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update doc for ReactionAqEqb #34

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Nov 30, 2024
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update doc for ReactionAqEqb #34

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36 changes: 29 additions & 7 deletions src/GenericReactions.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,31 @@ where to convert density units for `K_eqb`:

K_eqb' = K_eqb * rho_ref^K_density_power

The first name in the `Reactants` list is the new species concentration:
The first name in the `Reactants` list is the new species concentration `N`:
other species concentrations in `Reactants` and `Products` lists must already be
defined elsewhere in the model configuration.

The contribution of the new species to element totals or components is defined by the `N_components` vector,
The contribution of the new species to element totals or components is defined by the `N_components` vector, which may be empty eg to
just calculate an Omega or a gas partial pressure etc.

# Examples

## Gas partial pressure from concentration

solubility_H2:
class: ReactionAqEqb
parameters:
Reactants: ["pH2"]
Products: ["H2_conc"]
K_eqb: 7.8e-1 # mol m-3 atm-1 at 298.15 K
K_power: -1.0 # pH2 = H2_conc * K_eqb^-1
variable_attributes:
pH2%units: atm

Compilation of Henry's law coefficients: https://www.henrys-law.org/ which is
R. Sander: Compilation of Henry's law constants (version 5.0.0) for water as solvent, Atmos. Chem. Phys., 23, 10901-12440 (2023), doi:10.5194/acp-23-10901-2023

Unit conversions: 1 mol m^-3 Pa-1 = 1.01325e5 mol m-3 atm-1

# Parameters
$(PARS)
Expand All @@ -47,8 +67,8 @@ Base.@kwdef mutable struct ReactionAqEqb{P} <: PB.AbstractReaction
description="multiple K_eqb * rho_ref^K_density_power to convert units: 0.0 for K_eqb in mol m-3, 1.0 for K_eqb in mol kg-1, etc"),
PB.ParDouble("K_power", -1.0,
description="exponent of K_eqb"),
PB.ParStringVec("N_components", ["2*TN_calc_conc"] ,
description="contribution of new species to element or component total concentrations (or empty vector to just define an Omega)"),
PB.ParStringVec("N_components", String[],
description="contribution of new species to element or component total eg '[\"2*TN_calc\"]' to add `2*N_conc*volume` to `TN_calc` (or empty vector to just define an Omega)"),
)

component_stoichs::Vector{Float64} = Float64[]
Expand All @@ -59,9 +79,8 @@ function PB.register_methods!(rj::ReactionAqEqb)

@info "register_methods! $(PB.fullname(rj))"

vars = [
PB.VarDep("volume", "m3", "cell solute volume"),
]
vars = PB.VariableReaction[]

K_density_power = rj.pars.K_density_power[]
if !iszero(K_density_power)
push!(vars, PB.VarDep("rho_ref", "kg m-3", "reference density"))
Expand Down Expand Up @@ -98,6 +117,9 @@ function PB.register_methods!(rj::ReactionAqEqb)
push!(rj.component_stoichs, stoich)
push!(component_vars, PB.VarContrib(name, "mol", "total moles"))
end
if !isempty(rj.component_stoichs)
push!(vars, PB.VarDep("volume", "m3", "cell solute volume"))
end

PB.setfrozen!(rj.pars.Reactants, rj.pars.Products, rj.pars.N_components)

Expand Down
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