From noreply at r-forge.r-project.org Fri Oct 17 02:48:16 2025 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 17 Oct 2025 02:48:16 +0200 (CEST) Subject: [CHNOSZ-commits] r935 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/OBIGT/testing inst/extdata/thermo vignettes Message-ID: <20251017004816.4994F18430C@r-forge.r-project.org> Author: jedick Date: 2025-10-17 02:48:15 +0200 (Fri, 17 Oct 2025) New Revision: 935 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/NEWS.Rd pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv pkg/CHNOSZ/inst/extdata/thermo/refs.csv pkg/CHNOSZ/vignettes/OBIGT.Rmd pkg/CHNOSZ/vignettes/OBIGT.bib Log: Update bib info for Terry Seward GCA issue Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2025-08-22 03:21:37 UTC (rev 934) +++ pkg/CHNOSZ/DESCRIPTION 2025-10-17 00:48:15 UTC (rev 935) @@ -1,6 +1,6 @@ -Date: 2025-08-21 +Date: 2025-10-17 Package: CHNOSZ -Version: 2.2.0-4 +Version: 2.2.0-5 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 2025-08-22 03:21:37 UTC (rev 934) +++ pkg/CHNOSZ/inst/NEWS.Rd 2025-10-17 00:48:15 UTC (rev 935) @@ -68,10 +68,10 @@ \item Add palladium and platinum hydrosulfide complexes (Pd(HS)\s{4}\S{-2} and Pt(HS)\s{4}\S{-2}) from - \href{https://doi.org/10.1016/j.gca.2024.12.019}{Laskar et al. (2024)}. + \href{https://doi.org/10.1016/j.gca.2024.12.019}{Laskar et al. (2025)}. \item Add aqueous uranyl complexes from - \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. + \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2025)}. Move aqueous uranium species from \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock, Sassani and Betz (1997)} (except for HUO\s{4}\S{-}) to optional data. @@ -189,7 +189,7 @@ \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)}. + \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2025)}. \item Add FAQ questions: Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2025-08-22 03:21:37 UTC (rev 934) +++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2025-10-17 00:48:15 UTC (rev 935) @@ -682,16 +682,16 @@ HNbO3F-,NA,HNbO3F-,aq,AKK+20,NA,2021-03-20,HKF,cal,-297901,-318676,68.03,-104.73,75.003,12.2344,22.0907,-2.9325,-3.6922,-50.4591,-24.311,0.5913,-1 HTaO3F-,NA,HTaO3F-,aq,AKK+20,NA,2021-03-20,HKF,cal,-296835,-300079,128.05,-148.17,86.4,14.0434,25.5077,-4.6685,-3.8748,-69.9033,-33.2161,1.3079,-1 H2WO4,NA,H2WO4,aq,LXW21,NA,2021-09-27,HKF,cal,-232653,-276736.39,-10.757,125.839,-114.547,-13.9096,-41.7437,22.1569,-1.0533,79.916,22.5989,0,0 -UO2OH+,UO2OH+,UO2OH+,aq,MBA+24,NA,2024-04-23,HKF,cal,-277188,-300762,6.48,77.91,20.7,4.7507,3.8183,4.2494,-2.9369,56.0019,12.8361,0.4531,1 -UO3,UO3,UO3,aq,MBA+24,NEA20.1,2024-04-23,HKF,cal,-267659,-292369,2.67,-0.8,14.8,3.7774,1.4418,5.1834,-2.8386,5.3475,-3.1975,-0.038,0 +UO2OH+,UO2OH+,UO2OH+,aq,MBA+25,NA,2024-04-23,HKF,cal,-277188,-300762,6.48,77.91,20.7,4.7507,3.8183,4.2494,-2.9369,56.0019,12.8361,0.4531,1 +UO3,UO3,UO3,aq,MBA+25,NEA20.1,2024-04-23,HKF,cal,-267659,-292369,2.67,-0.8,14.8,3.7774,1.4418,5.1834,-2.8386,5.3475,-3.1975,-0.038,0 HUO4-,HUO4-,HUO4-,aq,SSB97,NA,1994-05-18,HKF,cal,-314800,-362900,-20.2,22.1,18.4,4.9364,4.2748,4.0637,-2.9556,36.9351,1.4672,1.9339,-1 -UO2Cl+,UO2Cl+,UO2Cl+,aq,MBA+24,NA,2024-04-23,HKF,cal,-259342,-283192,-7.92,53.65,33.12,6.5237,8.1473,2.5479,-3.1158,43.792,7.8937,0.6712,1 -UO2Cl2,UO2Cl2,UO2Cl2,aq,MBA+24,NA,2024-04-23,HKF,cal,-289862,-317554,21.47,6.28,63.63,10.4596,17.7573,-1.2292,-3.5131,9.4946,-1.7562,-0.038,0 -UO2SO4,UO2SO4,UO2SO4,aq,MBA+24,NA,2024-04-23,HKF,cal,-410182,-460211,-1.04,109.16,21.21,4.6545,3.5834,4.3417,-2.9271,69.7926,19.2018,-0.038,0 -UO2(SO4)2-2,UO2(SO4)2-2,UO2(SO4)2-2,aq,MBA+24,NA,2024-04-23,HKF,cal,-589461,-673514,21.8,67.87,36.69,7.7597,11.165,1.3618,-3.2406,72.4911,10.7898,2.8819,-2 -UO2CO3,UO2CO3,UO2CO3,aq,MBA+24,NA,2024-04-23,HKF,cal,-367270,-403994,12.78,-59.3,2.31,2.0683,-2.7313,6.8236,-2.6661,-0.8475,-28.9369,-0.038,0 -UO2(CO3)2-2,UO2(CO3)2-2,UO2(CO3)2-2,aq,MBA+24,NA,2024-04-23,HKF,cal,-502825,-564657,34.72,-28.8,-1.11,2.521,-1.626,6.3892,-2.7118,-42.4375,18.8896,2.6863,-2 -UO2(CO3)3-4,UO2(CO3)3-4,UO2(CO3)3-4,aq,MBA+24,NA,2024-04-23,HKF,cal,-635898,-741562,-6.14,-48.3,-4.53,3.3318,0.3538,5.6111,-2.7936,-59.7866,34.9856,6.4701,-4 +UO2Cl+,UO2Cl+,UO2Cl+,aq,MBA+25,NA,2024-04-23,HKF,cal,-259342,-283192,-7.92,53.65,33.12,6.5237,8.1473,2.5479,-3.1158,43.792,7.8937,0.6712,1 +UO2Cl2,UO2Cl2,UO2Cl2,aq,MBA+25,NA,2024-04-23,HKF,cal,-289862,-317554,21.47,6.28,63.63,10.4596,17.7573,-1.2292,-3.5131,9.4946,-1.7562,-0.038,0 +UO2SO4,UO2SO4,UO2SO4,aq,MBA+25,NA,2024-04-23,HKF,cal,-410182,-460211,-1.04,109.16,21.21,4.6545,3.5834,4.3417,-2.9271,69.7926,19.2018,-0.038,0 +UO2(SO4)2-2,UO2(SO4)2-2,UO2(SO4)2-2,aq,MBA+25,NA,2024-04-23,HKF,cal,-589461,-673514,21.8,67.87,36.69,7.7597,11.165,1.3618,-3.2406,72.4911,10.7898,2.8819,-2 +UO2CO3,UO2CO3,UO2CO3,aq,MBA+25,NA,2024-04-23,HKF,cal,-367270,-403994,12.78,-59.3,2.31,2.0683,-2.7313,6.8236,-2.6661,-0.8475,-28.9369,-0.038,0 +UO2(CO3)2-2,UO2(CO3)2-2,UO2(CO3)2-2,aq,MBA+25,NA,2024-04-23,HKF,cal,-502825,-564657,34.72,-28.8,-1.11,2.521,-1.626,6.3892,-2.7118,-42.4375,18.8896,2.6863,-2 +UO2(CO3)3-4,UO2(CO3)3-4,UO2(CO3)3-4,aq,MBA+25,NA,2024-04-23,HKF,cal,-635898,-741562,-6.14,-48.3,-4.53,3.3318,0.3538,5.6111,-2.7936,-59.7866,34.9856,6.4701,-4 Ta(OH)3F3-,Ta(OH)3F3-,Ta(OH)3F3-,aq,HET+24,NA,2024-12-26,HKF,cal,-464794,NA,49.87,102.537,60.003,8.517,72.6759,-126.173,-6.85,94.3167,6.6323,0.5706,-1 TaF7-2,TaF7-2,TaF7-2,aq,HET+24,NA,2024-12-26,HKF,cal,-585453,NA,46.13,-57.1404,60.309,4.4045,-109.973,371.972,0.8805,268.318,-150.173,3.3215,-2 Sn+4,Sn+4,Sn+4,aq,LYX23,NA,2025-01-05,HKF,cal,600,-18083.8,-112.9,-56.12,-61.76,-5.3731,-20.9004,13.9648,-1.915,9.0585,-14.4665,3.884,4 @@ -700,8 +700,8 @@ SnCl+,SnCl+,SnCl+,aq,LYX23,NA,2025-01-05,HKF,cal,-39962,-41670,17.5442,8.7913,9.2717,3.1277,-0.1446,5.8069,-2.773,13.8796,-1.2438,0.278,1 SnCl2,SnCl2,SnCl2,aq,LYX23,NA,2025-01-05,HKF,cal,-72232,-81852,33.2825,13.9082,37.0637,6.8239,8.8804,2.2598,-3.1461,13.9676,-0.2015,-0.038,0 SnCl3-,SnCl3-,SnCl3-,aq,LYX23,NA,2025-01-05,HKF,cal,-103547,-121668,47.0481,4.2091,68.0292,11.3814,20.0081,-2.1139,-3.6061,17.0106,-2.1772,0.9093,-1 -Pd(HS)4-2,Pd(HS)4-2,Pd(HS)4-2,aq,LBP24,NA,2025-02-15,HKF,cal,-11724,NA,52.919,-3.05,125.4,19.729,40.39,-10.1248,-4.4487,-6.481,12.5693,2.4,-2 -Pt(HS)4-2,Pt(HS)4-2,Pt(HS)4-2,aq,LBP24,NA,2025-02-15,HKF,cal,-14980,NA,45.303,48.502,126.9,19.9782,40.9985,-10.364,-4.4739,50.4082,10.5321,2.53,-2 +Pd(HS)4-2,Pd(HS)4-2,Pd(HS)4-2,aq,LBP25,NA,2025-02-15,HKF,cal,-11724,NA,52.919,-3.05,125.4,19.729,40.39,-10.1248,-4.4487,-6.481,12.5693,2.4,-2 +Pt(HS)4-2,Pt(HS)4-2,Pt(HS)4-2,aq,LBP25,NA,2025-02-15,HKF,cal,-14980,NA,45.303,48.502,126.9,19.9782,40.9985,-10.364,-4.4739,50.4082,10.5321,2.53,-2 YF+2,YF+2,YF+2,aq,LMW+13,NA,2025-06-01,HKF,cal,-237220,NA,-33.37,55.17,-31.65,-1.9638,-12.5762,10.6931,-2.2591,53.0391,8.2035,1.5936,2 YF2+,YF2+,YF2+,aq,LMW+13,NA,2025-06-01,HKF,cal,-308470,NA,-14.33,108.105,-28.19,-1.8049,-12.1883,10.5407,-2.2751,76.4665,18.9864,0.7611,1 CdCl+,NA,CdCl+,aq,HB24,BZA10,2023-07-07,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 Modified: pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv 2025-08-22 03:21:37 UTC (rev 934) +++ pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv 2025-10-17 00:48:15 UTC (rev 935) @@ -1,11 +1,11 @@ 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 -KHSO4,NA,KHSO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-246551,NA,52.892,43.67,36.82,6.8032,8.8337,2.278,-3.1442,31.8025,5.8381,0,0 -KSO4-,NA,KSO4-,aq,TAT+24,NA,2024-11-30,HKF,cal,-246636,NA,60.893,-136.37,30.4,6.8612,6.0072,3.3889,-3.0273,-63.7366,-30.8131,1.0996,-1 -H2SO4,NA,H2SO4,aq,TAT+24,NA,2024-11-30,HKF,cal,-178211,NA,28.058,67.18,83.42,13.1225,24.5891,-3.9144,-3.7955,45.8348,10.5047,0,0 -AuHS,NA,AuHS,aq,TAT+24,NA,2024-11-30,HKF,cal,8208,NA,38.583,26.25,45.73,8.0227,11.8073,1.1093,-3.2671,-49.3817,37.2185,0,0 -AuHS(H2S)3,NA,AuHS(H2S)3,aq,TAT+24,NA,2024-11-30,HKF,cal,-13146,NA,174.161,111.89,145.3,21.6476,45.0745,-11.966,-4.6424,-48.4088,78.8834,0,0 -Au(HS)2-,NA,Au(HS)2-,aq,TAT+24,NA,2024-11-30,HKF,cal,3532,NA,71.791,-30.47,67.97,11.5845,20.504,-2.3089,-3.6266,1.6472,-8.8534,1.5338,-1 -Au2S2-2,NA,Au2S2-2,aq,TAT+24,NA,2024-11-30,HKF,cal,28054,NA,78.65,-119.3,83.58,14.2429,26.9949,-4.86,-3.895,-35.3863,-27.3368,3.079,-2 +KHSO4,NA,KHSO4,aq,TAT+25,NA,2024-11-30,HKF,cal,-246551,NA,52.892,43.67,36.82,6.8032,8.8337,2.278,-3.1442,31.8025,5.8381,0,0 +KSO4-,NA,KSO4-,aq,TAT+25,NA,2024-11-30,HKF,cal,-246636,NA,60.893,-136.37,30.4,6.8612,6.0072,3.3889,-3.0273,-63.7366,-30.8131,1.0996,-1 +H2SO4,NA,H2SO4,aq,TAT+25,NA,2024-11-30,HKF,cal,-178211,NA,28.058,67.18,83.42,13.1225,24.5891,-3.9144,-3.7955,45.8348,10.5047,0,0 +AuHS,NA,AuHS,aq,TAT+25,NA,2024-11-30,HKF,cal,8208,NA,38.583,26.25,45.73,8.0227,11.8073,1.1093,-3.2671,-49.3817,37.2185,0,0 +AuHS(H2S)3,NA,AuHS(H2S)3,aq,TAT+25,NA,2024-11-30,HKF,cal,-13146,NA,174.161,111.89,145.3,21.6476,45.0745,-11.966,-4.6424,-48.4088,78.8834,0,0 +Au(HS)2-,NA,Au(HS)2-,aq,TAT+25,NA,2024-11-30,HKF,cal,3532,NA,71.791,-30.47,67.97,11.5845,20.504,-2.3089,-3.6266,1.6472,-8.8534,1.5338,-1 +Au2S2-2,NA,Au2S2-2,aq,TAT+25,NA,2024-11-30,HKF,cal,28054,NA,78.65,-119.3,83.58,14.2429,26.9949,-4.86,-3.895,-35.3863,-27.3368,3.079,-2 AuOH,NA,AuOH,aq,TAZ24,NA,2024-11-30,HKF,cal,-25947,NA,33.492,18.03,46.58,8.1395,12.0926,0.9972,-3.2789,1.6058,8.0824,0,0 AuCl,NA,AuCl,aq,TAZ24,NA,2024-11-30,HKF,cal,-1900,NA,52.2,-71.9,50.8,8.7165,13.5013,0.4435,-3.3371,-35.9711,-17.6806,0,0 AuCl2-,NA,AuCl2-,aq,TAZ24,NA,2024-11-30,HKF,cal,-36572,NA,43.5,9.5,68.52,11.4087,20.0747,-2.1401,-3.6089,16.8432,-0.463,0.7031,-1 Modified: pkg/CHNOSZ/inst/extdata/thermo/refs.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-08-22 03:21:37 UTC (rev 934) +++ pkg/CHNOSZ/inst/extdata/thermo/refs.csv 2025-10-17 00:48:15 UTC (rev 935) @@ -326,12 +326,12 @@ 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. Jov?-Col?n",2024,"Appl. Geochem. 169, 106032","Mg(OH)2-MgCl2-H2O phases",https://doi.org/10.1016/j.apgeochem.2024.106032 -LBP24,"C. Laksar et al.",2024,"Geochim. Cosmochim. Acta","Pd(HS)4-2 and Pt(HS)4-2",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 +LBP25,"C. Laksar et al.",2025,"Geochim. Cosmochim. Acta 406, 134-147","Pd(HS)4-2 and Pt(HS)4-2",https://doi.org/10.1016/j.gca.2024.12.019 +MBA+25,"A. Migdisov, E. Bastrakov et al.",2025,"Geochim. Cosmochim. Acta 406, 326-339","uranyl carbonate, chloride, sulfate, and hydroxide complexes",https://doi.org/10.1016/j.gca.2024.04.023 RSS+24,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","alkylamines, benzylamines, and aminiums",https://doi.org/10.1016/j.gca.2024.03.013 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 SO4-2-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 +TAT+25,"B. R. Tagirov, N. N. Akinfiev et al.",2025,"Geochim. Cosmochim. Acta 406, 285-304","Au-(hydro)sulfide species and SO4-2-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+3 and derived species",https://chnosz.net OBIGT.1,"J. M. Dick",2017,"OBIGT database in CHNOSZ","GHS (Tr) of the polymorph that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the polymorphs that are stable at higher temperatures.",https://chnosz.net OBIGT.3,"J. M. Dick",2017,"OBIGT database in CHNOSZ","AuCl4- renamed to AuCl4-3",https://chnosz.net Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2025-08-22 03:21:37 UTC (rev 934) +++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2025-10-17 00:48:15 UTC (rev 935) @@ -272,7 +272,7 @@