OBIGT: Remove temperature limit of Cp equations

git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@808 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
jedick · Nov 14, 2023 · 8cc30da · 8cc30da
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
-Date: 2023-09-22
+Date: 2023-11-14
 Package: CHNOSZ
-Version: 2.0.0-27
+Version: 2.0.0-28
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -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 2.0.0-26 (2023-09-19)}{
+\section{Changes in CHNOSZ version 2.0.0-28 (2023-11-14)}{
 
     \itemize{
 
@@ -62,6 +62,12 @@
       update several others (Arg\S{+}, Arg\S{-}, Asp\S{-}, Glu\S{-}, His\S{+},
       Lys\S{+}, Lys\S{-}, and Tyr\S{-}). Thanks to Grayson Boyer.
 
+      \item In the default (inorganic_cr.csv) and optional (SUPCRT92.csv) data
+      files, remove T values that represent temperature limit of Cp equations
+      (these are now listed as NA). Temperatures of polymorphic phase
+      transitions and melting or decomposition temperatures (only available for
+      some minerals) have been retained. See FAQ for more details.
+
     }
 
 }

diff --git a/inst/extdata/OBIGT/SUPCRT92.csv b/inst/extdata/OBIGT/SUPCRT92.csv
diff --git a/inst/extdata/OBIGT/inorganic_cr.csv b/inst/extdata/OBIGT/inorganic_cr.csv
diff --git a/inst/extdata/OBIGT/refs.csv b/inst/extdata/OBIGT/refs.csv
@@ -5,8 +5,7 @@ Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https:
 Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,https://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",https://www.worldcat.org/oclc/14154292
 BKK77,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","willemite Cp",https://www.worldcat.org/oclc/695258
-HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals and phase transitions",https://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",https://www.worldcat.org/oclc/13594862
+HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals and polymorphic phase transitions",https://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",https://www.worldcat.org/oclc/13594862
 RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,https://doi.org/10.3133/b1452
 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
@@ -65,7 +64,8 @@ RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 213
 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 &deg;C",https://doi.org/10.3133/b2131
 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
+RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (melting temperature and G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
+RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","anhydrite, bunsenite, chalcocite, covellite, cuprite, galena, gold, halite, pyrite, silver, sodium oxide, cassiterite, uraninite, zincite (melting or decomposition temperature)",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
@@ -220,7 +220,7 @@ ZZL+16,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","data listed in sprons
 ZZL+16.1,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","As(&alpha;): V listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
 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
-OBIGT.1,"J. M. Dick",2017,"OBIGT database in CHNOSZ","GHS (T<sub>r</sub>) of the phase that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) of the phases that are stable at higher temperatures.",https://chnosz.net
+OBIGT.1,"J. M. Dick",2017,"OBIGT database in CHNOSZ","GHS (T<sub>r</sub>) of the polymorph that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) of the polymorphs that are stable at higher temperatures.",https://chnosz.net
 OBIGT.3,"J. M. Dick",2017,"OBIGT database in CHNOSZ","AuCl<sub>4</sub><sup>-</sup> renamed to AuCl<sub>4</sub><sup>-3</sup>",https://chnosz.net
 OBIGT.4,"J. M. Dick",2017,"OBIGT database in CHNOSZ","charge of NpO<sub>2</sub>(Oxal), La(Succ)<sup>+</sup>, NH<sub>4</sub>(Succ)<sup>-</sup>, and NpO<sub>2</sub>(Succ) as listed by @PSK99",https://chnosz.net
 OBIGT.5,"J. M. Dick",2017,"OBIGT database in CHNOSZ","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH<sub>2</sub>NH<sub>2</sub>] were printed in Table 6 of @DLH06; corrected values are used here.",https://chnosz.net

diff --git a/inst/tinytest/test-subcrt.R b/inst/tinytest/test-subcrt.R
@@ -58,8 +58,9 @@ expect_message(subcrt(iacanthite), "subcrt: temperature\\(s\\) of 623.15 K and a
 expect_equal(subcrt("acanthite")$out$acanthite$polymorph, c(1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3), info = info)
 # The reaction coefficients in the output should be unchanged 20171214
 expect_equal(subcrt(c("bunsenite", "nickel", "oxygen"), c(-1, 1, 0.5))$reaction$coeff, c(-1, 1, 0.5), info = info) 
-# Properties are NA only above (not at) the transition temperature 20191111
-expect_equal(is.na(subcrt("rhodochrosite", T = c(699:701), P = 1, convert = FALSE)$out[[1]]$G), c(FALSE, FALSE, TRUE), info = info)
+## TODO: replace/revise this test after removal of temperature limit of Cp equations 20231114
+## Properties are NA only above (not at) the temperature limit 20191111
+#expect_equal(is.na(subcrt("rhodochrosite", T = c(699:701), P = 1, convert = FALSE)$out[[1]]$G), c(FALSE, FALSE, TRUE), info = info)
 
