[CHNOSZ-commits] r259 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man man/macros vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 16 16:30:48 CEST 2017
Author: jedick
Date: 2017-10-16 16:30:48 +0200 (Mon, 16 Oct 2017)
New Revision: 259
Added:
pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/cgl.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/macros/macros.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/vignettes/obigt.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
Log:
add SUPCRTBL data (aqueous SiO2 and Al species and As minerals)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/DESCRIPTION 2017-10-16 14:30:48 UTC (rev 259)
@@ -1,6 +1,6 @@
-Date: 2017-10-14
+Date: 2017-10-16
Package: CHNOSZ
-Version: 1.1.0-57
+Version: 1.1.0-58
Title: Thermodynamic Calculations for Geobiochemistry
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/cgl.R
===================================================================
--- pkg/CHNOSZ/R/cgl.R 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/R/cgl.R 2017-10-16 14:30:48 UTC (rev 259)
@@ -47,8 +47,11 @@
} else {
# use constant heat capacity if the coefficients are not available
Cp <- PAR$Cp
- CpdT <- PAR$Cp*(T - Tr)
+ intCpdT <- PAR$Cp*(T - Tr)
intCpdlnT <- PAR$Cp*log(T / Tr)
+ # in case Cp is listed as NA, set the integrals to 0 at Tr
+ intCpdT[T==Tr] <- 0
+ intCpdlnT[T==Tr] <- 0
}
# volume and its integrals
if(PAR$name %in% c("quartz", "coesite")) {
@@ -73,7 +76,12 @@
if(property[i] == "V") values[, i] <- V
if(property[i] == "E") values[, i] <- rep(NA, ncond)
if(property[i] == "kT") values[, i] <- rep(NA, ncond)
- if(property[i] == "G") values[, i] <- PAR$G - PAR$S*(T - Tr) + intCpdT - T*intCpdlnT + intVdP
+ if(property[i] == "G") {
+ # calculate S * (T - Tr), but set it to 0 at Tr (in case S is NA)
+ Sterm <- PAR$S*(T - Tr)
+ Sterm[T==Tr] <- 0
+ values[, i] <- PAR$G - Sterm + intCpdT - T*intCpdlnT + intVdP
+ }
if(property[i] == "H") values[, i] <- PAR$H + intCpdT + intVdP - T*intdVdTdP
if(property[i] == "S") values[, i] <- PAR$S + intCpdlnT - intdVdTdP
}
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/data/refs.csv 2017-10-16 14:30:48 UTC (rev 259)
@@ -17,14 +17,15 @@
BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,https://doi.org/10.1016/0016-7037(83)90066-2
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
-Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522","minerals",https://doi.org/10.1093/petrology/29.2.445
+Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522",minerals,https://doi.org/10.1093/petrology/29.2.445
SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",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
-Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344","annite",http://ammin.geoscienceworld.org/content/75/3-4/328
+Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344",annite,http://ammin.geoscienceworld.org/content/75/3-4/328
Ber90.1,"R. G. Berman",1990,"Am. Mineral. 75, 328-344","almandine and ilmenite: modified H and/or S",http://ammin.geoscienceworld.org/content/75/3-4/328
Eva90,"B. W. Evans",1990,"Lithos 25, 3-23","glaucophane and pumpellyite",https://doi.org/10.1016/0024-4937(90)90003-J
SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O
SH90.1,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","formic acid, formate, and propanoate",https://doi.org/10.1016/0016-7037(90)90429-O
+BN91,"J. W. Ball and D. K. Nordstrom",1991,"User's manual for WATEQ4F, with revised thermodynamic data base and text cases for calculating speciation of major, trace, and redox elements in natural waters. USGS Open-File Report 91-183","arsenopyrite: G",https://pubs.er.usgs.gov/publication/ofr91183
SHD91,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","G and H revisions for K- and Al-bearing silicates",https://doi.org/10.1016/0016-7037(89)90341-4
SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
@@ -45,6 +46,7 @@
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
SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes not included in later slop files.",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>,http://dx.doi.org/10.1016/0016-7037(95)00403-3
AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F
DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3
DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
@@ -80,11 +82,16 @@
PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes",https://doi.org/10.1016/S0016-7037(01)00678-0
PS01.1,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","acetic acid, propanoic acid, and methane",https://doi.org/10.1016/S0016-7037(01)00678-0
Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",https://doi.org/10.1016/S0016-7037(01)00761-X
+Ste01,"A. Stefansson",2001,"Chem. Geol. 172, 225-250",aqueous H<sub>4</sub>SiO<sub>4</sub>,http://dx.doi.org/10.1016/S0009-2541(00)00263-1
SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
+TS01,"B. Tagirov and J. Schott",2001,"Geochim. Cosmochim. Acta 65, 3965-3992","aqueous Al species",http://dx.doi.org/10.1016/S0016-7037(01)00705-0
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-bearing minerals",
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>,
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
+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
HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",https://doi.org/10.1016/j.jct.2005.10.013
LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",https://doi.org/10.1016/j.gca.2006.04.010
LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",https://doi.org/10.1016/j.gca.2006.04.010
@@ -94,6 +101,7 @@
DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",https://doi.org/10.5194/bg-3-311-2006
DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acids HKF parameters",https://doi.org/10.5194/bg-3-311-2006
DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides",https://doi.org/10.5194/bg-3-311-2006
+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
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",https://doi.org/10.1007/s00254-006-0578-5
@@ -126,6 +134,8 @@
SLOP15.7,"E. L. Shock et al.",2015,"slop15.dat computer data file","hexanol, heptanol, and octanol: "Minor differences in Gibbs energy, entropy, omega, a<sub>1</sub>, a<sub>2</sub>, a<sub>3</sub>, a<sub>4</sub> and c<sub>1</sub> values compared to @SH90."",http://geopig.asu.edu/?q=tools
CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid cycle metabolites",https://doi.org/10.1016/j.gca.2016.08.028
CS16.1,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid species HKF a<sub>1</sub>--a<sub>4</sub> parameters",https://doi.org/10.1016/j.gca.2016.08.028
+ZZL+16,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","data listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
+ZZL+16.1,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","As(α): V data listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
CHNOSZ.1,"J. M. Dick",2017,"CHNOSZ package documentation","GHS (T<sub>r</sub>) of the phase 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 phases that are stable at higher temperatures.",http://chnosz.net
CHNOSZ.2,"J. M. Dick",2017,"CHNOSZ package documentation","alanate and glycinate: GHS as used by @DLH06",http://chnosz.net
CHNOSZ.3,"J. M. Dick",2017,"CHNOSZ package documentation","metal-amino acid complexes: GHS were recalculated by adding the differences between values from @AH97b and @DLH06 for alanate or glycinate to the properties of the complexes reported by @SK95.",http://chnosz.net
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/demo/00Index 2017-10-16 14:30:48 UTC (rev 259)
@@ -1,23 +1,23 @@
-sources cross-check the reference list with the thermodynamic database
-protein.equil chemical activities of two proteins in metastable equilibrium
-affinity affinities of metabolic reactions and amino acid synthesis
-NaCl equilibrium constant for aqueous NaCl dissociation
-density density of H2O, inverted from IAPWS-95 equations
-ORP temperature dependence of oxidation-reduction potential for redox standards
-revisit coefficient of variation of metastable equilibrium activities of proteins
-findit minimize the standard deviation of logarithms of activities of sulfur species
+sources Cross-check the reference list with the thermodynamic database
+protein.equil Chemical activities of two proteins in metastable equilibrium
+affinity Affinities of metabolic reactions and amino acid synthesis
+NaCl Equilibrium constant for aqueous NaCl dissociation
+density Density of H2O, inverted from IAPWS-95 equations
+ORP Temperature dependence of oxidation-reduction potential for redox standards
+revisit Coefficient of variation of metastable equilibrium activities of proteins
+findit Minimize the standard deviation of logarithms of activities of sulfur species
ionize ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK
-buffer minerals and aqueous species as buffers of hydrogen fugacity
-protbuff chemical activities buffered by thiol peroxidases or sigma factors
-yeastgfp subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams
+buffer Minerals and aqueous species as buffers of hydrogen fugacity
+protbuff Chemical activities buffered by thiol peroxidases or sigma factors
+yeastgfp Subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams
mosaic Eh-pH diagram for iron oxides, sulfides and carbonate with two sets of changing basis species
-copper another example of mosaic(): complexation of copper with glycine species
-solubility solubility of calcite or CO2(gas) as a function of pH
+copper Another example of mosaic(): complexation of copper with glycine species
+solubility Solubility of calcite or CO2(gas) as a function of pH
wjd Gibbs energy minimization: prebiological atmospheres and cell periphery of yeast
dehydration log K of dehydration reactions; SVG file contains tooltips and links
-bugstab formation potential of microbial proteins in colorectal cancer
-Shh affinities of transcription factors relative to Sonic hedgehog
-activity_ratios mineral stability plots with activity ratios on the axes
+bugstab Formation potential of microbial proteins in colorectal cancer
+Shh Affinities of transcription factors relative to Sonic hedgehog
+activity_ratios Mineral stability plots with activity ratios on the axes
adenine HKF parameters regressed from heat capacity and volume of aqueous adenine
DEW Deep Earth Water (DEW) model for high pressures
lambda Effects of lambda transtion on thermodynamic properties of quartz
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/inst/NEWS 2017-10-16 14:30:48 UTC (rev 259)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-57 (2017-10-14)
+CHANGES IN CHNOSZ 1.1.0-58 (2017-10-16)
---------------------------------------
MAJOR CHANGES:
@@ -79,23 +79,27 @@
*everything* (the database and all computational and system settings).
