[CHNOSZ-commits] r671 - in pkg/CHNOSZ: . inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 8 04:22:33 CEST 2021
Author: jedick
Date: 2021-04-08 04:22:32 +0200 (Thu, 08 Apr 2021)
New Revision: 671
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/DEW.Rd
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/IAPWS95.Rd
pkg/CHNOSZ/man/add.OBIGT.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/eos.Rd
pkg/CHNOSZ/man/equilibrate.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/ionize.aa.Rd
pkg/CHNOSZ/man/nonideal.Rd
pkg/CHNOSZ/man/objective.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/thermo.Rd
pkg/CHNOSZ/man/util.blast.Rd
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/man/util.formula.Rd
pkg/CHNOSZ/man/util.protein.Rd
pkg/CHNOSZ/man/util.water.Rd
pkg/CHNOSZ/man/water.Rd
Log:
Use \doi macro in Rd files
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/DESCRIPTION 2021-04-08 02:22:32 UTC (rev 671)
@@ -1,6 +1,6 @@
Date: 2021-04-08
Package: CHNOSZ
-Version: 1.4.0-40
+Version: 1.4.0-41
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/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/inst/CHECKLIST 2021-04-08 02:22:32 UTC (rev 671)
@@ -77,8 +77,5 @@
- Ensure all Rd files have \concept{...} as listed in CHNOSZ-package.Rd
-- Instead of \doi{...}, use \url{https://doi.org/...}. The \doi macro
- generates a large (ca. 265K) build/partial.rdb file (see WRE 1.3.2).
-
- Run R_PAPERSIZE=letter R CMD Rd2pdf chnosz/
and fix any lines truncated by page margins
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -10,7 +10,7 @@
\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 1.4.0-38 (2021-04-07)}{
+\section{Changes in CHNOSZ version 1.4.1 (2021-04-08)}{
\subsection{NEW FEATURES}{
\itemize{
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -51,7 +51,7 @@
}
\references{
-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}
+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. \doi{10.1016/0098-3004(92)90029-Q}
}
\keyword{package}
Modified: pkg/CHNOSZ/man/DEW.Rd
===================================================================
--- pkg/CHNOSZ/man/DEW.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/DEW.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -51,9 +51,9 @@
}
\references{
-Sverjensky, D. A., Harrison, B. and Azzolini, D. (2014) 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}
+Sverjensky, D. A., Harrison, B. and Azzolini, D. (2014) 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. \doi{10.1016/j.gca.2013.12.019}
-Zhang, Z. and Duan, Z. (2005) Prediction of the \emph{PVT} properties of water over wide range of temperatures and pressures from molecular dynamics simulation. \emph{Phys. Earth Planet. Inter.} \bold{149}, 335--354. \url{https://doi.org/10.1016/j.pepi.2004.11.003}
+Zhang, Z. and Duan, Z. (2005) Prediction of the \emph{PVT} properties of water over wide range of temperatures and pressures from molecular dynamics simulation. \emph{Phys. Earth Planet. Inter.} \bold{149}, 335--354. \doi{10.1016/j.pepi.2004.11.003}
}
\concept{Water properties}
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -111,9 +111,9 @@
}
\references{
- Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \url{https://doi.org/10.1006/jcht.1997.0192}
+ Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \doi{10.1006/jcht.1997.0192}
- Schulte, M. D., Shock, E. L. and Wood, R. H. (1995) The temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3919--3930. \url{https://doi.org/10.1016/S0016-7037(01)00717-7}
+ Schulte, M. D., Shock, E. L. and Wood, R. H. (1995) The temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3919--3930. \doi{10.1016/S0016-7037(01)00717-7}
}
Modified: pkg/CHNOSZ/man/IAPWS95.Rd
===================================================================
--- pkg/CHNOSZ/man/IAPWS95.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/IAPWS95.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -43,7 +43,7 @@
}
\references{
-Wagner, W. and Pruss, A. (2002) The IAPWS formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use. \emph{J. Phys. Chem. Ref. Data} \bold{31}, 387--535. \url{https://doi.org/10.1063/1.1461829}
+Wagner, W. and Pruss, A. (2002) The IAPWS formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use. \emph{J. Phys. Chem. Ref. Data} \bold{31}, 387--535. \doi{10.1063/1.1461829}
}
\concept{Water properties}
Modified: pkg/CHNOSZ/man/add.OBIGT.Rd
===================================================================
--- pkg/CHNOSZ/man/add.OBIGT.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/add.OBIGT.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -145,15 +145,15 @@
\references{
Apps, J. and Spycher, N. (2004) \emph{Data qualification for thermodynamic data used to support THC calculations}. DOC.20041118.0004 ANL-NBS-HS-000043 REV 00. Bechtel SAIC Company, LLC.
