[CHNOSZ-commits] r859 - in pkg/CHNOSZ: . inst inst/extdata inst/extdata/OBIGT/testing inst/extdata/adds vignettes

Wed Dec 25 07:05:31 CET 2024

Author: jedick
Date: 2024-12-25 07:05:30 +0100 (Wed, 25 Dec 2024)
New Revision: 859

Added:
   pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
   pkg/CHNOSZ/inst/extdata/refs.csv
   pkg/CHNOSZ/vignettes/OBIGT.Rmd
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
OBIGT/testing: add REE from Migdisov et al. (2009)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2024-12-25 03:04:01 UTC (rev 858)
+++ pkg/CHNOSZ/DESCRIPTION	2024-12-25 06:05:30 UTC (rev 859)
@@ -1,6 +1,6 @@
 Date: 2024-12-25
 Package: CHNOSZ
-Version: 2.1.0-31
+Version: 2.1.0-32
 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	2024-12-25 03:04:01 UTC (rev 858)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2024-12-25 06:05:30 UTC (rev 859)
@@ -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 2.1.0-30 (2024-12-25)}{
+\section{Changes in CHNOSZ version 2.1.0-31 (2024-12-25)}{
 
   \subsection{OBIGT DEFAULT DATA}{
     \itemize{
@@ -25,7 +25,12 @@
       and related U-bearing minerals from
       \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}.
 
-      \item Move americium complexes from \file{slop98.dat} back to
+      \item For compatibility with the above change, aqueous uranium species
+      other than HUO\s{4}\S{-} from
+      \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)}
+      have been moved to optional data (\file{SLOP98.csv}).
+
+      \item Move americium complexes from \file{SLOP98.csv} back to
       \file{inorganic_aq.csv} (entropy of the element Am has been available for
       checking GHS self-consistency since version 1.4.0).
 
@@ -47,46 +52,24 @@
   \subsection{OBIGT OPTIONAL DATA}{
     \itemize{
 
-      \item Aqueous uranium species other than HUO\s{4}\S{-} from
-      \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)}
-      have been moved to \file{SLOP98.csv}.
-
       \item Make new directory \file{OBIGT/testing} to hold optional data files
-      for testing (currently \file{SiO2.csv}, \file{GEMSFIT.csv},
-      \file{IGEM.csv}, and \file{Sandia.csv}).
+      for testing, including \file{SiO2.csv} and \file{GEMSFIT.csv} in addition
+      to those listed below.
 
-      \item Add \file{IGEM.csv}: updated data for Au and Cu complexes and
+      \item Add \file{testing/IGEM.csv}: Au and Cu complexes and
       SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS.
       
-      \item Add \file{Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
+      \item Add \file{testing/Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
       \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
         (2024)}.
 
-    }
-  }
+      \item Add \file{testing/REE.csv}: REE(III) fluoride and chloride complexes from
+      \href{https://doi.org/10.1016/j.gca.2009.08.023}{Migdisov et al. (2009)}
+      (previously available in CHNOSZ verisons 0.9-5 to 1.0.8).
 
-  \subsection{DOCUMENTATION}{
-
-    \itemize{
-
-      \item Add FAQ question: Why are mineral stability boundaries curved on
-      mosaic diagrams?
-
-      \item Add \file{demo/total_S.R}: total activity of S--pH diagram for
-      Fe-S-O-C minerals.
-
-      \item Add \file{demo/uranyl.R}: total (carbonate|sulfate)-pH diagrams
-      for uranyl species, after
-      \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}.
-
-      \item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes,
-      and add solubility contours for Fe and Au.
-
     }
-
   }
 
-
   \subsection{OTHER CHANGES}{
     \itemize{
 
@@ -106,12 +89,33 @@
       
       \item For better readability, formulas of species are no longer
       subscripted by \code{axis.label()} (via \code{expr.species()}). An
-      example of the new formatting is log \emph{f}O\s{2}). Similar formatting
+      example of the new formatting is log \emph{f}O\s{2}. Similar formatting
       for other expressions has been used in the vignettes.
 
