[CHNOSZ-commits] r609 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Oct 6 12:17:47 CEST 2020 

Author: jedick
Date: 2020-10-06 12:17:46 +0200 (Tue, 06 Oct 2020)
New Revision: 609

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
OBIGT: Add cobalt and Co sulfides


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-10-04 21:50:21 UTC (rev 608)
+++ pkg/CHNOSZ/DESCRIPTION	2020-10-06 10:17:46 UTC (rev 609)
@@ -1,6 +1,6 @@
-Date: 2020-10-05
+Date: 2020-10-06
 Package: CHNOSZ
-Version: 1.3.6-82
+Version: 1.3.6-83
 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.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2020-10-04 21:50:21 UTC (rev 608)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2020-10-06 10:17:46 UTC (rev 609)
@@ -9,7 +9,7 @@
 \newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
 \newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
 
-\section{Changes in CHNOSZ version 1.3.6-82 (2020-10-05)}{
+\section{Changes in CHNOSZ version 1.3.6-83 (2020-10-06)}{
 
   \subsection{MAJOR CHANGES}{
     \itemize{
@@ -80,7 +80,7 @@
     \itemize{
 
       \item Dates in the \samp{date} column have been converted to use ISO 8601
-      extended format (e.g. 2020-08-16). The accessory function \code{today},
+      extended format (e.g. 2020-08-16). The accessory function \code{today()},
       to render the current date using the previous format, has been removed.
 
       \item Update species parameters for the 2019 version of the Deep Earth
@@ -113,6 +113,13 @@
       \href{https://doi.org/10.1016/j.oregeorev.2019.103289}{Liu and Xiao,
         2020}.
 
+      \item \samp{inorganic_cr.csv}: Add linnaeite (Co\s{3}S\s{4}) and
+      Co-pentlandite (Co\s{9}S\s{8}) from
+      \href{https://www.worldcat.org/oclc/801856147}{Vaughan and Craig, 1978}
+      and cattierite (CoS\s{2}) and cobalt from
+      \href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway,
+        1995}.
+
       \item Add GHS for almandine, dickite, fluorphlogopite, glaucophane,
       grunerite, larnite, pyrope (\samp{SUPCRT92.csv}) and bromellite
       (\samp{inorganic_cr.csv}) from
@@ -293,6 +300,8 @@
 
       \item TODO: add wustite from Robie and Hemingway (1995).
 
+      \item TODO: document type = 'loga.balance' (for solubility contours) in ?diagram.
+
     }
   }
 

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2020-10-04 21:50:21 UTC (rev 608)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv	2020-10-06 10:17:46 UTC (rev 609)
@@ -143,3 +143,7 @@
 manganese,NA,Mn,cr,RH95,NA,2020-08-15,J,0,0,32.01,26.19,7.354,0,41.345,-2.7217,313.29,-1.3745,0,0,980
 Mn(OH)2,NA,Mn(OH)2,cr,WEP+82.1,SUF+98,2020-08-15,J,-615000,-695400,99.2,114.7,NA,139.61,-85.25,0,0,0,0,0,700
 huebnerite,NA,MnWO4,cr,RH95,LX20,2020-09-10,J,-1235400,-1337600,132.5,NA,41.89,155.68,91.5,0.53,-1170,-5.31,0,0,1000
+linnaeite,NA,Co3S4,cr,VC78,RH95.8,2020-10-06,cal,-83400,-85800,44.1,39.72,62.55,39.72,0,0,0,0,0,0,937
+cattierite,NA,CoS2,cr,RH95,NA,2020-10-06,J,-145100,-150900,74.8,68.26,25.52,65.82,30.32,-5.87,0,0,0,0,1223
+Co-pentlandite,NA,Co9S8,cr,VC78,MP20,2020-10-06,cal,-199500,-203400,125,96.67,141.78,96.67,0,0,0,0,0,0,1107
+cobalt,NA,Co,cr,RH95,NA,2020-10-06,J,0,0,30.04,24.81,6.67,0,41.844,-1.5646,268.75,-1.6498,0,0,700

