 ™©gÎ]²)
 ÔÔTõÑTþšùDsQœ`—û4>¤«(•_9EK˜fð õO+«ò, cñ!0½ŸQd~¨û@§NÞ¨NNÄ»þטЫ.Ý/±‹îÛPL
@@ -30,7 +30,6 @@
 j'H:ª7Ž´ì5x¼ŽßÖz	zSR©ë0A-ù©L¡mŒÞJŽ•vÀ5@ÅÀ…(„~Ð>c¬øé&·šåˆw	y¦yVþSý
 Ø“Ó’hoÓ¸74E„N"ÊãNhxân‡OɱWZVì1V®Æ=ا#“UiV†C™xW4LÖ(•`à1â	ÿ¹îû¢—OJŽ&>^k‘l7dO×ôGÿ_šRüxÙÄï5§OX' Ýý‚o*Íh:TÔU·ä	iSwIqƱ®ž‰@Ùfû5Ð<ZnƒÄj&eëêÇarÕɉ%jºlŠ#q’Ô~bÃßt.qlIóV˜v;M$ãÃéŽ<ZVPï•ó¸å Á/kJ–}lmFv)ãÃÍ;)¥jY¶ ¢=ŠræG+
 ™
-–xjåX]Šok¿8ÎYe¬„Ouj©'41Ñ€'*&µ€p ¥‚ãt+á¤ãt­0 Ž}Œˆ8e½1RUHÞÁ7Y-~ÂNinw‹@rf´É!µW&ÍNßáGS+ÖšÈe+c¡è=ÌcÍ™ŽÉ“£š(²#wuÚ’õb.ànÌWÒÛ…”/µÓœ_ÏÓÞt´Ö´ãviÏ1?+X6Gâߨ]ûÈ"‘\äÐ[2À¾ÔV‚q¯»ÿåI|D½lB3=DN÷׬yf¤¢*që:¦ô°1™"²°²—O-X#*^Û£’î²b¯yPßH“Ãhªs/\•B¹w¢(ΑLdöˆ*Níû^ÂÚßß`§ÿªJŠd†ªZÒô•³x{öýú(öÔÖÒ¾iäÑ9RËÂüñC‘ë(„
-4³áŽ¤Ç"•,ÃóËfØŠaäG,{"½"»\Ñ 
-®®®ã«LÀE„’é¼gàNçzd]ò´E'ˆ¿‰8ÊÕÀ`ö8¥s¥Nó#xn»þcÓÖ¨7˜ÊÏß‚œq%ät/íz‰>äìÔ<ÂÑ<D)Ž	á·õb÷),he]”Í4A?Ð+™)̲÷û@ƒ‰¨F at s^Ø}¶@êþÿJÆšq÷H<¿7gë~ :R[N1T9)v…(Ò‹ÇôºZF°ËÐÀå¾ëie>!+ȧÇ4X/ÚiҚ㟸اÑagu£.K%Xî—uÏUþ©¢ÿ3!*KÅ s
-„öšQ Ü%Ãw  À—Κ±Ägû    YZ
\ No newline at end of file
+–xjåX]Šok¿8ÎYe¬„Ouj©'41Ñ€'*&µ€p ¥‚ãt+á¤ãt­0 Ž}Œˆ8e½1RUHÞÁ7Y-~ÂNinw‹@rf´É!µW&ÍNßáGS+ÖšÈe+c¡è=ÌcÍ™ŽÉ“£š(²#wuÚ’õb.ànÌWÒÛ…”/µÓœ_ÏÓÞt´Ö´ãviÏ1?+X6Gâߨ]ûÈ"‘\äÐ[2À¾ÔV‚q¯»ÿåI|D½lB3=DN÷׬yf¤¢UY¦9h©VÇåvšÃÊw™Á¹Î`ªŽ\ó~Û*Œ4»xßï–M†»OS%²å#f-èùŒUô¼˜ìpèµ\·ý»¬%&7_’ã‹„Ú	œ=bA‡ù‚Ù‘e¥=üNB}…&`¿.ì\QMDI'÷$®–§ëë—ê’TŠÓ¤”³@3xʹcýIòÎ8ß´Åó ØuÈýe¾òVë7!Lº¿í„¨¦f˲]		f€ARuV9ÚÝ6>ˆæö@–Hc	ã…ëºþ}¸ƒ51=|(-aëÉü~.DÝ"épûhñÉç>^‹æh[ˬä¼mJ•„nûÆ%4®	q¿ÌèÂÿ=öÑF²%á ×Z†«ZO>î×EƒûˆþB-Ù¢ye
+”L§­€åî»­§Ñbf)”UâK‘À!-!ƒ­ásFQ9vo’
+G^·¾]JÅ®ij»Ç­•4   É°M¥²“Øh Ú%Ãw  Ýt—L±Ägû    YZ
\ No newline at end of file

