[CHNOSZ-commits] r599 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 15 12:28:47 CEST 2020
Author: jedick
Date: 2020-08-15 12:28:47 +0200 (Sat, 15 Aug 2020)
New Revision: 599
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/man/DEW.Rd
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/eos.Rd
pkg/CHNOSZ/man/eqdata.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/mosaic.Rd
pkg/CHNOSZ/man/nonideal.Rd
pkg/CHNOSZ/man/objective.Rd
pkg/CHNOSZ/man/retrieve.Rd
pkg/CHNOSZ/man/solubility.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/thermo.Rd
pkg/CHNOSZ/man/util.fasta.Rd
pkg/CHNOSZ/man/water.Rd
pkg/CHNOSZ/tests/testthat/test-util.data.R
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/OBIGT.bib
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/mklinks.sh
Log:
Add Mn(OH)2 and move Mn-O-H example (using retrieve()) to anintro.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/DESCRIPTION 2020-08-15 10:28:47 UTC (rev 599)
@@ -1,6 +1,6 @@
Date: 2020-08-15
Package: CHNOSZ
-Version: 1.3.6-72
+Version: 1.3.6-73
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/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/R/util.data.R 2020-08-15 10:28:47 UTC (rev 599)
@@ -211,7 +211,7 @@
if(!is.na(calcval)) {
if(!is.na(refval)) {
if(abs(diff) > tol) {
- message(paste("checkEOS: ", prop, " of ", eos$name, " ", eos$state, " (", rownames(eos),
+ message(paste("checkEOS: ", prop, " of ", eos$name, "(", eos$state,
") differs by ", round(diff,2), " ", units, " from tabulated value", sep=""))
return(calcval)
}
@@ -245,7 +245,7 @@
if(!is.na(refval)) {
diff <- calcval - refval
if(abs(diff) > thermo$opt$G.tol) {
- message(paste("checkGHS: G of ", ghs$name, " ", ghs$state, " (", rownames(ghs),
+ message(paste("checkGHS: G of ", ghs$name, "(", ghs$state,
") differs by ", round(diff), " ", ghs$E_units, " mol-1 from tabulated value", sep=""))
return(calcval)
}
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -9,7 +9,7 @@
\newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
\newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
-\section{Changes in CHNOSZ version 1.3.6-71 (2020-08-15)}{
+\section{Changes in CHNOSZ version 1.3.6-73 (2020-08-15)}{
\subsection{MAJOR CHANGES}{
\itemize{
@@ -92,6 +92,11 @@
\href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway,
1995}.
+ \item \samp{inorganic_cr.csv}: Add amorphous Mn(OH)\s{2} from
+ \href{https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf}{Wagman et al., 1982}
+ (GHS) and \href{https://doi.org/10.1016/S0925-8388(98)00739-7}{Senoh et
+ al., 1998} (estimated Cp values).
+
\item Add GHS for almandine, dickite, fluorphlogopite, glaucophane,
grunerite, larnite, pyrope (\samp{SUPCRT92.csv}) and bromellite
(\samp{inorganic_cr.csv}) from
@@ -249,14 +254,14 @@
\item TODO: move H2O92D.f and R wrapper to a separate package (so people
don't have to compile anything to install CHNOSZ updates).
- \item TODO: get retrieve() into more examples/demos
-
\item TODO: convert dates in OBIGT to ISO 8601 format (2020-08-12).
\item TODO: get entropies for Am, Pu, Cm, Np.
- \item TODO: use default colors for 'fill' in diagram().
+ \item TODO: link to multi-metal.Rmd from anintro.Rmd.
+ \item TODO: add empty diagram -> exceed.Ttr hint to anintro.Rmd.
