[CHNOSZ-commits] r860 - in pkg/CHNOSZ: . inst inst/extdata inst/extdata/OBIGT/testing inst/extdata/adds vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 25 09:02:37 CET 2024
Author: jedick
Date: 2024-12-25 09:02:36 +0100 (Wed, 25 Dec 2024)
New Revision: 860
Added:
pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.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 germanium, indium, gallium, and cadmium species from Huston and Bastrakov (2024)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2024-12-25 06:05:30 UTC (rev 859)
+++ pkg/CHNOSZ/DESCRIPTION 2024-12-25 08:02:36 UTC (rev 860)
@@ -1,6 +1,6 @@
Date: 2024-12-25
Package: CHNOSZ
-Version: 2.1.0-32
+Version: 2.1.0-33
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 06:05:30 UTC (rev 859)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 08:02:36 UTC (rev 860)
@@ -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 2.1.0-31 (2024-12-25)}{
+\section{Changes in CHNOSZ version 2.1.0-33 (2024-12-25)}{
\subsection{OBIGT DEFAULT DATA}{
\itemize{
@@ -67,6 +67,10 @@
\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).
+ \item Add \file{testing/GA.csv}: Germanium, indium, gallium, and cadmium
+ species from \href{https://doi.org/10.1080/08120099.2024.2423772}{Huston
+ and Bastrakov (2024)}.
+
}
}
Added: pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/GA.csv 2024-12-25 08:02:36 UTC (rev 860)
@@ -0,0 +1,46 @@
+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
+CdCl+,NA,CdCl+,aq,BZA10,NA,07.Jul.2023,HKF,cal,-52629,NA,7.06,11.12,2.2,2.2303,-2.3357,6.6681,-2.6824,16.6723,-0.7693,0.4372,1
+CdCl2,NA,CdCl2,aq,BZA10,NA,07.Jul.2023,HKF,cal,-84883,NA,25.72,116.01,42.21,7.5221,10.5852,1.5895,-3.2166,73.7023,20.5956,-0.0495,0
+CdCl3-,NA,CdCl3-,aq,BZA10,NA,07.Jul.2023,HKF,cal,-115399,NA,45.15,97.78,63.47,10.8045,18.5994,-1.5605,-3.5479,72.0244,16.8832,0.9378,-1
+CdCl4-2,NA,CdCl4-2,aq,BZA10,NA,07.Jul.2023,HKF,cal,-145583,NA,50.61,42.52,81.35,13.8329,25.9938,-4.4669,-3.8536,53.6766,5.6267,2.4766,-2
+cadmium,Cd,Cd,cr,RH95.9,NA,07.Jul.2023,CGL,J,0,0,51.8,25.98,13.005,0,-0.038115,-134020,300.44,-1.43E-05,0,0,594.18
+monteponite,Mtp,CdO,cr,Bla17,NA,07.Jul.2023,CGL,J,-228661,-258350,54.8,43.65,15.59,47.26,0.00636,-490000,0,0,0,0,1273
+"Cd(OH)2 (cr)","Cd(OH)2 (cr)",Cd(OH)2,cr,Bla17,NA,07.Jul.2023,CGL,J,-472900,-559850,96,80,29.67,104.67,0.00279,-2267000,0,0,0,0,1273
+greenockite,Gnk,CdS,cr,RH95.9,NA,07.Jul.2023,CGL,J,-146100,-149600,72.2,47.3,29.93,35.38,0.01503,-533300,235.7,-2.4E-06,0,0,1100
+"CdSO4 (cr)","CdSO4 (cr)",CdSO4,cr,Bla17,NA,07.Jul.2023,CGL,J,-822631,-933280,123.04,100.4,44.44,77.32,0.0774,0,0,0,0,0,1273
+otavite,Ota,CdCO3,cr,Bla17,NA,07.Jul.2023,CGL,J,-674698,-75263,103.88,89.11,34.3,57.77,0.11693,-313000,0,0,0,0,1273
+GaOH+2,GaOH+2,GaOH+2,aq,Bla17,NA,07.Jul.2023,HKF,J,-383045,-368550,126.692,170.42,-5.707,0.5188,-31.2921,36.3548,-10.3303,62.4713,11.2717,-10.3303,2
+Ga(OH)2+,Ga(OH)2+,Ga(OH)2+,aq,Bla17,NA,07.Jul.2023,HKF,J,-594881,-672710,50.292,77.94,9.63,12.8156,-1.2636,24.5559,-11.5729,69.4628,3.2217,-0.2343,1
+Ga(OH)3,Ga(OH)3,Ga(OH)3,aq,Bla17,NA,07.Jul.2023,HKF,J,-805462,-928286,132.633,112.46,30.964,25.1124,28.7608,12.7528,-12.8156,91.7091,10.2131,0,0
+Ga(OH)4-,Ga(OH)4-,Ga(OH)4-,aq,Bla17,NA,07.Jul.2023,HKF,J,-1021440,-1212749,136.189,114.19,49.552,34.4996,67.3536,-2.4204,-14.4118,158.148,-4.3221,4.2731,-1
+GaSO4+,GaSO4+,GaSO4+,aq,HB24,NA,07.Jul.2023,HKF,cal,-219750,-262279,-42.5,-47.98,-3.9,1.6345,-3.7905,7.2399,-2.6223,-12.8072,-10.9423,1.1948,1