-Bazarkina, E. F., Zotov, A. V., and Akinfiev, N. N. (2010) Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1-1000 bar and 25°C. \emph{Geology of Ore Deposits} \bold{52}, 167--178. \url{https://doi.org/10.1134/S1075701510020054}
+Bazarkina, E. F., Zotov, A. V., and Akinfiev, N. N. (2010) Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1-1000 bar and 25°C. \emph{Geology of Ore Deposits} \bold{52}, 167--178. \doi{10.1134/S1075701510020054}
-Kitadai, N. (2014) Thermodynamic prediction of glycine polymerization as a function of temperature and pH consistent with experimentally obtained results. \emph{J. Mol. Evol.} \bold{78}, 171--187. \url{https://doi.org/10.1007/s00239-014-9616-1}
+Kitadai, N. (2014) Thermodynamic prediction of glycine polymerization as a function of temperature and pH consistent with experimentally obtained results. \emph{J. Mol. Evol.} \bold{78}, 171--187. \doi{10.1007/s00239-014-9616-1}
-Shock, E. L., Helgeson, H. C. and Sverjensky, D. A. (1989) Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of inorganic neutral species. \emph{Geochim. Cosmochim. Acta} \bold{53}, 2157--2183. \url{https://doi.org/10.1016/0016-7037(89)90341-4}
+Shock, E. L., Helgeson, H. C. and Sverjensky, D. A. (1989) Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of inorganic neutral species. \emph{Geochim. Cosmochim. Acta} \bold{53}, 2157--2183. \doi{10.1016/0016-7037(89)90341-4}
-Stef{\aacute}nsson, A. (2001) Dissolution of primary minerals of basalt in natural waters. I. Calculation of mineral solubilities from 0\degC to 350\degC. \emph{Chem. Geol.} \bold{172}, 225--250. \url{https://doi.org/10.1016/S0009-2541(00)00263-1}
+Stef{\aacute}nsson, A. (2001) Dissolution of primary minerals of basalt in natural waters. I. Calculation of mineral solubilities from 0\degC to 350\degC. \emph{Chem. Geol.} \bold{172}, 225--250. \doi{10.1016/S0009-2541(00)00263-1}
-Sverjensky, D. A., Shock, E. L., and Helgeson, H. C. (1997) Prediction of the thermodynamic properties of aqueous metal complexes to 1000 °C and 5 kbar. \emph{Geochim. Cosmochim. Acta} \bold{61}, 1359--1412. \url{https://doi.org/10.1016/S0016-7037(97)00009-4}
+Sverjensky, D. A., Shock, E. L., and Helgeson, H. C. (1997) Prediction of the thermodynamic properties of aqueous metal complexes to 1000 °C and 5 kbar. \emph{Geochim. Cosmochim. Acta} \bold{61}, 1359--1412. \doi{10.1016/S0016-7037(97)00009-4}
}
\concept{Thermodynamic data}
Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/affinity.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -102,7 +102,7 @@
}
\references{
-Helgeson, H. C., Richard, L, McKenzie, W. F., Norton, D. L. and Schmitt, A. (2009) A chemical and thermodynamic model of oil generation in hydrocarbon source rocks. \emph{Geochim. Cosmochim. Acta} \bold{73}, 594--695. \url{https://doi.org/10.1016/j.gca.2008.03.004}
+Helgeson, H. C., Richard, L, McKenzie, W. F., Norton, D. L. and Schmitt, A. (2009) A chemical and thermodynamic model of oil generation in hydrocarbon source rocks. \emph{Geochim. Cosmochim. Acta} \bold{73}, 594--695. \doi{10.1016/j.gca.2008.03.004}
}
\concept{Main workflow}
Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/basis.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -71,9 +71,9 @@
}
\references{
-Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}:e2238. \url{https://doi.org/10.7717/peerj.2238}
+Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}:e2238. \doi{10.7717/peerj.2238}
-Dick, J. M. (2017) Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. \emph{PeerJ} \bold{5}:e3421 \url{https://doi.org/10.7717/peerj.3421}
+Dick, J. M. (2017) Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. \emph{PeerJ} \bold{5}:e3421 \doi{10.7717/peerj.3421}
}
\examples{
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/berman.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -124,11 +124,11 @@
\references{
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}
+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. \doi{10.1093/petrology/29.2.445}
