data: Thermodynamic Database and System Settings

Description Usage Format References See Also Examples

Description

Run data(thermo) to initialize or reset all of the data used in CHNOSZ. This includes the computational settings, thermodynamic database, and system settings (chemical species).

The system settings are changed using basis and species. To restore the default system settings (no species loaded), run basis("").

The thermodynamic database is changed using add.obigt and mod.obigt. To restore the default database, run data(OBIGT).

The computational settings are changed using water, P.units, T.units, E.units, and some other commands (e.g. mod.buffer).

Some settings can only be changed by direct manipulation of thermo$opt. In an interactive session, this should be done using the super-assignment operator (e.g. thermo$opt$Berman <<- TRUE) so that the thermo object is not copied to the global environment. (Doing so would cause problems, as many functions are designed to access the thermo object in the CHNOSZ environment.)

To restore the default computational settings, thermodynamic database, and system settings, run data(thermo).

The data files provided with CHNOSZ are in the data and extdata/OBIGT directories of the package. The *.csv files in these directories are used to build the thermo data object in an environment named CHNOSZ. The structure of the thermo object is described below.

Usage

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Format

References

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

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\degC. Comp. Geosci. 18, 899–947. https://doi.org/10.1016/0098-3004(92)90029-Q

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/?q=tools.

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

Other data files, including those supporting the examples and vignettes, are documented separately at extdata.

Examples

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## where are the data files in CHNOSZ?
system.file("data", package="CHNOSZ")
system.file("extdata", package="CHNOSZ")

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

CHNOSZ documentation built on Dec. 14, 2017, 9:37 a.m.