+Ga(SO4)2-,Ga(SO4)2-,Ga(SO4)2-,aq,HB24,NA,07.Jul.2023,HKF,cal,-400818,-473276,-6,-69.45,32.69,1.9788,-3.3569,7.0695,-2.6402,-17.1818,-27.5761,1.7204,-1
+gallium,Ga,Ga,cr,Pan82,NA,07.Jul.2023,CGL,cal,0,0,9.758,6.25,11.803,6.496,0.0002,0,0,0,0,0,302.9
+"Ga2O3 (cr)","Ga2O3 (cr)",Ga2O3,cr,Pan82,NA,07.Jul.2023,CGL,cal,-238620,-260300,20.31,22.02,31.87,27.135,0.003144,-538000,0,0,0,0,2000
+"GaOOH (cr)","GaOOH (cr)",GaOOH,cr,Bla17,NA,07.Jul.2023,CGL,J,-627893,-705329,51.61,86.24,19.7,54.39,0.06418,1130000,0,0,0,0,1273
+"GaS (cr)","GaS (cr)",GaS,cr,PMW87.1,NA,07.Jul.2023,CGL,cal,-48927,-50000,13.82,11.02,26.37,10.705,0.004912,-102100,0,0,0,0,1000
+"Ga2S3 (cr)","Ga2S3 (cr)",Ga2S3,cr,BKK77.1,NA,07.Jul.2023,CGL,cal,NA,-122800,33.4,24.999,62.505,21.63,0.0113,0,0,0,0,0,1363
+Ge(OH)4,Ge(OH)4,Ge(OH)4,aq,PS98,NA,28.Nov.2019,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,PS98,NA,28.Nov.2019,HKF,cal,-218500,-260500,27.14,18,27.14,5.96,6.77,3.09,-3.06,27.66,0.63,1.2,-1
+germanium,Ge,Ge,cr,RH95.9,NA,28.Nov.2019,CGL,J,0,0,31.09,5.59,13.63,24.033,0.003049,-157140,0.84921,-2.5E-08,0,0,1211.4
+"GeO2 (hex)","GeO2 (hex)",GeO2,cr,PS98,NA,28.Nov.2019,CGL,cal,-119700,-132600,13.21,12.45,24.44,14.623,0.003296,-280500,0,0,0,0,1273
+argutite,"GeO2 (tetr)",GeO2,cr,PS98,NA,28.Nov.2019,CGL,cal,-124600,-138700,9.49,11.99,17.42,16.457,0.002178,-454900,0,0,0,0,1273
+"GeS (cr)","GeS (cr)",GeS,cr,OC95,NA,28.Nov.2019,CGL,J,-62276,-61195,66.93,47.77,25.53,45.6,0.0146,-197000,0,0,0,0,930
+"GeS2 (cr)","GeS2 (cr)",GeS2,cr,NRH74,NA,28.Nov.2019,CGL,cal,-44800,-45300,20.9,15.7,22.27,15.665,0.002624,-66401,0,0,0,0,1273
+"GeS2 (alpha)","GeS2 (alpha)",GeS2,cr,MMO+11,NA,28.Nov.2019,CGL,J,NA,-124683,87.935,66.191,22.27,-66.63,0.1597,-7672000,0,-5.18E-05,52240,-1,1116
+InCl+2,InCl+2,InCl+2,aq,BS23,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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,NA,07.Jul.2023,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,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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,BS23,NA,07.Jul.2023,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
+indium,In,In,cr,Pan82,NA,07.Jul.2023,CGL,cal,0,0,13.82,6.389,15.76,2.62,0.009254,82700,0,0,0,0,429.78
+"In2O3 (cr)",In2O3,In2O3,cr,Pan82,NA,07.Jul.2023,CGL,cal,-198537,-221270,24.9,24,38.67,29.323,0.001936,-524500,0,0,0,0,1327
+"InS (cr)",InS,InS,cr,PMW87.1,NA,07.Jul.2023,CGL,cal,-30652,-32000,16.96,11.5,28.36,11.613,0.003112,-92500,0,0,0,0,965
+"In2S3 (cr)",In2S3,In2S3,cr,PMW87.1,NA,07.Jul.2023,CGL,cal,-81564,-85000,39.1,28.2,66.5,30.434,0.001416,-235600,0,0,0,0,660
+"In2(SO4)3 (cr)",In2(SO4)3,In2(SO4)3,cr,BKK77.1,NA,07.Jul.2023,CGL,cal,NA,-651400,72.2,65.739,150.53,47.85,0.06,0,0,0,0,0,943
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-25 06:05:30 UTC (rev 859)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-25 08:02:36 UTC (rev 860)
@@ -399,4 +399,22 @@
"SUPCRT92","greenalite","cr","cal",,,142507
"SUPCRT92","grunerite","cr","cal",9.72,,
"SUPCRT92","halloysite","cr","cal",-1.6,,
+"GA","cadmium","cr","J",-22.72,,
+"GA","otavite","cr","J",,,677368
+"GA","GaOH+2","aq","J",9.07,,
+"GA","Ga(OH)4-","aq","J",-3.75,,
+"GA","GaSO4+","aq","cal",2.05,,
+"GA","Ga(SO4)2-","aq","cal",-19.44,-36.42,
+"GA","germanium","cr","J",17.63,,
+"GA","InCl+2","aq","cal",,,7343
+"GA","InCl2+","aq","cal",,,7350
+"GA","InCl3","aq","cal",,,7358
+"GA","InF+2","aq","cal",,,7346
+"GA","InF2+","aq","cal",,,7357
