[CHNOSZ-commits] r764 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 10 04:54:00 CET 2023
Author: jedick
Date: 2023-02-10 04:53:59 +0100 (Fri, 10 Feb 2023)
New Revision: 764
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/add.OBIGT.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
OBIGT/inorganic_cr.csv: Update linnaeite and Co-pentlandite
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-12-29 04:53:18 UTC (rev 763)
+++ pkg/CHNOSZ/DESCRIPTION 2023-02-10 03:53:59 UTC (rev 764)
@@ -1,6 +1,6 @@
-Date: 2022-12-29
+Date: 2023-02-10
Package: CHNOSZ
-Version: 1.9.9-55
+Version: 1.9.9-56
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/R/add.OBIGT.R
===================================================================
--- pkg/CHNOSZ/R/add.OBIGT.R 2022-12-29 04:53:18 UTC (rev 763)
+++ pkg/CHNOSZ/R/add.OBIGT.R 2023-02-10 03:53:59 UTC (rev 764)
@@ -91,11 +91,15 @@
thermo$OBIGT$state[ispecies[iold[i]]] <- state
thermo$OBIGT$model[ispecies[iold[i]]] <- model
}
- # Tell user if they're the same, otherwise update the data entry
- if(isTRUE(all.equal(oldprop, args[iold[i], ], check.attributes = FALSE)))
+ # Convert NA to NA_real_ so no change is detected 20230210
+ newprop <- args[iold[i], ]
+ newprop[is.na(newprop)] <- NA_real_
+ if(isTRUE(all.equal(oldprop, newprop, check.attributes = FALSE))) {
+ # No change to OBIGT; tell the user about it
message("mod.OBIGT: no change for ", speciesname[iold[i]], "(", state, ")")
- else {
- thermo$OBIGT[ispecies[iold[i]], icol] <- args[iold[i], ]
+ } else {
+ # Update the data in OBIGT
+ thermo$OBIGT[ispecies[iold[i]], icol] <- newprop
assign("thermo", thermo, CHNOSZ)
message("mod.OBIGT: updated ", speciesname[iold[i]], "(", state, ")")
}
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2022-12-29 04:53:18 UTC (rev 763)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2023-02-10 03:53:59 UTC (rev 764)
@@ -12,7 +12,7 @@
% links to vignettes 20220723
\newcommand{\viglink}{\ifelse{html}{\out{<a href="../CHNOSZ/doc/#1.html"><strong>#1.Rmd</strong></a>}}{\bold{#1.Rmd}}}
-\section{Changes in CHNOSZ version 1.9.9-54 (2022-12-13)}{
+\section{Changes in CHNOSZ version 1.9.9-56 (2023-02-10)}{
\subsection{MAJOR USER-VISIBLE CHANGES}{
\itemize{
@@ -64,6 +64,17 @@
(Co\s{3}O\s{4}), and zinc from \href{https://doi.org/10.3133/b2131}{Robie
and Hemingway (1995)}.
+ \item \samp{OBIGT/inorganic_cr.csv}: Modify linnaeite (Co\s{3}S\s{4}) to
+ use 25 \degC parameters from \href{https://doi.org/10.3133/b2131}{Robie
+ and Hemingway (1995)} and heat capacity coefficients from
+ \href{https://www.worldcat.org/oclc/16131757}{Pankratz et al. (1987)}.
+
+ \item \samp{OBIGT/inorganic_cr.csv}: Modify Co-pentlandite
+ (Co\s{9}S\s{8}) to use parameters from
+ \href{https://www.worldcat.org/oclc/16131757}{Pankratz et al. (1987)} as
+ listed by \href{https://doi.org/10.5382/econgeo.4895}{Williams-Jones and
+ Vasyukova (2022)}.
+
\item \samp{OBIGT/organic_aq.csv}: Correct formulas of Na(Mal)-, K(Mal)-,
and Dy(Mal)+. Thanks to Grayson Boyer.