- In add.obigt(), using 'file' without a file suffix now can be used to
- locate corresponding files (such as CHNOSZ_aq.csv or DEW_aq.csv) in
- the extdata/OBIGT package directory.
+ locate corresponding files (such as DEW_aq.csv or SUPCRTBL.csv) in the
+ extdata/OBIGT package directory.
- add.obigt() gets new argument 'species' for selecting species to add.
-- Add DEW_aq.csv with aqueous species data from the DEW spreadsheet
- (May 2017 version). Species with data that do not differ from the
- default database in CHNOSZ are not included. Currently, detailed
- reference keys and descriptions (in thermo$refs) are given for
- selected species only.
-
- Add Berman_cr.csv with names and formulas for minerals whose
thermodynamic properties are calculated using the Berman, 1988
equations. The state "cr_Berman" is used to distinguish these
minerals from the Helgeson data. The parameters themselves are
stored in extdata/Berman/*.csv.
+- Add DEW_aq.csv with aqueous species data from the DEW spreadsheet
+ (May 2017 version). Species with data that do not differ from the
+ default database in CHNOSZ are not included. Currently, detailed
+ reference keys and descriptions (in thermo$refs) are given for
+ selected species only. [Optional Data; not loaded by data(thermo).]
+
+- Add SUPCRTBL.csv with mineral and aqueous species data from
+ spronsbl.dat (http://www.indiana.edu/~hydrogeo/supcrtbl.html), as
+ described by Zimmer et al., 2016. [Optional Data.]
+
- Update HKF parameters of adenine based on experimental heat capacity
and volume data (Lowe et al., 2017). Add demo/adenine.R comparing
the updates with the previous data (LaRowe and Helgeson, 2006).
Added: pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/SUPCRTBL.csv 2017-10-16 14:30:48 UTC (rev 259)
@@ -0,0 +1,33 @@
+name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+Al+3,NA,Al+3,aq,TS01,NA,25.Aug.06,-116510,NA,-81.203,-28.56,-45.3,-3.3984,-16.0789,12.0699,-2.1143,14.4295,-8.8523,2.7403,3
+Al(OH)4-,NA,Al(OH)4-,aq,TS01,NA,25.Aug.06,-312087,NA,24.748,23.06,46.3,8.4938,12.9576,0.657,-3.3147,55.7265,-11.4047,1.0403,-1
+AlOH+2,NA,AlOH+2,aq,TS01,NA,25.Aug.06,-166425,NA,-43.29,-8.97,-20.6,-0.4532,-8.8878,9.2434,-2.4116,15.4131,-4.8618,1.5897,2
+Al(OH)2+,NA,Al(OH)2+,aq,TS01,NA,25.Aug.06,-214987,NA,-6.584,9.76,3.86,2.4944,-1.6909,6.4146,-2.7091,16.7439,-1.0465,0.5324,1
+Al(OH)3,NA,Al(OH)3,aq,TS01,NA,25.Aug.06,-263321,NA,14.185,23.65,27.02,5.4624,5.556,3.5662,-3.0087,20.027,1.7829,0,0
+AlF+2,NA,AlF+2,aq,TS01,NA,25.Aug.06,-193374,NA,-52.413,-3.41,-17.74,0.0486,-7.6626,8.7618,-2.4622,21.3382,-3.7292,1.882,2
+AlF2+,NA,AlF2+,aq,TS01,NA,25.Aug.06,-268382,NA,-29.84,20.88,9.58,3.4523,0.648,5.4953,-2.8058,27.4906,1.2187,0.996,1
+AlF3,NA,AlF3,aq,TS01,NA,25.Aug.06,-341248,NA,-14.45,40.33,35.6,6.6365,8.4227,2.4395,-3.1272,29.8025,5.1806,0,0
+AlF4-,NA,AlF4-,aq,TS01,NA,25.Aug.06,-411835,NA,-6.691,45.3,57.74,10.3172,17.4096,-1.0929,-3.4987,48.4334,6.193,1.7229,-1
+Al(OH)2F2-,NA,Al(OH)2F2-,aq,TS01,NA,25.Aug.06,-361765,NA,45.062,34.18,52.02,9.3237,14.9838,-0.1394,-3.3984,1.8352,21.1478,1.1651,-1
+Al(OH)2F,NA,Al(OH)2F,aq,TS01,NA,25.Aug.06,-291441,NA,25.181,19.55,21.52,4.7098,3.7184,4.2885,-2.9327,17.6241,0.9477,0,0
