[CHNOSZ-commits] r385 - in pkg/CHNOSZ: . data inst inst/extdata/OBIGT tests/testthat vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Feb 8 04:57:39 CET 2019 

Author: jedick
Date: 2019-02-08 04:57:38 +0100 (Fri, 08 Feb 2019)
New Revision: 385

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
   pkg/CHNOSZ/tests/testthat/test-recalculate.R
   pkg/CHNOSZ/tests/testthat/test-revisit.R
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
OBIGT: recalculate GHS of HSiO3-


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-02-07 06:43:08 UTC (rev 384)
+++ pkg/CHNOSZ/DESCRIPTION	2019-02-08 03:57:38 UTC (rev 385)
@@ -1,6 +1,6 @@
-Date: 2019-02-07
+Date: 2019-02-08
 Package: CHNOSZ
-Version: 1.1.3-92
+Version: 1.1.3-93
 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/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2019-02-07 06:43:08 UTC (rev 384)
+++ pkg/CHNOSZ/data/refs.csv	2019-02-08 03:57:38 UTC (rev 385)
@@ -43,6 +43,7 @@
 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
 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
 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
@@ -122,10 +123,10 @@
 LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","pyridine and piperidine",https://doi.org/10.1016/j.tca.2006.06.008
 DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",https://doi.org/10.5194/bg-3-311-2006
 DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acids HKF parameters",https://doi.org/10.5194/bg-3-311-2006
-DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides Cp, V, and HKF c1, c2, omega parameters",https://doi.org/10.5194/bg-3-311-2006
+DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides Cp, V, and HKF c<sub>1</sub>, c<sub>2</sub>, ω parameters",https://doi.org/10.5194/bg-3-311-2006
 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 c1, c2, omega 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
 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
@@ -162,7 +163,7 @@
 SLOP15.4,"E. L. Shock et al.",2015,"slop15.dat computer data file","adipic acid and n-dodecanoate: "Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of @Sho95."",http://geopig.asu.edu/?q=tools
 SLOP15.5,"E. L. Shock et al.",2015,"slop15.dat computer data file","n-octanoate: "Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of @Sho95."",http://geopig.asu.edu/?q=tools
 SLOP15.6,"E. L. Shock et al.",2015,"slop15.dat computer data file",""Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements."",http://geopig.asu.edu/?q=tools
-SLOP15.7,"E. L. Shock et al.",2015,"slop15.dat computer data file","hexanol, heptanol, and octanol: "Minor differences in Gibbs energy, entropy, omega, a<sub>1</sub>, a<sub>2</sub>, a<sub>3</sub>, a<sub>4</sub> and c<sub>1</sub> values compared to @SH90."",http://geopig.asu.edu/?q=tools
+SLOP15.7,"E. L. Shock et al.",2015,"slop15.dat computer data file","hexanol, heptanol, and octanol: "Minor differences in Gibbs energy, entropy, ω, a<sub>1</sub>, a<sub>2</sub>, a<sub>3</sub>, a<sub>4</sub> and c<sub>1</sub> values compared to @SH90."",http://geopig.asu.edu/?q=tools
 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
@@ -176,6 +177,7 @@
 CHNOSZ.8,"J. M. Dick",2017,"CHNOSZ package documentation","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here.",http://chnosz.net
 CHNOSZ.9,"J. M. Dick",2019,"CHNOSZ package documentation","recalculated values of Cp (those in @AKAE19 appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)",http://chnosz.net
 CHNOSZ.10,"J. M. Dick",2019,"CHNOSZ package documentation","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: replace Ti with Tl",http://chnosz.net
+CHNOSZ.11,"J. M. Dick",2019,"CHNOSZ package documentation","HSiO<sub>3</sub><sup>-</sup>: GHS recalculated by adding difference from SiO<sub>2</sub> [@SSH97] to updated values for SiO<sub>2</sub> [@AS04]",http://chnosz.net
 LCT17,"A. R. Lowe, J. S. Cox and P. R. Tremaine",2017,"J. Chem. Thermodynamics 112, 129-145","adenine HKF parameters",https://doi.org/10.1016/j.jct.2017.04.005
 DEW17,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","other data from Aqueous Species Table in spreadsheet (see detailed references there)",http://www.dewcommunity.org
 DEW17.1,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for ions",http://www.dewcommunity.org