+"GA","InF3","aq","cal",,,7367
+"GA","InF4-","aq","cal",,,7378
+"GA","InSO4+","aq","cal",3.64,,7358
+"GA","In(SO4)2-","aq","cal",-19.05,-33.6,7380
+"GA","InHS+2","aq","cal",,,7362
+"GA","In(HS)2+","aq","cal",,,7389
"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 06:05:30 UTC (rev 859)
+++ pkg/CHNOSZ/inst/extdata/refs.csv 2024-12-25 08:02:36 UTC (rev 860)
@@ -4,8 +4,10 @@
Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https://www.worldcat.org/oclc/693388901
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
+NRH74,"Naumov, G. B., Ryzhenko, B. N., & Khodakovsky, I. L.",1974,"Handbook of Thermodynamic Data (U.S. Geol. Surv.)","GeS<sub>2</sub>",https://www.worldcat.org/oclc/8139446
RH72,"R. A. Robie and B. S. Hemingway",1972,"Am. Mineral. 57, 1768-1781","nesquehonite Cp",https://pubs.geoscienceworld.org/msa/ammin/article-pdf/57/11-12/1768/4256711/am-1972-1768.pdf
BKK77,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","willemite Cp",https://www.worldcat.org/oclc/695258
+BKK77.1,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","Ga<sub>2</sub>S<sub>3</sub> and In<sub>2</sub>(SO<sub>4</sub>)<sub>3</sub>",https://www.worldcat.org/oclc/695258
HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229",minerals,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
@@ -12,6 +14,7 @@
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
RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://doi.org/10.3133/b1452
RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://doi.org/10.3133/b1452
+Pan82,"L. B. Pankratz",1987,"Thermodynamic Properties of Elements and Oxides (U.S. Bureau of Mines Bull. 672)","gallium, Ga<sub>2</sub>O<sub>3</sub>, indium, In<sub>2</sub>O<sub>3</sub>",https://catalog.hathitrust.org/Record/102119912
PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","Mn(OH)<sub>2</sub> (amorphous) and MgSO<sub>4</sub>",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
@@ -20,6 +23,7 @@
Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845
JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365
PMW87,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","cattierite, linnaeite, and Co-pentlandite",https://www.worldcat.org/oclc/16131757
+PMW87.1,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","GaS, InS, and In<sub>2</sub>S<sub>3</sub>",https://www.worldcat.org/oclc/16131757
RA87,"E. J. Reardon and D. K. Armstrong",1987,"Geochim. Cosmochim. Acta 51, 63-72","celestite GHS",https://doi.org/10.1016/0016-7037(87)90007-X
RS87,"J. R. Ruaya and T. M. Seward",1987,"Geochim. Cosmochim. Acta 51, 121-130",HCl,https://doi.org/10.1016/0016-7037(87)90013-5
Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522",minerals,https://doi.org/10.1093/petrology/29.2.445
@@ -56,6 +60,7 @@
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
HDM+94,"A. W. Hakin et al.",1994,"J. Chem. Soc., Faraday Trans. 90, 2027-2035","glutamic acid",https://doi.org/10.1039/FT9949002027
+OC95,"P. A. G. O'Hare and L. A. Curtiss",1995,"J. Chem. Thermodynamics 27, 643-662","GeS",https://doi.org/10.1006/jcht.1995.0066
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
@@ -68,6 +73,7 @@
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","phase stability limit",https://doi.org/10.3133/b2131
RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","brucite V",https://doi.org/10.3133/b2131
+RH95.9,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","germanium, cadmium, and greenockite (CdS)",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
