[CHNOSZ-commits] r919 - 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
Thu Jun 5 08:55:17 CEST 2025
Author: jedick
Date: 2025-06-05 08:55:16 +0200 (Thu, 05 Jun 2025)
New Revision: 919
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv
pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/refs.csv
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Corrected {U+0394}H{U+00B0}f of In+3 and derived species
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/DESCRIPTION 2025-06-05 06:55:16 UTC (rev 919)
@@ -1,6 +1,6 @@
-Date: 2025-06-03
+Date: 2025-06-05
Package: CHNOSZ
-Version: 2.1.0-90
+Version: 2.1.0-91
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 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2025-06-05 06:55:16 UTC (rev 919)
@@ -15,18 +15,18 @@
\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 2.1.0-90 (2025-06-04)}{
+\section{Changes in CHNOSZ version 2.1.0-91 (2025-06-05)}{
\subsection{OBIGT DATABASE FORMAT}{
\itemize{
\item Mineral species whose \code{T} value is a Cp equation limit or
- phase transition temperature are indicated by \samp{CGL} or \samp{CGL_Ttr},
- respectively, in \code{model}. At conditions above the \code{T} limit,
- \code{subcrt()} extrapolates values and produces a warning for \samp{CGL}
- species or returns NA values for \samp{CGL_Ttr} species. The addition of
- \samp{CGL_Ttr} replaces the previous strategy of using signed values of
- \code{T}.
+ phase transition temperature are indicated by \samp{CGL} or
+ \samp{CGL_Ttr}, respectively, in \code{model}. At temperatures above the
+ \code{T} limit, \code{subcrt()} extrapolates values and produces a
+ warning for \samp{CGL} species or returns NA values for \samp{CGL_Ttr}
+ species. The addition of \samp{CGL_Ttr} replaces the previous strategy of
+ using signed values of \code{T}.
}
}
@@ -93,7 +93,7 @@
\href{https://doi.org/10.2113/gsecongeo.80.5.1365}{Jackson and Helgeson
(1985)} to optional data.
- \item Add spherocobaltite (CoCO<sub>3</sub>) from
+ \item Add spherocobaltite (CoCO\s{3}) from
\href{https://doi.org/10.1007/978-3-662-02293-1}{Barin et al. (1977)}.
\item Add CoSO\s{4} and beta-Nb\s{2}O\s{5} from
@@ -100,10 +100,16 @@
\href{https://www.worldcat.org/oclc/8139446}{Naumov et al. (1974)}. A PDF
of this publication is available from the
\href{https://ntrl.ntis.gov/NTRL/}{National Technical Reports Library}.
-
+
\item Move americium complexes from optional to default data. Entropy of
the element Am has been listed in \file{element.csv} since CHNOSZ 1.4.0.
+ \item Corrected Δ\emph{H}°\s{f} by -7335 cal/mol to maintain GHS
+ consistency for In\s{+3} and derived species. This is in addition to the
+ correction for S° previously noted by
+ \href{https://doi.org/10.1016/0016-7037(88)90181-0}{Shock and Helgeson
+ (1988)}.
+
\item Fix sign of \emph{c} parameter for nesquehonite. Thanks to James
Leong and Grayson Boyer.
