Species

Species is a composite type (introduced by the keyword struct) and is defined by a human-readable name, a chemical symbol/notation, an underlying Formula object holding composition, charge, and string representations, a physical state aggregate_state, a species class, as well as an extensible map of custom properties (molar mass, thermodynamic data, etc.)

struct Species{T<:Number} <: AbstractSpecies
    name::String
    symbol::String
    formula::Formula{T}
    aggregate_state::AggregateState
    class::Class
    properties::OrderedDict{Symbol,PropertyType}
end

Species construction

Species can be created from:

• a Formula

fH2O = Formula("H2O")
H2O = Species(fH2O)

Species{Int64}
           name: H2O
         symbol: H2O
        formula: H2O ◆ H₂O
          atoms: H => 2, O => 1
         charge: 0
aggregate_state: AS_UNDEF
          class: SC_UNDEF
     properties: M = 0.0180149999937744 kg mol⁻¹

• a string

HSO4⁻ = Species("HSO₄⁻")

Species{Int64}
           name: HSO₄⁻
         symbol: HSO₄⁻
        formula: HSO₄⁻ ◆ HSO4-
          atoms: H => 1, S => 1, O => 4
         charge: -1
aggregate_state: AS_UNDEF
          class: SC_UNDEF
     properties: M = 0.09706399996645676 kg mol⁻¹

• a dictionary

CO2 = Species(Dict(:C => 1, :O => 2))

Species{Int64}
           name: CO₂
         symbol: CO₂
        formula: CO2 ◆ CO₂
          atoms: O => 2, C => 1
         charge: 0
aggregate_state: AS_UNDEF
          class: SC_UNDEF
     properties: M = 0.04400899998479143 kg mol⁻¹

CO2 = Species(Dict(:Si => 1, :O => 3), -2)

Species{Int64}
           name: SiO₃-2
         symbol: SiO₃-2
        formula: SiO3-2 ◆ SiO₃-2
          atoms: Si => 1, O => 3
         charge: -2
aggregate_state: AS_UNDEF
          class: SC_UNDEF
     properties: M = 0.0760819999737077 kg mol⁻¹

Keyword arguments such as name, symbol, aggregate_state, class can be added during construction.

fH₂O = Formula("H2O")
H₂O = Species(fH₂O; name="Water", symbol="H₂O@", aggregate_state=AS_AQUEOUS, class=SC_AQSOLVENT)

Species{Int64}
           name: Water
         symbol: H₂O@
        formula: H2O ◆ H₂O
          atoms: H => 2, O => 1
         charge: 0
aggregate_state: AS_AQUEOUS
          class: SC_AQSOLVENT
     properties: M = 0.0180149999937744 kg mol⁻¹

And symbol accept unicode characters.

CO₂ = Species(Dict(:C=>1, :O=>2); name="Carbon dioxide", symbol="CO₂⤴", aggregate_state=AS_GAS, class=SC_GASFLUID)

Species{Int64}
           name: Carbon dioxide
         symbol: CO₂⤴
        formula: CO2 ◆ CO₂
          atoms: O => 2, C => 1
         charge: 0
aggregate_state: AS_GAS
          class: SC_GASFLUID
     properties: M = 0.04400899998479143 kg mol⁻¹

vapour = Species("H2O"; name="Vapour", symbol="H₂O⤴", aggregate_state=AS_GAS, class=SC_GASFLUID)
vapour == H₂O

Species properties

The molar mass is systematically calculated and integrated into the species properties. The heat capacity function is also integrated as a predefined function of the Species structure. This function is expressed as follows:

\[{C_p}^° = a_0 + a_1 T + a_2 T^{−2} + a_3 T^{−0.5}\]

Other species properties are open and left to the discretion of users. We can of course imagine that these properties could contain thermodynamic properties such as the Gibbs energy of formation or even the entropy variation, these properties themselves being temperature dependent. These properties must nevertheless respect one of the following types: Number, AbstractVector{<:Number}, Function, AbstractString.

Imagine, for example, that we wanted to construct the $CO_2$ molecule with some of its thermodynamic properties. The Gibbs energy of formation of this species is equal to $-394.39\; KJ/mol$. This property, intrinsic to the species, can be added simply as follows:

using DynamicQuantities, ModelingToolkit
CO₂.ΔfG⁰ = -394.39u"kJ/mol"

-394390.0 m² kg s⁻² mol⁻¹

Heat capacity, on the other hand, is introduced in the following way:

coeffs = [:a₀ => 44.22u"J/K/mol", :a₁ => 0.0088u"J/mol/K^2", :a₂ => -861.904e6u"J*K/mol", :a₃ => 0.0u"J/mol/√K"]
CO₂.Cp = ThermoFunction(:Cp, coeffs; ref=[:T=>298.15u"K", :P=>1u"bar"])

44.22 + 0.0088T + -8.61904e8 / (T^2) ♢ unit=[m² kg s⁻² K⁻¹ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]

CO₂.Cp()

Other functions can be added to species. For example, we can add a rate to the CO2 species:

CO₂.rate = ThermoFunction(:((c₁+c₂*t)/(c₃+c₄*√t)), [:c₁ => 1.0, :c₂ => 2.0u"1/s", :c₃ => 3.0, :c₄ => 4.0u"1/√s"])
CO₂.rate(1u"s")

0.42857142857142855