[CHNOSZ-commits] r910 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/misc inst/extdata/thermo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri May 30 08:34:47 CEST 2025
Author: jedick
Date: 2025-05-30 08:34:46 +0200 (Fri, 30 May 2025)
New Revision: 910
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/refs.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/vignettes/OBIGT.bib
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
Add REE minerals from Migdisov et al. (2016)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-05-27 11:21:10 UTC (rev 909)
+++ pkg/CHNOSZ/DESCRIPTION 2025-05-30 06:34:46 UTC (rev 910)
@@ -1,6 +1,6 @@
-Date: 2025-05-27
+Date: 2025-05-30
Package: CHNOSZ
-Version: 2.1.0-81
+Version: 2.1.0-82
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 2025-05-27 11:21:10 UTC (rev 909)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2025-05-30 06:34:46 UTC (rev 910)
@@ -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 2.1.0-78 (2025-05-26)}{
+\section{Changes in CHNOSZ version 2.1.0-82 (2025-05-30)}{
\subsection{OBIGT DEFAULT DATA}{
\itemize{
@@ -43,10 +43,13 @@
\item Add alkylamines, benzylamines, and aminiums from
\href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}.
- \item Add cerianite (CeO\s{2}), chromite (FeCr\s{2}O\s{4}), and
- cassiterite (SnO\s{2}) from \href{https://doi.org/10.3133/b2131}{Robie
- and Hemingway (1995)}.
+ \item Add REE minerals from the compilation of
+ \href{https://doi.org/10.1016/j.chemgeo.2016.06.005}{Migdisov et al.
+ (2016)} with modifications.
+ \item Add chromite (FeCr\s{2}O\s{4}), and cassiterite (SnO\s{2}) from
+ \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}.
+
\item Move americium complexes from \file{SLOP98.csv} (entropy of the
element Am has been available for checking GHS self-consistency since
version 1.4.0).
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2025-05-27 11:21:10 UTC (rev 909)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2025-05-30 06:34:46 UTC (rev 910)
@@ -159,6 +159,75 @@
beta-UO2(OH)2,Sho,UO2(OH)2,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-1398683,-1533800,138,141,0,41.8,0.2,3530000,0,0,0,0,1273
Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL_Ttr,J,-3011454,-3203800,275.9,227.3,0,262.83,0.014653,-3549000,0,0,0,0,1273
chromite,Chr,FeCr2O4,cr,RH95,NA,2024-05-23,CGL,J,-1344500,-1445500,146,133.58,44.01,301.8,-0.04157,487700,-2803,1.147E-05,0,0,1800
-cerianite,Cei,CeO2,cr,RH95,NA,2024-05-23,CGL,J,-1024600,-1088700,62.3,61.63,23.85,80.29,0.005699,-729400,-209.9,0,0,0,1800
cassiterite,Cst,SnO2,cr,RH95,NA,2025-01-17,CGL_Ttr,J,-515800,-577600,49.02,53.22,21.55,76.04,0.007364,-2224000,0,0,0,0,1903
aluminum,Al,Al,cr,RH95,NA,2025-04-28,CGL_Ttr,J,0,0,28.3,24.21,9.999,41.32,-0.01988,-126500,-181.6,1.93E-05,0,0,933.5
+La2O3,La2O3,La2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1703890,-1791600,127.32,108.78,49.99,120.6805,0.013424,-1413668,0,0,0,0,2313
+Ce2O3,Ce2O3,Ce2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1709280,-1799800,148.1,115,46.47,113.736,0.028434,-641205,0,0,0,0,2392
+CeO2,CeO2,CeO2,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1026338,-1090400,62.29,61.63,24.61,74.4814,0.005837,-1297100,0,0,0,0,3083