+
}
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2020-08-15 10:28:47 UTC (rev 599)
@@ -115,7 +115,7 @@
natrojarosite,NA,NaFe3(SO4)2(OH)6,cr,SAJ00,NA,13.Apr.09,cal,-778370,-877892,91.396,NA,NA,147.321,21.8,-48.7,0,0,0,0,NA
melanterite,NA,FeSO4*7H2O,cr,PK95,NA,13.Apr.09,cal,-599366.6,-720028.7,97.801,NA,NA,0,0,0,0,0,0,0,NA
gypsum,NA,CaSO4*2H2O,cr,RH95.7,Kel60.3,22.Nov.15,cal,-429493,-483509,46.32,NA,74.69,21.84,76,0,0,0,0,0,400
-MgSO4,NA,MgSO4,cr,WEP+82.2,NA,24.Nov.15,cal,-279780,-307100,21.89,NA,NA,23.06,0,0,0,0,0,0,NA
+MgSO4,NA,MgSO4,cr,WEP+82.1,NA,24.Nov.15,cal,-279780,-307100,21.89,NA,NA,23.06,0,0,0,0,0,0,NA
"arsenic,alpha",NA,As,cr,NA03,ZZL+16.1,16.Oct.17,J,0,0,35.63,24.43,12.96,NA,NA,NA,NA,NA,NA,NA,NA
arsenolite,NA,As2O3,cr,NA03,NA,16.Oct.17,J,-576340,-657270,107.38,96.88,NA,NA,NA,NA,NA,NA,NA,NA,NA
claudetite,NA,As2O3,cr,NA03,NA,16.Oct.17,J,-576530,-655670,113.37,96.98,NA,NA,NA,NA,NA,NA,NA,NA,NA
@@ -141,3 +141,4 @@
bixbyite,NA,Mn2O3,cr,RH95,NA,15.Aug.20,J,-882100,-959000,113.7,101.81,31.37,162.4,12.11,10.46,-1317,0.3462,0,0,1400
hausmannite,NA,Mn3O4,cr,RH95,NA,15.Aug.20,J,-1282500,-1384500,164.1,142.02,46.95,-7.432,94.87,-67.12,3396,0,0,0,1400
manganese,NA,Mn,cr,RH95,NA,15.Aug.20,J,0,0,32.01,26.19,7.354,0,41.345,-2.7217,313.29,-1.3745,0,0,980
+Mn(OH)2,NA,Mn(OH)2,cr,WEP+82.1,SUF+98,15.Aug.20,J,-615000,-695400,99.2,114.7,NA,139.61,-85.25,0,0,0,0,0,700
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-08-15 10:28:47 UTC (rev 599)
@@ -15,8 +15,7 @@
RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://pubs.er.usgs.gov/publication/b1452
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",manganosite,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
-WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",MgSO<sub>4</sub>,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
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
HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",H<sub>2</sub>O,https://www.worldcat.org/oclc/858456124
Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845
@@ -111,6 +110,7 @@
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
SS98a.3,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","Pd<sup>+2</sup> and Pt<sup>+2</sup> and their complexes",https://doi.org/10.1016/S0016-7037(98)00049-0
+SUF+98,"H. Senoh et al.",1998,"J. Alloys Compd. 280, 114-124","Mn(OH)<sub>2</sub>: Cp coefficients from linear fit to values estimated by @SUF+98",https://doi.org/10.1016/S0925-8388(98)00739-7
HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",https://doi.org/10.1016/S0016-7037(99)00276-8
MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253",actinides,http://rimg.geoscienceworld.org/content/38/1/221
PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-08-15 10:28:47 UTC (rev 599)
@@ -249,24 +249,24 @@
"OBIGT",1974,"orpiment","cr","J",,,-1036
"OBIGT",1982,"dawsonite","cr","J",,,19466
"OBIGT",1984,"ferberite","cr","J",1.21,,
-"OBIGT",2011,"octadecane","cr","cal",-2.63,,
-"OBIGT",2012,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2013,"eicosane","cr","cal",-2.79,,
-"OBIGT",2014,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2015,"docosane","cr","cal",-2.63,,
-"OBIGT",2016,"tricosane","cr","cal",-5.22,,
-"OBIGT",2017,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2018,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2019,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2020,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2072,"carbazole","cr","cal",-43.39,,
-"OBIGT",2113,"triphenylene","cr","cal",,,541
-"OBIGT",2426,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2584,"ethylene","gas","cal",-4.59,,
-"OBIGT",2594,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2904,"nonacontane","liq","cal",,,635
-"OBIGT",2911,"2-methyloctane","liq","cal",10,,
-"OBIGT",3324,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",2012,"octadecane","cr","cal",-2.63,,
+"OBIGT",2013,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2014,"eicosane","cr","cal",-2.79,,
+"OBIGT",2015,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2016,"docosane","cr","cal",-2.63,,
+"OBIGT",2017,"tricosane","cr","cal",-5.22,,
+"OBIGT",2018,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2019,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2020,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2021,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2073,"carbazole","cr","cal",-43.39,,
+"OBIGT",2114,"triphenylene","cr","cal",,,541
+"OBIGT",2427,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2585,"ethylene","gas","cal",-4.59,,
+"OBIGT",2595,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2905,"nonacontane","liq","cal",,,635
+"OBIGT",2912,"2-methyloctane","liq","cal",10,,
+"OBIGT",3325,"5,6-dithiadecane","liq","cal",2,,
"DEW",8,"AlO2(SiO2)-","aq","cal",,,-897
"DEW",17,"BO(OH)","aq","cal",,,-1111
"DEW",19,"Ca(HCO3)+","aq","cal",,,-2971
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/man/DEW.Rd
===================================================================
--- pkg/CHNOSZ/man/DEW.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/DEW.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -26,7 +26,7 @@
\details{
The Deep Earth Water (DEW) model, described by Sverjensky et al., 2014, extends the applicability of the revised HKF equations of state to 60 kbar.