-Berman, R. G. and Aranovich, L. Ya. (1996) Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al{\s2}O{\s3}-TiO{\s2}-SiO{\s2}. \emph{Contrib. Mineral. Petrol.} \bold{126}, 1-24. \url{https://doi.org/10.1007/s004100050233}
+Berman, R. G. and Aranovich, L. Ya. (1996) Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al{\s2}O{\s3}-TiO{\s2}-SiO{\s2}. \emph{Contrib. Mineral. Petrol.} \bold{126}, 1-24. \doi{10.1007/s004100050233}
-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}
+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. \doi{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{https://www.worldcat.org/oclc/13594862}
}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/diagram.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -302,17 +302,17 @@
Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57.
-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}
+Dick, J. M. (2019) CHNOSZ: Thermodynamic calculations and diagrams for geochemistry. \emph{Front. Earth Sci.} \bold{7}:180. \doi{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{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{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}
+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. \doi{10.1111/j.1472-4669.2007.00099.x}
-Majzlan, J., Navrotsky, A., McClesky, R. B. and Alpers, C. N. (2006) Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe\s{2}(SO\s{4})\s{3}(H\s{2}O)\s{5}. \emph{Eur. J. Mineral.} \bold{18}, 175--186. \url{https://doi.org/10.1127/0935-1221/2006/0018-0175}
+Majzlan, J., Navrotsky, A., McClesky, R. B. and Alpers, C. N. (2006) Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe\s{2}(SO\s{4})\s{3}(H\s{2}O)\s{5}. \emph{Eur. J. Mineral.} \bold{18}, 175--186. \doi{10.1127/0935-1221/2006/0018-0175}
-Tagirov, B. and Schott, J. (2001) Aluminum speciation in crustal fluids revisited. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3965--3992. \url{https://doi.org/10.1016/S0016-7037(01)00705-0}
+Tagirov, B. and Schott, J. (2001) Aluminum speciation in crustal fluids revisited. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3965--3992. \doi{10.1016/S0016-7037(01)00705-0}
}
Modified: pkg/CHNOSZ/man/eos.Rd
===================================================================
--- pkg/CHNOSZ/man/eos.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/eos.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -96,21 +96,21 @@
\references{
- Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. \emph{Geochim. Cosmochim. Acta} \bold{67}, 613--629. \url{https://doi.org/10.1016/S0016-7037(02)01141-9}
+ Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. \emph{Geochim. Cosmochim. Acta} \bold{67}, 613--629. \doi{10.1016/S0016-7037(02)01141-9}
- Helgeson, H. C., Kirkham, D. H. and Flowers, G. C. (1981) Theoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures. IV. Calculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600\degC and 5 Kb. \emph{Am. J. Sci.} \bold{281}, 1249--1516. \url{https://doi.org/10.2475/ajs.281.10.1249}
+ Helgeson, H. C., Kirkham, D. H. and Flowers, G. C. (1981) Theoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures. IV. Calculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600\degC and 5 Kb. \emph{Am. J. Sci.} \bold{281}, 1249--1516. \doi{10.2475/ajs.281.10.1249}
- Helgeson, H. C., Owens, C. E., Knox, A. M. and Richard, L. (1998) Calculation of the standard molal thermodynamic properties of crystalline, liquid, and gas organic molecules at high temperatures and pressures. \emph{Geochim. Cosmochim. Acta} \bold{62}, 985--1081. \url{https://doi.org/10.1016/S0016-7037(97)00219-6}
+ Helgeson, H. C., Owens, C. E., Knox, A. M. and Richard, L. (1998) Calculation of the standard molal thermodynamic properties of crystalline, liquid, and gas organic molecules at high temperatures and pressures. \emph{Geochim. Cosmochim. Acta} \bold{62}, 985--1081. \doi{10.1016/S0016-7037(97)00219-6}
- 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}
