CHNOSZ (version 1.0.0)

swap.basis: Swap Basis Species

Description

Swap the basis species defining a chemical system. One basis species is replaced by a new one with a different chemical formula.

Usage

basis.matrix(basis = get("thermo")$basis)
  element.mu(basis = get("thermo")$basis, T = 25)
  basis.logact(emu, basis = get("thermo")$basis, T = 25)
  swap.basis(species, species2)

Arguments

basis

dataframe, a basis definition

T

numeric, temperature in Kelvin

emu

numeric, chemical potentials of elements

species

character, names or formulas of species, or numeric, indices of species

species2

character or numeric, a species to swap in to the basis definition

encoding

UTF-8

Details

To change the basis definition, specify the names or formulas of the new basis species in the first argument. When the basis definition is changed, any species of interest that were present are deleted, unless the new basis definition has exactly the same elements as before. In that case, the species are kept and the activities of the new basis species are set so that the chemical potentials of the elements at 25 $^{\circ}$C and 1 bar are unchanged.

See Also

basis for defining the basis species, a prerequisite for swapping. Tests (using test_that) showing common error conditions are in inst/tests.

Examples

data(thermo)
## swapping basis species
# start with a preset basis definition
b1 <- basis("CHNOS+")
# swap H2 for O2
(b2 <- swap.basis("O2", "H2"))
# the logarithm of activity calculated for H2
# is equal to the one calculated from the equilibrium constant
# for H2O = H2 + 0.5O2
logK <- subcrt(c("O2","H2","H2O"), c(-0.5,-1,1), T=25)$out$logK
# the equilibrium value of logaH2 
# (for logaH2O = 0 and logfO2 = -80)
(logaH2 <- -logK + 40)
stopifnot(all.equal(logaH2, b2$logact[5]))
# put O2 back in
b3 <- swap.basis("H2", "O2")
# we have returned to starting point
stopifnot(all.equal(b1$logact, b3$logact))

## demonstrating the interconvertibility between 
## chemical potentials of elements and logarithms 
## of activities of basis species at high temperature
basis("CHNOS+")
bl1 <- basis()$logact
emu <- element.mu(T=100)
bl2 <- basis.logact(emu, T=100)
# note that basis.logact produces a named array
stopifnot(all.equal(bl1, as.numeric(bl2)))

## swapping basis species while species are defined
## and using numeric species indices
basis("MgCHNOPS+") 
# load species whose names contain "ATP"
species(info.approx("ATP "))
# swap in CO2(g) for CO2(aq)
iCO2g <- info("CO2", "gas")
swap.basis("CO2", iCO2g)
a1 <- affinity()
# swap in CH4(g) for CO2(g)
iCH4g <- info("CH4", "gas")
swap.basis(iCO2g, iCH4g)
a2 <- affinity()
# the equilibrium fugacity of CH4 is *very* low
# swap in CO2(aq) for CH4(g)
iCO2a <- info("CO2", "aq")
swap.basis(iCH4g, iCO2a)
a3 <- affinity()
# swapping the basis species didn't affect the affinities
# of the formation reactions of the species, since
# the chemical potentials of the elements were unchanged
stopifnot(all.equal(a1$values, a2$values))
stopifnot(all.equal(a1$values, a3$values))