@@ -100,12 +106,13 @@
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
+PS98,"G. S. Pokrovski and J. Schott",1998,"Geochim. Cosmochim. Acta 62, 1631-1642","GeO<sub>2</sub> (hex) and (tetr) (augite) and Ge hydroxide and oxyhydroxide complexes",https://doi.org/10.1016/S0016-7037(98)00081-7
RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1
-SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools
-SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "G<sub>f</sub> and H<sub>f</sub> from @SS93a TMM"",http://geopig.asu.edu/?q=tools
-SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools
-SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",http://geopig.asu.edu/?q=tools
-SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",http://geopig.asu.edu/?q=tools
+SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",https://doi.org/10.5281/zenodo.2630820
+SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "G<sub>f</sub> and H<sub>f</sub> from @SS93a TMM"",https://doi.org/10.5281/zenodo.2630820
+SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",https://doi.org/10.5281/zenodo.2630820
+SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",https://doi.org/10.5281/zenodo.2630820
+SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",https://doi.org/10.5281/zenodo.2630820
SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",https://doi.org/10.1016/S0016-7037(98)00049-0
SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",https://doi.org/10.1016/S0016-7037(98)00049-0
SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh<sup>+3</sup>,https://doi.org/10.1016/S0016-7037(98)00049-0
@@ -144,6 +151,7 @@
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
ZZX+05,"Y. Zhu et al.",2005,"J. Hazard. Mater. A120, 37-44","barium arsenate and barium hydrogen arsenate: G",https://doi.org/10.1016/j.jhazmat.2004.12.025
+electron,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",https://chnosz.net
ARHB06,"C. Akilan et al.",2006,"ChemPhysChem 7, 2319-2330",MgSO<sub>4</sub>,https://doi.org/10.1002/cphc.200600342
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
@@ -162,11 +170,10 @@
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
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
-electron,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",https://chnosz.net
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
-SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)<sup>+2</sup>",http://geopig.asu.edu/?q=tools
-SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high-temperature HKF parameters from @AP01",http://geopig.asu.edu/?q=tools
+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
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
Ric08,"L. Richard",2008,"personal communication",alkenes,
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
@@ -175,6 +182,7 @@
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
+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
AML10.1,"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
@@ -182,6 +190,7 @@
MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",https://doi.org/10.1007/s12665-009-0369-x
Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",https://doi.org/10.1007/s10498-010-9102-3
LBT+11,"W. Liu et al.",2011,"Geochim. Cosmochim. Acta 75, 1227-1248","Co-chloride complexes",https://doi.org/10.1016/j.gca.2010.12.002