+ 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. \doi{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{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}
+ 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. \doi{10.1016/0016-7037(88)90181-0}
- Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 \degC and 5 kbar. \emph{J. Chem. Soc. Faraday Trans.} \bold{88}, 803--826. \url{https://doi.org/10.1039/FT9928800803}
+ Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 \degC and 5 kbar. \emph{J. Chem. Soc. Faraday Trans.} \bold{88}, 803--826. \doi{10.1039/FT9928800803}
- Tanger, J. C. IV and Helgeson, H. C. (1988) Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Revised equations of state for the standard partial molal properties of ions and electrolytes. \emph{Am. J. Sci.} \bold{288}, 19--98. \url{https://doi.org/10.2475/ajs.288.1.19}
+ Tanger, J. C. IV and Helgeson, H. C. (1988) Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Revised equations of state for the standard partial molal properties of ions and electrolytes. \emph{Am. J. Sci.} \bold{288}, 19--98. \doi{10.2475/ajs.288.1.19}
}
Modified: pkg/CHNOSZ/man/equilibrate.Rd
===================================================================
--- pkg/CHNOSZ/man/equilibrate.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/equilibrate.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -141,7 +141,7 @@
}
\references{
- Dick, J. M. (2008) Calculation of the relative metastabilities of proteins using the CHNOSZ software package. \emph{Geochem. Trans.} \bold{9}:10. \url{https://doi.org/10.1186/1467-4866-9-10}
+ Dick, J. M. (2008) Calculation of the relative metastabilities of proteins using the CHNOSZ software package. \emph{Geochem. Trans.} \bold{9}:10. \doi{10.1186/1467-4866-9-10}
}
\concept{Main workflow}
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2021-04-07 23:01:18 UTC (rev 670)
+++ pkg/CHNOSZ/man/examples.Rd 2021-04-08 02:22:32 UTC (rev 671)
@@ -87,67 +87,67 @@
}
\references{
-Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. \emph{Geochim. Cosmochim. Acta} \bold{67}, 613--629. \url{https://doi.org/10.1016/S0016-7037(02)01141-9}
+Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. \emph{Geochim. Cosmochim. Acta} \bold{67}, 613--629. \doi{10.1016/S0016-7037(02)01141-9}
-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 Tagirov, B. R. (2014) Zn in hydrothermal systems: Thermodynamic description of hydroxide, chloride, and hydrosulfide complexes. \emph{Geochem. Int.} \bold{52}, 197--214. \doi{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.
Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57.
-Amend, J. P. and Shock, E. L. (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. \emph{Science} \bold{281}, 1659--1662. \url{https://doi.org/10.1126/science.281.5383.1659}
+Amend, J. P. and Shock, E. L. (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. \emph{Science} \bold{281}, 1659--1662. \doi{10.1126/science.281.5383.1659}
-Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. \emph{FEMS Microbiol. Rev.} \bold{25}, 175--243. \url{https://doi.org/10.1016/S0168-6445(00)00062-0}
+Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. \emph{FEMS Microbiol. Rev.} \bold{25}, 175--243. \doi{10.1016/S0168-6445(00)00062-0}
-Amend, J. P., Aronson, H. S., Macalady, J. and LaRowe, D. E. (2020) Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. \emph{Environ. Microbiol.} \bold{22}, 1971--1976. \url{https://doi.org/10.1111/1462-2920.14982}
+Amend, J. P., Aronson, H. S., Macalady, J. and LaRowe, D. E. (2020) Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. \emph{Environ. Microbiol.} \bold{22}, 1971--1976. \doi{10.1111/1462-2920.14982}
-Azadi, M. R., Karrech, A., Attar, M. and Elchalakani, M. (2019) Data analysis and estimation of thermodynamic properties of aqueous monovalent metal-glycinate complexes. \emph{Fluid Phase Equilib.} \bold{480}, 25-40. \url{https://doi.org/10.1016/j.fluid.2018.10.002}
