phr_pH_fix_definition: fix pH or pe of a reaction
In paleolimbot/tidyphreeqc: Tidy geochemical modeling using PHREEQC

Description Usage Arguments Details Value See Also Examples

While you can state the initial pH and pe of a SOLUTION at its definition, during a reaction, e.g. with an EQUILIBRIUM_PHASE, these initial conditions can (will!) change. This does not always match the true behavior of the system that the modeller is trying to depict. Sometimes the pH and/or pe of a system are supposed to be held at a constant value. PHREEQC does not come with a build-in way of fixing pe/pH, but the User's guide to PHREEQC provides something of an official workaround by defining pseudo-phases capable of locking pH or pe at defined values. The functions described here provide practical shortcuts to these workarounds.

phr_pH_fix_definition()

phr_pe_fix_definition()

phr_pH_fix(pH, number = NA, name = "", formula = "HCl",
  amount = 10)

phr_pe_fix(pe, number = NA, name = "", formula = "O2", amount = 10)

`pH`	The desired final pH-value of the solution
`number`	The number of the component
`name`	The name of the component
`formula`	The chemical formula that is added or substractet from the solution until the desired equilibrium conditions are reached
`amount`	The amount of the species defined by `formula` available to try to reach desired equilibrium conditions
`pe`	The desired final pe-value of the solution

The theory behind pe_fix and pH_fix is, that the presence of an additional phase controls the pe/pH of a system by reaction. For example: if phr_pH_fix is called with default formula = HCl in a simulation, PHREEQC will add or substract Hydrochloric acid to or from your system, until the specified pH is reached. Note that this will likely modify the amount of Cl in your system. Make sure this does not affect the implications of your results! It is possible to use any chemical to control pH/pe, e.g. switching from HCl to NaOH or from O2 to NaMnO4, as long as the Elements involved are defined as SOLUTION_MASTER_SPECIES.

Becaue pe_fix and pH_fix rely on the equilibration with pseudo-species, they have to be defined in a PHASES block first, either in your Database or in your PHREEQC-programm. This can be done via calls to phr_pH_fix_definition() and phr_pe_fix_definition(). See the examples section dor details on the implementation.

A phr_input_section()

https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/html/final-77.html#pgfId-338379

# Fixing pH
sol <- phr_solution(pH = 7)
pH_def <- phr_pH_fix_definition()
pH_set <- phr_pH_fix(pH = 3)
sel <- phr_selected_output(pH = TRUE)

res_pH <- phr_run(
  phr_input(sol, pH_def, pH_set, sel)
) %>%
tibble::as_tibble()

res_pH[res_pH$state == "react", "pH"]

# Fixing pe
sol <- phr_solution(pe = 2)
pe_def <- phr_pe_fix_definition()
pe_set <- phr_pe_fix(pe = 8)
sel <- phr_selected_output(pe = TRUE)

res_pe <- phr_run(
  phr_input(sol, pe_def, pe_set, sel)
) %>%
tibble::as_tibble()

res_pe[res_pe$state == "react", "pe"]

# When there is more than one EQUILIBRIUM_PHASE in one simulation run,
# all have to be defined in the same EQUILIBRIUM_PHASE block. Thus, the
# shortcut-functions who provide a one-phase-only block wont work. In this
# case, define your pe_fix and pH-fix directly inside your call to
# phr_equilibrium_phases(). Keep an eye on the negative prefix, though!

sol <-  phr_solution(pH = 7, pe = 4)
# You still need to define the pseudo-phases
pH_def <- phr_pH_fix_definition()
pe_def <- phr_pe_fix_definition()

phases <- phr_equilibrium_phases(
 Calcite = c(0, 0.001), # somewhat alkaline phase
 Fix_pH = c("-3", "HCl", "10"), # -3 --> pH = 3
 Fix_pe = c("-8", "O2", "10") # -8 --> pe = 8
)
sel <- phr_selected_output(pH = TRUE, pe = TRUE)
res_multi <- phr_run(
  phr_input(sol, pH_def, pe_def, phases, sel)
) %>%
tibble::as_tibble()

res_multi[res_pe$state == "react", c("pH", "pe")]