-This implementation of DEW is based on the VBA macro code in the May, 2017 version of the DEW spreadsheet downloaded from \url{http://dewcommunity.org}.
+This implementation of DEW is based on the VBA macro code in the May, 2017 version of the DEW spreadsheet downloaded from \url{http://dewcommunity.org/}.
The spreadsheet provides multiple options for some calculations; here the default equations for density of water (Zhang and Duan, 2005), dielectric constant (Sverjensky et al., 2014) and Gibbs energy of water (integral of volume, equation created by Brandon Harrison) are used.
Comments in the original code indicate that \code{calculateGibbsOfWater} is valid for 100 \le \T \le 1000 \degC and \P \ge 1000 bar.
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/berman.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -122,7 +122,7 @@
}
\references{
-Anderson, G. M. (2005) \emph{Thermodynamics of Natural Systems}, 2nd ed., Cambridge University Press, 648 p. \url{http://www.worldcat.org/oclc/474880901}
+Anderson, G. M. (2005) \emph{Thermodynamics of Natural Systems}, 2nd ed., Cambridge University Press, 648 p. \url{https://www.worldcat.org/oclc/474880901}
Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
@@ -130,7 +130,7 @@
Berman, R. G. (2007) winTWQ (version 2.3): A software package for performing internally-consistent thermobarometric calculations. \emph{Open File} \bold{5462}, Geological Survey of Canada, 41 p. \url{https://doi.org/10.4095/223425}
-Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{http://www.worldcat.org/oclc/13594862}
+Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{https://www.worldcat.org/oclc/13594862}
}
\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/buffer.Rd
===================================================================
--- pkg/CHNOSZ/man/buffer.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/buffer.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -131,7 +131,7 @@
}
\references{
-Garrels, R. M. (1960) \emph{Mineral Equilibria}. Harper & Brothers, New York, 254 p. \url{http://www.worldcat.org/oclc/552690}
+Garrels, R. M. (1960) \emph{Mineral Equilibria}. Harper & Brothers, New York, 254 p. \url{https://www.worldcat.org/oclc/552690}
}
\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/diagram.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -289,9 +289,9 @@
Dick, J. M. (2019) CHNOSZ: Thermodynamic calculations and diagrams for geochemistry. \emph{Front. Earth Sci.} \bold{7}:180. \url{https://doi.org/10.3389/feart.2019.00180}
-Helgeson, H. C. (1970) A chemical and thermodynamic model of ore deposition in hydrothermal systems. \emph{Mineral. Soc. Amer. Spec. Pap.} \bold{3}, 155--186. \url{http://www.worldcat.org/oclc/583263}
+Helgeson, H. C. (1970) A chemical and thermodynamic model of ore deposition in hydrothermal systems. \emph{Mineral. Soc. Amer. Spec. Pap.} \bold{3}, 155--186. \url{https://www.worldcat.org/oclc/583263}
-Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{http://www.worldcat.org/oclc/13594862}
+Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{https://www.worldcat.org/oclc/13594862}
LaRowe, D. E. and Helgeson, H. C. (2007) Quantifying the energetics of metabolic reactions in diverse biogeochemical systems: electron flow and ATP synthesis. \emph{Geobiology} \bold{5}, 153--168. \url{https://doi.org/10.1111/j.1472-4669.2007.00099.x}
Modified: pkg/CHNOSZ/man/eos.Rd
===================================================================
--- pkg/CHNOSZ/man/eos.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/eos.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -103,7 +103,7 @@
