inst/tinytest/test-water.lines.R

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

# This is a long test ... only run it "at home" 20220131
if(!at_home()) exit_file("Skipping long test")

# Load default settings for CHNOSZ
reset()

# Testing revised water.lines 2017-06-04

# Change to TRUE to show plots (for additional testing)
plot.it <- FALSE
# Change to FALSE to make base plots (for additional testing)
limit.water <- TRUE

# Function to count the number of species on a diagram (not including NA fields)
nspecies <- function(a) length(na.omit(unique(as.numeric(diagram(a, limit.water = limit.water, plot.it = plot.it, balance = 1)$predominant))))

res <- 25

info <- "water.lines() masks H2 and O2 fields on diagrams with pH as x-axis"
if(plot.it) par(mfrow = c(3, 6))
Ts <- c(25, 100, 25)
logaH2O <- c(0, 0, -5)
for(i in 1:3) {
  T <- Ts[i]
  basis(c("H2O", "H+", "e-"), c(logaH2O[i], -7, -7))
  species(c("H2O", "O2", "H2"), c("liq", "gas", "gas"))
  # Eh-pH
  n1 <- nspecies(affinity(pH = c(-2, 16, res), Eh = c(-1, 1.5, res), T = T))
  # pe-pH
  n2 <- nspecies(affinity(pH = c(-2, 16, res), pe = c(-20, 25, res), T = T))
  # logfO2-pH
  swap.basis("e-", "oxygen")
  n3 <- nspecies(affinity(pH = c(-2, 16, res), O2 = c(-90, 10, res), T = T))
  # logaO2-pH
  swap.basis("oxygen", "O2")
  n4 <- nspecies(affinity(pH = c(-2, 16, res), O2 = c(-90, 10, res), T = T))
  # logfH2-pH
  swap.basis("O2", "hydrogen")
  n5 <- nspecies(affinity(pH = c(-2, 16, res), H2 = c(-50, 10, res), T = T))
  # logaH2-pH
  swap.basis("hydrogen", "H2")
  n6 <- nspecies(affinity(pH = c(-2, 16, res), H2 = c(-50, 10, res), T = T))
  expect_equal(c(n1, n2, n3, n4, n5, n6), c(1, 1, 1, 1, 1, 1), info = info)
}

if(plot.it) par(mfrow = c(3, 6))
basis(c("H2O", "H+", "e-"), c(0, -7, -7))
species(c("H2O", "O2", "H2"), c("liq", "gas", "gas"))

info <- "water.lines() masks H2 and O2 fields on diagrams with T as x-axis"
n1 <- nspecies(affinity(T = c(0, 200, res), Eh = c(-1, 1.5, res)))  # Eh-T
n2 <- nspecies(affinity(T = c(0, 200, res), pe = c(-20, 25, res)))  # pe-T
swap.basis("e-", "oxygen"); n3 <- nspecies(affinity(T = c(0, 200, res), O2 = c(-90, 10, res)))  # logfO2-T
swap.basis("oxygen", "O2"); n4 <- nspecies(affinity(T = c(0, 200, res), O2 = c(-90, 10, res)))  # logaO2-T
swap.basis("O2", "hydrogen"); n5 <- nspecies(affinity(T = c(0, 200, res), H2 = c(-50, 10, res)))  # logfH2-T
swap.basis("hydrogen", "H2"); n6 <- nspecies(affinity(T = c(0, 200, res), H2 = c(-50, 10, res)))  # logaH2-T
expect_equal(c(n1, n2, n3, n4, n5, n6), c(1, 1, 1, 1, 1, 1), info = info)

info <- "water.lines() masks H2 and O2 fields on diagrams with P as x-axis"
swap.basis("H2", "e-")
n1 <- nspecies(affinity(P = c(1, 5000, res), Eh = c(-1, 1.5, res)))  # Eh-P
n2 <- nspecies(affinity(P = c(1, 5000, res), pe = c(-20, 25, res)))  # pe-P
swap.basis("e-", "oxygen"); n3 <- nspecies(affinity(P = c(1, 5000, res), O2 = c(-90, 10, res)))  # logfO2-P
swap.basis("oxygen", "O2"); n4 <- nspecies(affinity(P = c(1, 5000, res), O2 = c(-90, 10, res)))  # logaO2-P
swap.basis("O2", "hydrogen"); n5 <- nspecies(affinity(P = c(1, 5000, res), H2 = c(-50, 10, res)))  # logfH2-P
swap.basis("hydrogen", "H2"); n6 <- nspecies(affinity(P = c(1, 5000, res), H2 = c(-50, 10, res)))  # logaH2-P
expect_equal(c(n1, n2, n3, n4, n5, n6), c(1, 1, 1, 1, 1, 1), info = info)

info <- "water.lines() masks H2 and O2 fields on diagrams with T as y-axis"
swap.basis("H2", "e-")
n1 <- nspecies(affinity(Eh = c(-1, 1.5, res), T = c(0, 200, res)))  # T-Eh
n2 <- nspecies(affinity(pe = c(-20, 25, res), T = c(0, 200, res)))  # T-pe
swap.basis("e-", "oxygen"); n3 <- nspecies(affinity(O2 = c(-90, 10, res), T = c(0, 200, res)))  # T-logfO2
swap.basis("oxygen", "O2"); n4 <- nspecies(affinity(O2 = c(-90, 10, res), T = c(0, 200, res)))  # T-logaO2
swap.basis("O2", "hydrogen"); n5 <- nspecies(affinity(H2 = c(-50, 10, res), T = c(0, 200, res)))  # T-logfH2
swap.basis("hydrogen", "H2"); n6 <- nspecies(affinity(H2 = c(-50, 10, res), T = c(0, 200, res)))  # T-logaH2
expect_equal(c(n1, n2, n3, n4, n5, n6), c(1, 1, 1, 1, 1, 1), info = info)