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-06-20 02:59:49 UTC (rev 531)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-06-27 00:51:15 UTC (rev 532)
@@ -20,6 +20,7 @@
 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
 WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",MgSO<sub>4</sub>,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
 BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,https://doi.org/10.1016/0016-7037(83)90066-2
+HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables","H<sub>2</sub>O",http://www.worldcat.org/oclc/858456124
 Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845
 JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365
 RA87,"E. J. Reardon and D. K. Armstrong",1987,"Geochim. Cosmochim. Acta 51, 63-72","celestite GHS",https://doi.org/10.1016/0016-7037(87)90007-X
@@ -41,6 +42,7 @@
 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` data file",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html
+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
@@ -90,6 +92,7 @@
 TZA97,"B. R. Tagirov, A. V. Zotov and N. N. Akinfiev",2007,"Geochim. Cosmochim. Acta 61, 4267-4280","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00274-3
 ST97,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylammonium chloride HKF parameters",https://doi.org/10.1023/A:1022977006327
 ST97.1,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylamine HKF parameters",https://doi.org/10.1023/A:1022977006327
+proton,"OBIGT",1997,"Hydrogen-ion convention","'The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature' [@JOH92]",http://chnosz.net
 HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6
 HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6
 RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1
@@ -149,6 +152,7 @@
 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
 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
+electron,"OBIGT",2006,"See CHNOSZ vignette obigt.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",http://chnosz.net
 Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain",
 MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes; linked to properties of arsenate and arsenite from @SSWS97",https://doi.org/10.1007/s00254-006-0578-5
 SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)<sup>+2</sup>",http://geopig.asu.edu/?q=tools

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

Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib	2020-06-20 02:59:49 UTC (rev 531)
+++ pkg/CHNOSZ/vignettes/obigt.bib	2020-06-27 00:51:15 UTC (rev 532)
@@ -1192,16 +1192,16 @@
   pages         = {172},
 }
 
- at Incollection{NA03,
-  author        = {Nordstrom, D. Kirk and Archer, Donald G.},
-  booktitle     = {Arsenic in Groundwater},
-  publisher     = {Springer},
-  title         = {{A}rsenic thermodynamic data and environmental geochemistry},
-  year          = {2003},
-  editor        = {Welch, Alan H. and Stollenwerk, Kenneth G.},
-  pages         = {1--25},
-  address       = {New York},
-  doi           = {10.1007/0-306-47956-7_1},
+ at InCollection{NA03,
+  author    = {Nordstrom, D. Kirk and Archer, Donald G.},
+  booktitle = {Arsenic in Groundwater},
+  publisher = {Springer},
+  title     = {{A}rsenic thermodynamic data and environmental geochemistry},
+  year      = {2003},
+  address   = {New York},
+  editor    = {Welch, Alan H. and Stollenwerk, Kenneth G.},
+  pages     = {1--25},
+  doi       = {10.1007/0-306-47956-7_1},
 }
 
 @Article{LMR06,
@@ -1525,3 +1525,19 @@
   note      = {Translated by George J. Soleimani},
   url       = {https://trove.nla.gov.au/work/22192707},
 }
+
+ at TechReport{electron,
+  author      = {OBIGT},
+  institution = {OBIGT database in CHNOSZ},
+  title       = {Non-zero entropy of the electron based on the hydrogen-ion convention},
+  year        = {2006},
+  note        = {Because the standard thermodynamic properties of the formation reaction of H+ (0.5H2(g) = H+ + e-) are defined to be zero, the standard entropy of e- is half that of H2(g).},
+}
+
+ at TechReport{proton,
+  author      = {OBIGT},
+  institution = {OBIGT database in CHNOSZ},
+  title       = {Hydrogen-ion convention},
+  year        = {1997},
+  note        = {"The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature" [@JOH92]},
+}

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