data: Thermodynamic Database and System Definition

Description

Please read the important Warning at CHNOSZ-package.

The core data files provided with CHNOSZ are in the data directory of the package. These *.csv files are used to build the thermo data object on loading the package. Additional (extra) data files, supporting the examples and vignettes, are documented separately at extdata.

The thermo object holds the thermodynamic database of properties of species, some thermodynamic constants and operational parameters for functions in CHNOSZ, the properties of elements, references to literature sources of thermodynamic data, compositions of chemical activity buffers, and amino acid compositions of proteins. The thermo object also holds intermediate data used in calculations, in particular the definitions of basis species and species of interest input by the user, and the calculated properties of water so that subsequent calculations at the same temperature-pressure conditions can be accelerated.

The thermo object is a list composed of data.frames or lists each representing a class of data. The object is created in an environment named thermo; see sideeffects for details. It is created upon loading the package, through a call to data(thermo) in .onAttach. At any time, the user can restore the data object to its initial state by calling data(thermo). This is sometimes a useful command to use during an interactive session, when previous definitions of basis species and species of interest are longer desired.

The function add.obigt is available to update the thermodynamic database in use in a running session. For example, one can run add.obigt("mydata.csv") after loading the package, and the data in that file will be added to the database. The format of this file must be the same as the OBIGT.csv file provided with CHNOSZ. Although changes made using add.obigt are lost when the current R session is closed, the data can always be restored the next time as long as the user has the mydata.csv (or other) file available.

The first example below shows how to find the installation locations of OBIGT.csv and other *.csv files. Making changes to these files is not recommended, because incompatible changes can leave the package unusable; also, the files will be overwritten whenver the package is installed (or updated). Instead, use these files as templates for creating your own database files.

Usage

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Format

The items in the thermo object are documented below.

References

Amend, J. P. and Helgeson, H. C. (1997b) Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. Part 1. L-alpha-amino acids. J. Chem. Soc., Faraday Trans. 93, 1927–1941. http://dx.doi.org/10.1039/a608126f

Cox, J. D., Wagman, D. D. and Medvedev, V. A., eds. (1989) CODATA Key Values for Thermodynamics. Hemisphere Publishing Corporation, New York, 271 p. http://www.worldcat.org/oclc/18559968

Dick, J. M., LaRowe, D. E. and Helgeson, H. C. (2006) Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. Biogeosciences 3, 3110–336. http://www.biogeosciences.net/3/311/2006/bg-3-311-2006.html

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 1000°C. Comp. Geosci. 18, 899–947. http://dx.doi.org/10.1016/0098-3004(92)90029-Q

Shock, E. L. and Koretsky, C. M. 1995 Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. Geochim. Cosmochim. Acta 59, 1497–1532. http://dx.doi.org/10.1016/0016-7037(95)00058-8

Shock, E. L. et al. 1998 SLOP98.dat (computer data file). http://geopig.asu.edu/supcrt92_data/slop98.dat, accessed on 2005-11-05. Current location: http://geopig.asu.edu/sites/default/files/slop98.dat.

Wagman, D. D., Evans, W. H., Parker, V. B., Schumm, R. H., Halow, I., Bailey, S. M., Churney, K. L. and Nuttall, R. L. (1982) The NBS tables of chemical thermodynamic properties. Selected values for inorganic and C1 and C2 organic substances in SI units. J. Phys. Chem. Ref. Data 11 (supp. 2), 1–392. https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf

See Also

add.obigt for thermodynamic data from local .csv files.

Examples

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## where are OBIGT.csv and the other data 
## files on your installation?
system.file("data",package="CHNOSZ")

## exploring thermo$obigt
# what physical states there are
unique(thermo$obigt$state)
# formulas of ten species at random
n <- nrow(thermo$obigt)
thermo$obigt$formula[runif(10)*n]

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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