Maier, C. G. and Kelley, K. K. (1932) An equation for the representation of high-temperature heat content data. \emph{J. Am. Chem. Soc.} \bold{54}, 3243--3246. \url{https://doi.org/10.1021/ja01347a029}
- Robie, R. A. and Hemingway, B. S. (1995) \emph{Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (\eqn{10^5} Pascals) Pressure and at Higher Temperatures}. U. S. Geol. Surv., Bull. 2131, 461 p. \url{http://www.worldcat.org/oclc/32590140}
+ Robie, R. A. and Hemingway, B. S. (1995) \emph{Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (\eqn{10^5} Pascals) Pressure and at Higher Temperatures}. U. S. Geol. Surv., Bull. 2131, 461 p. \url{https://www.worldcat.org/oclc/32590140}
Shock, E. L. and Helgeson, H. C. (1988) Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Correlation algorithms for ionic species and equation of state predictions to 5 kb and 1000\degC. \emph{Geochim. Cosmochim. Acta} \bold{52}, 2009--2036. \url{https://doi.org/10.1016/0016-7037(88)90181-0}
Modified: pkg/CHNOSZ/man/eqdata.Rd
===================================================================
--- pkg/CHNOSZ/man/eqdata.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/eqdata.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -40,9 +40,9 @@
}
\references{
- Wolery, T. J. (1992) EQ3/6, A Software Package for Geochemical Modeling of Aqueous Systems: Package Overview and Installation Guide (Version 7.0). Lawrence Livermore National Laboratory, UCRL-MA-110662 PT I. \url{http://www.wipp.energy.gov/library/cra/2009_cra/references/Others/Wolery_1992_EQ36_A_Software_Package_for_Geochemical_Modeling_of_Aqueous_Systems_ERMS241375.pdf}
+ Wolery, T. J. (1992) EQ3/6, A Software Package for Geochemical Modeling of Aqueous Systems: Package Overview and Installation Guide (Version 7.0). Lawrence Livermore National Laboratory, UCRL-MA-110662 PT I. \url{https://www.wipp.energy.gov/library/cra/2009_cra/references/Others/Wolery_1992_EQ36_A_Software_Package_for_Geochemical_Modeling_of_Aqueous_Systems_ERMS241375.pdf}
- Wolery, T. J. and Daveler, S. A. (1992) EQ6, A Computer Program for Reaction Path Modeling of Aqueous Geochemical Systems: Theoretical Manual, User's Guide, and Related Documentation (Version 7.0). Lawrence Livermore National Laboratory, UCRL-MA-110662 PT IV. \url{http://www.wipp.energy.gov/library/cra/2009_cra/references/Others/Wolery_Daveler_1992_EQ36_A_Computer_Program_for_Reaction_Path_Modeling_of_Aqueous_Geochemical_Systems_ERMS241379.pdf}
+ Wolery, T. J. and Daveler, S. A. (1992) EQ6, A Computer Program for Reaction Path Modeling of Aqueous Geochemical Systems: Theoretical Manual, User's Guide, and Related Documentation (Version 7.0). Lawrence Livermore National Laboratory, UCRL-MA-110662 PT IV. \url{https://www.wipp.energy.gov/library/cra/2009_cra/references/Others/Wolery_Daveler_1992_EQ36_A_Computer_Program_for_Reaction_Path_Modeling_of_Aqueous_Geochemical_Systems_ERMS241379.pdf}
}
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/examples.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -88,7 +88,7 @@
Akinfiev, N. N. and Tagirov, B. R. (2014) Zn in hydrothermal systems: Thermodynamic description of hydroxide, chloride, and hydrosulfide complexes. \emph{Geochem. Int.} \bold{52}, 197--214. \url{https://doi.org/10.1134/S0016702914030021}
-Akinfiev, N. N. and Zotov, A. V. (2001) Thermodynamic description of chloride, hydrosulfide, and hydroxo complexes of Ag(I), Cu(I), and Au(I) at temperatures of 25-500\degC and pressures of 1-2000 bar. \emph{Geochem. Int.} \bold{39}, 990--1006. \url{http://pleiades.online/cgi-perl/search.pl/?type=abstract&name=geochem&number=10&year=1&page=990}