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/DEW.csv 2025-06-05 06:55:16 UTC (rev 919)
@@ -110,7 +110,7 @@
HSO4-,HSO4(-),HSO4-,aq,SSWS97,DEW17.3,2017-09-26,DEW,cal,-180630,-212500,30,5.3,35.2,8.9201,4.2097,1.3083,-2.953,20.096,-1.955,1.1748,-1
HSO5-,HSO5(-),HSO5-,aq,SSWS97,DEW17.3,2017-09-26,DEW,cal,-152370,-185380,50.7,29.2,50.7,11.7798,6.9324,-0.9747,-3.0656,31.2126,2.9134,0.8611,-1
HVO4-2,HVO4(-2),HVO4-2,aq,SSWS97,DEW17.3,2017-09-26,DEW,cal,-233000,-277000,4,-48.3,17.4,6.4118,1.8216,3.3107,-2.8543,6.9054,-12.8732,3.1527,-2
-In+3,In(+3),In+3,aq,SSWS97,DEW17.2,2017-09-26,DEW,cal,-23400,-25000,-63,-34.9,-42.2,-8.3223,-2.0934,13.9778,-2.6925,8.7478,-10.1438,2.5003,3
+In+3,In(+3),In+3,aq,SSWS97,DEW17.201,2017-09-26,DEW,cal,-23400,-32335,-63,-34.9,-42.2,-8.3223,-2.0934,13.9778,-2.6925,8.7478,-10.1438,2.5003,3
isobutane,Isobutane,C4H10,aq,SH90,DEW17.22,2017-09-26,DEW,cal,36,-36230,40.02,133.92,82.81,17.46,12.34,-5.51,-3.29,92.3,19.12,-0.3,0
KCl,KCl(0),KCl,aq,OH88,DEW17.23,2017-09-26,DEW,cal,-98850,NA,34,-1.5,34,8.1715,3.4969,1.9059,-2.9236,6.2088,-3.3402,0.1,0
KOH,KOH(0),KOH,aq,HP97,SHA14.3,2017-09-26,DEW,cal,-102800,-180000,36.3,-6.5,20.3,5.6931,1.1373,3.8845,-2.826,6.7794,-4.3587,0.48,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv 2025-06-05 06:55:16 UTC (rev 919)
@@ -301,7 +301,7 @@
CoCl+,CoCl+,CoCl+,aq,SSH97.3,NA,2007-10-16,HKF,cal,-45157,-53965,-11.27,17.02,-1.5,1.8028,-3.3766,7.0702,-2.6394,22.7656,0.4323,0.7191,1
CuCl,CuCl,CuCl,aq,SSH97.3,NA,1997-10-02,HKF,cal,-22608,-26338,22.06,19.64,17.22,4.1084,2.253,4.8575,-2.8721,17.3292,0.967,-0.038,0
CuCl2-,CuCl2-,CuCl2-,aq,SSH97.3,NA,1997-10-02,HKF,cal,-58038,-72903,26.96,32.99,45.43,8.3943,12.7182,0.7442,-3.3047,36.7555,3.6846,1.2219,-1
-InCl+2,InCl+2,InCl+2,aq,SSH97.3,NA,1997-10-07,HKF,cal,-59226,-66209,-38.8,1.57,-21.67,-0.6441,-9.3513,9.4185,-2.3924,22.2354,-2.7149,1.6444,2
+InCl+2,InCl+2,InCl+2,aq,SSH97.3,OBIGT25,1997-10-07,HKF,cal,-59226,-73544,-38.8,1.57,-21.67,-0.6441,-9.3513,9.4185,-2.3924,22.2354,-2.7149,1.6444,2
ZnCl+,ZnCl+,ZnCl+,aq,SSH97.3,NA,1997-09-16,HKF,cal,-66850,-66240,23,19.9,-1.28,1.6583,-3.7293,7.2088,-2.6248,19.6947,1.0191,0.2025,1
ZnCl2,ZnCl2,ZnCl2,aq,SSH97.3,NA,1997-09-16,HKF,cal,-98300,-109080,27.03,34.7,24.82,5.1486,4.7929,3.8592,-2.9771,26.1528,4.0338,-0.038,0
ZnCl3-,ZnCl3-,ZnCl3-,aq,SSH97.3,NA,1997-10-02,HKF,cal,-129310,-151060,25,41.97,53.9,9.5636,15.5732,-0.3779,-3.4227,42.2912,5.5147,1.2513,-1
@@ -308,7 +308,7 @@
Zn(Ac)+,Zn(Ac)+,ZnCH3COO+,aq,SSH97.4,NA,1997-09-18,HKF,cal,-125660,-155120,9.4,86.2,21.52,4.8484,4.06,4.1473,-2.9468,60.4626,14.5244,0.41,1
Zn(Ac)2,Zn(Ac)2,Zn(CH3COO)2,aq,SSH97.4,NA,1997-09-18,HKF,cal,-216450,-271500,22.47,193.3,73.02,11.7443,20.8978,-2.4707,-3.6429,119.1022,36.3407,-0.038,0