     }
   }
 
+  \subsection{DOCUMENTATION}{
+
+    \itemize{
+
+      \item Add FAQ question: Why are mineral stability boundaries curved on
+      mosaic diagrams?
+
+      \item Add \file{demo/total_S.R}: total activity of S--pH diagram for
+      Fe-S-O-C minerals.
+
+      \item Add \file{demo/uranyl.R}: total (carbonate|sulfate)-pH diagrams
+      for uranyl species, after
+      \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}.
+
+      \item Revise \file{demo/sum_S.R} for log \emph{f}O\s{2} - log \emph{m} ΣS
+      diagram and add solubility contours for Fe and Au.
+
+    }
+
+  }
+
   \subsection{REMOVED FEATURES}{
     \itemize{
 

Added: pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/REE.csv	2024-12-25 06:05:30 UTC (rev 859)
@@ -0,0 +1,43 @@
+name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+LaF+2,NA,LaF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-236290,NA,-28.9,38.62,-36.67,-2.6763,-14.316,11.377,-2.1872,42.7211,4.8321,1.5259,2
+CeF+2,NA,CeF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-234190,NA,-24.92,25.38,-42.85,-3.5448,-16.4364,12.2104,-2.0995,34.4101,2.1345,1.4656,2
+PrF+2,NA,PrF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-235200,NA,-25.4,21.48,-40.63,-3.2382,-15.6879,11.9162,-2.1305,32.1968,1.3417,1.473,2
+NdF+2,NA,NdF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-233150,NA,-26.48,24.73,-41.72,-3.3812,-16.0371,12.0534,-2.116,34.2449,2.0023,1.4892,2
+SmF+2,NA,SmF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232090,NA,-27.08,-5.4,-40.5,-3.2108,-15.621,11.8899,-2.1332,16.6719,-4.1344,1.4983,2
+EuF+2,NA,EuF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-210450,NA,-28.85,-11.08,-39.73,-3.0953,-15.339,11.7791,-2.1449,13.5854,-5.2922,1.5251,2
+GdF+2,NA,GdF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-231710,NA,-25.91,-11.83,-38.73,-2.9753,-15.046,11.6639,-2.157,12.7413,-5.4446,1.4806,2
+TbF+2,NA,TbF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232790,NA,-30.21,-21.45,-38.53,-2.9233,-14.919,11.614,-2.1622,7.7005,-7.4034,1.5458,2
+DyF+2,NA,DyF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232030,NA,-29.52,-27.14,-39.08,-3.0025,-15.1125,11.69,-2.1543,4.2664,-8.5636,1.5353,2
+HoF+2,NA,HoF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-234580,NA,-28.53,-22.87,-40.09,-3.1464,-15.4638,11.8281,-2.1397,6.6315,-7.6938,1.5203,2
+ErF+2,NA,ErF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-233060,NA,-32.54,-26.35,-41.66,-3.3383,-15.9323,12.0123,-2.1204,5.1506,-8.4013,1.581,2
+TmF+2,NA,TmF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-233080,NA,-31.84,-30.14,-41.66,-3.3423,-15.942,12.0161,-2.12,2.8337,-9.1731,1.5705,2
+YbF+2,NA,YbF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-226300,NA,-30.41,-36.41,-43.34,-3.5804,-16.5233,12.2446,-2.0959,-1.0405,-10.4509,1.5488,2
+LuF+2,NA,LuF+2,aq,MWW09,NA,2010-07-03,HKF,cal,-232530,NA,-36.16,-32.88,-43.9,-3.6241,-16.6301,12.2865,-2.0915,1.8202,-9.7329,1.6359,2
+LaCl+2,NA,LaCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-196390,NA,-47.06,94.49,-17.46,0.0563,-7.6438,8.7545,-2.463,77.9764,16.2138,1.8009,2
+CeCl+2,NA,CeCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-193910,NA,-46.15,111.04,-23.65,-0.796,-9.7248,9.5724,-2.377,87.5448,19.5834,1.7871,2
+PrCl+2,NA,PrCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-194950,NA,-54.19,148.14,-21.42,-0.4448,-8.8673,9.2354,-2.4124,110.4007,27.1413,1.9089,2
+NdCl+2,NA,NdCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-192950,NA,-51.92,122.49,-22.51,-0.607,-9.2633,9.391,-2.3961,95.0531,21.916,1.8745,2