+Akinfiev, N. N. and Zotov, A. V. (2001) Thermodynamic description of chloride, hydrosulfide, and hydroxo complexes of Ag(I), Cu(I), and Au(I) at temperatures of 25-500\degC and pressures of 1-2000 bar. \emph{Geochem. Int.} \bold{39}, 990--1006. \url{https://pleiades.online/cgi-perl/search.pl/?type=abstract&name=geochem&number=10&year=1&page=990}
Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57. \url{https://doi.org/10.1149/1.1344532}
@@ -102,7 +102,7 @@
Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
-Bowers, T. S., Jackson, K. J. and Helgeson, H. C. (1984) \emph{Equilibrium Activity Diagrams for Coexisting Minerals and Aqueous Solutions at Pressures and Temperatures to 5 kb and 600\degC}, Springer-Verlag, Berlin, 397 p. \url{http://www.worldcat.org/oclc/11133620}
+Bowers, T. S., Jackson, K. J. and Helgeson, H. C. (1984) \emph{Equilibrium Activity Diagrams for Coexisting Minerals and Aqueous Solutions at Pressures and Temperatures to 5 kb and 600\degC}, Springer-Verlag, Berlin, 397 p. \url{https://www.worldcat.org/oclc/11133620}
Canovas, P. A., III and Shock, E. L. (2016) Geobiochemistry of metabolism: Standard state thermodynamic properties of the citric acid cycle. \emph{Geochim. Cosmochim. Acta} \bold{195}, 293--322. \url{https://doi.org/10.1016/j.gca.2016.08.028}
@@ -110,7 +110,7 @@
Dick, J. M. (2015) Chemical integration of proteins in signaling and development. \emph{bioRxiv}. \url{https://doi.org/10.1101/015826}
-Garrels, R. M. and Christ, C. L. (1965) \emph{Solutions, Minerals, and Equilibria}, Harper & Row, New York, 450 p. \url{http://www.worldcat.org/oclc/517586}
+Garrels, R. M. and Christ, C. L. (1965) \emph{Solutions, Minerals, and Equilibria}, Harper & Row, New York, 450 p. \url{https://www.worldcat.org/oclc/517586}
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\degC. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{https://doi.org/10.1016/0098-3004(92)90029-Q}
@@ -128,7 +128,7 @@
Stef{\aacute}nsson, A. and Seward, T. M. (2004) Gold(I) complexing in aqueous sulphide solutions to 500\degC at 500 bar. \emph{Geochim. Cosmochim. Acta} \bold{68}, 4121--4143. \url{https://doi.org/10.1016/j.gca.2004.04.006}
-Stumm, W. and Morgan, J. J. (1996) \emph{Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters}, John Wiley & Sons, New York, 1040 p. \url{http://www.worldcat.org/oclc/31754493}
+Stumm, W. and Morgan, J. J. (1996) \emph{Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters}, John Wiley & Sons, New York, 1040 p. \url{https://www.worldcat.org/oclc/31754493}
Sverjensky, D. A., Harrison, B. and Azzolini, D. (2014a) Water in the deep Earth: The dielectric constant and the solubilities of quartz and corundum to 60 kb and 1,200 \degC. \emph{Geochim. Cosmochim. Acta} \bold{129}, 125--145. \url{https://doi.org/10.1016/j.gca.2013.12.019}
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/extdata.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -111,7 +111,7 @@
Richard, L. and Helgeson, H. C. (1998) Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. \emph{Geochim. Cosmochim. Acta} \bold{62}, 3591--3636. \url{https://doi.org/10.1016/S0016-7037(97)00345-1}
-Robie, R. A. and Hemingway, B. S. (1995) \emph{Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (\eqn{10^5} Pascals) Pressure and at Higher Temperatures}. U. S. Geol. Surv., Bull. 2131, 461 p. \url{http://www.worldcat.org/oclc/32590140}
+Robie, R. A. and Hemingway, B. S. (1995) \emph{Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (\eqn{10^5} Pascals) Pressure and at Higher Temperatures}. U. S. Geol. Surv., Bull. 2131, 461 p. \url{https://www.worldcat.org/oclc/32590140}