Zn(Ac)3-,Zn(Ac)3-,Zn(CH3COO)3-,aq,SSH97.4,SLOP16.2,1998-06-02,HKF,cal,-305740,-408093,25,316.5,130.4,20.0332,41.1373,-10.4257,-4.4796,203.1827,61.4365,1.2513,-1
-InF+2,InF+2,InF+2,aq,SSH97.6,NA,1997-10-09,HKF,cal,-97016,-98718,-23.53,5.84,-40.87,-3.3507,-15.96,12.016,-2.1192,22.5771,-1.8453,1.4099,2
+InF+2,InF+2,InF+2,aq,SSH97.6,OBIGT25,1997-10-09,HKF,cal,-97016,-106053,-23.53,5.84,-40.87,-3.3507,-15.96,12.016,-2.1192,22.5771,-1.8453,1.4099,2
Ag+,Ag+,Ag+,aq,SH88.3,NA,1997-11-07,HKF,cal,18427,25275,17.54,7.9,-0.8,1.7285,-3.5608,7.1496,-2.6318,12.7862,-1.4254,0.216,1
Al+3,Al+3,Al+3,aq,SSWS97.2,NA,1997-11-07,HKF,cal,-115609,-126834,-77.7,-32.5,-44.4,-3.3802,-17.0071,14.5185,-2.0758,10.7,-8.06,2.753,3
Au+,Au+,Au+,aq,SSWS97.2,SH88.1,1997-11-13,HKF,cal,39000,47900,25.6,-0.3,12.5,3.5312,0.8428,5.4139,-2.8137,7.5089,-3.0956,0.1648,1
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2025-06-05 06:55:16 UTC (rev 919)
@@ -179,7 +179,7 @@
Fr+,Fr+,Fr+,aq,SSWS97,NA,1997-11-11,HKF,cal,-70500,-62500,35.1,-6.5,21.5,4.7139,3.7284,4.2849,-2.933,2.5442,-4.3586,0.0203,1
Be+2,Be+2,Be+2,aq,SSWS97,NA,1997-11-11,HKF,cal,-90550,-91500,-32.1,-5.8,-20.9,-0.5718,-9.1742,9.3462,-2.3996,17.0245,-4.216,1.5475,2
Ra+2,Ra+2,Ra+2,aq,SSWS97,NA,1997-11-11,HKF,cal,-134200,-126100,12.9,-14.3,-12.3,0.374,-6.8598,8.4279,-2.4953,5.7496,-5.9474,0.8644,2
-In+3,In+3,In+3,aq,SSWS97,SH88.1,1997-11-11,HKF,cal,-23400,-25000,-63,-15.6,-35.5,-2.2361,-13.2378,10.9433,-2.2316,20.3744,-6.2122,2.5346,3
+In+3,In+3,In+3,aq,SSWS97,SH88.5,1997-11-11,HKF,cal,-23400,-32335,-63,-15.6,-35.5,-2.2361,-13.2378,10.9433,-2.2316,20.3744,-6.2122,2.5346,3
Tl+,Tl+,Tl+,aq,SSWS97,SH88.1,1997-11-11,HKF,cal,-7740,1280,30,-4.2,18.2,4.2884,2.6903,4.691,-2.8901,4.6024,-3.89,0.0974,1
Tl+3,Tl+3,Tl+3,aq,SSWS97,SH88.1,1997-11-11,HKF,cal,51300,47000,-46,-0.2,-27,-1.1607,-10.6078,9.9017,-2.3404,27.0098,-3.0752,2.2752,3
CN-,CN-,CN-,aq,SSWS97,NA,1997-11-11,HKF,cal,41200,36000,22.5,-17.7,23.9,5.4714,5.5813,3.5497,-3.0096,7.6773,-6.64,1.29,-1
@@ -716,14 +716,14 @@
Ga(SO4)2-,Ga(SO4)2-,Ga(SO4)2-,aq,HB24,HB24.1,2023-07-07,HKF,cal,-400818,-473276,-6,-69.45,32.69,1.9788,-3.3569,7.0695,-2.6402,-17.1818,-27.5761,1.7204,-1
Ge(OH)4,Ge(OH)4,Ge(OH)4,aq,HB24,PS98.1,2019-11-28,HKF,cal,-231200,-267000,47.83,50,54.9,9.29,14.9,-0.11,-3.4,57.1,-3.5,0,0
GeO(OH)3-,GeO(OH)3-,GeO(OH)3-,aq,HB24,PS98.1,2019-11-28,HKF,cal,-218500,-260500,27.14,18,27.14,5.96,6.77,3.09,-3.06,27.66,0.63,1.2,-1
-InCl+2,InCl+2,InCl+2,aq,HB24,BS23,2023-07-07,HKF,cal,-58530.66,-65513.139,-38.803,44.059,-12.821,-2.446,6.363,-2.992,-3.042,47.137,5.94,1.644,2
-InCl2+,InCl2+,InCl2+,aq,HB24,BS23,2023-07-07,HKF,cal,-92119.729,-107898.655,-26.056,84.938,12.449,-2.094,5.446,36.329,-3.004,64.639,14.267,0.944,1
