[CHNOSZ-commits] r529 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/thermo man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Jun 17 07:35:12 CEST 2020 

Author: jedick
Date: 2020-06-17 07:35:12 +0200 (Wed, 17 Jun 2020)
New Revision: 529

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   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/man/palply.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
OBIGT: update arsenopyrite using data from Naumov et al., 1971


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-06-15 23:52:13 UTC (rev 528)
+++ pkg/CHNOSZ/DESCRIPTION	2020-06-17 05:35:12 UTC (rev 529)
@@ -1,6 +1,6 @@
 Date: 2020-06-16
 Package: CHNOSZ
-Version: 1.3.6-6
+Version: 1.3.6-7
 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/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2020-06-15 23:52:13 UTC (rev 528)
+++ pkg/CHNOSZ/inst/NEWS	2020-06-17 05:35:12 UTC (rev 529)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.6-4 (2020-06-16)
+CHANGES IN CHNOSZ 1.3.6-6 (2020-06-16)
 --------------------------------------
 
 - OBIGT/organic_aq.csv, AkDi.csv, DEW_aq.csv: Remove "methane" as the
@@ -16,6 +16,9 @@
 - subcrt(): change 'action.unbalanced' argument to 'autobalance',
   which provides the ability to prevent autobalancing.
 
+- OBIGT/inorganic_aq.csv: Update arsenopyrite with data from Naumov et
+  al., 1974 (via Unitherm).
+
 CHANGES IN CHNOSZ 1.3.6 (2020-03-16)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2020-06-15 23:52:13 UTC (rev 528)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2020-06-17 05:35:12 UTC (rev 529)
@@ -1,4 +1,4 @@
-ý7zXZ  æÖ´F !   t/å£à;¶ ] 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;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¸”
 k×&ªßóƒ™Ôi×øtÍsiÛ¢©¯óóª]1û¹ËÿÔC)9$~6Ӎd‡VìGêÐèp1®¹ Ãw\â,Ðþ0×<§wý¹á,ÑË|ñƒ3H€AÃXvÔŒÿÞ?g²øÐD•'b¹ªbØè)BÐw 1E¨È T—!®„JuqM†dk¿¢.I¾óÒOKZ"c‘)…9©1c*7hö?d€Ì_Òì`¹}-bgÊ‹aË©+Z«€…Gç†0P'¿¬YÚ×ö"¾aZ·ù4Uaf(LjÚSÞ‡òÔ&áIyۍí|ûQ Uˆ:,lêH¾!ÉÓa#õsÍ¥]q«ìNå…ÜÚ<¥ò™<Ô½³X
 ™©gÎ]²)
 ÔÔTõÑTþšùDsQœ`—û4>¤«(•_9EK˜fð õO+«ò, cñ!0½ŸQd~¨û@§NÞ¨NNÄ»þטЫ.Ý/±‹îÛPL
@@ -30,5 +30,7 @@
 j'H:ª7Ž´ì5x¼ŽßÖz	zSR©ë0A-ù©L¡mŒÞJŽ•vÀ5@ÅÀ…(„~Ð>c¬øé&·šåˆw	y¦yVþSý
 Ø“Ó’hoÓ¸74E„N"ÊãNhxân‡OɱWZVì1V®Æ=ا#“UiV†C™xW4LÖ(•`à1â	ÿ¹îû¢—OJŽ&>^k‘l7dO×ôGÿ_šRüxÙÄï5§OX' Ýý‚o*Íh:TÔU·ä	iSwIqƱ®ž‰@Ùfû5Ð<ZnƒÄj&eëêÇarÕɉ%jºlŠ#q’Ô~bÃßt.qlIóV˜v;M$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|D½o’SEúύ†äÒ)WÅlÐ6à%öÊCû ýMÉ«~ÑË~9®´&,u»v‘ÜcÇ»j¶O)dË79À@DO)¹±Ü/6Î.Åüíû&ü€åCÅ™}#ã›<Ô@ÒMˆÚø׶÷ÞèòE±Õ•P[=±á1ɪ<¼_Ô|°Í‚âü.öä1Ûj-ÃϱӍ«¨ãêC)b?>½Màßg=§[‹"Ëxp˜·{Édd2#p±äÃ	¨âäQÉ/„©tpdÕkôrpòЭ’Rôx
->»o{Ý“Þ¾$’µM"ÛùK¥´N…/Ök"n¼Ë¥ùç:óOÂÉn]ÇÆ£PbEÙ…µIbÏLa«¡Å¸}™ø¢!ðydÔ<j+-E‘Ä˜í¬†ÏÏBAZ¦6AÙç”O—,Í	æ,†wºÚ£‚—NƲ¬óXߍQ;ªÔË”\qˆ]ЁAIVn ½ß€ÌT{ ¼%·w  Q¯gv±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¤¢*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