+Azadi, M. R., Karrech, A., Attar, M. and Elchalakani, M. (2019) Data analysis and estimation of thermodynamic properties of aqueous monovalent metal-glycinate complexes. \emph{Fluid Phase Equilib.} \bold{480}, 25-40. \doi{10.1016/j.fluid.2018.10.002}
-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}
+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. \doi{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{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}
+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. \doi{10.1016/j.gca.2016.08.028}
-Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLoS ONE} \bold{6}, e22782. \url{https://doi.org/10.1371/journal.pone.0022782}
+Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLoS ONE} \bold{6}, e22782. \doi{10.1371/journal.pone.0022782}
-Dick, J. M. (2015) Chemical integration of proteins in signaling and development. \emph{bioRxiv}. \url{https://doi.org/10.1101/015826}
+Dick, J. M. (2015) Chemical integration of proteins in signaling and development. \emph{bioRxiv}. \doi{10.1101/015826}
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}
+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. \doi{10.1016/0098-3004(92)90029-Q}
-LaRowe, D. E. and Amend, J. P. (2016) The energetics of anabolism in natural settings. \emph{ISME J.} \bold{10}, 1285--1295. \url{https://doi.org/10.1038/ismej.2015.227}
+LaRowe, D. E. and Amend, J. P. (2016) The energetics of anabolism in natural settings. \emph{ISME J.} \bold{10}, 1285--1295. \doi{10.1038/ismej.2015.227}
-Lowe, A. R., Cox, J. S. and Tremaine, P. R. (2017) Thermodynamics of aqueous adenine: Standard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from \emph{T} = 278.15 K to 393.15 K. \emph{J. Chem. Thermodyn.} \bold{112}, 129--145. \url{https://doi.org/10.1016/j.jct.2017.04.005}
+Lowe, A. R., Cox, J. S. and Tremaine, P. R. (2017) Thermodynamics of aqueous adenine: Standard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from \emph{T} = 278.15 K to 393.15 K. \emph{J. Chem. Thermodyn.} \bold{112}, 129--145. \doi{10.1016/j.jct.2017.04.005}
-Lu, P. and Zhu, C. (2011) Arsenic Eh--pH diagrams at 25\degC and 1 bar. \emph{Environ. Earth Sci.} \bold{62}, 1673--1683. \url{https://doi.org/10.1007/s12665-010-0652-x}
+Lu, P. and Zhu, C. (2011) Arsenic Eh--pH diagrams at 25\degC and 1 bar. \emph{Environ. Earth Sci.} \bold{62}, 1673--1683. \doi{10.1007/s12665-010-0652-x}
-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}
+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. \doi{10.2138/rmg.2013.75.5}
Pourbaix, M. (1974) \emph{Atlas of Electrochemical Equilibria in Aqueous Solutions}, NACE, Houston, TX and CEBELCOR, Brussels. \url{https://www.worldcat.org/oclc/563921897}
-Schulte, M. D. and Shock, E. L. (1995) Thermodynamics of Strecker synthesis in hydrothermal systems. \emph{Orig. Life Evol. Biosph.} \bold{25}, 161--173. \url{https://doi.org/10.1007/BF01581580}
+Schulte, M. D. and Shock, E. L. (1995) Thermodynamics of Strecker synthesis in hydrothermal systems. \emph{Orig. Life Evol. Biosph.} \bold{25}, 161--173. \doi{10.1007/BF01581580}
-Shock, E. L. and Koretsky, C. M. (1995) Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. \emph{Geochim. Cosmochim. Acta} \bold{59}, 1497--1532. \url{https://doi.org/10.1016/0016-7037(95)00058-8}
+Shock, E. L. and Koretsky, C. M. (1995) Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. \emph{Geochim. Cosmochim. Acta} \bold{59}, 1497--1532. \doi{10.1016/0016-7037(95)00058-8}
-Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 \degC and 5 kbar. \emph{J. Chem. Soc. Faraday Trans.} \bold{88}, 803--826. \url{https://doi.org/10.1039/FT9928800803}
+Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 \degC and 5 kbar. \emph{J. Chem. Soc. Faraday Trans.} \bold{88}, 803--826. \doi{10.1039/FT9928800803}
-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}
+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. \doi{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{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}
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 671
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