+AlOHF2,NA,AlOHF2,aq,TS01,NA,25.Aug.06,-308085,NA,42.004,15.45,16.02,3.9572,1.8807,5.0108,-2.8567,15.2213,0.1126,0,0
+AlSO4+,NA,AlSO4+,aq,TS01,NA,25.Aug.06,-298759,NA,-46.724,106.7,-6.17,1.833,-3.3057,7.0494,-2.6423,90.7261,18.7002,2.4143,1
+NaAl(OH)3F,NA,NaAl(OH)3F,aq,TS01,NA,25.Aug.06,-398892,NA,71.594,28.2,48,8.3333,12.5657,0.811,-3.2985,22.6935,2.7097,0,0
+NaAl(OH)2F2,NA,NaAl(OH)2F2,aq,TS01,NA,25.Aug.06,-403511,NA,128.933,24.2,42.4,7.567,10.6947,1.5464,-3.2211,20.3493,1.8949,0,0
+NaAl(OH)4,NA,NaAl(OH)4,aq,TS01,DPS+96,25.Aug.06,-374611,-413601,48.8,32.2,53.6,9.1267,14.3411,0.1121,-3.3719,60.7157,-14.0523,0,0
+AlH3SiO4+2,NA,AlH3SiO4+2,aq,TS01,NA,25.Aug.06,-425860,NA,13.57,-71.9,-13.93,0.16,-7.23,8.61,-2.48,37.07,-49.66,0.88,2
+H4SiO4,NA,H4SiO4,aq,Ste01,NA,31.Aug.06,-312919.933078394,-348676.147227533,45.1003824091778,15.0095602294455,52.3,18.7299235181644,-21.2600382409178,18.6199808795411,-1.20004780114723,58.0305927342256,-20.789913957935,0.0869024856596558,0
+SiO2,NA,SiO2,aq,AS04,ZZL+16,16.Oct.17,-199539.9,-212179,11.12811,NA,NA,1.9,1.7,20,-2.7,32.22,-25.29001,0.3427103,0
+"arsenic,alpha",NA,As,cr,NA03,ZZL+16.1,16.Oct.17,0,0,8.515774378585085,5.838910133843212,12.96,NA,NA,NA,NA,NA,NA,NA,NA
+arsenolite,NA,As2O3,cr,NA03,NA,16.Oct.17,-137748.56596558317,-157091.3001912046,25.664435946462714,23.154875717017205,NA,NA,NA,NA,NA,NA,NA,NA,NA
+claudetite,NA,As2O3,cr,NA03,NA,16.Oct.17,-137793.97705544933,-156708.8910133843,27.09608030592734,23.178776290630974,NA,NA,NA,NA,NA,NA,NA,NA,NA
+As2O5,NA,As2O5,cr,NA03,NA,16.Oct.17,-185172.08413001912,-219309.27342256214,25.20076481835564,27.70076481835564,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"realgar,alpha",NA,AsS,cr,NA03,NA,16.Oct.17,-7480.879541108986,-7600.38240917782,15.033460803059272,11.233269598470363,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"realgar,beta",NA,AsS,cr,NA03,NA,16.Oct.17,-7385.277246653919,-7409.177820267686,15.176864244741873,11.233269598470363,NA,NA,NA,NA,NA,NA,NA,NA,NA
+orpiment,NA,As2S3,cr,NA03,NA,16.Oct.17,-20291.586998087954,-20506.692160611852,39.14913957934991,38.95793499043977,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"orpiment,amorphous",NA,As2S3,cr,NA03,NA,16.Oct.17,-18355.640535372848,-15989.483747609942,47.801147227533455,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+arsenopyrite,NA,FeAsS,cr,BN91,ZZL+16,16.Oct.17,-33843.21223709369,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+scorodite,NA,FeAsO4.2H2O,cr,LMR06,ZZL+16,16.Oct.17,-307619.5028680688,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"ferric arsenate,amorphous",NA,FeAsO4.2H2O,cr,LMR06,ZZL+16,16.Oct.17,-303771.51051625237,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"barium arsenate",NA,Ba3(AsO4)2,cr,ZZX+05,ZZL+16,16.Oct.17,-739749.0439770555,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"barium hydrogen arsenate",NA,BaHAsO4.H2O,cr,ZZX+05,ZZL+16,16.Oct.17,-367746.1759082218,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/man/examples.Rd 2017-10-16 14:30:48 UTC (rev 259)
@@ -35,26 +35,26 @@
See the comments in the source code for more information about each demo.
\tabular{ll}{
