[CHNOSZ-commits] r921 - in pkg/CHNOSZ: . inst inst/extdata/thermo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 5 23:56:46 CEST 2025
Author: jedick
Date: 2025-06-05 23:56:45 +0200 (Thu, 05 Jun 2025)
New Revision: 921
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/thermo/refs.csv
pkg/CHNOSZ/vignettes/FAQ.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
Add FAQ question: Where do the names CHNOSZ, OBIGT, and subcrt come from?
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-06-05 08:35:13 UTC (rev 920)
+++ pkg/CHNOSZ/DESCRIPTION 2025-06-05 21:56:45 UTC (rev 921)
@@ -1,6 +1,6 @@
-Date: 2025-06-05
+Date: 2025-06-06
Package: CHNOSZ
-Version: 2.1.0-92
+Version: 2.1.0-93
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/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2025-06-05 08:35:13 UTC (rev 920)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2025-06-05 21:56:45 UTC (rev 921)
@@ -167,6 +167,9 @@
\item Add FAQ question: Why are mineral stability boundaries curved on
mosaic diagrams?
+ \item Add FAQ question: Where do the names CHNOSZ, OBIGT, and subcrt come
+ from?
+
}
}
Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-06-05 08:35:13 UTC (rev 920)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-06-05 21:56:45 UTC (rev 921)
@@ -46,7 +46,7 @@
OH90,"E. H. Oelkers and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 727-738","Debye-Hückel extended term parameter (<i>b</i><sub>$\gamma$</sub>)",https://doi.org/10.1016/0016-7037(90)90368-U
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
HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,https://pubs.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,"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
SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
JUN92,"C. de Capitani",1992,"JUN92.bs database supplied with Theriak/Domino software","data as listed in `JUN92.bs` data file",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html
@@ -59,7 +59,7 @@
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
-SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal-acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J
+SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J
SK93.1,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","Ag, Au, Cu(I) and Al acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J
SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",https://doi.org/10.1006/icar.1993.1185
SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,https://doi.org/10.1016/0016-7037(93)90337-V
@@ -147,7 +147,7 @@
VPT01,"O. Vidal, T. Parra and F. Trotet",2001,"Am. J. Sci. 301, 557-592","daphnite and Mg-amesite",https://doi.org/10.2475/ajs.301.6.557
GKL02,"R. N. Goldberg et al.",2002,"J. Phys. Chem. Ref. Data 31, 231-370","glycine, diglycine, and triglycine (+1 and -1 ions) GHS",https://doi.org/10.1063/1.1416902
AD03.1,"N. N. Akinfiev and L. W. Diamond",2003,"Geochim. Cosmochim. Acta 67, 613-629","dissolved gas species; parameters estimated from the experimental Henry's constant",https://doi.org/10.1016/S0016-7037(02)01141-9
-AD03.2,"N. N. Akinfiev and L. W. Diamond",2003,"Geochim. Cosmochim. Acta 67, 613-629","dissolved gas species; parameters estimated from standard-state properties at 25 ° C",https://doi.org/10.1016/S0016-7037(02)01141-9
+AD03.2,"N. N. Akinfiev and L. W. Diamond",2003,"Geochim. Cosmochim. Acta 67, 613-629","dissolved gas species; parameters estimated from standard state properties at 25 ° C",https://doi.org/10.1016/S0016-7037(02)01141-9
KK03,"R. J. M. Konings and A. Kovács",2003,"Thermodynamic properties of the lanthanide(III) halides, in Handbook on the Physics and Chemistry of Rare Earths","REE chlorides and fluorides",https://doi.org/10.1016/S0168-1273(02)33003-4
MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",https://doi.org/10.2138/am-2003-5-614
NA03,"D. K. Nordstrom and D. G. Archer",2003,"Arsenic thermodynamic data and environmental geochemistry. In Arsenic in Groundwater, eds. Welch and Stollenwerk, Kluwer","As oxide and sulfide minerals",
@@ -165,7 +165,7 @@
AVZP06,"N. N. Akinfiev et al.",2006,"Geochem. Int. 44, 867-878",AgCl<sub>3</sub><sup>-2</sup>,https://doi.org/10.1134/S0016702906090035