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-06-15 23:52:13 UTC (rev 528)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-06-17 05:35:12 UTC (rev 529)
@@ -6,6 +6,7 @@
 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
 BK73,"I. Barin and O. Knacke",1973,"Thermochemical Properties of Inorganic Substances","scheelite Cp",http://www.worldcat.org/oclc/695258
+NRK74,"G. B. Naumov, B. N. Ryzhenko and I. L. Khodakovskii",1974,"Handbook of Thermodynamic Data, U. S. Geological Survey, Water Resources Division","arsenopyrite",https://trove.nla.gov.au/work/22192707
 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
@@ -35,7 +36,6 @@
 Pol90,"D. A. Polya",1990,"Trans. Inst. Min. Metall. 99, B120-B124","ferberite G, S and Cp (Cp coefficients multiplied by 4.184 to convert to J, as listed in @WS00, but who give a 2nd term that is off by a factor of 10). Cp at 25 °C is from @LW74.",
 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",boehmite,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
@@ -106,6 +106,7 @@
 MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253",actinides,http://rimg.geoscienceworld.org/content/38/1/221
 PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5
 PSK99.1,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","Al(Mal)<sup>+</sup> and Al(Oxal)<sup>+</sup>",https://doi.org/10.1016/S0016-7037(99)00146-5
+SB99,"Yu. Shvarov and E. Bastrakov",1999,"HCh: A software package for geochemical equilibrium modelling. User's Guide","data from HCh Unitherm database",http://pid.geoscience.gov.au/dataset/ga/25473
 SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",https://doi.org/10.2138/rmg.2000.40.9
 WS00,"S. A. Wood and I. M. Samson",2000,"Econ. Geol. 95, 143-182","scheelite and ferberite; GHS and V of scheelite and V of ferberite are from @RHF78.",https://doi.org/10.2113/gsecongeo.95.1.143
 AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,https://doi.org/10.1016/S0016-7037(01)00707-4

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

Modified: pkg/CHNOSZ/man/palply.Rd
===================================================================
--- pkg/CHNOSZ/man/palply.Rd	2020-06-15 23:52:13 UTC (rev 528)
+++ pkg/CHNOSZ/man/palply.Rd	2020-06-17 05:35:12 UTC (rev 529)
@@ -19,7 +19,7 @@
 }
 
 \details{
-\code{palply} is a wrapper function to run \code{parallel::parLapply} (see \code{\link[parallel]{clusterApply}}) if length of \code{X} > \code{\link{thermo}$opt$paramin} and multiple cores are available, otherwise it runs \code{\link{lapply}}.
+\code{palply} is a wrapper function to run \code{\link[parallel:clusterApply]{parallel::parLapply}} if length of \code{X} > \code{\link{thermo}$opt$paramin} and multiple cores are available, otherwise it runs \code{\link{lapply}}.
 Note that \code{parLapply} is called with \code{methods} set to FALSE.
 If lots of package startup messages are created when running \code{parallel::makeCluster} (which is called by \code{palply}), it can probably be stopped by adding a test for \code{\link{interactive}} sessions around any \code{\link{library}} commands in the \code{\link{Rprofile}}.
 }