+Pr2O3,Pr2O3,Pr2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1720040,-1809900,152.7,118.15,54.16,121.6594,0.025561,-989420,0,0,0,0,2310
+Nd2O3,Nd2O3,Nd2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1719840,-1806900,158.7,111.34,52.61,117.1079,0.028137,-1258450,0,0,0,0,2379
+Sm2O3,Sm2O3,Sm2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1734664,-1823000,150.6,114.52,46.02,129.7953,0.019031,-1862270,0,0,0,0,2190
+Eu2O3-monocl,Eu2O3,Eu2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1555060,-1650400,143.5,122.3,49.74,133.3906,0.016644,-1424350,0,0,0,0,2327
+Eu2O3-cubic,Eu2O3,Eu2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1565043,-1662500,136.4,123.9,49.74,136.2978,0.014988,-1499300,0,0,0,0,2327
+EuO,EuO,EuO,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-564358,-593200,83.6,NA,19.77,46.5453,0.00736,0,0,0,0,0,1793
+Gd2O3-monocl,Gd2O3,Gd2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1734203,-1819700,157.1,105.1,48.24,114.6104,0.015234,-1249170,0,0,0,0,2430
+Gd2O3-cubic,Gd2O3,Gd2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1766570,NA,150.6,105.52,48.24,114.8086,0.017291,-1283970,0,0,0,0,2430
+TbO2,TbO2,TbO2,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-915111,-972200,86.9,NA,24.67,73.259,0.013202,-1042400,0,0,0,0,1400
+Tb2O3,Tb2O3,Tb2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1777260,-1865200,159.2,116,46.68,120.6682,0.022172,-1002610,0,0,0,0,1823
+Dy2O3,Dy2O3,Dy2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1771740,-1863400,149.8,116.27,45.8,121.2302,0.015276,-845800,0,0,0,0,2223
+Ho2O3,Ho2O3,Ho2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1793280,-1883300,156.38,114.98,44.96,121.934,0.010116,-886280,0,0,0,0,2538
+Er2O3,Er2O3,Er2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1810380,-1900100,153.13,108.49,44.21,123.2921,0.008622,-1544330,0,0,0,0,2538
+Tm2O3,Tm2O3,Tm2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1795080,-1889300,139.7,116.73,43.26,128.4322,0.005232,-1178910,0,0,0,0,2588
+Yb2O3,Yb2O3,Yb2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1726740,-1814500,133.1,115.35,46.25,130.6438,0.003346,-1448200,0,0,0,0,2687
+Lu2O3,Lu2O3,Lu2O3,cr,MWBC16,KBK+14,2025-05-28,CGL_Ttr,J,-1792670,-1877000,126.79,101.75,41.91,122.4593,0.00729,-2034140,0,0,0,0,2762
+Y2O3,Y2O3,Y2O3,cr,MWBC16,MK04,2025-05-28,CGL,J,-1844070,-1932800,98.96,103.4,46.16,122.91,0.00743,-1931300,0,0,0,0,2000
+La(OH)3,La(OH)3,La(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1284200,-1416100,117.81,NA,43.35,174.6003,0.011336,796396,0,0,-20746.01,-1,1273
+Pr(OH)3,Pr(OH)3,Pr(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1280900,-1413800,131.7,NA,41.8,174.6003,0.009677,858653,0,0,-20698.87,-1,1273
+Nd(OH)3,Nd(OH)3,Nd(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1283000,-1415600,129.87,NA,40.65,174.6003,0.010826,983534,0,0,-21241.87,-1,1273
+Eu(OH)3,Eu(OH)3,Eu(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1180600,-1319100,119.88,NA,39.76,174.6003,0.027272,791828,0,0,-20557.44,-1,1273
+Gd(OH)3,Gd(OH)3,Gd(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1276200,-1408900,126.63,NA,38.72,174.6003,0.014341,967638,0,0,-22925.02,-1,1273
