[CHNOSZ-commits] r824 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT inst/extdata/thermo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 6 14:27:36 CET 2024
Author: jedick
Date: 2024-02-06 14:27:35 +0100 (Tue, 06 Feb 2024)
New Revision: 824
Modified:
pkg/CHNOSZ/.Rbuildignore
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/logB.to.OBIGT.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
OBIGT: Add carrollite from von der Heyden et al. (2024)
Modified: pkg/CHNOSZ/.Rbuildignore
===================================================================
--- pkg/CHNOSZ/.Rbuildignore 2024-01-11 12:10:40 UTC (rev 823)
+++ pkg/CHNOSZ/.Rbuildignore 2024-02-06 13:27:35 UTC (rev 824)
@@ -2,3 +2,4 @@
vignettes/clean.sh
LICENSE
^\.github$
+inst/extdata/src
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2024-01-11 12:10:40 UTC (rev 823)
+++ pkg/CHNOSZ/DESCRIPTION 2024-02-06 13:27:35 UTC (rev 824)
@@ -1,6 +1,6 @@
-Date: 2024-01-10
+Date: 2024-02-06
Package: CHNOSZ
-Version: 2.0.0-43
+Version: 2.0.0-44
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/logB.to.OBIGT.R
===================================================================
--- pkg/CHNOSZ/R/logB.to.OBIGT.R 2024-01-11 12:10:40 UTC (rev 823)
+++ pkg/CHNOSZ/R/logB.to.OBIGT.R 2024-02-06 13:27:35 UTC (rev 824)
@@ -133,7 +133,7 @@
logK <- suppressMessages(subcrt(species, coeffs, T = T, P = P)$out$logK)
# Calculate the mean absolute difference
mad <- mean(abs(logK - logB))
- message(paste("logB.to.OBIGT: mean absolute difference between logB (experimental) and logK (calculated) is", round(mad, 4)))
+ message(paste("logB.to.OBIGT: mean difference between logB (experimental) and logK (calculated) is", round(mad, 4)))
# Check that calculated values are close to input values
stopifnot(all.equal(logK, logB, tolerance = tolerance, scale = 1))
# Return the species index in OBIGT
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2024-01-11 12:10:40 UTC (rev 823)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2024-02-06 13:27:35 UTC (rev 824)
@@ -15,7 +15,7 @@
\newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
\newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{Δ<I>G</I>°}}{ΔG°}}}
-\section{Changes in CHNOSZ version 2.0.0-42 (2023-01-09)}{
+\section{Changes in CHNOSZ version 2.0.0-44 (2023-02-06)}{
\subsection{NEW FEATURES}{
\itemize{
@@ -67,6 +67,15 @@
NA for \DG0 and issuing a message is now reserved for phase stability
limits (i.e., melting, vaporization, or decomposition). See \viglink{FAQ}
for details.
+
+ \item Add carrollite (Cu\s{0.92}Co\s{2.07}S\s{4}) from
+ \href{https://doi.org/10.3749/2300028}{von der Heyden et al. (2024)}.
+
+ \item Modify cattierite (CoS\s{2}) and linnaeite (Co\s{3}S\s{4}) 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 Add 36 charged amino acids from
\href{https://doi.org/10.1007/s11084-015-9428-3}{Kitadai (2015)} and
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-01-11 12:10:40 UTC (rev 823)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-02-06 13:27:35 UTC (rev 824)
@@ -144,9 +144,6 @@
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,"tricobalt tetrasulfide",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,"cobalt disulfide",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,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
@@ -153,3 +150,8 @@
guite,"tricobalt tetroxide",Co3O4,cr,RH95,NA,2022-06-21,CGL,J,-802200,-918800,109.3,123.39,39.77,131.6,0.06602,-2480000,0,0,0,0,-1000
"cobalt monoxide",NA,CoO,cr,RH95,NA,2022-06-21,CGL,J,-214100,-237900,52.8,43.34,11.64,-30.47,0.02946,-4166000,1932,0,0,0,2078
zinc,NA,Zn,cr,RH95,NA,2022-07-15,CGL,J,0,0,41.63,25.39,9.162,29.09,-0.003507,0,-63.66,1.161E-05,0,0,692.7
+Co-pentlandite,NA,Co9S8,cr,PMW87,WV22,2023-02-10,CGL,J,-816330,-850930,410.752,43.32,149.33,39.5,0.0271,-379000,0,0,0,0,-1107
+linnaeite,"tricobalt tetrasulfide",Co3S4,cr,PMW87,WV22,2024-02-05,CGL,J,-346347,-358990,175.937,162.63,63.12,153,0.0825,-1340000,0,0,0,0,-937
+cattierite,"cobalt disulfide",CoS2,cr,PMW87,WV22,2024-02-05,CGL,J,-147365,-153140,74.793,68.26,25.52,65.82,0.0303,-587000,0,0,0,0,-1223
+carrollite,NA,Cu0.92Co2.07S4,cr,HDR+24,NA,2024-02-05,CGL,J,-331140,-344460,176.33,158.48,63.91,197.951,-0.0298,-2687000,0,0,0,0,377
+carrollite,NA,Cu0.92Co2.07S4,cr2,HDR+24,NA,2024-02-05,CGL,J,-331157,-345026,174.49,NA,63.91,234.11,-0.18038,0,0,0,0,0,650
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-01-11 12:10:40 UTC (rev 823)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-02-06 13:27:35 UTC (rev 824)
@@ -18,8 +18,7 @@
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
+PMW87,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","cattierite, linnaeite, and Co-pentlandite",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
@@ -288,3 +287,4 @@
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
+HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93","carrollite",https://doi.org/10.3749/2300028
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2024-01-11 12:10:40 UTC (rev 823)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2024-02-06 13:27:35 UTC (rev 824)
@@ -278,7 +278,7 @@
@Book{Kel60,
author = {Kelley, K. K.},
publisher = {U. S. Bureau of Mines},
- title = {{C}ontributions to the {D}ata in {T}heoretical {M}etallurgy {XIII}: {H}igh {T}emperature {H}eat {C}ontent, {H}eat {C}apacities and {E}ntropy {D}ata for the {E}lements and {I}norganic {C}ompounds},
+ title = {Contributions to the Data in Theoretical Metallurgy {XIII}: High Temperature Heat Content, Heat Capacities and Entropy Data for the Elements and Inorganic Compounds},
year = {1960},
series = {Bulletin 584},
pages = {232},
@@ -749,7 +749,7 @@
@Article{SH88,
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: {C}orrelation algorithms for ionic species and equation of state predictions to 5 kb and 1000°{C}},
+ title = {Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Correlation algorithms for ionic species and equation of state predictions to 5 kb and 1000°{C}},
year = {1988},
number = {8},
pages = {2009--2036},
@@ -1779,3 +1779,14 @@
series = {Bulletin},
url = {https://www.worldcat.org/oclc/16131757},
}
+
+ at Article{HDR+24,
+ author = {{von der Heyden}, Bjorn P. and Dick, Jeffrey and Rosenfels, Ryan C. and Carlton, Luke and Lilova, Kristina and Navrotsky, Alexandra and Subramani, Tamilarasan and Woodfield, Brian F. and Gibson, Alexis},
+ journal = {The Canadian Journal of Mineralogy and Petrology},
+ title = {Growth and stability of stratiform carrollite ({CuCo\textsubscript{2}S\textsubscript{4}}) in the {T}enke-{F}ungurume ore district, {C}entral {A}frican {C}opperbelt},
+ year = {2024},
+ number = {1},
+ pages = {77--93},
+ volume = {62},
+ doi = {10.3749/2300028},
+}
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