-InCl3,InCl3,InCl3,aq,HB24,BS23,2023-07-07,HKF,cal,-124358.201,-152376.136,-24.855,107.036,40.603,-1.604,4.172,79.3,-2.951,68.62,18.769,-0.03,0
-InF+2,InF+2,InF+2,aq,HB24,BS23,2023-07-07,HKF,cal,-97424.777,-99126.775,-23.527,48.161,-31.931,-2.328,6.056,-36.052,-3.029,47.381,6.776,1.41,2
-InF2+,InF2+,InF2+,aq,HB24,BS23,2023-07-07,HKF,cal,-169539.617,-181812.026,-19.166,94.733,-27.953,-2.044,5.317,-31.841,-2.999,69.469,16.262,0.845,1
-InF3,InF3,InF3,aq,HB24,BS23,2023-07-07,HKF,cal,-240426.641,-268312.027,-31.717,124.115,-23.522,-1.604,4.172,-28.216,-2.951,78.629,22.247,-0.03,0
-InF4-,InF4-,InF4-,aq,HB24,BS23,2023-07-07,HKF,cal,-308448.762,-358424.759,-65.994,136.307,-18.585,-2.948,7.667,-8.325,-3.096,110.376,24.731,2.64,-1
-InSO4+,InSO4+,InSO4+,aq,HB24,HB24.1,2023-07-07,HKF,cal,-205423,-236952,-26.5,-38.05,-1.65,1.8605,-3.2387,7.023,-2.6451,-10.7845,-7.3551,0.9525,1
-In(SO4)2-,In(SO4)2-,In(SO4)2-,aq,HB24,HB24.1,2023-07-07,HKF,cal,-386081,-447540,10,-60.49,32.19,2.2048,-2.8051,6.8526,-2.663,-15.3567,-24.9589,1.4781,-1
-InHS+2,InHS+2,InHS+2,aq,HB24,BS23,2023-07-07,HKF,cal,-34864.521,-41566.732,-41.307,57.552,-9.961,-2.464,6.408,1.951,-3.044,55.357,8.689,1.678,2
-In(HS)2+,In(HS)2+,In(HS)2+,aq,HB24,BS23,2023-07-07,HKF,cal,-41008.506,-55299.1,-27.954,117.159,18.495,-2.107,5.481,46.584,-3.006,83.771,20.831,0.971,1
+InCl+2,InCl+2,InCl+2,aq,HB24,BS23,2023-07-07,HKF,cal,-58530.66,-72848.139,-38.803,44.059,-12.821,-2.446,6.363,-2.992,-3.042,47.137,5.94,1.644,2
+InCl2+,InCl2+,InCl2+,aq,HB24,BS23,2023-07-07,HKF,cal,-92119.729,-115233.655,-26.056,84.938,12.449,-2.094,5.446,36.329,-3.004,64.639,14.267,0.944,1
+InCl3,InCl3,InCl3,aq,HB24,BS23,2023-07-07,HKF,cal,-124358.201,-159711.136,-24.855,107.036,40.603,-1.604,4.172,79.3,-2.951,68.62,18.769,-0.03,0
+InF+2,InF+2,InF+2,aq,HB24,BS23,2023-07-07,HKF,cal,-97424.777,-106461.775,-23.527,48.161,-31.931,-2.328,6.056,-36.052,-3.029,47.381,6.776,1.41,2
+InF2+,InF2+,InF2+,aq,HB24,BS23,2023-07-07,HKF,cal,-169539.617,-189147.026,-19.166,94.733,-27.953,-2.044,5.317,-31.841,-2.999,69.469,16.262,0.845,1
+InF3,InF3,InF3,aq,HB24,BS23,2023-07-07,HKF,cal,-240426.641,-275647.027,-31.717,124.115,-23.522,-1.604,4.172,-28.216,-2.951,78.629,22.247,-0.03,0
+InF4-,InF4-,InF4-,aq,HB24,BS23,2023-07-07,HKF,cal,-308448.762,-365759.759,-65.994,136.307,-18.585,-2.948,7.667,-8.325,-3.096,110.376,24.731,2.64,-1
+InSO4+,InSO4+,InSO4+,aq,HB24,HB24.2,2023-07-07,HKF,cal,-205423,-244287,-26.5,-38.05,-1.65,1.8605,-3.2387,7.023,-2.6451,-10.7845,-7.3551,0.9525,1
+In(SO4)2-,In(SO4)2-,In(SO4)2-,aq,HB24,HB24.2,2023-07-07,HKF,cal,-386081,-454875,10,-60.49,32.19,2.2048,-2.8051,6.8526,-2.663,-15.3567,-24.9589,1.4781,-1
