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Species

ChemistryLab.AbstractSpecies — Type
abstract type AbstractSpecies end

Abstract base type for all chemical species representations.

All concrete species types (Species, CemSpecies) inherit from this type.

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ChemistryLab.AggregateState — Type
@enum AggregateState

Enumeration for species aggregate states.

Values

  • AS_UNDEF: undefined state.
  • AS_AQUEOUS: aqueous solution.
  • AS_CRYSTAL: crystalline solid.
  • AS_GAS: gas phase.
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ChemistryLab.Class — Type
@enum Class

Enumeration for species chemical classes.

Values

  • SC_UNDEF: undefined class.
  • SC_AQSOLVENT: aqueous solvent.
  • SC_AQSOLUTE: aqueous solute.
  • SC_COMPONENT: component.
  • SC_GASFLUID: gas or fluid.
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ChemistryLab.Species — Type
struct Species{T<:Number} <: AbstractSpecies

Standard chemical species representation using atomic composition.

Fields

  • name::String: human-readable name.
  • symbol::String: species symbol.
  • formula::Formula{T}: chemical formula with stoichiometric coefficients.
  • aggregate_state::AggregateState: physical state.
  • class::Class: chemical class.
  • properties::OrderedDict{Symbol,PropertyType}: thermodynamic and other properties.

Examples

julia> s = Species("H2O"; name="Water", aggregate_state=AS_AQUEOUS);

julia> atoms(s)
OrderedDict{Symbol, Int64} with 2 entries:
  :H => 2
  :O => 1
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Base.isequal — Method
Base.isequal(s1::AbstractSpecies, s2::AbstractSpecies) -> Bool

Compare two species for equality based on formula, aggregate state, and class.

Examples

julia> s1 = Species("H2O"; aggregate_state=AS_AQUEOUS);

julia> s2 = Species("H₂O"; aggregate_state=AS_AQUEOUS);

julia> s1 == s2
true
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ChemistryLab.charge — Method
charge(s::AbstractSpecies) -> Int8

Return the formal charge of the species.

Examples

julia> s1 = Species("Ca(HSiO3)+");

julia> charge(s1) == 1
true
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ChemistryLab.CemSpecies — Type
struct CemSpecies{T<:Number,S<:Number} <: AbstractSpecies

Cement chemistry species representation using oxide notation.

Fields

  • name::String: human-readable name.
  • symbol::String: species symbol.
  • formula::Formula{T}: atomic composition formula.
  • cemformula::Formula{S}: oxide notation formula.
  • aggregate_state::AggregateState: physical state.
  • class::Class: chemical class.
  • properties::OrderedDict{Symbol,PropertyType}: thermodynamic and other properties.

Examples

julia> s = CemSpecies("C3A"; name="Tricalcium aluminate");

julia> oxides(s)
OrderedDict{Symbol, Int64} with 2 entries:
  :C => 3
  :A => 1
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ChemistryLab.name — Method
name(s::AbstractSpecies) -> String

Return the name of the species.

Examples

julia> s1 = Species("H2O"; aggregate_state=AS_AQUEOUS);

julia> s1.name == "H2O"
true
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ChemistryLab.formula — Method
formula(s::AbstractSpecies) -> Formula

Return the Formula object associated with the species.

Examples

julia> s1 = Species("H2O"; aggregate_state=AS_AQUEOUS);

julia> formula(s1) == Formula("H2O")
true
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ChemistryLab.atoms — Method
atoms(s::AbstractSpecies) -> OrderedDict{Symbol,Number}

Return the atomic composition (element => coefficient) of the species.

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ChemistryLab.atoms_charge — Method
atoms_charge(s::AbstractSpecies) -> OrderedDict{Symbol,Number}

Return atomic composition including the charge as a :Zz key if non-zero.

Examples

julia> s = Species("Ca+2");

julia> atoms_charge(s)
OrderedDict{Symbol, Int64} with 2 entries:
  :Ca => 1
  :Zz => 2
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ChemistryLab.oxides — Function
oxides(s::CemSpecies) -> OrderedDict{Symbol,Number}

Return the oxide composition of the cement species.

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ChemistryLab.oxides_charge — Function
oxides_charge(s::CemSpecies) -> OrderedDict{Symbol,Number}

Return oxide composition including the charge as a :Zz key if non-zero.

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Missing docstring.

Missing docstring for components. Check Documenter's build log for details.

ChemistryLab.aggregate_state — Method
aggregate_state(s::AbstractSpecies) -> AggregateState

Return the aggregate state of the species.

Examples

julia> s1 = Species("H2O"; aggregate_state=AS_AQUEOUS);

julia> aggregate_state(s1) == AS_AQUEOUS
true
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ChemistryLab.properties — Method
properties(s::AbstractSpecies) -> OrderedDict{Symbol,PropertyType}

Return the properties dictionary of the species.

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ChemistryLab.apply — Method
apply(func::Function, s::S, args...; kwargs...) where {S<:AbstractSpecies} -> S

Apply a function element-wise to all numeric components and properties of a species.

Arguments

  • func: function to apply.
  • s: source species.
  • args...: additional arguments for func.
  • kwargs...: keyword arguments (including potential overrides for name, symbol, etc.).

Returns

  • New species with transformed values.

Handles Quantity types, attempting to preserve dimensions when possible.

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