BL06,"A. V. Bandura and S. N. Lvov",2006,"J. Phys. Chem. Ref. Data 35, 15-30",OH<sup>-</sup>,https://doi.org/10.1063/1.1928231
HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",https://doi.org/10.1016/j.jct.2005.10.013
-LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",https://doi.org/10.1016/j.gca.2006.04.010
+LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic acid bases, nucleosides, and nucleotides",https://doi.org/10.1016/j.gca.2006.04.010
LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",https://doi.org/10.1016/j.gca.2006.04.010
LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",https://doi.org/10.1016/j.tca.2006.06.008
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
@@ -181,9 +181,9 @@
PK06,"K. Popa and R.J.M. Konings",2006,"Thermochim. Acta 445, 49-52","REE phosphates (monazites) [different G than @MWBC16]",https://doi.org/10.1016/j.tca.2006.03.023
SGX+06,"A. V. Sharygin et al.",2006,"Geochim. Cosmochim. Acta 70, 5169-5182",KSO<sub>4</sub><sup>-</sup>,https://doi.org/10.1016/j.gca.2006.07.034
Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain",
-MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes; linked to properties of arsenate and arsenite from @SSWS97",https://doi.org/10.1007/s00254-006-0578-5
+MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal arsenate and arsenite complexes; linked to properties of arsenate and arsenite from @SSWS97",https://doi.org/10.1007/s00254-006-0578-5
SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)<sup>+2</sup>",https://doi.org/10.5281/zenodo.2630820
-SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high-temperature HKF parameters from @AP01",https://doi.org/10.5281/zenodo.2630820
+SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high temperature HKF parameters from @AP01",https://doi.org/10.5281/zenodo.2630820
ZW07,"S. P. Ziemer and E. M. Woolley",2007,"J. Chem. Thermodynamics 39, 645-666",glutamate,https://doi.org/10.1016/j.jct.2006.08.008
PPB+08,"E. Perfetti et al.",2008,"Geochim. Cosmochim. Acta 72, 713-731","arsenopyrite, loellingite, and westerveldite",https://doi.org/10.1016/j.gca.2007.11.017
PPB+08.1,"E. Perfetti et al.",2008,"Geochim. Cosmochim. Acta 72, 713-731","As(OH)<sub>3</sub> and AsO(OH)<sub>3</sub>",https://doi.org/10.1016/j.gca.2007.11.017
@@ -195,7 +195,7 @@
MWW09,"A. A. Migdisov, A. E. Williams-Jones and T. Wagner",2009,"Geochim. Cosmochim. Acta 73, 7087-7109","REE F<sup>-</sup> and Cl<sup>-</sup> complexes",https://doi.org/10.1016/j.gca.2009.08.023
JSW09,"K. T. Jacob et al.",2009,"J. Chem. Thermodynamics 41, 748-753",beta-Ta<sub>2</sub>O<sub>5</sub>,https://doi.org/10.1016/j.jct.2008.12.006
BZA10,"E. F. Bazarkina, A. V. Zotov and N. N. Akinfiev",2010,"Geol. Ore Deposits 52, 167-178","Cd chloride complexes",https://doi.org/10.1134/S1075701510020054
-AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010
+AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010
AML10.1,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","Np and Am chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010
AZ10,"N. N. Akinfiev and A. V. Zotov",2010,"Geochem. Int. 48, 714-720","MHS and M(HS)<sub>2</sub><sup>-</sup> (M = Au<sup>+</sup>, Ag<sup>+</sup>, or Cu<sup>+</sup>)",https://doi.org/10.1134/S0016702910070074
DS10,"J. Delgado Martin and A. Soler i Gil",2010,"Eur. J. Mineral. 22, 363-380","hedenbergite, andradite, ferro-actinolite, grunerite, and ilvaite",https://doi.org/10.1127/0935-1221/2010/0022-2021
@@ -249,7 +249,7 @@
ZZL+16.2,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","Cp parameters listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
ZZL+16.3,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","dawsonite GHS",https://doi.org/10.1016/j.cageo.2016.02.013
Bla17,"P. Blanc",2017,"Thermoddem: Update for the 2017 version","monteponite, Cd(OH)<sub>2</sub>, CdSO<sub>4</sub>, otavite, and GaOOH",https://thermoddem.brgm.fr/page/brgm-reports
-Bla17.1,"P. Blanc",2017,"Thermoddem: Update for the 2017 version","Ga-hydroxide complexes",https://thermoddem.brgm.fr/page/brgm-reports
+Bla17.1,"P. Blanc",2017,"Thermoddem: Update for the 2017 version","Ga hydroxide complexes",https://thermoddem.brgm.fr/page/brgm-reports