+InHS+2,InHS+2,InHS+2,aq,HB24,BS23,2023-07-07,HKF,cal,-34864.521,-48901.732,-41.307,57.552,-9.961,-2.464,6.408,1.951,-3.044,55.357,8.689,1.678,2
+In(HS)2+,In(HS)2+,In(HS)2+,aq,HB24,BS23,2023-07-07,HKF,cal,-41008.506,-62634.1,-27.954,117.159,18.495,-2.107,5.481,46.584,-3.006,83.771,20.831,0.971,1
Modified: pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/inst/extdata/misc/OBIGT_check.csv 2025-06-05 06:55:16 UTC (rev 919)
@@ -28,7 +28,6 @@
"OBIGT","WO4-2","aq","cal",,,19984
"OBIGT","PO4-3","aq","cal",,-1.72,
"OBIGT","UO2+2","aq","cal",-1.1,,
-"OBIGT","In+3","aq","cal",,,7335
"OBIGT","P2O7-4","aq","cal",,-2.11,
"OBIGT","HP2O7-3","aq","cal",,-1.42,
"OBIGT","SO3-2","aq","cal",,-1.02,
@@ -124,17 +123,8 @@
"OBIGT","Ga(OH)4-","aq","J",-3.75,,
"OBIGT","GaSO4+","aq","cal",2.05,,
"OBIGT","Ga(SO4)2-","aq","cal",-19.44,-36.42,
-"OBIGT","InCl+2","aq","cal",,,7343
-"OBIGT","InCl2+","aq","cal",,,7350
-"OBIGT","InCl3","aq","cal",,,7358
-"OBIGT","InF+2","aq","cal",,,7346
-"OBIGT","InF2+","aq","cal",,,7357
-"OBIGT","InF3","aq","cal",,,7367
-"OBIGT","InF4-","aq","cal",,,7378
-"OBIGT","InSO4+","aq","cal",3.64,,7358
-"OBIGT","In(SO4)2-","aq","cal",-19.05,-33.6,7380
-"OBIGT","InHS+2","aq","cal",,,7362
-"OBIGT","In(HS)2+","aq","cal",,,7389
+"OBIGT","InSO4+","aq","cal",3.64,,
+"OBIGT","In(SO4)2-","aq","cal",-19.05,-33.6,
"OBIGT","CH4","aq","cal",-2.61,,
"OBIGT","hexane","aq","cal",1.43,3.21,
"OBIGT","ethylene","aq","cal",6.12,-3.82,
@@ -361,7 +351,6 @@
"DEW","HCN","aq","cal",,,907
"DEW","Hg2+2","aq","cal",,,9334
"DEW","HPO4-2","aq","cal",,-1.02,
-"DEW","In+3","aq","cal",,,7335
"DEW","KOH","aq","cal",,,-71448
"DEW","MgHCO3+","aq","cal",,,686
"DEW","MgOH+","aq","cal",,,11274
@@ -398,11 +387,9 @@
"SLOP98","PtCl4-2","aq","cal",-13.86,,
"SLOP98","Pt(SO4)3-4","aq","cal",,-1.79,-2915
"SLOP98","UO4-2","aq","cal",,-1.11,
-"SLOP98","InCl+2","aq","cal",,,7342
"SLOP98","ZnCl3-","aq","cal",,,2264
"SLOP98","Zn(Ac)+","aq","cal",,,-4547
"SLOP98","Zn(Ac)3-","aq","cal",,,-13968
-"SLOP98","InF+2","aq","cal",,,7347
"SLOP98","Al+3","aq","cal",1.74,,
"SLOP98","Th+4","aq","cal",,-1.14,
"SLOP98","AsO4-3","aq","cal",,-1.65,
Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-06-05 06:55:16 UTC (rev 919)
@@ -35,6 +35,7 @@
SH88.2,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",H<sub>2</sub>AsO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
SH88.3,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",Ag<sup>+</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
SH88.4,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","K<sup>+</sup>, Na<sup>+</sup>, Ca<sup>+2</sup>, Mg<sup>+2</sup>, Cl<sup>-</sup>, and OH<sup>-</sup>",https://doi.org/10.1016/0016-7037(88)90181-0
