Thermodynamic Calculations for Geobiochemistry
What is it?
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.
After Helgeson, 1970.
- R commands
basis(c("Fe", "O2", "S2"), c("cr1", "gas", "gas"))
species(c("iron", "ferrous-oxide", "magnetite", "hematite", "pyrite", "pyrrhotite"))
a <- affinity(S2 = c(-50, 0, 400), O2 = c(-70, -30, 400), T = 200)
diagram(a, fill = "heat")
title(main=paste("Fe-S-O, 200 °C, 1 bar", "After Helgeson, 1970", sep = "\n"))
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.
Download and documentation
- Output from examples (including figures) (2015)
- Animations of equilibrium activity diagrams (2013)
Reaction path calculations in CHNOSZ (2009) (Removed Sep. 2017)
Around the web
CHNOSZ is on R-Forge. Updates to the package will be made there before being posted to this website or to CRAN. Get the latest development version using:
install.packages("CHNOSZ", repos = "http://R-Forge.R-project.org")
Mentioned on Chemistry StackExchange: sodium oxide hydration and thermodynamic data.
- canprot (on Github and CRAN) is a new package that uses CHNOSZ for compositional and thermodynamic analysis of proteomic datasets.
This site hosts the online manual and the vignettes from the package:
See the papers in PeerJ (2016, 2017) for more information.
CHNOSZ is free software made available under the GPL.
The maintainer of this package is Jeffrey Dick. Please contact me at email@example.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