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2022-12-29 04:53:18 UTC (rev 763)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2023-02-10 03:53:59 UTC (rev 764)
@@ -144,9 +144,9 @@
manganese,NA,Mn,cr,RH95,NA,2020-08-15,CGL,J,0,0,32.01,26.19,7.354,0,0.041345,-272170,313.29,-1.3745E-05,0,0,980
Mn(OH)2,NA,Mn(OH)2,cr,WEP+82.1,SUF+98,2020-08-15,CGL,J,-615000,-695400,99.2,114.7,NA,139.61,-0.08525,0,0,0,0,0,700
huebnerite,NA,MnWO4,cr,RH95,LX20,2020-09-10,CGL,J,-1235400,-1337600,132.5,NA,41.89,155.68,0.0915,53000,-1170,-5.31E-05,0,0,1000
-linnaeite,NA,Co3S4,cr,VC78,RH95.8,2020-10-06,CGL,cal,-83400,-85800,44.1,39.72,62.55,39.72,0,0,0,0,0,0,937
+linnaeite,NA,Co3S4,cr,RH95,PMW87.1,2023-02-10,CGL,J,-334900,-347500,176,162.6321,62.55,153,0.0825,-1340000,0,0,0,0,937
cattierite,NA,CoS2,cr,RH95,NA,2020-10-06,CGL,J,-145100,-150900,74.8,68.26,25.52,65.82,0.03032,-587000,0,0,0,0,1223
-Co-pentlandite,NA,Co9S8,cr,VC78,MP20,2020-10-06,CGL,cal,-199500,-203400,125,96.67,141.78,96.67,0,0,0,0,0,0,1107
+Co-pentlandite,NA,Co9S8,cr,PMW87,WV22,2023-02-10,CGL,J,-816330,NA,410.752,NA,149.33,39.5,0.0271,-379000,0,0,0,0,1107
cobalt,NA,Co,cr,RH95,NA,2020-10-06,CGL,J,0,0,30.04,24.81,6.67,0,0.041844,-156460,268.75,-1.6498E-05,0,0,700
wustite,NA,Fe0.947O,cr,RH95,NA,2020-11-10,CGL,J,-244900,-266300,56.6,48.13,12.04,-19.3,0.03017,-2533000,1501,0,0,0,1652
willemite,NA,Zn2SiO4,cr,RH95,BKK77,2021-03-22,CGL,J,-1523100,-1636700,131.4,123.3,52.42,144.892,0.036945,-3029200,0,0,0,0,1785
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2022-12-29 04:53:18 UTC (rev 763)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2023-02-10 03:53:59 UTC (rev 764)
@@ -12,7 +12,6 @@
RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://doi.org/10.3133/b1452
RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://doi.org/10.3133/b1452
RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://doi.org/10.3133/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
@@ -20,6 +19,8 @@
HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",H<sub>2</sub>O,https://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
+PMW87,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","Co-pentlandite",https://www.worldcat.org/oclc/16131757
+PMW87.1,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","linnaeite Cp",https://www.worldcat.org/oclc/16131757
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
RS87,"J. R. Ruaya and T. M. Seward",1987,"Geochim. Cosmochim. Acta 51, 121-130",HCl,https://doi.org/10.1016/0016-7037(87)90013-5
Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522",minerals,https://doi.org/10.1093/petrology/29.2.445
@@ -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","gypsum, manganese, manganosite, pyrolusite, bixbyite, hausmannite, huebnerite, cattierite, cobalt, cobalt monoxide, guite, wustite, willemite, and zinc",https://doi.org/10.3133/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum, manganese, manganosite, pyrolusite, bixbyite, hausmannite, huebneritecobalt, cobalt monoxide, guite, cattierite, linnaeite, wustite, willemite, and zinc",https://doi.org/10.3133/b2131
RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://doi.org/10.3133/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://doi.org/10.3133/b2131
RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, halloysite, pyrope: GHS and Cp at 25 °C",https://doi.org/10.3133/b2131
@@ -65,7 +66,6 @@
RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
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://doi.org/10.3133/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://doi.org/10.3133/b2131
-RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","linnaeite V",https://doi.org/10.3133/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
Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,https://doi.org/10.1016/0016-7037(95)00403-3
@@ -283,6 +283,6 @@
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
AKK+20,"N. N. Akinfiev et al.",2020,"Geochim. Cosmochim. Acta 280, 102-115","Nb and Ta species",https://doi.org/10.1016/j.gca.2020.04.009
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
LXW21,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","H<sub>2</sub>WO<sub>4</sub>",https://doi.org/10.1016/j.chemgeo.2021.120488
LXW21.1,"X. Liu, C. Xiao and Y. Wang",2021,"Chem. Geol. 584, 120488","scheelite Cp",https://doi.org/10.1016/j.chemgeo.2021.120488
+WV22,"A. E. Williams-Jones and O. V. Vasyukova",2022,"Econ. Geol. 117, 513-528","parameters listed here",https://doi.org/10.5382/econgeo.4895
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2022-12-29 04:53:18 UTC (rev 763)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2023-02-10 03:53:59 UTC (rev 764)
@@ -34,7 +34,7 @@
@Article{AH97b,
