thermo {CHNOSZ}R Documentation

Thermodynamic Database and System Definition

Description

Data files provided with CHNOSZ are in the data and extdata directories of the package. The *.csv files under data and extdata/OBIGT are used to build the thermo data object on loading the package. Other 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. 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.

Usage

data(thermo)

Format

The items in the thermo object are documented below.

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°C. 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

add.obigt

Examples


## 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]

[Package CHNOSZ version 1.1.0 Index]