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2020-06-15 23:52:13 UTC (rev 528)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2020-06-17 05:35:12 UTC (rev 529)
@@ -36,6 +36,7 @@
 o2 <- "O<sub>2</sub>"
 h2o <- "H<sub>2</sub>O"
 sio2 <- "SiO<sub>2</sub>"
+ch4 <- "CH<sub>4</sub>"
 ```
 
 ```{r setup, include=FALSE}
@@ -248,25 +249,39 @@
 
 <span style="color:green">`info()`</span> provides an interface to the thermodynamic database packaged with CHNOSZ.
 Suppose you are interested in the thermodynamic properties of aqueous methane.
-You can search for the species by name:
-```{r info_methane}
-info("methane")
+Because the database is assembled with aqueous species first, they take precedence over other states.
+Searching by chemical formula alone gives the first matching species, in this case aqueous methane:
+```{r info_CH4}
+info("CH4")
 ```
 
-The number that is returned can be used to identify the species for other functions in CHNOSZ.
-Multiple entries exist for methane; the index of the `aq` (aqueous) species is returned by default.
-```{marginfigure}
-This convention applies to organic species, but for inorganic species, the English name refers to the gas (<span style='color:green'>`info("oxygen")`</span>) while the chemical formula is used to identify the aqueous species (<span style='color:green'>`info("O2")`</span>).
+The number that is returned is the species index in the database.
+A second argument can be used to specify a physical state with lower precedence:
+```{r info_CH4_gas}
+info("CH4", "gas")
 ```
-A second argument can be used to specify a different physical state:
-```{r info_methane_gas}
-info("methane", "gas")
+
+While some species are identified only by chemical formula, others have distinct names (in English) listed in the database.
+For `r ch4` and inorganic substances that are represented by both gaseous and aqueous forms, the name is applied only to the gas.
+However, the names of organic substances other than methane are applied to aqueous species, which have precedence, and those in other states.
+The following commands get the species indices for some common gases:
+```{r info_names_gas}
+info("methane")
+info("oxygen")
+info("carbon dioxide")
 ```
 
+A special case is sulfur; the name refers to both the native mineral, which has precedence, and the gas.
+These two phases can be identifed with the formulas S<sub>2</sub> and S, respectively.
+```{r info_sulfur_S2}
+info("sulfur")
+info("S2")
+```
+
 Taking the species number of aqueous methane returned by <span style="color:green">`info()`</span>, use the function again to retrieve the set of standard molal thermodynamic properties and equations of state parameters:
-```{r info_imethane, message=FALSE}
-imethane <- info("methane")
-info(imethane)
+```{r iCH4, message=FALSE}
+iCH4 <- info("CH4")
+info(iCH4)
 ```
 
 Liquid water is species number 1; it has NA entries in the database because specialized functions are used to compute its properties:
@@ -297,22 +312,22 @@
 
 ## Counting elements, chemical formulas, <span style="color:green">`ZC()`</span>
 
-Continuing with the example of methane, let's look at its chemical formula:
-```{r info_imethane_formula, message=FALSE}
-info(imethane)$formula
+Continuing with the example of aqueous methane, let's look at its chemical formula:
+```{r info_CH4_formula, message=FALSE}
+info(iCH4)$formula
 ```
 
 We can use <span style="color:green">`makeup()`</span> to count the elements in the formula, followed by <span style="color:green">`as.chemical.formula()`</span> to rewrite the formula on one line:
-```{r makeup_imethane}
-makeup(imethane)
-as.chemical.formula(makeup(imethane))
+```{r makeup_iCH4}
+makeup(iCH4)
+as.chemical.formula(makeup(iCH4))
 ```
 