- \code{sources} \tab cross-check the reference list with the thermodynamic database \cr
- \code{protein.equil} \tab chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011) \cr
- \code{affinity} \tab affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001) \cr
- \code{NaCl} \tab * equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992) \cr
- \code{density} \tab * density of \H2O, inverted from IAPWS-95 equations (\code{\link{rho.IAPWS95}}) \cr
- \code{ORP} \tab * temperature dependence of oxidation-reduction potential for redox standards \cr
- \code{revisit} \tab * coefficient of variation of metastable equilibrium activities of proteins \cr
- \code{findit} \tab * minimize the standard deviation of logarithms of activities of sulfur species \cr
+ \code{sources} \tab Cross-check the reference list with the thermodynamic database \cr
+ \code{protein.equil} \tab Chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011) \cr
+ \code{affinity} \tab Affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001) \cr
+ \code{NaCl} \tab * Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992) \cr
+ \code{density} \tab * Density of \H2O, inverted from IAPWS-95 equations (\code{\link{rho.IAPWS95}}) \cr
+ \code{ORP} \tab * Temperature dependence of oxidation-reduction potential for redox standards \cr
+ \code{revisit} \tab * Coefficient of variation of metastable equilibrium activities of proteins \cr
+ \code{findit} \tab * Minimize the standard deviation of logarithms of activities of sulfur species \cr
\code{ionize} \tab ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK \cr
- \code{buffer} \tab * minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995) \cr
- \code{protbuff} \tab chemical activities buffered by thiol peroxidases or sigma factors \cr
- \code{yeastgfp} \tab * subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams (Dick, 2009) \cr
+ \code{buffer} \tab * Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995) \cr
+ \code{protbuff} \tab Chemical activities buffered by thiol peroxidases or sigma factors \cr
+ \code{yeastgfp} \tab * Subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams (Dick, 2009) \cr
\code{mosaic} \tab * Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965) \cr
- \code{copper} \tab * another example of \code{\link{mosaic}}: complexation of Cu with glycine (Aksu and Doyle, 2001) \cr
- \code{solubility} \tab * solubility of calcite (cf. Manning et al., 2013) or \CO2 (cf. Stumm and Morgan, 1996) \cr
+ \code{copper} \tab * Another example of \code{\link{mosaic}}: complexation of Cu with glycine (Aksu and Doyle, 2001) \cr
+ \code{solubility} \tab * Solubility of calcite (cf. Manning et al., 2013) or \CO2 (cf. Stumm and Morgan, 1996) \cr
\code{wjd} \tab * Gibbs energy minimization: prebiological atmospheres (Dayhoff et al., 1964) and cell periphery of yeast \cr
- \code{dehydration} \tab * log K of dehydration reactions; SVG file contains tooltips and links \cr
- \code{bugstab} \tab * formation potential of microbial proteins in colorectal cancer (Dick, 2016) \cr
- \code{Shh} \tab * affinities of transcription factors relative to Sonic hedgehog (Dick, 2015) \cr
- \code{activity_ratios} \tab * mineral stability plots with activity ratios on the axes \cr