+Tb(OH)3,Tb(OH)3,Tb(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1281100,-1414800,128.37,NA,37.66,174.6003,0.012288,1137175,0,0,-22959.94,-1,1273
+Ho(OH)3,Ho(OH)3,Ho(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1297400,-1431100,130.04,NA,37.26,174.6003,0.021297,1148144,0,0,-23562.31,-1,1273
+Y(OH)3,Y(OH)3,Y(OH)3,cr,MWBC16,DRT98,2025-05-28,CGL,J,-1338500,-1472300,99.21,NA,37.51,174.6003,0.021297,1148144,0,0,-23562.31,-1,1273
+LaCl3,LaCl3,LaCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-995890,-1071600,137.57,98.03,65.95,74.9288,0.051654,684520,0,0,0,0,1133
+CeCl3,CeCl3,CeCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-983610,-1059700,151.42,98.6,64.22,90.9772,0.035812,-271530,0,0,0,0,1090
+PrCl3,PrCl3,PrCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-982720,-1058600,153.3,98.95,64.15,85.6511,0.039524,134650,0,0,0,0,1060
+NdCl3,NdCl3,NdCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-965560,-1040900,153.43,99.24,63.08,87.2834,0.038586,40210,0,0,0,0,1032
+SmCl3,SmCl3,SmCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-949550,-1025300,150.12,99.54,89.81,95.3748,0.033444,-516135,0,0,0,0,950
+EuCl3,EuCl3,EuCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-855390,-935400,144.06,106.98,63.13,100.9736,0.030092,-263620,0,0,0,0,894
+GdCl3,GdCl3,GdCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-943280,-1018200,151.42,97.78,60.74,88.7959,0.031444,-34750,0,0,0,0,875
+TbCl3,TbCl3,TbCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-935170,-1010600,154.85,97.8,75.36,86.292,0.038598,0,0,0,0,0,783
+DyCl3,DyCl3,DyCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-923340,-993100,175.4,100.5,68.87,104.5279,-0.027019,0,0,4.53E-05,0,0,924
+HoCl3,HoCl3,HoCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-928290,-997700,177.1,101.9,92.03,100.382,0.005091,0,0,0,0,0,993
+ErCl3,ErCl3,ErCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-925020,-994400,175.1,99.78,87.84,101.4247,-0.016327,0,0,3.63E-05,0,0,1049
+TmCl3,TmCl3,TmCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-926200,-996300,173.5,100,69.52,102.0423,-0.017956,0,0,3.73E-05,0,0,1095
+YbCl3,YbCl3,YbCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-892360,-959500,169.3,101.4,68.11,104.8985,-0.02384,0,0,4.06E-05,0,0,1138
+LuCl3,LuCl3,LuCl3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-917760,-987100,153,96.62,90.66,98.3259,-0.01795,0,0,4.1E-05,0,0,1198
+LaF3,LaF3,LaF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1656370,-1699500,106.98,90.29,33.74,255.8744,-0.16815,-774231,-1972.378,8.48E-05,0,0,1766
+CeF3,CeF3,CeF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1641370,-1689200,115.23,93.47,29.84,103.2577,-0.0129896,-720870,0,2.47E-05,0,0,1703
+PrF3,PrF3,PrF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1641370,-1689100,121.22,92.65,32.56,130.5994,-0.0325026,-2655590,0,1.82E-05,0,0,1670
+NdF3,NdF3,NdF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1634370,-1679400,120.79,92.42,31.75,103.3867,0.0016669,-1101170,0,1.04E-05,0,0,1649
+SmF3,SmF3,SmF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1624370,-1700700,116.5,91.7,31.85,169.0564,-0.076809,-4840760,0,0,0,0,743