 For organic species, a calculation of the average oxidation state of carbon (`r zc`) is possible given the species index, chemical formula, or elemental count:
-```{r ZC_imethane, message=FALSE}
-ZC(imethane)
-ZC(info(imethane)$formula)
-ZC(makeup(imethane))
+```{r ZC_iCH4, message=FALSE}
+ZC(iCH4)
+ZC(info(iCH4)$formula)
+ZC(makeup(iCH4))
 ```
 
 # Calculating thermodynamic properties
@@ -359,17 +374,17 @@
 The default units of temperature, pressure, and energy are °C, bar, and calories.
 The functions <span style="color:red">`T.units()`</span>, <span style="color:red">`P.units()`</span>, and <span style="color:red">`E.units()`</span> can be used to change the units used by various functions in CHNOSZ.
 What is the Gibbs energy in J/mol of aqueous methane at 298.15 K and 0.1 MPa?
-```{r units_methane, message=FALSE}
+```{r units_CH4, message=FALSE}
 T.units("K")
 P.units("MPa")
 E.units("J")
-subcrt("methane", T = 298.15, P = 0.1)$out$methane$G
+subcrt("CH4", T = 298.15, P = 0.1)$out$CH4$G
 ```
 
 A related function, <span style="color:green">`convert()`</span>, can be used to convert given values between units.
 Let's convert the standard Gibbs energy of aqueous methane listed in the database from cal/mol to J/mol:
 ```{r convert_G, message=FALSE}
-convert(info(info("methane"))$G, "J")
+convert(info(info("CH4"))$G, "J")
 ```
 
 As expected, we get the same result from both operations.
@@ -459,14 +474,14 @@
 By identifying species *other than* the basis species, the reactions will be automatically balanced.
 This produces the balanced reaction for acetoclastic methanogenesis:
 ```{r subcrt_acetoclastic, message=FALSE}
-subcrt(c("acetate", "methane"), c(-1, 1))$reaction
+subcrt(c("acetate", "CH4"), c(-1, 1))$reaction
 ```
 
 We can similarly consider reactions for hydrogenotrophic methanogenesis as well as acetate oxidation (without production of methane):
 ```{r subcrt_methanogenesis, message=FALSE}
 acetate_oxidation <- subcrt("acetate", -1)
-hydrogenotrophic <- subcrt("methane", 1)
-acetoclastic <- subcrt(c("acetate", "methane"), c(-1, 1))
+hydrogenotrophic <- subcrt("CH4", 1)
+acetoclastic <- subcrt(c("acetate", "CH4"), c(-1, 1))
 ```
 
 Use <span style="color:green">`describe.reaction()`</span> to write the reactions on a plot:
@@ -505,7 +520,7 @@
 basis(c("H2", "pH"), c(-3.92, 7.3))
 ```
 ```{r affinity_acetoclastic, message=FALSE}
-subcrt(c("acetate", "methane"), c(-1, 1),
+subcrt(c("acetate", "CH4"), c(-1, 1),
        c("aq", "gas"), logact = c(-3.4, -0.18), T = 55, P = 50)$out
 ```
 
@@ -512,7 +527,7 @@
 The new `A` column shows the affinity; the other columns are unaffected and still show the standard-state properties.
 Let's repeat the calculation for hydrogenotrophic methanogenesis.
 ```{r affinity_hydrogenotrophic, message=FALSE}
-subcrt("methane", 1, "gas", logact = -0.18, T = 55, P = 50)$out
+subcrt("CH4", 1, "gas", logact = -0.18, T = 55, P = 50)$out
 ```
 
 Under the specified conditions, the affinities of hydrogenotrophic and acetoclastic methanogenesis are somewhat greater than and less than 20 kJ, respectively.
@@ -525,7 +540,7 @@
 To make the code neater, we write a function that can run any of the reactions:
 ```{r rxnfun, message=FALSE}
 rxnfun <- function(coeffs) {
-  subcrt(c("acetate", "methane"), coeffs,
+  subcrt(c("acetate", "CH4"), coeffs,
          c("aq", "gas"), logact = c(-3.4, -0.18), T = 55, P = 50)$out
 }
 ```
@@ -747,17 +762,17 @@
 rb <- read.csv(file, check.names = FALSE)
 ```
 