+SH88.5,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","values of GHS; corrected H for In<sup>+3</sup> [@OBIGT25]",https://doi.org/10.1016/0016-7037(88)90181-0
SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4
SHS89.1,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183",SiO<sub>2</sub>,https://doi.org/10.1016/0016-7037(89)90341-4
Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344",annite,http://ammin.geoscienceworld.org/content/75/3-4/328
@@ -247,14 +248,6 @@
ZZL+16.1,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","As(α): 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 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
-OBIGT.6,"J. M. Dick",2019,"OBIGT database in CHNOSZ","recalculated values of Cp (those in @AKAE19 appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)",https://chnosz.net
-OBIGT.7,"J. M. Dick",2019,"OBIGT database in CHNOSZ","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: change Ti to Tl",https://chnosz.net
-OBIGT.8,"J. M. Dick",2019,"OBIGT database in CHNOSZ","GHS recalculated by adding difference from SiO<sub>2</sub> [@SSH97] to updated values for SiO<sub>2</sub> [@AS04]",https://chnosz.net
-OBIGT.9,"J. M. Dick",2021,"OBIGT database in CHNOSZ","diaminopimelic acid, putrescine and spermidine: parameters recalculated to account for a missing [-CH2NH2] group in the group additivity equations",https://chnosz.net
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
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
@@ -265,6 +258,7 @@
DEW17.05,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(Al<sup>+3</sup>: parameters in DEW spreadsheet are the same as in @SSWS97)",http://www.dewcommunity.org
DEW17.1,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a<sub>1</sub> for ions",http://www.dewcommunity.org
DEW17.2,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a<sub>1</sub> for cations",http://www.dewcommunity.org
+DEW17.201,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a<sub>1</sub> for cations [corrected H for In<sup>+3</sup>; @OBIGT25]",http://www.dewcommunity.org
DEW17.3,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a<sub>1</sub> for complex species",http://www.dewcommunity.org
DEW17.4,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with a<sub>1</sub> equal to the sum of the ions",http://www.dewcommunity.org
DEW17.5,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","BaCl<sup>+</sup>, CaCl<sup>+</sup>, CaCl<sup>2</sup>: with new V from the sum of a<sub>1</sub> values of ions",http://www.dewcommunity.org
@@ -321,7 +315,7 @@
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","data compilation for Co minerals",https://doi.org/10.5382/econgeo.4895
-BS23,"G. Boyer and E. Shock",2023,"The Complicator (prototype) (v0.0.2)","In complexes",https://doi.org/10.5281/zenodo.8206644