+GdF3,GdF3,GdF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1621370,-1699300,114.77,88.39,27.37,102.3403,0.0060945,-1401620,0,0,0,0,1347
+TbF3,TbF3,TbF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1618370,-1695900,118.97,90.5,30.14,97.5769,0.0198845,-1156100,0,0,0,0,1446
+DyF3,DyF3,DyF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1616870,-1692000,118.07,88.94,31.02,91.2338,0.0282118,-926687,0,-3.16E-06,0,0,1426
+HoF3,HoF3,HoF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1624370,-1697800,120.34,88.6,29.27,131.7639,-0.0650032,-2463830,0,4.425E-05,0,0,1416
+ErF3,ErF3,ErF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1614370,-1693600,116.86,90.07,29.99,121.3374,-0.0303149,-2155640,0,2.27E-05,0,0,1388
+TmF3,TmF3,TmF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1614370,-1693700,114.98,90.8,25.06,115.6209,-0.0171827,-1853060,0,1.29E-05,0,0,1325
+YbF3,YbF3,YbF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1587370,-1655100,111.84,89.4,29,103.7012,0.0092366,-1516080,0,0,0,0,1267
+LuF3,LuF3,LuF3,cr,MWBC16,KK03,2025-05-28,CGL_Ttr,J,-1610370,-1679900,94.83,87.07,33.49,89.0368,0.0192857,-685980,0,0,0,0,1230
+LaPO4,LaPO4,LaPO4,cr,MWBC16,PK06,2025-05-28,CGL,J,-1850500,-1969700,108.28,101.28,47.48,121.13,0.030116,-2562500,0,0,0,0,1273
+CePO4,CePO4,CePO4,cr,MWBC16,PK06,2025-05-28,CGL,J,-1849900,-1969500,119.97,106.63,46.5,125.21,0.027894,-2408500,0,0,0,0,1273
+PrPO4,PrPO4,PrPO4,cr,MWBC16,PK06,2025-05-28,CGL,J,-1841900,-1961800,123.2,106.04,46.3,124.5,0.030374,-2449500,0,0,0,0,1273
+NdPO4,NdPO4,NdPO4,cr,MWBC16,PK06,2025-05-28,CGL,J,-1848400,-1967900,122.9,104.92,45.5,132.96,0.022541,-3100900,0,0,0,0,1273
+SmPO4,SmPO4,SmPO4,cr,MWBC16,PK06,2025-05-28,CGL,J,-1847000,-1965800,122.5,105.59,44.19,133.13,0.023468,-3068700,0,0,0,0,1273
+EuPO4,EuPO4,EuPO4,cr,MWBC16,PK06,2025-05-28,CGL,J,-1741600,-1864400,117.2,111.49,45.48,137.56,0.017693,-2785400,0,0,0,0,1273
+GdPO4,GdPO4,GdPO4,cr,MWBC16,PK06,2025-05-28,CGL,J,-1840800,-1958500,124.57,102.21,43.53,133.24,0.012793,-3097200,0,0,0,0,1273
+TbPO4,TbPO4,TbPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1855900,-1971100,138.1,NA,44.8,165.51,0.01904,-661298.2,-1024.372,1.187E-05,0,0,1273
+DyPO4,DyPO4,DyPO4,cr,MWBC16,GHFW16,2025-05-28,CGL,J,-1829100,-1950600,119,NA,44.27,185.5,0,-3261000,-751.9,0,0,0,1273
+HoPO4,HoPO4,HoPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1857000,-1971600,142.3,NA,43.75,0,0,0,0,0,0,0,1273
+ErPO4,ErPO4,ErPO4,cr,MWBC16,GHFW16,2025-05-28,CGL,J,-1832500,-1954100,116.6,NA,43.29,264.19,-0.03543,491967.5,-2752.696,9.42E-06,0,0,1273
+TmPO4,TmPO4,TmPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1849300,-1964700,138.1,NA,42.7,0,0,0,0,0,0,0,1273
+YbPO4,YbPO4,YbPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1817000,-1929400,133.9,NA,41.11,247.56,-0.02291,256022.1,-2463.215,6.87E-06,0,0,1273
+LuPO4,LuPO4,LuPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1840600,-1955400,117.2,NA,41.9,268.28,-0.04472,570634.2,-2803.989,1.1187E-05,0,0,1273
+YPO4,YPO4,YPO4,cr,MWBC16,NLM+15,2025-05-28,CGL,J,-1872400,-1987700,108.8,NA,44.57,134.06,0.01833,-3490000,-52.4841,4.24E-07,0,0,1273