-We take a selection of the species from Shock and Canovas (2010) with activities equal to 10<sup>-6</sup>; methane is assigned an activity of 10<sup>-3</sup>.
+We take a selection of the species from Shock and Canovas (2010) with activities equal to 10<sup>-6</sup>; aqueous `r ch4` is assigned an activity of 10<sup>-3</sup>.
 We will write the synthesis reactions of organic species in terms of these basis species:
 ```{marginfigure}
-The constant activity of methane is a simplification of the calculation reported by Shock and Canovas (2010).
-The code here could be expanded to vary the activity of methane.
+The constant activity of CH<sub>4</sub> is a simplification of the calculation reported by Shock and Canovas (2010).
+The code here could be expanded to vary the activity of CH<sub>4</sub>.
 ```
 ```{r rainbow_species, results="hide"}
 basis(c("CO2", "H2", "NH4+", "H2O", "H2S", "H+"))
 species("CH4", -3)
 species(c("adenine", "cytosine", "aspartic acid", "deoxyribose",
-          "methane", "leucine", "tryptophan", "n-nonanoic acid"), -6)
+          "CH4", "leucine", "tryptophan", "n-nonanoic acid"), -6)
 ```
 
 Now we can calculate affinities along the transect of changing temperature and activities of five basis species.

Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib	2020-06-15 23:52:13 UTC (rev 528)
+++ pkg/CHNOSZ/vignettes/obigt.bib	2020-06-17 05:35:12 UTC (rev 529)
@@ -1,4 +1,3 @@
-% Encoding: UTF-8
 
 @Article{AML10,
   author        = {Accornero, Marina and Marini, Luigi and Lelli, Matteo},
@@ -90,13 +89,13 @@
 }
 
 @Article{CS16,
-  author        = {Canovas, III, Peter A. and Shock, Everett L.},
-  journal       = {Geochimica et Cosmochimica Acta},
-  title         = {{G}eobiochemistry of metabolism: {S}tandard state thermodynamic properties of the citric acid cycle},
-  year          = {2016},
-  volume        = {195},
-  pages         = {293--322},
-  doi           = {10.1016/j.gca.2016.08.028},
+  author    = {Canovas, III, Peter A. and Shock, Everett L.},
+  journal   = {Geochimica et Cosmochimica Acta},
+  title     = {{G}eobiochemistry of metabolism: {S}tandard state thermodynamic properties of the citric acid cycle},
+  year      = {2016},
+  pages     = {293--322},
+  volume    = {195},
+  doi       = {10.1016/j.gca.2016.08.028},
 }
 
 @Article{DSM+97,
@@ -475,8 +474,8 @@
   journal   = {Earth and Planetary Science Letters},
   title     = {{S}tability and abundance of the trisulfur radical ion in hydrothermal fluids},
   year      = {2015},
+  pages     = {298--309},
   volume    = {411},
-  pages     = {298--309},
   doi       = {10.1016/j.epsl.2014.11.035},
   issn      = {0012-821X},
 }
@@ -763,6 +762,14 @@
   doi       = {10.1016/S0016-7037(96)00339-0},
 }
 
+ at Manual{SB99,
+  title        = {{HC}h: {A} software package for geochemical equilibrium modelling. {U}ser's {G}uide},
+  author       = {Shvarov, Yuri and Bastrakov, Evgeniy},
+  organization = {Australian Geological Survey Organisation, Record 1999/25},
+  year         = {1999},
+  url          = {http://pid.geoscience.gov.au/dataset/ga/25473},
+}
+
 @Article{Ste01,
   author    = {Stefánsson, Andri},
   journal   = {Chemical Geology},
@@ -875,14 +882,14 @@
 }
 