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-02-07 06:43:08 UTC (rev 384)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-02-08 03:57:38 UTC (rev 385)
@@ -26,6 +26,8 @@
 
 - check reverse dependencies: ecipex and canprot packages
 
+- vignettes/obigt.bib: check correct year for CHNOSZ reference
+
 - documentation links: after installation, run doc/mklinks.sh
   and insert the modified anintro.html in the package
 

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-02-07 06:43:08 UTC (rev 384)
+++ pkg/CHNOSZ/inst/NEWS	2019-02-08 03:57:38 UTC (rev 385)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-92 (2019-02-07)
+CHANGES IN CHNOSZ 1.1.3-93 (2019-02-08)
 ---------------------------------------
 
 BUG FIXES
@@ -162,13 +162,21 @@
 - Update aqueous Au species with data from Akinfiev and Zotov, 2001
   and 2010, and Pokrovski et al., 2014.
 
-- Move superseded data for aqueous Au species to SLOP98.csv.
+- Move SUPCRTBL updates (As and Al minerals and aqueous species and
+  SiO2(aq)) into default database.
 
-- Move SUPCRTBL updates into default database.
+- Values for SiO2(aq) are taken from Apps and Spycher, 2004. Thanks
+  to John Apps for providing the document.
 
-- Add test-recalculate.R to check that some recalculated values are
-  correctly entered in OBIGT.
+- Recalculate GHS for HSiO3- by adding difference from SiO2(aq)
+  (Sverjensky et al., 1997) to updated values for SiO2(aq).
 
+- Add test-recalculate.R to check that recalculated values are correctly
+  entered in OBIGT.
+
+- Move superseded data for aqueous Au, As, and Al species, SiO2 and
+  HSiO3- to OBIGT/SLOP98.csv.
+
 - Add or update glycine, diglycine, and triglycine (zwitterions and
   ions), and diketopiperazine, [Gly] and [UPBB] groups from Kitadai,
   2014.

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv	2019-02-07 06:43:08 UTC (rev 384)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv	2019-02-08 03:57:38 UTC (rev 385)
@@ -16,6 +16,7 @@
 AsO2-,AsO2-,AsO2-,aq,"SSWS97.3 [S98]",NA,11.Nov.97,-83650,-102540,9.7,-28,6.9,3.2101,0.0554,5.7305,-2.7812,3.4104,-8.7381,1.482,-1
 HAsO2,HAsO2,HAsO2,aq,"SSWS97.3 [S98]",NA,11.Nov.97,-96240,-109110,30.1,2.9,28.3,5.5984,5.8913,3.428,-3.0224,6.799,-2.4438,-0.1158,0
 SiO2,NA,SiO2,aq,"SHS89.1 [S92]",NA,13.Jan.89,-199190,-209775,18,-76.1,16.1,1.9,1.7,20,-2.7,29.1,-51.2,0.1291,0
+HSiO3-,HSiO3-,HSiO3-,aq,"SSH97 [S98]",NA,18.Sep.97,-242801,-273872,5,-21,5,2.9735,-0.5158,5.9467,-2.7575,8.1489,-7.3123,1.5511,-1
 AlO2-,AlO2-,AlO2-1,aq,"SSWS97.4 [S98]",NA,07.Nov.97,-198693,-222125,-7.22,-11.9,10,3.7221,3.9954,-1.5879,-2.9441,15.2391,-5.4585,1.7418,-1
 Al+3,Al+3,Al+3,aq,"SSWS97.4 [S98]",NA,07.Nov.97,-115609,-126834,-77.7,-32.5,-44.4,-3.3802,-17.0071,14.5185,-2.0758,10.7,-8.06,2.753,3
 AlOH+2,AlOH+2,AlOH+2,aq,"SSWS97.4 [S98]",NA,13.Nov.97,-165475,-183300,-44.2,13.2,-2.2,2.0469,-2.7813,6.8376,-2.6639,29.7923,-0.3457,1.7247,2