Modified: pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv 2025-05-27 11:21:10 UTC (rev 909)
+++ pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv 2025-05-30 06:34:46 UTC (rev 910)
@@ -312,6 +312,19 @@
"OBIGT","ferberite","cr","J",1.21,,
"OBIGT","willemite","cr","J",-1.47,,
"OBIGT","rutherfordine","cr","J",-14.37,,
+"OBIGT","Eu(OH)3","cr","J",,,-860
+"OBIGT","LaF3","cr","J",,,32632
+"OBIGT","CeF3","cr","J",,,29974
+"OBIGT","PrF3","cr","J",,,28646
+"OBIGT","NdF3","cr","J",,,30967
+"OBIGT","GdF3","cr","J",,,-1160
+"OBIGT","DyF3","cr","J",,,2653
+"OBIGT","HoF3","cr","J",,,3835
+"OBIGT","ErF3","cr","J",,,-1560
+"OBIGT","TmF3","cr","J",,,-852
+"OBIGT","YbF3","cr","J",,,7468
+"OBIGT","LuF3","cr","J",,,8083
+"OBIGT","CePO4","cr","J",,,681
"OBIGT","octadecane","cr","cal",-2.63,,
"OBIGT","nonadecane","cr","cal",-13.32,,
"OBIGT","eicosane","cr","cal",-2.79,,
Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-05-27 11:21:10 UTC (rev 909)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-05-30 06:34:46 UTC (rev 910)
@@ -64,7 +64,7 @@
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","aluminum, bixbyite, cassiterite, cattierite, cerianite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, zinc",https://doi.org/10.3133/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","aluminum, bixbyite, cassiterite, cattierite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, 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
@@ -104,6 +104,7 @@
TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",https://doi.org/10.1016/S1251-8050(97)83981-X
TZA97,"B. R. Tagirov, A. V. Zotov and N. N. Akinfiev",2007,"Geochim. Cosmochim. Acta 61, 4267-4280","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00274-3
ST97,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylammonium chloride HKF parameters",https://doi.org/10.1023/A:1022977006327
+DRT98,"I. I. Diakonov et al.",1998,"Chem. Geol. 151, 327-347","REE hydroxides",https://doi.org/10.1016/S0009-2541(98)00088-6
proton,OBIGT,1997,"Hydrogen-ion convention","""The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature"" [@JOH92]",https://chnosz.net
HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6
HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6
@@ -142,6 +143,7 @@
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
+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",
NA03.1,"D. K. Nordstrom and D. G. Archer",2003,"Arsenic thermodynamic data and environmental geochemistry. In Arsenic in Groundwater, eds. Welch and Stollenwerk, Kluwer","aqueous As oxides and sulfides",
@@ -148,6 +150,7 @@
MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",https://doi.org/10.2138/am-2003-5-613
AS04,"J. Apps and N. Spycher",2004,"Data qualification for thermodynamic data used to support THC calculations. Bechtel SAIC Company, LLC. ANL-NBS-HS-000043 REV 00 (DOC.20041118.0004)","aqueous SiO<sub>2</sub>",
Got04,"M. Gottschalk",2004,"Rev. Mineral. Geochem. 56, 83-124","zoisite, clinozoisite, and epidote",https://doi.org/10.2138/gsrmg.56.1.83
+MK04,"L. R. Morse and R. J. M. Konings",2004,"Thermochemistry of binary rare earth oxides, in Binary Rare Earth Oxides",Y<sub>2</sub>O<sub>3</sub>,https://doi.org/10.1007/1-4020-2569-6_7
MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",https://doi.org/10.1007/s00269-004-0405-z
SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",https://doi.org/10.1016/j.gca.2003.06.001
VPV05,"O. Vidal, T. Parra and P. Viellard",2005,"Am. Mineral. 90, 347-358",Fe-amesite,https://doi.org/10.2138/am.2005.1554
@@ -170,6 +173,7 @@
LEB+06,"W. Liu et al.",2006,"Chem. Geol. 231, 326-349","FeCl<sub>2</sub><sup>+</sup>, FeCl<sub>3</sub>, FeCl<sub>4</sub><sup>-</sup>",https://doi.org/10.1016/j.chemgeo.2006.02.005
LMR06,"D. Langmuir et al.",2006,"Geochim. Cosmochim. Acta 70, 2942-2956","scorodite and amorphous ferric arsenate: G",https://doi.org/10.1016/j.gca.2006.03.006
MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175
+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
@@ -205,6 +209,7 @@
FDM+14,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","CO<sub>2</sub>, HCO<sub>3</sub><sup>-</sup>, CO<sub>3</sub><sup>-2</sup>, CaCO<sub>3</sub>, Ca<sup>+2</sup>",https://doi.org/10.1016/j.gca.2014.01.030
FDM+14.1,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","aragonite; source of data: `berman.dat`",https://doi.org/10.1016/j.gca.2014.01.030
Kit14,"N. Kitadai",2014,"J. Mol. Evol. 78, 171-187","glycine, diglycine, and triglycine (zwitterions and ions); diketopiperazine, [Gly] and [UPBB] groups",https://doi.org/10.1007/s00239-014-9616-1
+KBK+14,"R. J. M. Konings et al.",2014,"J. Phys. Chem. Ref. Data 43, Article 013101","REE oxides",https://doi.org/10.1063/1.4825256
PAB+14,"G. S. Pokrovski, N. N. Akinfiev et al., 2014",2014,"Geol. Soc. Spec. Publ. 402, 9-70","corrected H of AuHS",https://doi.org/10.1144/SP402.4
SBS14,"A. Stefánsson, P. Benézéth and J. Schott",2014,"Geochim. Cosmochim. Acta 138, 21-31",Mg(HCO<sub>3</sub>)<sup>+</sup>,https://doi.org/10.1016/j.gca.2014.04.008
SHA14,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","SiO<sub>2</sub> and Si<sub>2</sub>O<sub>4</sub>",https://doi.org/10.1016/j.gca.2013.12.019
@@ -212,10 +217,13 @@
SHA14.2,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","BO(OH): Revised May 2013",https://doi.org/10.1016/j.gca.2013.12.019
SHA14.3,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","Fitted to @HP97 data with a<sub>1</sub> pred. from the sum of the ions and used to predict the volume",https://doi.org/10.1016/j.gca.2013.12.019
SHA14.4,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","BO<sub>2</sub><sup>-</sup>: revised a<sub>1</sub>-a<sub>4</sub> using delkappan for BO<sub>2</sub><sup>-</sup> instead of B(OH)<sub>4</sub><sup>-</sup> used by @SH88; @SSWS97",https://doi.org/10.1016/j.gca.2013.12.019
+GHFW16,"A. P. Gysi et al.",2016,"Thermochim. Acta 627–629, 61-67","REE phosphates (xenotimes) [different S for DyPO<sub>4</sub> than @MWBC16]",https://doi.org/10.1016/j.tca.2016.01.016
Kit15,"N. Kitadai",2015,"Origins Life Evol. Biospheres 45, 377-409","charged amino acids",https://doi.org/10.1007/s11084-015-9428-3
Kit15.1,"N. Kitadai",2015,"Origins Life Evol. Biospheres 45, 377-409","charged amino acids GHS (Arg<sup>+</sup>, Arg<sup>-</sup>, Asp<sup>-</sup>, Glu<sup>-</sup>, His<sup>+</sup>, Lys<sup>+</sup>, Lys<sup>-</sup>, and Tyr<sup>-</sup>)",https://doi.org/10.1007/s11084-015-9428-3