 @Article{ZZL+16,
-  author        = {Kurt Zimmer and Yilun Zhang and Peng Lu and Yanyan Chen and Guanru Zhang and Mehmet Dalkilic and Chen Zhu},
-  journal       = {Computers \& Geosciences},
-  title         = {{SUPCRTBL}: {A} revised and extended thermodynamic dataset and software package of {SUPCRT}92},
-  year          = {2016},
-  volume        = {90},
-  pages         = {97--111},
-  doi           = {10.1016/j.cageo.2016.02.013},
-  issn          = {0098-3004},
+  author    = {Kurt Zimmer and Yilun Zhang and Peng Lu and Yanyan Chen and Guanru Zhang and Mehmet Dalkilic and Chen Zhu},
+  journal   = {Computers \& Geosciences},
+  title     = {{SUPCRTBL}: {A} revised and extended thermodynamic dataset and software package of {SUPCRT}92},
+  year      = {2016},
+  pages     = {97--111},
+  volume    = {90},
+  doi       = {10.1016/j.cageo.2016.02.013},
+  issn      = {0098-3004},
 }
 
 @Book{CWM89,
@@ -999,14 +1006,14 @@
 }
 
 @Article{LCT17,
-  author        = {Alexander R. Lowe and Jenny S. Cox and Peter R. Tremaine},
-  journal       = {Journal of Chemical Thermodynamics},
-  title         = {{T}hermodynamics of aqueous adenine: {S}tandard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from ${T}$ = 278.15 {K} to 393.15 {K}},
-  year          = {2017},
-  volume        = {112},
-  pages         = {129--145},
-  doi           = {10.1016/j.jct.2017.04.005},
-  issn          = {0021-9614},
+  author    = {Alexander R. Lowe and Jenny S. Cox and Peter R. Tremaine},
+  journal   = {Journal of Chemical Thermodynamics},
+  title     = {{T}hermodynamics of aqueous adenine: {S}tandard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from ${T}$ = 278.15 {K} to 393.15 {K}},
+  year      = {2017},
+  pages     = {129--145},
+  volume    = {112},
+  doi       = {10.1016/j.jct.2017.04.005},
+  issn      = {0021-9614},
 }
 
 @Misc{DEW17,
@@ -1197,17 +1204,6 @@
   doi           = {10.1007/0-306-47956-7_1},
 }
 
- at TechReport{BN91,
-  author        = {Ball, James W. and Nordstrom, D. Kirk},
-  title         = {{U}ser's manual for {WATEQ}4{F}, with revised thermodynamic data base and text cases for calculating speciation of major, trace, and redox elements in natural waters},
-  institution   = {U. S. Geological Survey},
-  year          = {1991},
-  type          = {Open-File Report},
-  number        = {91-183},
-  address       = {Menlo Park, CA},
-  url           = {https://pubs.er.usgs.gov/publication/ofr91183},
-}
-
 @Article{LMR06,
   author    = {Langmuir, Donald and Mahoney, John and Rowson, John},
   journal   = {Geochimica et Cosmochimica Acta},
@@ -1490,9 +1486,9 @@
   journal   = {Geomicrobiology Journal},
   title     = {{T}he energetics of fermentation in natural settings},
   year      = {2019},
-  volume    = {36},
   number    = {6},
   pages     = {492-505},
+  volume    = {36},
   doi       = {10.1080/01490451.2019.1573278},
 }
 
@@ -1519,3 +1515,13 @@
   issn      = {0021-9614},
 }
 
+ at Book{NRK74,
+  author    = {Naumov, Georgii Borisovich and Ryzhenko, Boris Nikolaevich and Khodakovskii, Igor L'vovich},
+  editor    = {Ivan Barnes and Velma Speltz},
+  publisher = {U.S. Geological Survey, Water Resources Division},
+  title     = {Handbook of Thermodynamic Data},
+  year      = {1974},
+  address   = {Menlo Park, Calif.},
+  note      = {Translated by George J. Soleimani},
+  url       = {https://trove.nla.gov.au/work/22192707},
+}

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