+BS23,"G. Boyer and E. Shock",2023,"The Complicator (prototype) (v0.0.2)","In complexes; corrected H [@OBIGT25]",https://doi.org/10.5281/zenodo.8206644
AZ23,"N. N. Akinfiev and A. V. Zotov",2023,"Geol. Ore Deposits 65, 1-10","Cu<sup>+</sup> and CuO<sup>-</sup>",https://doi.org/10.1134/S1075701523010026
LYX23,"X. Liu, P. Yu and C. Xiao",2023,"Geosci. Front. 14, 101624","Sn<sup>+2</sup>, Th<sup>+4</sup>, and Sn chloride complexes",https://doi.org/10.1016/j.gsf.2023.101624
TTA+23,"N. D. Trofimov, B. R. Tagirov et al.",2023,"Chem. Geol. 625, 121413","Cu hydrosulfide and chloride complexes",https://doi.org/10.1016/j.chemgeo.2023.121413
@@ -328,7 +322,8 @@
HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93",carrollite,https://doi.org/10.3749/2300028
HET+24,"B. Hu, B. Etschmann et al.",2024,"Geochim. Cosmochim. Acta","Ta(OH)<sub>3</sub>F<sub>3</sub><sup>-</sup> and TaF<sub>7</sub><sup>-2</sup>",https://doi.org/10.1016/j.gca.2024.10.019
HB24,"D. L. Huston and E. Bastrakov",2024,"Aust. J. Earth Sci. 71, 1125-1155","data compilation for Cd, Ga, Ge, and In minerals and aqueous species",https://doi.org/10.1080/08120099.2024.2423772
-HB24.1,"D. L. Huston and E. Bastrakov",2024,"Aust. J. Earth Sci. 71, 1125-1155","Ga and In sulfate complexes [algorithms based on @SSH97]",https://doi.org/10.1080/08120099.2024.2423772
+HB24.1,"D. L. Huston and E. Bastrakov",2024,"Aust. J. Earth Sci. 71, 1125-1155","Ga sulfate complexes [algorithms based on @SSH97]",https://doi.org/10.1080/08120099.2024.2423772
+HB24.2,"D. L. Huston and E. Bastrakov",2024,"Aust. J. Earth Sci. 71, 1125-1155","In sulfate complexes [algorithms based on @SSH97]; corrected H [@OBIGT25]",https://doi.org/10.1080/08120099.2024.2423772
KBJ24,"A. W. Knight, C. R. Bryan and C. F. Jové-Colón",2024,"Appl. Geochem. 169, 106032","Mg(OH)<sub>2</sub>-MgCl<sub>2</sub>-H<sub>2</sub>O phases",https://doi.org/10.1016/j.apgeochem.2024.106032
LBP24,"C. Laksar et al.",2024,"Geochim. Cosmochim. Acta","Pd(HS)<sub>4</sub><sup>-2</sup> and Pt(HS)<sub>4</sub><sup>-2</sup>",https://doi.org/10.1016/j.gca.2024.12.019
MBA+24,"A. Migdisov, E. Bastrakov et al.",2024,"Geochim. Cosmochim. Acta","uranyl carbonate, chloride, sulfate, and hydroxide complexes",https://doi.org/10.1016/j.gca.2024.04.023
@@ -336,3 +331,12 @@
RSS+24.1,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","corrected V for tripropylaminium",https://doi.org/10.1016/j.gca.2024.03.013
TAT+24,"B. R. Tagirov, N. N. Akinfiev et al.",2024,"Geochim. Cosmochim. Acta","Au-(hydro)sulfide species and SO<sub>4</sub><sup>-2</sup>-bearing species",https://doi.org/10.1016/j.gca.2024.08.022