 # Use calories for comparisons with SUPCRT92
 E.units("cal")

diff --git a/vignettes/FAQ.Rmd b/vignettes/FAQ.Rmd
@@ -620,4 +620,39 @@ Here are the three plots that we made:
 
 *Answered on 2023-09-08.*
 
+### What is purpose of the "T" column for minerals and solid and liquid organic species?
+
+The purposes of this column are 1) to list the temperature(s) of transition(s) between polymorphs of a mineral (^) and 2) to indicate the temperature above which a phase is not stable (i.e., melting of a solid or vaporization of a liquid).
+This column does not list the T limit for the Maier-Kelley equation (see Historical Remarks below).
+
+These cases are handled by subcrt() as follows (note that the units of T in the OBIGT database are Kelvin, but subcrt() by default uses &deg;C):
+- For polymorphic transitions, the properties of specific polymorphs are returned:
+
+(^) In both SUPCRT92 and OBIGT, quicksilver, tin, sulfur, and selenium are each listed as minerals with one or more polymorphic transitions, but the highest-temperature polymorph actually represents the liquid state.
+
+- For phase transitions, G of the requested phase is set to NA above the transition temperature:
+
+- If T for a phase is set to NA, then no upper temerature limit is imposed by subcrt().
+
+Historial Remarks:
+Data for minerals from Helgeson et al. (1978) are provided in the default OBIGT database (if they don't conflict with Berman (1988)) and optional SUPCRT92 database.
+The original SUPCRT92 package included "Tmax" values to indicate the (estimated) maximum temperature of validity of the Maier-Kelley equation for heat capacity.
+Calculations at temperatures higher than Tmax produced the warning "CAUTION: BEYOND T LIMIT OF CP COEFFS FOR A MINERAL OR GAS", but the calculated values of thermodynamnic properties were still output by SUPCRT92.
+It follows that "Tmax" in SUPCRT92 does not necessarily correspond to the melting or decomposition temperature of the mineral.
+Except as described below, Tmax values have been *removed* from OBIGT in the development version of CHNOSZ, with the result that subcrt() no longer imposes an uppper temperature limit for the majority of minerals.
+
+OBIGT's T column non-exhaustively lists melting temperatures for minerals, some of which were taken from SUPCRT92's Tmax values while others were taken from RH95 or other sources.
+The minerals with available temperatures of melting (or decomposition or other phase transition, not including polymorphs) include anhydrite, bunsenite, bromellite, chalcocite, chlorargyrite, cinnabar, copper, covellite, cuprite, galena, gold, halite, iron, nickel, pyrite, pyrrhotite, silver, sphalerite, strontianite, sylvite, cassiterite, uraninite, zincite, manganosite, wustite, cobalt monoxide, and zinc.
+Many organic solids and liquids have melting and vaporization temperatures listed as well.
+However, no melting temperatures are listed for minerals represented by the Berman (1988) equations.
+
+If subcrt() is run at temperatures above the melting or vaporization temperature, then values of G and logK are reported as NA and a message is produced (e.g. "XXX").
+This is a design decision that is intended to discourage the user from choosing unrealistic physical states.
+If you want to calculate the extrapolated properties of a phase above its listed transition temperature, then set exceed.Ttr to TRUE.
+
+In general, the removal of Tmax values from SUPCRT92 makes CHNOSZ more permissive with respect to the temperature range of calculations.
+However, OBIGT now uses the decomposition temperature of covellite (780 K from Robie and Hemingway, 1995) in contrast to the previous Tmax from SUPCRT92 (1273 K, which is referenced to an "estimated" Cp equation on p. 62 of Kelley (1960)).
+
+*Answered on 2023-11-14.*
+
 ## References