CHNOSZ {CHNOSZ}R Documentation

Chemical Thermodynamics and Activity Diagrams

Description

CHNOSZ is a software package for calculating the standard molal thermodynamic properties and chemical affinities of reactions in geobiochemical systems and for visualizing the stable or metastable equilibrium reference state on chemical speciation and predominance diagrams.

Usage

  CHNOSZ()

Details

CHNOSZ is a package for thermodynamic calculations and graphical analysis.

The functions in CHNOSZ perform three primary tasks: 1) calculation of the standard molal Gibbs energies and other thermodynamic properties of species and reactions. 2) calculation of the activity products of formation reactions of the species of interest from the basis species. The basis species stand for the descriptive compositional variables, i.e. perfectly mobile components (Korzhinskii, 1965). 3) combination of the results of (1) and (2) to generate diagrams showing the equilibrium distributions of species as a function of temperature, pressure, and chemical activities or fugacities of the basis species (which may include pH and Eh if the proton and electron are in the basis).

Note: The CHNOSZ function exists so that this overview page can be linked to the rest of the documentation. All this function does is run the “getting started” examples below. Read further for the functions that really do the work.

Here is some help on getting started with CHNOSZ:

Acknowledgement: This material is based upon work supported by the National Science Foundation under grant EAR-0847616.

References

Korzhinskii, D. S., 1965. The theory of systems with perfectly mobile components and processes of mineral formation. Am. J. Sci., 263, 193-205.

Examples

  

  ### Getting Started
  
  ## standard thermodynamic properties of species
  subcrt('H2O')
  subcrt('alanine')
  subcrt('LYSC_CHICK')  # a protein
  # custom temperature range
  T <- seq(0,500,100)
  subcrt('H2O',T=T,P=1000)
  # temperature - pressure grid
  P <- seq(1000,4000,1000)
  subcrt('H2O',T=T,P=P,grid='P')
  
  ## information about species
  # query the database using formulas
  info('C6H12O6')
  info('SiO2')
  # query using names
  info('quartz')
  t <- info(c('glucose','mannose'))
  # show the equations of state parameters
  info(t)
  # approximate matches for names or formulas
  info('acid ')
  info('SiO2 ')

  ## standard thermodynamic properties of reactions
  # fermentation example
  info(c('fructose','ethanol'))
  subcrt(c('fructose','C2H5OH','CO2'),c(-1,2,2))
  # weathering example -- also see transfer()
  subcrt(c('k-feldspar','H2O','H+','kaolinite','K+','SiO2'),
    c(-2,-1,-2,1,2,4))
  # partial reaction auto-completion is possible
  basis(c('SiO2','H2O','K+','H+','O2'))
  subcrt(c('k-feldspar','kaolinite'),c(-2,1))
 
  ## chemical affinities
  # basis species
  basis(c('CO2','H2O','O2'))
  # species of interest
  species(c('CH4','C2H4O2','CO2'))
  # chemical affinities of formation reactions
  # take off $values for complete output
  affinity()$values
  affinity(O2=c(-90,-60,5))$values
  


[Package CHNOSZ version 0.8 Index]