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
DEW17.01,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(acetic acid, glycine, methanol, propanoic acid, propanol: parameters in DEW spreadsheet are the same as in @PS01)",http://www.dewcommunity.org
DEW17.02,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(ethanol: parameters in DEW spreadsheet are different from @PS01; no comment provided)",http://www.dewcommunity.org
@@ -295,7 +295,7 @@
BDat17.1,"D. A. Sverjensky et al.",2017,"berman.dat file in SUPCRT92b.zip on the DEW website","antigorite: "Oct. 21, 2016: Revised volume coefficients consistent with @HDR06 and @YIY+14 "",http://www.dewcommunity.org/resources.html
MWKL17,"G. D. Miron et al.",2017,"Am. J. Sci. 317, 755-806","aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl",https://doi.org/10.2475/07.2017.01
MWKL17.1,"G. D. Miron et al.",2017,"Am. J. Sci. 317, 755-806","ΔG°<sub>f</sub> values",https://doi.org/10.2475/07.2017.01
-AKAE19,"M. R. Azadi et al.",2019,"Fluid Phase Equilib. 480, 25-40","metal-glycinate complexes",https://doi.org/10.1016/j.fluid.2018.10.002
+AKAE19,"M. R. Azadi et al.",2019,"Fluid Phase Equilib. 480, 25-40","metal glycinate complexes",https://doi.org/10.1016/j.fluid.2018.10.002
DEW19,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(values listed in DEW spreadsheet)",http://www.dewcommunity.org
DEW19.1,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(values from @HS19 listed in DEW spreadsheet)",http://www.dewcommunity.org
DEW19.2,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","MgOH<sup>+</sup>: Revised by Dimitri, January, 2019; with minimum volume needed",http://www.dewcommunity.org
Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd 2025-06-05 08:35:13 UTC (rev 920)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd 2025-06-05 21:56:45 UTC (rev 921)
@@ -208,7 +208,7 @@
This vignette was compiled on `r Sys.Date()` with CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
-## How is 'CHNOSZ' pronounced?
+## How is CHNOSZ pronounced?
As one syllable that starts with an *sh* sound and [rhymes with *Oz*](https://en.wiktionary.org/wiki/Rhymes:English/%C9%92z).
CHNOSZ and [schnoz](https://en.wiktionary.org/wiki/schnozz) are homophones.
@@ -215,6 +215,24 @@
*Added on 2023-05-22.*
+## Where do the names CHNOSZ, OBIGT, and subcrt come from?
+
+CHNOSZ has the symbols for five elements (carbon, hydrogen, nitrogen, oxygen, and sulfur) and charge (Z).
+These letters appear as the column names in the stoichiometric matrix for ionized proteins, which were the subject of JMD's PhD thesis.
+
+OBIGT was originally an abbreviation for the OrganoBioGeoTherm software package written by John Donovan,
+a Windows interface to SUPCRT92 that was first mentioned in print by @RH98.
+That package incorporated a database that was used as the starting point for the current OBIGT database.
+
+The name of the `subcrt()` function is loosely based on the SUPCRT92 software package.
+SUPCRT is an abbreviation for supercritical [@JOH92], but `subcrt()` is just a different name and is not limited to subcritical conditions.
+
+I would like to acknowledge Jan Amend for the suggestion to use a different function name than SUPCRT
+and for possibly being the first person to try to pronounce CHNOSZ while looking at the program's output.
+That interaction at the 2007 Goldschmidt conference led me to use CHNOSZ as the name for the package.
+
+*Added on 2025-06-05.*
+
## How should CHNOSZ be cited?
* This paper is the general reference for CHNOSZ: @Dic19.
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2025-06-05 08:35:13 UTC (rev 920)
+++ pkg/CHNOSZ/vignettes/vig.bib 2025-06-05 21:56:45 UTC (rev 921)
@@ -272,6 +272,17 @@
doi = {10.1126/science.1199911},
}
+ at Article{RH98,
+ author = {Richard, Laurent and Helgeson, Harold C.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest},
+ year = {1998},
+ number = {23-24},
+ pages = {3591--3636},
+ volume = {62},
+ doi = {10.1016/S0016-7037(97)00345-1},
+}
+
@Book{RH95,
author = {Robie, Richard A. and Hemingway, Bruce S.},
publisher = {U.S. Geological Survey},
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