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2019-02-07 06:43:08 UTC (rev 384)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2019-02-08 03:57:38 UTC (rev 385)
@@ -1,4 +1,4 @@
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+ý7zXZ  æÖ´F !   t/å£à¯z4] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù¦cL;ù"ß“<²ëbï¨gò;ø¥Kä‡¥Šfœ‘1Æw?oz†ÆCþ­aì]IØŽ¨Ý5i‡*U9œ—X‘×0wã±tGƒØꪥáýA¢æ‰Yo|Û¥XQ$š{ÃÏ16¦\O¯]x¡˜t%	­È~žA2Ké¹¾2õ
 MöÜØëÏuÛ2CŒûÄíl,Úó̉ßÿߏ ðõë>I“,t¿bßPK“ä7t(emA-PÄQÀ]Æå ›·8Ó.fø|šöÛ©–V[ŒÖ΃è=ÍñK¸®ŸÿVTmÚ­~vwÓ
 æ2/	ѺWaÓás¼-×ú‚¢Îp÷lVsýáêÕH˜¬ßuÔ˜ÑÍ ´%²XFöîk#ÅéêÁ£‹èÿ»+ÒÇ(ë¬m5’St5”FaÉa˜jNч8®à€>zÄÑ°3MwS%Ò°ÛÚøî+Ú3x¨Ù`cw`¤; $ˆ(‘ú¼ý˜‘P„>’ºµ•>ò1b¿ºòQAÊáîÈç?>6o©=Ñ-¥((äŠpNÚÊÄiéä¹ÒVOL·A®˜ï9	c»E3ñÂXPœ¸¾¼kjsÌóíÔ¢Y!&oÀªw(Ò•3³+ƒ"îՁÖÈ–ò;	±£R6eW뒍Î![˼îör¿O>O»<¹‡ÕÆË&œÔºYÙ²r|¸¡à‘kzí:$’6"&x´½{D71Ÿt\Z’²8dwï>*ˆh\t½”€tyï‚)BÿîêÂn<ç9lÓN!3ŒÏÙz	'  ú}Üí±nVº,0uVeåÈÜ›¼¤
 jò–˜×Þ|Bƒ´d^7&KK¾-
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 cŒO_´®2Á¾ƒ&r.w
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Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2019-02-07 06:43:08 UTC (rev 384)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2019-02-08 03:57:38 UTC (rev 385)
@@ -1,4 +1,5 @@
