CHNOSZ is a package for thermodynamic calculations, primarily with applications in geochemistry and compositional biology. It can be used to calculate the standard molal thermodynamic properties and chemical affinities of reactions relevant to geobiochemical processes, and to visualize the equilibrium activities of species on chemical speciation and predominance diagrams.
To view the manual, run help.start() then select ‘Packages’ and ‘CHNOSZ’. Examples in the function help pages can be run by pasting the code block into the R console.
Be sure to check out the vignette titled An Introduction to CHNOSZ, which is available by following the link in help.start to ‘User guides, package vignettes and other documentation’.
Run the command examples() to run all of the examples provided in CHNOSZ. This should take about a minute.
Each help page (other than this one) has been given one of the following “concept index entries”:
Main workflow: info, subcrt, basis, species, affinity, equilibrate, diagram
Extended workflow: swap.basis, buffer, mosaic, objective, revisit, findit, EOSregress, wjd
Thermodynamic calculations: util.formula, makeup, util.units, eos, berman, nonideal, util.misc
Water properties: water, util.water, DEW, IAPWS95
Protein properties: protein, protein.info, add.protein, util.fasta, util.protein, util.seq, ionize.aa, yeast
Other tools: examples, eqdata, taxonomy, util.blast
Utility functions: util.expression, util.plot, util.array, util.matrix, util.list, util.test, palply
These concept entries are visible to help.search (aka ??).
For example, help pages related to thermodynamic data can be listed using ??"thermodynamic data".
All thermodynamic data and examples are provided on an as-is basis.
It is up to you to check not only the accuracy of the data, but also the suitability of the data AND computational techniques for your problem.
By combining data taken from different sources, it is possible to build an inconsistent and/or nonsensical calculation.
An attempt has been made to provide a default database (OBIGT) that is internally consistent, but no guarantee can be made.
If there is any doubt about the accuracy or suitability of data for a particular problem, please consult the primary sources (see thermo.refs).
This package would not exist without the encouragement and groudbreaking work of the late Professor Harold C. Helgeson.
The revised Helgeson-Kirkham-Flowers equations of state are used in this package, together with thermodynamic properties of minerals and aqueous species from many papers coauthored by Helgeson.
CHNOSZ uses Fortran code from H2O92D.f in the SUPCRT92 package (Johnson et al., 1992), with only minor modifications (masking of WRITE and STOP statements made for compatibility with the R environment and keep valTP flag TRUE to permit sub-zero C calculations).
Work on this package at U.C. Berkeley from ca. 2003 to 2008 was supported by research grants to HCH 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 EAR-0847616.
The files in extdata/bison are derived from BLAST calculations made on the Saguaro high performance computer at Arizona State University.
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000C. Comp. Geosci. 18, 899--947. https://doi.org/10.1016/0098-3004(92)90029-Q