inst/tinytest/test-swap.basis.R

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

# Load default settings for CHNOSZ
reset()

info <- "swap.basis raises errors when needed"
expect_error(swap.basis(c("CO2", "H2O")), "requires an existing basis definition", info = info)
basis("CHNOS+")
expect_error(swap.basis(c("CO2", "H2O")), "two species must be identified", info = info)
expect_error(swap.basis(c("CO2", "H2O"), c("HCO3-", "H2O")), "can only swap one species for one species", info = info)
expect_error(swap.basis("CH4", "C2H5OH"), "basis species .* is not defined", info = info)
expect_error(swap.basis("CO2", "C60"), "is not available", info = info)
expect_error(swap.basis("CO2", "H2"), "the number of basis species is greater than the number of elements and charge", info = info)

info <- "basis.logact only accepts defined elements"
# Setup basis species with two elements: C and H
basis(c("graphite", "H2"), c("cr", "gas"))
# We can't get basis activities with one element
expect_error(basis.logact(c(C = 1)), "number of elements in 'emu' is less than those in basis", info = info)

# 20181111
info <- "Swapping works with a buffer (no recalculation of activities)"
basis("FeCHNOS+")
oldb <- basis("O2", "PPM")
# Before version 1.1.3-57, this gave Error in value * (-log(10) * R * T) : non-numeric argument to binary operator
newb <- swap.basis("O2", "hydrogen")
# NOTE: logact includes "PPM" for O2 (old) and H2 (new)
expect_identical(oldb$logact, newb$logact, info = info)

# 20200728 moved from swap-basis.Rd
info <- "Swapping doesn't affect affinities of formation reactions of species"
## Swapping basis species while species are defined
## and using numeric species indices
basis("MgCHNOPS+") 
# Load some Mg-ATP species
species(c("MgATP-2", "MgHATP-", "MgH2ATP", "Mg2ATP"))
# Swap in CO2(g) for CO2(aq)
swap.basis("CO2", "carbon dioxide")
a1 <- affinity()
# Swap in CH4(g) for CO2(g)
swap.basis("carbon dioxide", "methane")
a2 <- affinity()
# The equilibrium fugacity of CH4 is *very* low
# Swap in CO2(aq) for CH4(g)
swap.basis("methane", "CO2")
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
expect_equal(a1$values, a2$values, info = info)
expect_equal(a1$values, a3$values, info = info)