Shock, E. and Canovas, P. (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. \emph{Geofluids} \bold{10}, 161--192. \url{https://doi.org/10.1111/j.1468-8123.2010.00277.x}
Modified: pkg/CHNOSZ/man/mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/mosaic.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/mosaic.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -95,7 +95,7 @@
}
\references{
- Garrels, R. M. and Christ, C. L. (1965) \emph{Solutions, Minerals, and Equilibria}, Harper & Row, New York, 450 p. \url{http://www.worldcat.org/oclc/517586}
+ Garrels, R. M. and Christ, C. L. (1965) \emph{Solutions, Minerals, and Equilibria}, Harper & Row, New York, 450 p. \url{https://www.worldcat.org/oclc/517586}
}
\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/nonideal.Rd
===================================================================
--- pkg/CHNOSZ/man/nonideal.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/nonideal.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -224,11 +224,11 @@
\references{
Alberty, R. A. (2001) Effect of temperature on standard transformed Gibbs energies of formation of reactants at specified pH and ionic strength and apparent equilibrium constants of biochemical reactions. \emph{J. Phys. Chem. B} \bold{105}, 7865--7870. \url{https://doi.org/10.1021/jp011308v}
-Alberty, R. A. (2003) \emph{Thermodynamics of Biochemical Reactions}, John Wiley & Sons, Hoboken, New Jersey, 397 p. \url{http://www.worldcat.org/oclc/51242181}
+Alberty, R. A. (2003) \emph{Thermodynamics of Biochemical Reactions}, John Wiley & Sons, Hoboken, New Jersey, 397 p. \url{https://www.worldcat.org/oclc/51242181}
Clarke, E. C. W. and Glew, D. N. (1980) Evaluation of Debye-Hückel limiting slopes for water between 0 and 150 °C. \emph{J. Chem. Soc. Faraday Trans.} \bold{76}, 1911--1916. \url{https://doi.org/10.1039/f19807601911}
-Garrels, R. M. and Christ, C. L. (1965) \emph{Solutions, Minerals, and Equilibria}, Harper & Row, New York, 450 p. \url{http://www.worldcat.org/oclc/517586}
+Garrels, R. M. and Christ, C. L. (1965) \emph{Solutions, Minerals, and Equilibria}, Harper & Row, New York, 450 p. \url{https://www.worldcat.org/oclc/517586}
Helgeson, H. C. (1969) Thermodynamics of hydrothermal systems at elevated temperatures and pressures. \emph{Am. J. Sci.} \bold{267}, 729--804. \url{https://doi.org/10.2475/ajs.267.7.729}
Modified: pkg/CHNOSZ/man/objective.Rd
===================================================================
--- pkg/CHNOSZ/man/objective.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/objective.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -113,7 +113,7 @@
\references{
- Anderson, G. M. (2005) \emph{Thermodynamics of Natural Systems}, 2nd ed., Cambridge University Press, 648 p. \url{http://www.worldcat.org/oclc/474880901}
+ Anderson, G. M. (2005) \emph{Thermodynamics of Natural Systems}, 2nd ed., Cambridge University Press, 648 p. \url{https://www.worldcat.org/oclc/474880901}
Dick, J. M. and Shock, E. L. (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. \emph{PLoS ONE} \bold{8}, e72395. \url{https://doi.org/10.1371/journal.pone.0072395}
Modified: pkg/CHNOSZ/man/retrieve.Rd
===================================================================
--- pkg/CHNOSZ/man/retrieve.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/retrieve.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -39,7 +39,7 @@
}
\seealso{
-\code{\link{info}}
+\code{\link{info}} for basic database searches; \viglink{anintro} for a diagram made with \code{retrieve}d species in the Mn-O-H system.
