Package ummisco.gama.chemmisol

Class Reaction

java.lang.Object
ummisco.gama.chemmisol.Reaction
public class Reaction extends Object
Describes a reaction that transforms reactants into products.

A reaction can be fully described by:

  • a list of reactives and products (reagents)
  • stoichiometric coefficients
  • a log K value

Let's consider the following example reaction: 

     n A + m B <-> k C + l D
A and B are reactants, C and D are products and n, m, k and l are corresponding stoichiometric coefficients.

By convention, the reaction is rewritten as 

     n A + m B - k C - l D <-> 0
so that stoichiometric coefficients of reactants are positive and stoichiometric coefficients of products are negative.

The equilibrium constant K is then defined according to the law of mass action as: 

    ([C]^k * [D]^l) / ([A]^n * [B]^m) = K
where the bracket notation denotes the activity of each component at equilibrium. By convention, the products form the numerator.

The Chemmisol convention is compliant with the conventions used by the reference VMinteq software, so that values used in the VMinteq database can be reused as is in Chemmisol. Reactions must be specified so that all reagents are defined in the chemical system as components, except one reagent, that represents the produced species of the reaction.

Examples

        try (ChemicalSystem system = new ChemicalSystem()) {
                // Defines the reaction PO4-3 + 4 H+ <-> H4PO3
                Reaction reaction = new Reaction("H4PO3", 13.192)
                        .addReagent("H4PO3", -1, Phase.AQUEOUS)
                        .addReagent("H+", 4, Phase.AQUEOUS)
                        .addReagent("PO4-3", 1, Phase.AQUEOUS);
                system.addReaction(reaction);

                // Implicitly defines H+ as a component
                system.fixPH(7);
                // Defines PO4-3 as a component
                system.addComponent(new ChemicalComponent(
                        "PO4-3", Phase.AQUEOUS, 0.1
                        );

                // The H4PO3 species is automatically added to the system, as the
                produced species of the reaction
                system.setUp();
        }
See Also:

  • Constructor Details

    • Reaction

      public Reaction(String name, double log_K)
      Initializes a new Reaction.
      Parameters:
      name - Name of the reaction. By convention, generally corresponds to the name of the produced species of the reaction.
      log_K - Value of log(K) where K is the equilibrium constant of the reaction.

  • Method Details

    • getName

      public String getName()
      Gets the name of this reaction. By convention, the name of the reaction generally corresponds to the name of its produced species. The name of each reaction must be unique within each chemical system.
      Returns:
      name of the reaction

    • getLogK

      public double getLogK()
      Gets the base 10 logarithm of this reaction.

      Let's consider the following example reaction: 

           n A + m B <-> k C + l D
      The log(K) value is such that at equilibrium: 
          ([C]^k * [D]^l) / ([A]^n * [B]^m) = K
      Returns:
      log(K) value of this reaction

    • addReagent

      public Reaction addReagent(String name, int coefficient, Phase phase)
      Adds a reagent to this reaction. Equivalent to addReagent(new Reagent(name, coefficient, phase).
      Parameters:
      name - Name of the reagent.
      coefficient - Stoichiometric coefficient associated to the reagent in this reaction.
      phase - Phase of the reagent.
      Returns:
      This reaction.
      See Also:

    • addReagent

      public Reaction addReagent(Reagent reagent)
      Adds a reagent to this reaction.

      The name of the reagent must correspond to the name of the species in the chemical system to which the reaction will be added. The corresponding species does not require to be already defined in the chemical system, but all reagents must be added to the reaction before ChemicalSystem.addReaction(Reaction) is called. While reagents corresponding to components must be defined explicitly in the chemical system, the produced species is automatically defined when the chemical system is set up.

      By convention, negative coefficients are associated to products and positive coefficients are associated to reactants.

      Parameters:
      reagent - Reagent to add to this reaction.
      Returns:
      This reaction.

    • getReagents

      public List<Reagent> getReagents()
      Gets the current list of reagents of this reaction.
      Returns:
      list of reagents