CHNOSZ

Thermodynamic Calculations and Diagrams for Geo(bio)chemistry

What is it?

The CHNOSZ package for R provides an integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. It has functions for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant.
The thermodynamic properties of liquid water are calculated using Fortran code from SUPCRT92 (Johnson et al., 1992) or an implementation in R of the IAPWS-95 formulation (Wagner and Pruß, 2002). 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). The corresponding high-temperature properties are calculated using the Berman-Brown (1985) equations for minerals and the revised Helgeson-Kirkham-Flowers (1981) equations for aqueous species. The HKF equations are augmented with the Deep Earth Water (DEW) model (Sverjensky et al., 2014) and estimates of parameters in the extended Debye-Hückel equation (Manning et al., 2013) to calculate standard-state properties and activity coefficients for given ionic strength at high pressure (to 6 GPa). Activity coefficients are implemented via adjusted standard Gibbs energies at specified ionic strength (Alberty, 1996), which converts all activity variables in the workflow to molalities. A related adjustment is available to convert standard Gibbs energies for gases from the 1 bar standard state used in SUPCRT to a variable-pressure standard state (Anderson and Crerar, 1993, Ch. 12).

Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, logfO2-T, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also has unique capabilities for comparing the compositional and thermodynamic properties of different proteins.

canprot is a package by the same author that uses CHNOSZ for compositional and thermodynamic analysis of proteomic datasets.

An example

After Yang et al., 2018.

Getting started

Download R from the Comprehensive R Archive Network (CRAN). Start 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

Around the web

canprot package

Download canprot from Github or CRAN. The online manual and the vignettes from the package can be viewed here:

See the papers in PeerJ (2016, 2017) for more information.

About

CHNOSZ and canprot are free software made available under the GPL.

The maintainer of these packages is Jeffrey Dick. Please contact him at j3ffdick@gmail.com.

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


Last updated: 2018-11-13