+SmCl+2,NA,SmCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191390,NA,-44.42,76.88,-21.3,-0.4843,-8.9637,9.2732,-2.4084,67.2886,12.6257,1.761,2
+EuCl+2,NA,EuCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-169620,NA,-42.31,55.98,-20.52,-0.3896,-8.7326,9.1824,-2.418,54.746,8.3675,1.729,2
+GdCl+2,NA,GdCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-190950,NA,-34.69,31.25,-19.52,-0.2964,-8.505,9.0929,-2.4274,39.2045,3.3318,1.6136,2
+TbCl+2,NA,TbCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191790,NA,-38.16,26.39,-19.33,-0.2506,-8.3931,9.0489,-2.432,36.8323,2.3408,1.6661,2
+DyCl+2,NA,DyCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191030,NA,-40.82,34.88,-19.88,-0.3106,-8.5396,9.1065,-2.426,42.1744,4.0696,1.7064,2
+HoCl+2,NA,HoCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-193750,NA,-41.14,43.23,-20.88,-0.4456,-8.8692,9.2361,-2.4123,47.1123,5.7705,1.7113,2
+ErCl+2,NA,ErCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-192230,NA,-41.84,29.13,-22.45,-0.6564,-9.384,9.4384,-2.3911,38.9461,2.8986,1.7219,2
+TmCl+2,NA,TmCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-192250,NA,-42.84,14.93,-22.46,-0.652,-9.3733,9.4342,-2.3915,30.7668,0.0075,1.7371,2
+YbCl+2,NA,YbCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-185320,NA,-38.84,-7.59,-24.13,-0.9035,-9.9872,9.6755,-2.3661,17.0158,-4.5799,1.6765,2
+LuCl+2,NA,LuCl+2,aq,MWW09,NA,2010-07-03,HKF,cal,-191690,NA,-42.08,-32.19,-24.69,-0.9615,-10.129,9.7313,-2.3603,3.0453,-9.5913,1.7255,2
+LaCl2+,NA,LaCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-227450,NA,-2.02,-8.19,6.83,2.9168,-0.6596,6.0093,-2.7517,6.6097,-4.7029,0.5747,1
+CeCl2+,NA,CeCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-224990,NA,9.64,-54.21,-0.06,1.9073,-3.1244,6.9781,-2.6498,-21.9709,-14.0772,0.3982,1
+PrCl2+,NA,PrCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-225970,NA,1.82,-22.59,2.42,2.2914,-2.1866,6.6095,-2.6886,-2.3592,-7.6362,0.5166,1
+NdCl2+,NA,NdCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-224000,NA,-1.36,-34.48,1.21,2.144,-2.5465,6.7509,-2.6737,-8.8885,-10.0582,0.5647,1
+SmCl2+,NA,SmCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222430,NA,-3.21,-34.9,2.56,2.3393,-2.0696,6.5635,-2.6934,-8.8795,-10.1437,0.5927,1
+EuCl2+,NA,EuCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-200660,NA,-10.02,-5.48,3.42,2.4959,-1.6871,6.4131,-2.7093,9.3035,-4.1509,0.6958,1
+GdCl2+,NA,GdCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-221990,NA,-7.61,-2.41,4.53,2.634,-1.3499,6.2806,-2.7232,10.7695,-3.5255,0.6593,1
+TbCl2+,NA,TbCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222840,NA,-12.4,-2.81,4.75,2.6916,-1.2094,6.2254,-2.729,11.1974,-3.607,0.7319,1
+DyCl2+,NA,DyCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222050,NA,-17.33,16.06,4.14,2.6363,-1.3444,6.2785,-2.7234,22.9371,0.2368,0.8065,1
+HoCl2+,NA,HoCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-224770,NA,-15.26,9.04,3.02,2.4712,-1.7476,6.4369,-2.7068,18.5365,-1.1932,0.7751,1
+ErCl2+,NA,ErCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-223270,NA,-20.65,4.65,1.27,2.2626,-2.2569,6.6371,-2.6857,16.7094,-2.0874,0.8569,1
+TmCl2+,NA,TmCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-223290,NA,-20.2,4.66,1.26,2.2586,-2.2666,6.6409,-2.6853,16.6521,-2.0854,0.85,1
+YbCl2+,NA,YbCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-216360,NA,-19.22,-4.55,-0.6,1.9985,-2.9017,6.8906,-2.659,11.1191,-3.9614,0.8351,1
+LuCl2+,NA,LuCl2+,aq,MWW09,NA,2010-07-03,HKF,cal,-222750,NA,-30.31,11.26,-1.23,1.9757,-2.9572,6.9124,-2.6567,21.9175,-0.7409,1.0031,1

Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2024-12-25 03:04:01 UTC (rev 858)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2024-12-25 06:05:30 UTC (rev 859)
@@ -399,4 +399,4 @@
 "SUPCRT92","greenalite","cr","cal",,,142507
 "SUPCRT92","grunerite","cr","cal",9.72,,
 "SUPCRT92","halloysite","cr","cal",-1.6,,
-"KBJ24","2-1-4 phase","cr","J",-4.39,,
+"Sandia","2-1-4 phase","cr","J",-4.39,,

Modified: pkg/CHNOSZ/inst/extdata/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/refs.csv	2024-12-25 03:04:01 UTC (rev 858)
+++ pkg/CHNOSZ/inst/extdata/refs.csv	2024-12-25 06:05:30 UTC (rev 859)
@@ -174,6 +174,7 @@
 GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805-6815","kieserite, starkeyite, hexahydrite, and epsomite",https://doi.org/10.1016/j.gca.2009.08.005
 HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695","kerogens (C128, C292, C406, C415, C515) and pyrobitumen (C<sub>54</sub>H<sub>42</sub>)",https://doi.org/10.1016/j.gca.2008.03.004
 LRB09,"K. H. Lemke, R. J. Rosenbauer and D. K. Bird",2009,"Astrobiology 9, 141-146","diglycine and diketopiperazine",https://doi.org/10.1089/ast.2008.0166
+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
 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

Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd	2024-12-25 03:04:01 UTC (rev 858)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd	2024-12-25 06:05:30 UTC (rev 859)
@@ -405,6 +405,10 @@
 This file also has H<sub>4</sub>SiO<sub>4</sub> from an earlier publication [@Ste01] that is roughly consistent with the SiO<sub>2</sub> here.
 See `demo(aluminum)` and the vignette [<span style="color:blue">*Regressing thermodynamic data*</span>](eos-regress.html) for examples.
 
+<h3>REE</h3>
+
+Rare earth element (REE(III)) fluoride and chloride complexes [@MWW09].
+
 <h3>GEMSFIT</h3>
 
 Internally consistent dataset for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl obtained with the [GEMSFIT](https://doi.org/10.1016/j.apgeochem.2014.10.013) package [@MWKH16;@MWKL17].

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2024-12-25 03:04:01 UTC (rev 858)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2024-12-25 06:05:30 UTC (rev 859)
@@ -456,6 +456,17 @@
   doi       = {10.1016/S0883-2927(00)00025-1},
 }
 
+ at Article{MWW09,
+  author    = {Migdisov, Art. A. and Williams-Jones, A. E. and Wagner, T.},
+  journal   = {Geochimica et Cosmochimica Acta},
+  title     = {An experimental study of the solubility and speciation of the {R}are {E}arth {E}lements ({III}) in fluoride- and chloride-bearing aqueous solutions at temperatures up to 300 °{C}},
+  year      = {2009},
+  number    = {23},
+  pages     = {7087--7109},
+  volume    = {73},
+  doi       = {10.1016/j.gca.2009.08.023},
+}
+
 @Article{OH88,
   author    = {Oelkers, Eric H. and Helgeson, Harold C.},
   journal   = {Journal of Physical Chemistry},