+ \code{dehydration} \tab * \logK of dehydration reactions; SVG file contains tooltips and links \cr
+ \code{bugstab} \tab * Formation potential of microbial proteins in colorectal cancer (Dick, 2016) \cr
+ \code{Shh} \tab * Affinities of transcription factors relative to Sonic hedgehog (Dick, 2015) \cr
+ \code{activity_ratios} \tab * Mineral stability plots with activity ratios on the axes \cr
\code{adenine} \tab * HKF parameters regressed from heat capacity and volume of aqueous adenine (Lowe et al., 2017) \cr
\code{DEW} \tab * Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b) \cr
\code{lambda} \tab * Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988) \cr
Modified: pkg/CHNOSZ/man/macros/macros.Rd
===================================================================
--- pkg/CHNOSZ/man/macros/macros.Rd 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/man/macros/macros.Rd 2017-10-16 14:30:48 UTC (rev 259)
@@ -21,6 +21,7 @@
% other common variables
\newcommand{\T}{\ifelse{latex}{\eqn{T}}{\ifelse{html}{\out{<I>T</I>}}{T}}}
\newcommand{\P}{\ifelse{latex}{\eqn{P}}{\ifelse{html}{\out{<I>P</I>}}{P}}}
+\newcommand{\logK}{\ifelse{latex}{\eqn{\log K}}{\ifelse{html}{\out{log<i>K</i>}}{log K}}}
\newcommand{\logfO2}{\ifelse{latex}{\eqn{\log f_{\mathrm{O_{2}}}}}{\ifelse{html}{\out{log<i>f</i><sub>O<sub>2</sub></sub>}}{logfO2}}}
\newcommand{\logfH2}{\ifelse{latex}{\eqn{\log f_{\mathrm{H_{2}}}}}{\ifelse{html}{\out{log<i>f</i><sub>H<sub>2</sub></sub>}}{logfH2}}}
\newcommand{\logaH2O}{\ifelse{latex}{\eqn{\log a_{\mathrm{H_{2}O}}}}{\ifelse{html}{\out{log<i>a</i><sub>H<sub>2</sub>O</sub>}}{logaH2O}}}
Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/man/subcrt.Rd 2017-10-16 14:30:48 UTC (rev 259)
@@ -97,7 +97,7 @@
Comparison of the output of \code{subcrt} with that of \acronym{SUPCRT92} indicates the two give similar values of properties for neutral aqueous species up to 1000 \degC and 5000 bar.
Changes were made in CHNOSZ 0.9-9 to improve the calculation of the \eqn{g}{g}- and \eqn{f}{f}-functions (Shock et al., 1992) for the partial derivatives of the omega parameter which are used by the \code{\link{hkf}} function, so thermodynamic properties of charged aqueous species over the temperature range 0 to 1000 \degC are now mostly consistent with \acronym{SUPCRT92}.
Note, however, that while \acronym{SUPCRT92} limits calculations at Psat to 350 \degC (\dQuote{beyond range of applicability of aqueous species equations}), there is no corresponding limit in place in \code{subcrt} (or \code{\link{hkf}}), so that inapplicable calculations will be performed up to the critical temperature (373.917 \degC) without any warning.
-It is probably for this reason that there is a noticeable jump in the value of logK at Psat shown in the one of the examples (\code{demo("NaCl")}).
+It is probably for this reason that there is a noticeable jump in the value of \logK at Psat shown in the one of the examples (\code{demo("NaCl")}).
A known bug is misidentification of the stable polymorph of some minerals at high temperature; an example of this bug is shown in the \code{\link{stopifnot}} at the end of the skarn example below.