+MMO+11,"Jiří Málek, Takefumi Mitsuhashi et al.",2011,"J. Chem. Thermodynamics 43, 405-409","GeS<sub>2</sub> (alpha)",https://doi.org/10.1016/j.jct.2010.10.011
RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",https://doi.org/10.1016/j.gca.2011.07.030
LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",https://doi.org/10.1016/j.gca.2011.11.041
LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",https://doi.org/10.1016/j.gca.2011.11.041
@@ -230,6 +239,7 @@
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, GaOOH, and 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
@@ -292,6 +302,7 @@
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","parameters listed here",https://doi.org/10.5382/econgeo.4895
+BS23,"G. Boyer and E. Shock",2023,"The Complicator (prototype)","In (indium) complexes",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
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
HDR+24,"B. P. von der Heyden et al.",2024,"Can. J. Mineral. Petrol. 62, 77-93",carrollite,https://doi.org/10.3749/2300028
@@ -301,3 +312,4 @@
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
+HB24,"D. L. Huston and E. Bastrakov",2024,"Aust. J. Earth Sci.","Ga and In sulfate complexes [algorithms based on @SSH97]",https://doi.org/10.1080/08120099.2024.2423772
Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-25 06:05:30 UTC (rev 859)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-25 08:02:36 UTC (rev 860)
@@ -421,6 +421,10 @@
Model for the Mg(OH)<sub>2</sub>-MgCl<sub>2</sub>-H<sub>2</sub>O system at 25 to 150 °C from researchers at Sandia National Laboratories [@KBJ24].
+<h3>GA</h3>
+
+Germanium, indium, gallium, and cadmium species from researchers at Geoscience Australia [@HB24].
+
<h3>Citations</h3>
```{r optreflist, results="asis", echo=FALSE}
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-25 06:05:30 UTC (rev 859)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2024-12-25 08:02:36 UTC (rev 860)
@@ -63,6 +63,17 @@
doi = {10.1111/j.1574-6976.2001.tb00576.x},
}
+ at Article{BZA10,
+ author = {Bazarkina, E. F. and Zotov, A. V. and Akinfiev, N. N.},
+ journal = {Geology of Ore Deposits},
+ title = {Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1-1000 bar and 25°{C}},
+ year = {2010},
+ number = {2},
+ pages = {167--178},
+ volume = {52},
+ doi = {10.1134/S1075701510020054},
+}
+
@Article{BH83,
author = {Bowers, Teresa Suter and Helgeson, Harold C.},
journal = {Geochimica et Cosmochimica Acta},
@@ -565,6 +576,18 @@
doi = {10.1016/j.epsl.2014.11.035},
}
+ at Article{PS98,
+ author = {Pokrovski, Gleb S. and Schott, Jacques},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{T}hermodynamic properties of aqueous {G}e({IV}) hydroxide complexes from 25 to 350°{C}: {I}mplications for the behavior of germanium and the {G}e/{S}i ratio in hydrothermal fluids},
+ year = {1998},
+ number = {9},
+ pages = {1631--1642},
+ volume = {62},
+ doi = {10.1016/S0016-7037(98)00081-7},
+ sourceid = {OBIGT06},
+}
+
@Article{PH95,
author = {Pokrovskii, Vitalii A. and Helgeson, Harold C.},
journal = {American Journal of Science},
@@ -756,14 +779,6 @@
doi = {10.2113/gsecongeo.104.8.1235},
}
- at Misc{SLOP98,
- author = {slop98.dat},
- title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92},
- howpublished = {Last updated on 1998-08-20. Accessed on 2019-04-08.},
- year = {1998},
- doi = {10.5281/zenodo.2630820},
-}
-
@Article{SH88,
author = {Shock, Everett L. and Helgeson, Harold C.},
journal = {Geochimica et Cosmochimica Acta},
