CHNOSZ

Chemical Thermodynamics and Activity Diagrams

What is it?

• A package for the R software environment.
• This package includes functions and data sets to support chemical thermodynamic modeling in biochemistry and low-temperature geochemistry. The features include calculation of the standard molal thermodynamic properties and chemical affinities of reactions involving minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous species; amino acid group additivity for the standard molal thermodynamic properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state for aqueous species; construction of equilibrium activity diagrams as a function of temperature, pressure, and chemical activities or fugacities of basis species.

An example

• Program script
  
  basis(c('Fe','O2','S2'))
  species(c('iron','ferrous-oxide','magnetite','hematite','pyrite','pyrrhotite'))
  a <- affinity(S2=c(-50,0),O2=c(-90,-10),T=200)
  diagram(a,color='heat')
  title(main=paste('Fe-S-O, 200 degrees C, 1 bar','After Helgeson, 1970',sep='\n'))
  
  
• Output

  

Quick Start

Install R if you don't have it already (from Comprehensive R Archive Network). Start up R, then use these commands to install and load the package and run the examples from the documentation.

On This Site

Download and Documentation

Other Stuff

anim	Animations of equilibrium activity diagrams
Rpad	Interface to CHNOSZ using the Rpad web-based analysis program
transfer	Reaction path calculations in CHNOSZ

Off This Site

• The CHNOSZ-help mailing list has been set up for users to post help requests, bug reports, and stay up to date with future releases (thanks to R-Forge for hosting).
• A paper in Geochemical Transactions describes the program and reports calculations for model surface-layer proteins in different organisms.
• See Figures Fast blog for highlights of new developments in the package.
• The figures from the documentation examples can also be found in the R Graphical Manual (probably for an older release of the package).

About

CHNOSZ is free software.

The author of this package is Jeffrey M. Dick. Please contact me at <jmdick@asu.edu>.

Work on this project at U.C. Berkeley through 2008 was supported by research grants from the U.S. National Science Foundation and Department of Energy. Professor Harold C. Helgeson (d. May 2007) was principal investigator on these grants and my research advisor during the initial stages of development of this software. In 2009-2011, this material is based upon work supported by the National Science Foundation under Grant No. EAR-0847616.

Updates will be posted as progress allows. The thermodynamic database represents the work of many different authors; don't forget to cite them appropriately in publications using this data! For a list of references, use the browse.refs() function in the package, or see its output here.