}
Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd 2017-10-14 15:09:27 UTC (rev 258)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd 2017-10-16 14:30:48 UTC (rev 259)
@@ -12,7 +12,7 @@
bibliography: obigt.bib
# so that these appear in the bibliography
nocite: |
- @SPRONS92, @SLOP98, @SLOP07, @SLOP15, @CHNOSZ, @JOH92, @WP02, @CWM89, @PRPG97, @TH88, @Kul06, @Sho09
+ @SPRONS92, @SLOP98, @SLOP07, @SLOP15, @CHNOSZ, @JOH92, @WP02, @CWM89, @PRPG97, @TH88, @Kul06, @Sho09, @HP11
csl: elementa.csl
---
@@ -39,8 +39,8 @@
dat <- read.csv(file, as.is=TRUE)
## exclude entries for phase transitions
#dat <- dat[!dat$state %in% c("cr2", "cr3", "cr4", "cr5", "cr6", "cr7", "cr8", "cr9"), ]
- # the class of substance, followed by number of species
- class <- gsub("_.*", "", csvfile)
+ # the class of substance (used as section header), followed by number of species
+ class <- gsub(".csv", "", gsub("_.*", "", csvfile))
substr(class, 1, 1) <- toupper(substr(class, 1, 1))
paste0("`", class, "` (", nrow(dat), ")")
}
@@ -107,13 +107,13 @@
```
This [vignette](index.html), produced on `r Sys.Date()`, documents the sources of thermodynamic data in CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
+Running `data(thermo)` creates the default database, which is present in the R session as `thermo$obigt`.
-The sections below correspond to CSV data files read by `data(thermo)`.
+The sections below correspond to CSV data files that are stored in the `extdata/OBIGT` package directory and read by `data(thermo)` (except for Optional Data).
In each section, the primary references (`ref1` in `thermo$obigt`) are listed in chronological order.
Any secondary references (`ref2`) are listed with bullet points.
Each reference is followed by the number of species, and a note (from `thermo$refs`).
Symbols show whether the data were present in the earliest of the sprons92.dat (ø), slop98.dat (\*), slop07.dat (†), or slop15.dat (‡) datafiles for the SUPCRT92 package.
-NOTE: URLs for the slop files and other data files cited below (`JUN92.bs`, `berman.dat`, and the DEW model spreadsheet) are given in the References.
Any additional comments are placed at the beginning of the sections.
Abbreviations used below are: Cp (heat capacity), GHS (standard Gibbs energy, enthalpy, entropy), HKF (Helgeson-Kirkham-Flowers equations), V (volume), T (temperature), P (pressure).
@@ -121,17 +121,19 @@
# Recent additions (late 2017)
-* Mineral data using the [Berman (1988)](https://doi.org/10.1093/petrology/29.2.445) equations are listed under [**Solids** / **Berman**](#berman-107).
+* Mineral data using the [Berman (1988)](https://doi.org/10.1093/petrology/29.2.445) equations are listed under **Solids** / **Berman**.
-* Aqueous species data intended for use with the [Deep Earth Water](http://www.dewcommunity.org/) model are listed under [**Optional Data** / **DEW**](#dew-199).
+* Aqueous species data intended for use with the [Deep Earth Water](http://www.dewcommunity.org/) model are listed under **Optional Data** / **DEW**.
-# Sources of data {.tabset .tabset-fade .tabset-sticky}
+* Updates included with [SUPCRTBL](http://www.indiana.edu/~hydrogeo/supcrtbl.html) are listed under **Optional Data** / **SUPCRTBL**.
+# Sources of data {.tabset .tabset-fade}
+
<!-- uncomment for full version -->
Use the tabs below to select a section for viewing.
Select "All at once" to show all sections.
-## Aqueous species {.tabset .tabset-pills .tabset-sticky}
+## Aqueous species {.tabset .tabset-pills}
### `r setfile("H2O_aq.csv")`
```{r H2O_aq, results="asis", echo=FALSE}
@@ -177,7 +179,7 @@
```{r reflist, results="asis", echo=FALSE}
```
-## Solids {.tabset .tabset-pills .tabset-sticky}
+## Solids {.tabset .tabset-pills}
### `r setfile("inorganic_cr.csv")`
```{r inorganic_cr, results="asis", echo=FALSE}
@@ -202,13 +204,13 @@
```{r reflist, results="asis", echo=FALSE}
```
-## Liquids {.tabset .tabset-pills .tabset-sticky}
+## Liquids {.tabset .tabset-pills}
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 259
More information about the CHNOSZ-commits
mailing list