author = {Amend, Jan P. and Helgeson, Harold C.},
journal = {Journal of the Chemical Society, Faraday Transactions},
- title = {{C}alculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. {P}art 1. \textsc{l}-{$\alpha$}-amino acids},
+ title = {Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. {P}art 1. \textsc{l}-{$\alpha$}-amino acids},
year = {1997},
number = {10},
pages = {1927--1941},
@@ -45,7 +45,7 @@
@Article{AP01,
author = {Amend, Jan P. and Plyasunov, Andrey V.},
journal = {Geochimica et Cosmochimica Acta},
- title = {{C}arbohydrates in thermophile metabolism: {C}alculation of the standard molal thermodynamic properties of aqueous pentoses and hexoses at elevated temperatures and pressures},
+ title = {Carbohydrates in thermophile metabolism: Calculation of the standard molal thermodynamic properties of aqueous pentoses and hexoses at elevated temperatures and pressures},
year = {2001},
number = {21},
pages = {3901--3917},
@@ -298,7 +298,7 @@
@Article{LA16,
author = {LaRowe, Douglas E. and Amend, Jan P.},
- journal = {ISME Journal},
+ journal = {The ISME Journal},
title = {The energetics of anabolism in natural settings},
year = {2016},
number = {6},
@@ -320,7 +320,7 @@
@Article{LH06a,
author = {LaRowe, Douglas E. and Helgeson, Harold C.},
journal = {Geochimica et Cosmochimica Acta},
- title = {{B}iomolecules in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures},
+ title = {Biomolecules in hydrothermal systems: Calculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures},
year = {2006},
number = {18},
pages = {4680--4724},
@@ -518,7 +518,7 @@
@Article{PS01,
author = {Plyasunov, Andrey V. and Shock, Everett L.},
journal = {Geochimica et Cosmochimica Acta},
- title = {{C}orrelation strategy for determining the parameters of the revised {H}elgeson-{K}irkham-{F}lowers model for aqueous nonelectrolytes},
+ title = {Correlation strategy for determining the parameters of the revised {H}elgeson-{K}irkham-{F}lowers model for aqueous nonelectrolytes},
year = {2001},
number = {21},
pages = {3879--3900},
@@ -664,7 +664,7 @@
@Article{SS93,
author = {Schulte, Mitchell D. and Shock, Everett L.},
journal = {Geochimica et Cosmochimica Acta},
- title = {{A}ldehydes in hydrothermal solution: {S}tandard partial molal thermodynamic properties and relative stabilities at high temperatures and pressures},
+ title = {Aldehydes in hydrothermal solution: Standard partial molal thermodynamic properties and relative stabilities at high temperatures and pressures},
year = {1993},
number = {16},
pages = {3835--3846},
@@ -708,7 +708,7 @@
@Article{Sho95,
author = {Shock, Everett L.},
journal = {American Journal of Science},
- title = {{O}rganic acids in hydrothermal solutions: {S}tandard molal thermodynamic properties of carboxylic acids and estimates of dissociation constants at high temperatures and pressures},
+ title = {Organic acids in hydrothermal solutions: Standard molal thermodynamic properties of carboxylic acids and estimates of dissociation constants at high temperatures and pressures},
year = {1995},
number = {5},
pages = {496--580},
@@ -749,7 +749,7 @@
@Article{SH90,
author = {Shock, Everett L. and Helgeson, Harold C.},
journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {S}tandard partial molal properties of organic species},
+ title = {Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of organic species},
year = {1990},
number = {4},
pages = {915--945},
@@ -793,7 +793,7 @@
@Article{SM93,
author = {Shock, Everett L. and McKinnon, William B.},
journal = {Icarus},
- title = {{H}ydrothermal processing of cometary volatiles---{A}pplications to {T}riton},
+ title = {Hydrothermal processing of cometary volatiles---{A}pplications to {T}riton},
year = {1993},
number = {2},
pages = {464--477},
@@ -1730,22 +1730,6 @@
doi = {10.1016/j.gca.2020.04.009},
}
- 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},
-}
-
@Article{LXW21,
author = {Xiangchong Liu and Changhao Xiao and Yong Wang},
journal = {Chemical Geology},
@@ -1766,3 +1750,24 @@
volume = {317},
doi = {10.2475/07.2017.01},
}
+
+ at Article{WV22,
+ author = {Williams-Jones, A. E. and Vasyukova, O. V.},
+ journal = {Economic Geology},
+ title = {Constraints on the genesis of cobalt deposits: {P}art {I}. {T}heoretical considerations},
+ year = {2022},
+ number = {3},
+ pages = {513--528},
+ volume = {117},
+ doi = {10.5382/econgeo.4895},
+}
+
+ at Book{PMW87,
+ author = {L. B. Pankratz and A. D. Mah and S. W. Watson},
+ publisher = {United States Department of the Interior, Bureau of Mines},
+ title = {Thermodynamic Properties of Sulfides},
+ year = {1987},
+ number = {689},
+ series = {Bulletin},
+ url = {https://www.worldcat.org/oclc/16131757},
+}
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