CHNOSZ: Thermodynamic Calculations and Diagrams for Geo(bio)chemistry

An integrated set of tools for thermodynamic calculations in geochemistry and compositional biology. The thermodynamic properties of liquid water are calculated using Fortran code from SUPCRT92 (Johnson et al., 1992 <doi:10.1016/0098-3004(92)90029-Q>) or an implementation in R of the IAPWS-95 formulation (Wagner and Pruß, 2002 <doi:10.1063/1.1461829>). Thermodynamic properties of other species are taken from a database for minerals and inorganic and organic aqueous species including biomolecules, or from amino acid group additivity for proteins (Dick et al., 2006 <doi:10.5194/bg-3-311-2006>). High-temperature properties are calculated using the Berman-Brown (1985) <doi:10.1007/BF00379451> equations for minerals and the revised Helgeson-Kirkham-Flowers (1981) <doi:10.2475/ajs.281.10.1249> equations for aqueous species. The HKF equations are augmented with the Deep Earth Water (DEW) model (Sverjensky et al., 2014 <doi:10.1016/j.gca.2013.12.019>) and estimates of parameters in the extended Debye-Hückel equation (Manning et al., 2013 <doi:10.2138/rmg.2013.75.5>) to calculate standard-state properties and activity coefficients for given ionic strength at high pressure (to 6 GPa). Functions are provided to calculate standard-state properties of species and reactions, define the basis species of a chemical system, automatically balance reactions, calculate the chemical affinities of formation reactions for selected species, calculate the equilibrium activities of those species, and plot the results on chemical activity diagrams.

Package details

AuthorJeffrey Dick [aut, cre] (0000-0002-0687-5890), R Core Team [ctb] (code derived from R's pmax())
MaintainerJeffrey Dick <[email protected]>
LicenseGPL (>= 2)
Version1.1.3-56
URL http://www.chnosz.net/ http://chnosz.r-forge.r-project.org/
Package repositoryView on R-Forge
Installation Install the latest version of this package by entering the following in R:
install.packages("CHNOSZ", repos="http://R-Forge.R-project.org")

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CHNOSZ documentation built on Nov. 8, 2018, 3 p.m.