thermo: Thermodynamic Database and System Settings

Description Usage Arguments Format References See Also Examples

View source: R/thermo.R

Description

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

The system settings are changed using basis and species. To clear the system settings (the default, i.e. no species loaded), run basis(""); to clear only the formed species, run species(delete = TRUE)

The thermodynamic database is changed using add.OBIGT and mod.OBIGT. To restore the default database without altering the species settings, run OBIGT().

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

All the data are stored in the thermo data object in an environment named CHNOSZ. thermo() is a convenience function to access or modify parts of this object, in particular some computational settings, for example, thermo("opt$ideal.H" = FALSE) (see nonideal).

The main data files provided with CHNOSZ, as *.csv files in the extdata/thermo and extdata/OBIGT directories of the package, are used to build the thermo object, which is described below.

Usage

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Arguments

...

list, one or more arguments whose names correspond to the component() to modify

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; moved to 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("extdata", package="CHNOSZ")
# What files make up OBIGT?
# Note: file names with _aq, _cr, _gas, or _liq
# are used in the default database
dir(system.file("extdata/OBIGT", 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]

## adding an element
old <- thermo()$element
# element symbol, state, source (can be anything),
# mass, entropy, and number in compound
Xprops <- data.frame(element = "X", state = "cr",
  source = "user", mass = 100, s = 100, n = 1)
new <- rbind(old, Xprops)
thermo(element = new)
# now "X" is recognized as an element in other functions
mass("X10")
# restore default settings to remove X
reset()

CHNOSZ documentation built on July 7, 2020, 3 p.m.