TAZ24,"B. R. Tagirov, N. N. Akinfiev and A. V. Zotov",2024,"Geol. Ore Deposits 66, 581--597","Au hydroxide and chloride complexes",https://doi.org/10.1134/S1075701524600403
+OBIGT25,OBIGT,2025,"OBIGT database in CHNOSZ","corrected H by -7335 cal/mol to maintain GHS consistency for In<sup>+3</sup> and derived species",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
+OBIGT.6,"J. M. Dick",2019,"OBIGT database in CHNOSZ","recalculated values of Cp (those in @AKAE19 appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)",https://chnosz.net
+OBIGT.7,"J. M. Dick",2019,"OBIGT database in CHNOSZ","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: change Ti to Tl",https://chnosz.net
+OBIGT.8,"J. M. Dick",2019,"OBIGT database in CHNOSZ","GHS recalculated by adding difference from SiO<sub>2</sub> [@SSH97] to updated values for SiO<sub>2</sub> [@AS04]",https://chnosz.net
+OBIGT.9,"J. M. Dick",2021,"OBIGT database in CHNOSZ","diaminopimelic acid, putrescine and spermidine: parameters recalculated to account for a missing [-CH2NH2] group in the group additivity equations",https://chnosz.net
Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2025-06-05 06:55:16 UTC (rev 919)
@@ -185,7 +185,7 @@
if(!identical(note, "")) note <- paste0(" *", note, "* ")
# Use bullets for ref2
if(whichref=="ref2") bullet <- "- " else bullet <- ""
- # Convert key (e.g. LD12.2) to ref in OBIGT.bib (e.g. LD12)
+ # Convert key with subreference (e.g. LD12.2) to reference in OBIGT.bib (e.g. LD12)
thisref <- gsub("\\..*$", "", thiskey)
# Replace SLOP98 with slop98.dat, etc.
# (we don't actually cite them here to keep the year from showing -- it's annoying to see e.g. "slop98.dat (1998)")
@@ -398,7 +398,7 @@
Besides using `add.OBIGT("DEW")` to load these data, you should also run `water("DEW")` to activate the DEW equations in CHNOSZ.
See `demo(DEW)` for some examples.
-Most of the comments below were transcribed from the DEW spreadsheet. (Comments in parentheses were added by JMD.)
+Most of the comments below were transcribed from the DEW spreadsheet. Comments in parentheses were added by JMD.
```{r optreflist, results="asis", echo=FALSE}
```
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2025-06-03 09:31:47 UTC (rev 918)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2025-06-05 06:55:16 UTC (rev 919)
@@ -2140,6 +2140,13 @@
doi = {10.1016/j.jct.2008.12.006},
}
+ at TechReport{OBIGT25,
+ author = {OBIGT},
+ title = {Corrected {Δ\emph{H}}°\textsubscript{f} by -7335 cal/mol to maintain {GHS} consistency for {In}\textsuperscript{+3} and derived species},
+ year = {2025},
+ school = {OBIGT database in CHNOSZ},
+}
+
@Article{Shv08,
author = {Shvarov, {\relax Yu}. V.},
journal = {Geochemistry International},
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