+NLM+15,"A. Navrotsky et al.",2015,"J. Chem. Thermodyn.","REE phosphates (xenotimes) [different G than @MWBC16]",https://doi.org/10.1016/j.jct.2015.04.008
PD15,"G. S. Pokrovski and J. Dubessy",2015,"Earth Planet. Sci. Lett. 411, 298-309","trisulfur radical ion",https://doi.org/10.1016/j.epsl.2014.11.035
LA16,"D. E. LaRowe and J. P. Amend",2016,"ISME J. 10, 1285-1295","fatty acids, saccharides, and other species",https://doi.org/10.1038/ismej.2015.227
+MWBC16,"A. A. Migdisov et al.",2016,"Chem. Geol. 439, 13-42","Compilation of data for REE minerals with modifications for OBIGT",https://doi.org/10.1016/j.chemgeo.2016.06.005
SLOP16.1,"E. L. Shock et al.",2016,"slop16.dat computer data file",""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."",https://doi.org/10.5281/zenodo.2630820
SLOP16.2,"E. L. Shock et al.",2016,"slop16.dat computer data file","Zn(Ac)<sub>3</sub><sup>-</sup>: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."",https://doi.org/10.5281/zenodo.2630820
SLOP16.3,"E. L. Shock et al.",2016,"slop16.dat computer data file","formaldehyde: "Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of @SS93."",https://doi.org/10.5281/zenodo.2630820
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2025-05-27 11:21:10 UTC (rev 909)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2025-05-30 06:34:46 UTC (rev 910)
@@ -127,6 +127,16 @@
doi = {10.1016/0016-7037(95)00403-3},
}
+ at Article{DRT98,
+ author = {Diakonov, I. I. and Ragnarsdottir, K. V. and Tagirov, B. R.},
+ journal = {Chemical Geology},
+ title = {Standard thermodynamic properties and heat capacity equations of rare earth hydroxides: {II}. {C}e({III})-, {P}r-, {S}m-, {E}u({III})-, {G}d-, {T}b-, {D}y-, {H}o-, {E}r-, {T}m-, {Y}b-, and {Y}-hydroxides. {C}omparison of thermochemical and solubility data},
+ year = {1998},
+ pages = {327--347},
+ volume = {151},
+ doi = {10.1016/S0009-2541(98)00088-6},
+}
+
@PhdThesis{Dic07,
author = {Dick, Jeffrey Michael},
school = {University of California},
@@ -1783,6 +1793,17 @@
doi = {10.1016/j.gca.2020.04.009},
}
+ at Article{KBK+14,
+ author = {Konings, Rudy J. M. and Beneš, Ondrej and Kovács, Attila and Manara, Dario and Sedmidubský, David and Gorokhov, Lev and Iorish, Vladimir S. and Yungman, Vladimir and Shenyavskaya, E. and Osina, E.},
+ journal = {Journal of Physical and Chemical Reference Data},
+ title = {The thermodynamic properties of the \emph{f}-elements and their compounds. Part 2. The lanthanide and actinide oxides},
+ year = {2014},
+ number = {1},
+ pages = {013101},
+ volume = {43},
+ doi = {10.1063/1.4825256},
+}
+
@Article{LXW21,
author = {Xiangchong Liu and Changhao Xiao and Yong Wang},
journal = {Chemical Geology},
@@ -1834,7 +1855,6 @@
pages = {101624},
volume = {14},
doi = {10.1016/j.gsf.2023.101624},
- issn = {1674-9871},
}
@Article{TTA+23,
@@ -1847,6 +1867,16 @@
doi = {10.1016/j.chemgeo.2023.121413},
}
+ at Article{MWBC16,
+ author = {A. Migdisov and A. E. Williams-Jones and J. Brugger and F. A. Caporuscio},
+ journal = {Chemical Geology},
