Chemical Thermodynamics and Activity Diagrams
What is it?
package offers an integrated set of tools for thermodynamic calculations in compositional biology and geochemistry.
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 can be used for calculating 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
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 (GitHub; manual) is a new package that uses CHNOSZ for compositional and thermodynamic analysis of proteomic datasets. The following vignettes showing oxidation and hydration state are available:
See the papers in PeerJ (2016) and bioRxiv (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 firstname.lastname@example.org.
Work on this project through 2008 was supported by research grants from the U.S. National Science Foundation and Department of Energy. In 2009-2011, development of this package was based upon work supported by the National Science Foundation under Grant No. EAR-0847616.
To cite CHNOSZ, use this reference: Dick, 2008. The thermodynamic database represents 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 browse.refs() function in the package, or access the table of references here.
Updated on 2017-03-12 by Jeffrey M. Dick