}
\examples{
@@ -62,13 +62,6 @@
# minerals in the system SiO2-MgO-CaO-CO2
retrieve(list("Si", "Mg", "Ca", "C", "O"), state="cr")
-
-# an Eh-pH diagram for Mn-bearing aqueous species
-basis(c("Mn+2", "H2O", "H+", "e-"))
-iMn <- retrieve("Mn", c("O", "H"), "aq")
-species(iMn)
-a <- affinity(pH = c(6, 14), Eh = c(-1, 1))
-diagram(a, fill = "terrain", limit.water = TRUE)
\dontshow{par(thermo()$opar)}
}
Modified: pkg/CHNOSZ/man/solubility.Rd
===================================================================
--- pkg/CHNOSZ/man/solubility.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/solubility.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -147,7 +147,7 @@
\references{
Manning, C. E., Shock, E. L. and Sverjensky, D. A. (2013) The chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: Experimental and theoretical constraints. \emph{Rev. Mineral. Geochem.} \bold{75}, 109--148. \url{https://doi.org/10.2138/rmg.2013.75.5}
-Stumm, W. and Morgan, J. J. (1996) \emph{Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters}, John Wiley & Sons, New York, 1040 p. \url{http://www.worldcat.org/oclc/31754493}
+Stumm, W. and Morgan, J. J. (1996) \emph{Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters}, John Wiley & Sons, New York, 1040 p. \url{https://www.worldcat.org/oclc/31754493}
}
\concept{Main workflow}
Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/subcrt.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -225,7 +225,7 @@
}
\references{
- Anderson, G. M. and Crerar, D. A. (1993) \emph{Thermodynamics in Geochemistry: The Equilibrium Model}, Oxford University Press. \url{http://www.worldcat.org/oclc/803272549}
+ Anderson, G. M. and Crerar, D. A. (1993) \emph{Thermodynamics in Geochemistry: The Equilibrium Model}, Oxford University Press. \url{https://www.worldcat.org/oclc/803272549}
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\degC. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{https://doi.org/10.1016/0098-3004(92)90029-Q}
Modified: pkg/CHNOSZ/man/thermo.Rd
===================================================================
--- pkg/CHNOSZ/man/thermo.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/thermo.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -276,7 +276,7 @@
}
\references{
-Cox, J. D., Wagman, D. D. and Medvedev, V. A., eds. (1989) \emph{CODATA Key Values for Thermodynamics}. Hemisphere Publishing Corporation, New York, 271 p. \url{http://www.worldcat.org/oclc/18559968}
+Cox, J. D., Wagman, D. D. and Medvedev, V. A., eds. (1989) \emph{CODATA Key Values for Thermodynamics}. Hemisphere Publishing Corporation, New York, 271 p. \url{https://www.worldcat.org/oclc/18559968}
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\degC. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{https://doi.org/10.1016/0098-3004(92)90029-Q}
Modified: pkg/CHNOSZ/man/util.fasta.Rd
===================================================================
--- pkg/CHNOSZ/man/util.fasta.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/util.fasta.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -48,7 +48,7 @@
\code{start} and/or \code{stop} can be provided to count a fragment of the sequence (extracted using \code{\link{substr}}).
If only one of \code{start} or \code{stop} is present, the other defaults to 1 (\code{start}) or the length of the sequence (\code{stop}).
-\code{uniprot.aa} returns a data frame of amino acid composition, in the format of \code{thermo()$protein}, retrieved from the protein sequence if it is available from UniProt (\url{http://uniprot.org}).
+\code{uniprot.aa} returns a data frame of amino acid composition, in the format of \code{thermo()$protein}, retrieved from the protein sequence if it is available from UniProt (\url{https://uniprot.org/}).
The \code{protein} argument corresponds to the \samp{Entry name} on the UniProt search pages.
}
Modified: pkg/CHNOSZ/man/water.Rd
===================================================================
--- pkg/CHNOSZ/man/water.Rd 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/man/water.Rd 2020-08-15 10:28:47 UTC (rev 599)
@@ -159,7 +159,7 @@
\references{
Archer, D. G. and Wang, P. M. (1990) The dielectric constant of water and Debye-Hückel limiting law slopes. \emph{J. Phys. Chem. Ref. Data} \bold{19}, 371--411. \url{https://doi.org/10.1063/1.555853}
-Haar, L., Gallagher, J. S. and Kell, G. S. (1984) \emph{NBS/NRC Steam Tables}. Hemisphere, Washington, D. C., 320 p. \url{http://www.worldcat.org/oclc/301304139}
+Haar, L., Gallagher, J. S. and Kell, G. S. (1984) \emph{NBS/NRC Steam Tables}. Hemisphere, Washington, D. C., 320 p. \url{https://www.worldcat.org/oclc/301304139}
Helgeson, H. C. and Kirkham, D. H. (1974) Theoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures. I. Summary of the thermodynamic/electrostatic properties of the solvent. \emph{Am. J. Sci.} \bold{274}, 1089--1098. \url{https://doi.org/10.2475/ajs.274.10.1089}
Modified: pkg/CHNOSZ/tests/testthat/test-util.data.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-util.data.R 2020-08-15 06:36:17 UTC (rev 598)
+++ pkg/CHNOSZ/tests/testthat/test-util.data.R 2020-08-15 10:28:47 UTC (rev 599)
@@ -2,9 +2,9 @@
test_that("checkGHS() and checkEOS() (via info()) produce messages", {
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 599
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