+ title = {Hydrothermal transport, deposition, and fractionation of the {REE}: Experimental data and thermodynamic calculations},
+ year = {2016},
+ pages = {13--42},
+ volume = {439},
+ doi = {10.1016/j.chemgeo.2016.06.005},
+}
+
@Book{NEA20,
author = {I. Grenthe and X. Gaona and A. Plyasunov and L. Rao and W. Runde and B. Grambow},
publisher = {OECD and Nuclear Energy Agency},
@@ -1931,7 +1961,6 @@
title = {Tantalum in hydrothermal fluids},
year = {2024},
doi = {10.1016/j.gca.2024.10.019},
- issn = {0016-7037},
}
@Article{AZ23,
@@ -2022,3 +2051,59 @@
year = {2024},
doi = {10.1016/j.gca.2024.12.019},
}
+
+ at InCollection{MK04,
+ author = {Morss, L. R. and Konings, R. J. M.},
+ booktitle = {Binary Rare Earth Oxides},
+ publisher = {Springer Netherlands},
+ title = {Thermochemistry of binary rare earth oxides},
+ year = {2004},
+ address = {Dordrecht},
+ editor = {Adachi, G. and Imanaka, N. and Kang, Z. C.},
+ pages = {163--188},
+ doi = {10.1007/1-4020-2569-6_7},
+}
+
+ at Article{NLM+15,
+ author = {Alexandra Navrotsky and Wingyee Lee and Aleksandra Mielewczyk-Gryn and Sergey V. Ushakov and Andre Anderko and Haohan Wu and Richard E. Riman},
+ journal = {The Journal of Chemical Thermodynamics},
+ title = {Thermodynamics of solid phases containing rare earth oxides},
+ year = {2015},
+ pages = {126--141},
+ volume = {88},
+ doi = {10.1016/j.jct.2015.04.008},
+}
+
+ at InCollection{KK03,
+ author = {R. J. M. Konings and A. Kovács},
+ booktitle = {Handbook on the Physics and Chemistry of Rare Earths},
+ publisher = {Elsevier},
+ title = {Thermodynamic properties of the lanthanide({III}) halides},
+ year = {2003},
+ editor = {K. A. Gschneidner and J.-C. G. Bünzli and V. K. Pecharsky},
+ pages = {147--247},
+ series = {Handbook on the Physics and Chemistry of Rare Earths},
+ volume = {33},
+ doi = {10.1016/S0168-1273(02)33003-4},
+}
+
+ at Article{GHFW16,
+ author = {Alexander P. Gysi and Daniel Harlov and Deusavan Costa Filho and Anthony E. Williams-Jones},
+ journal = {Thermochimica Acta},
+ title = {Experimental determination of the high temperature heat capacity of a natural xenotime-({Y}) solid solution and synthetic {DyPO}\textsubscript{4} and {ErPO}\textsubscript{4} endmembers},
+ year = {2016},
+ pages = {61--67},
+ volume = {627--629},
+ doi = {10.1016/j.tca.2016.01.016},
+}
+
+ at Article{PK06,
+ author = {K. Popa and R. J. M. Konings},
+ journal = {Thermochimica Acta},
+ title = {High-temperature heat capacities of {EuPO}\textsubscript{4} and {SmPO}\textsubscript{4} synthetic monazites},
+ year = {2006},
+ number = {1},
+ pages = {49--52},
+ volume = {445},
+ doi = {10.1016/j.tca.2006.03.023},
+}
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2025-05-27 11:21:10 UTC (rev 909)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2025-05-30 06:34:46 UTC (rev 910)
@@ -1865,7 +1865,7 @@
- `Shh`: Relative stabilities of transcription factors along redox and water activity gradient
- `carboxylase`: Predicted rank abundance with varying temperature and redox
- - `rank.affinity`: Affinity ranking for groupwise stability comparisons
+ - `rank.affinity`: Average rank of affinity for groupwise stability comparisons
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