@@ -1041,12 +1056,13 @@
volume = {78},
}
- at Misc{SLOP07,
- author = {slop07.dat},
- title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92},
- howpublished = {Last updated on 2008-04-17. Accessed on 2019-04-08.},
- year = {2007},
- doi = {10.5281/zenodo.2630820},
+ at Misc{BS23,
+ author = {Grayson Boyer and Everett Shock},
+ howpublished = {Zenodo},
+ note = {Version v0.0.2},
+ title = {The Complicator (prototype)},
+ year = {2023},
+ doi = {10.5281/zenodo.8206644},
}
@Misc{SLOP16,
@@ -1582,6 +1598,16 @@
doi = {10.1016/j.oregeorev.2019.103289},
}
+ at TechReport{Bla17,
+ author = {P. Blanc},
+ institution = {Bureau de Recherches Géologiques et Minières},
+ title = {Thermoddem: Update for the 2017 version},
+ year = {2017},
+ number = {BRGM/RP-66811-FR},
+ type = {Report},
+ url = {https://thermoddem.brgm.fr/page/brgm-reports},
+}
+
@TechReport{electron,
author = {OBIGT},
institution = {OBIGT database in CHNOSZ},
@@ -1896,3 +1922,81 @@
volume = {65},
doi = {10.1134/S1075701523010026},
}
+
+
+
+ at Article{HB24,
+ author = {Huston, D. L. and Bastrakov, E.},
+ journal = {Australian Journal of Earth Sciences},
+ title = {Germanium, indium, gallium and cadmium in zinc ores: a mineral system approach},
+ year = {2024},
+ doi = {10.1080/08120099.2024.2423772},
+}
+
+ at Misc{slo98,
+ author = {slop98.dat},
+ howpublished = {Last updated on 1998-08-20. Accessed on 2019-04-08.},
+ title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92},
+ year = {1998},
+ doi = {10.5281/zenodo.2630820},
+}
+
+ at Misc{slo07,
+ author = {slop07.dat},
+ howpublished = {Last updated on 2008-04-17. Accessed on 2019-04-08.},
+ title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92},
+ year = {2007},
+ doi = {10.5281/zenodo.2630820},
+}
+
+ at Book{Pan82,
+ author = {L. B. Pankratz},
+ publisher = {Bureau of Mines},
+ title = {Thermodynamic Properties of Elements and Oxides},
+ year = {1982},
+ number = {672},
+ series = {Bulletin},
+ url = {https://catalog.hathitrust.org/Record/102119912},
+}
+
+ at Article{MMO+11,
+ author = {Jiří Málek and Takefumi Mitsuhashi and Naoki Ohashi and Yuki Taniguchi and Hitoshi Kawaji and Tooru Atake},
+ journal = {The Journal of Chemical Thermodynamics},
+ title = {Heat capacity and thermodynamic properties of germanium disulfide at temperatures from {\emph{T}} = (2 to 1240) {K}},
+ year = {2011},
+ number = {3},
+ pages = {405--409},
+ volume = {43},
+ doi = {10.1016/j.jct.2010.10.011},
+}
+
+ at Article{OC95,
+ author = {P. A. G. O'Hare and L. A. Curtiss},
+ journal = {The Journal of Chemical Thermodynamics},
+ title = {Thermochemistry of (germanium + sulfur): {IV}. Critical evaluation of the thermodynamic properties of solid and gaseous germanium({II}) sulfide {GeS} and germanium({IV}) disulfide {GeS\textsubscript{2}}, and digermanium disulfide {Ge\textsubscript{2}S\textsubscript{2}}(g). Enthalpies of dissociation of bonds in {GeS}(g), {GeS\textsubscript{2}}(g), and {Ge\textsubscript{2}S\textsubscript{2}}(g)},
+ year = {1995},
+ number = {6},
+ pages = {643--662},
+ volume = {27},
+ doi = {10.1006/jcht.1995.0066},
+}
+
+ at Article{WS06,
+ author = {Scott A. Wood and Iain M. Samson},
+ journal = {Ore Geology Reviews},
+ title = {The aqueous geochemistry of gallium, germanium, indium and scandium},
+ year = {2006},
+ number = {1},
+ pages = {57--102},
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 860
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