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-10-04 21:50:21 UTC (rev 608)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-10-06 10:17:46 UTC (rev 609)
@@ -13,6 +13,7 @@
 RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://pubs.er.usgs.gov/publication/b1452
 RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://pubs.er.usgs.gov/publication/b1452
 RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://pubs.er.usgs.gov/publication/b1452
+VC78,"D. J. Vaughan and J. R. Craig",1978,"Mineral Chemistry of Metal Sulfides","linnaeite and Co-pentlandite",https://www.worldcat.org/oclc/801856147
 PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
 WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
 WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","Mn(OH)<sub>2</sub> (amorphous) and MgSO<sub>4</sub>",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
@@ -58,7 +59,7 @@
 HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P
 PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255
 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","manganese, manganosite, pyrolusite, bixbyite, hausmannite, and heubnerite",https://pubs.er.usgs.gov/publication/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","manganese, manganosite, pyrolusite, bixbyite, hausmannite, heubnerite, cattierite, and cobalt",https://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",https://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",https://pubs.er.usgs.gov/publication/b2131
 RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, pyrope (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
@@ -66,6 +67,7 @@
 RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://pubs.er.usgs.gov/publication/b2131
 RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
 RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",https://pubs.er.usgs.gov/publication/b2131
+RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","linnaeite V",https://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
@@ -275,5 +277,6 @@
 DEW19.6,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(Fe<sup>+2</sup>: HKF a<sub>1</sub>-a<sub>4</sub> parameters taken from @HS19, which are different from 2019 DEW spreadsheet)",http://www.dewcommunity.org
 HS19,"F. Huang and D. A. Sverjensky",2019,"Geochim. Cosmochim. Acta 254, 192-230","ions and metal complexes",https://doi.org/10.1016/j.gca.2019.03.027
 LA19,"D. E. LaRowe and J. P. Amend",2019,"Geomicrobiol. J. 36, 492-505","dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid",https://doi.org/10.1080/01490451.2019.1573278
-SPD+19,"B. St Clair et al.",2019,"ACS Earth Space Chem 3, 905-921","Metal carbonate and bicarbonate complexes and FeSO<sub>4</sub>",https://doi.org/10.1021/acsearthspacechem.9b00016
+SPD+19,"B. St Clair et al.",2019,"ACS Earth Space Chem 3, 905-921","metal carbonate and bicarbonate complexes and FeSO<sub>4</sub>",https://doi.org/10.1021/acsearthspacechem.9b00016
 LX20,"Liu and Xiao",2020,"Ore Geol. Rev. 117, 103289","huebnerite Cp",https://doi.org/10.1016/j.oregeorev.2019.103289
+MP20,"Materials Project",2020,"mp-1513: Co9S8","Co-pentlandite V calculated from density of Co<sub>9</sub>S<sub>8</sub> from Materials Project",https://doi.org/10.17188/1191033

Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2020-10-04 21:50:21 UTC (rev 608)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2020-10-06 10:17:46 UTC (rev 609)
@@ -255,24 +255,25 @@
 "OBIGT",2005,"orpiment","cr","J",,,-1036
 "OBIGT",2013,"dawsonite","cr","J",,,19466
 "OBIGT",2015,"ferberite","cr","J",1.21,,
-"OBIGT",2044,"octadecane","cr","cal",-2.63,,
-"OBIGT",2045,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2046,"eicosane","cr","cal",-2.79,,
-"OBIGT",2047,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2048,"docosane","cr","cal",-2.63,,
-"OBIGT",2049,"tricosane","cr","cal",-5.22,,
-"OBIGT",2050,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2051,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2052,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2053,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2105,"carbazole","cr","cal",-43.39,,
-"OBIGT",2146,"triphenylene","cr","cal",,,541
-"OBIGT",2459,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2617,"ethylene","gas","cal",-4.59,,
-"OBIGT",2627,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2937,"nonacontane","liq","cal",,,635
-"OBIGT",2944,"2-methyloctane","liq","cal",10,,
-"OBIGT",3357,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",2028,"Co-pentlandite","cr","cal",,,-3630
+"OBIGT",2048,"octadecane","cr","cal",-2.63,,
+"OBIGT",2049,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2050,"eicosane","cr","cal",-2.79,,
+"OBIGT",2051,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2052,"docosane","cr","cal",-2.63,,
+"OBIGT",2053,"tricosane","cr","cal",-5.22,,
+"OBIGT",2054,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2055,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2056,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2057,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2109,"carbazole","cr","cal",-43.39,,
+"OBIGT",2150,"triphenylene","cr","cal",,,541
+"OBIGT",2463,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2621,"ethylene","gas","cal",-4.59,,
+"OBIGT",2631,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2941,"nonacontane","liq","cal",,,635
+"OBIGT",2948,"2-methyloctane","liq","cal",10,,
+"OBIGT",3361,"5,6-dithiadecane","liq","cal",2,,
 "DEW",8,"AlO2(SiO2)-","aq","cal",,,-897
 "DEW",17,"BO(OH)","aq","cal",,,-1111
 "DEW",19,"Ca(HCO3)+","aq","cal",,,-2971

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

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2020-10-04 21:50:21 UTC (rev 608)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2020-10-06 10:17:46 UTC (rev 609)
@@ -1690,3 +1690,19 @@
   volume    = {280},
   doi       = {10.1016/S0925-8388(98)00739-7},
 }
+
+ at Book{VC78,
+  author    = {Vaughan, David J. and Craig, James R.},
+  publisher = {Cambridge University Press},
+  title     = {Mineral Chemistry of Metal Sulfides},
+  year      = {1978},
+  address   = {Cambridge},
+  url       = {https://www.worldcat.org/oclc/801856147},
+}
+
+ at Misc{MP20,
+  author    = {{Materials Project}},
+  title     = {mp-1513: Co9S8},
+  year      = {2020},
+  doi       = {10.17188/1191033},
+}

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