CHNOSZ

Chemical Thermodynamics and Activity Diagrams

What is it?

• A package for the R software environment.
• Description: Calculation of the standard molal thermodynamic properties and chemical affinities of reactions between and among minerals, inorganic, organic, and/or biomolecular aqueous and crystalline species. Incorporation of an extensive database of thermodynamic properties of species and algorithms for computing the standard thermodynamic properties of neutral and ionized proteins from amino acid group contributions. Generation of chemical speciation and predominance diagrams for stable and metastable equilibrium in open systems 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

  

Sitemap

faq	Frequently asked questions.
download	Download CHNOSZ or get the NEWS.
html	HTML version of the package documentation (including vignettes).
examples	Output from examples in the package documentation.
gallery	Selected examples and short discussion.
Rpad	Interface to CHNOSZ using the Rpad web-based analysis program.
transfer	Description of reaction path calculations in CHNOSZ, with movies.
yeast	Protein metastability in yeast (supporting information for a paper).

Installation

• Download and install R.
• Option 1: Install CHNOSZ using a package file from the Comprehensive R Archive Network.

  • Use this R command or a GUI equivalent: install.packages("CHNOSZ")

• Option 2: Install CHNOSZ using a package file available here.
  • On command line:

    R CMD INSTALL CHNOSZ_0.9.tar.gz

  • In Mac R GUI (Note the F.A.Q.):

    Packages & Data > Package Installer > (Repository) Local Source Package > At User Level > Install > CHNOSZ_0.9.tar.gz

  • In Windows R GUI:

    Packages > Install package(s) from local zip files > CHNOSZ_0.9.zip

Documentation

• A paper in Geochemical Transactions describes the program and reports calculations for model surface-layer proteins in different organisms.
• Download the PDF version of the program documentation or view it online. The same content is available through the R help system, after the package is loaded.
• Getting started: Open an R session, then use these commands to load the package and run the examples from the documentation:

  
  library(CHNOSZ)
  examples()

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.

Effective in 2009: This material is based upon work supported by the National Science Foundation under Grant No. EAR-0847616. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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 citations, see the file "source.csv" in the package.