CHNOSZ

Thermodynamic Calculations for Geobiochemistry

What is it?

This R package offers an integrated set of tools for thermodynamic calculations in geochemistry and compositional biology. Thermodynamic properties are taken from a database for minerals and inorganic and organic aqueous species including biomolecules, or from amino acid group additivity for proteins. High-temperature properties are calculated using the revised Helgeson-Kirkham-Flowers equations of state for aqueous species. Functions are provided to define a system using basis species, automatically balance reactions, calculate the chemical affinities of reactions for selected species, compute metastable equilibrium distributions of species, and plot the results on potential diagrams or equilibrium activity diagrams. Experimental features are available to calculate activity coefficients of aqueous species or for multidimensional optimization of thermodynamic variables using an objective function.

An example

After Helgeson, 1970.

Getting started

Download R from the Comprehensive R Archive Network (CRAN). Launch an R session, then use these commands to install and load the package and run the examples from the documentation.

install.packages("CHNOSZ")
library(CHNOSZ)
data(thermo)
examples()

Download and documentation

Older stuff

Around the web

About

CHNOSZ is free software made available under the GPL.

The maintainer of this package is Jeffrey Dick. Please contact me at j3ffdick@gmail.com.

To cite CHNOSZ, use this reference: Dick, 2008. The thermodynamic database is made possible by the work of many different authors. If you publish results of calculations using any of these data, please cite the primary data sources! For a list of references, use the thermo.refs() function in the package, or access the table of references here.


Updated on 2017-10-18 by Jeffrey M. Dick