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-ÔpÂiçõ1v×õní$6Ÿ^i¬6ÙaÅ(=O½R^ÿá3a¯éRU¬í„éñö”æÝÌ0eš¨YjQLC4å0/?Ï–2 at VlÆAi6× ªFƒ*§ß¹?ïx²{ ìÙ"VÉï§g0ø°¦Ž€/´]Å-G]*âôê뺰¾ºãþIS"®çé2fÒ±hp p¤ý_ at Aûsá¢(^š«‡šl<›ü­¼í”Å½B(ÄÛ”¡ÕY¯at“F'ß(Û”d¬œs«ØELÕ ³-ž‚rñbÑ„Óšöo¾"ŽäfºÃÞÞ€Ãa—Â-Ù—„ºíü¨dALð€†Ua03çÁÌö®GúÅ¿œeAÀàû¬‚¡»†æêU`àû6LUò6÷¸¿ªýP(—ce¤ËêñŒYIÚ”<CŒ4@Œ+ƒ[Ÿ—¢eßl]‘°<dôç= À I¬üÐôËðX®\|éɈ(¦Õr“5.R¦q#)«Ð¯µÎcÒöÔÃûì`G&;¢aÓʱ¨¬'Kž—;V7„/èMv*jI´‘¥¾—ì¥ =ÌçH³u”)uèQµ2áé­¹,æ˜Î¿*&(o‰^!ÙÂûQNsXôƒp¢˜ É`õ´þH°Çû±ì(	Ú£¥1&WLRbYdÄ>N”·ýÇÔ”ß÷™Ä•ºú0lé·'Á–Úyû ­×.¡ÜœrP  ±²÷‹) ¡Î¦©.¿·.|ÁùL'›BI^BƒZ+hýy÷òH£åÜŠ¼EÈ{¦~×Q¾ö$›3™¯|ÎHÁ®ÃòM+Á•"óÿ·Çä™±AÛ|Q‚ïÂHF.š•<íêàpºà1O­‹zyÆ`ÎÔ§hé  MvôM¹Bܸ:Ø}\¿‚štÉ%J‰	·" tËÂäþTð‹ÿ	¶4Þ:T´³Øf®þÎJ¬ãÊžÔi1\ý!ˉ å‰{?èP[Ó”éŸhi.”QrU<µò
-åÉJÊOÜš‰BÌ8z;úðžSô¸Qï÷š“8Ö—ÒøÃòÀýi|;M9‹—ûC(ÉÜq'tKaöåÆŒ¤ÚÃnüÁ
-¨{LÂ҉츧®ñ+<—iŠh%f/â.ïx:[u‰‡«‘RÐmÎkځ|c¾3Öð
-‹Ê怴˧9Ù…»Omàû.l{º¸	ðÀ/«”\QÂœÅà´Øƾôrh›¾©E¶'ÏNÚÅÝf¬¦Ç‘¢‰›ä¶sð^LGÛ(bBƒ#u”òRòa•U«VtN~B›»8pƒÒiy–u¦$ÖzmW£Áâl#<Ÿo%ïÜoDb•geMP„ô”MYïK„@ùm·û#uE+pKö~½‚Ã	heq‰ÓãAU¤{á==~“´™’”¡½›cò¼C\)ª\zSaçä…î™[ãwL0@~d÷SÐòõ¼ãŒ&Ô©(!m&g ¤a‚'uCLŸÉî+
-ñè^ÈPc⋁ ˜¢m¯æá-ñ#Ióhæ!>ÛFƒ¯Èk*©{la“p9ñ+BC…d°¼ÞþƒH–?j¸ãŨ¨­>zÿm߇péMóÿÙc,~*»ßW5 ³cPÑ£¾bALÿšzÕqr>’^|Ò‰h~äêË0ñÀÑŸ€B8ÂÔ¯Q&îzÅ[í7È£6'Cµ†¹Ì><tzÐ]WH1f×s9›ÅpJ Ó=äÑ·ÿ&²óf‹ÑE…"
-ß *˜bXô;£QØ“XN-6ÀÌ5—õ¹K"¼ˆEdDFáé,†7öHÉ«î%jß¿¿*BhŒ¶Úè
-Ó¢5ãœA!'`O]PÒMÈ›T A,â««°qKSZˆ‘÷
-LšJ¹´£ddªüÃXmxÍBøíB(­ù0žw±g‡b´Âù&Úþàƒß¨ëâú`©@OÆáA ×>©°/â
-44ù/ö͐–À„n˦ˆòñ;B;Ÿ»Æ.Ôð­èH!×âm²Åþã'‰Rx§]
-ðÜwriõ0}—³ÎOƒ'çãÓ:1â¡V€1õ-ÍdÎo¬§éÿ.Ðïò.¼gVðíÚ¹Z-Úsž
-úÉ„¤ýuÁÇq-ÎÚ¹V+,N4ÂVp¯iz.y›f*¨
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 385

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