Defining chemical systems#

This section covers the components of a chemical system as defined in MusicBox:

  • Species (see musica:musica.mechanism_configuration.Species)

  • Phases (see musica:musica.mechanism_configuration.Phase)

  • Reactions (see musica:musica.mechanism_configuration.Reactions)

  • Mechanisms (see musica:musica.mechanism_configuration.Mechanism)

As a reminder, this section assumes you have imported:

import musica.mechanism_configuration as mc

Species#

Chemical species are the fundamental units that participate in reactions, they can be defined using:

X = mc.Species(name="X")
Y = mc.Species(name="Y")
Z = mc.Species(name="Z")

species = {"X":X,"Y":Y,"Z":Z}

Species can be initialized with various chemistry-related paramaters (e.g., molecular weight, density, etc.). See the musica.mechanism_configuration.Species documentation for further details.

Phases#

Species can be grouped into a phase. At present MUSICA and therefore MusicBox can only support a single gas phase, but support for more phases is coming in the future:

gas = mc.Phase(name="gas",species=list(species.values()))

Reactions#

Reactions are defined using rate-based classes such as musica:musica.mechanism_configuration.Arrhenius. Each class takes a unique set of rate parameters and the participating species:

arr1 = mc.Arrhenius(name="X->Y", A=4.0e-3, C=50, reactants=[species["X"]], products=[species["Y"]], gas_phase=gas)
arr2 = mc.Arrhenius(name="Y->Z", A=4.0e-3, C=50, reactants=[species["Y"]], products=[species["Z"]], gas_phase=gas)

For passing later on into a Mechanism (see musica:musica.mechanism_configuration.Mechanism), it is helpful to store your selected reactions into a dictionary:

rxns = {r.name: r for r in [arr1, arr2]}

Note

Several other reaction types are made available for use in MusicBox. For a full list of supported reactions types as well as their parameters, please see the Reactions page in the OpenAtmos Mechanism Configuration documentation.

Mechanisms#

A mechanism defines a collection of chemical species, their associated phases, and the reactions between them. Mechanisms can be defined as follows:

mechanism = mc.Mechanism(name="tutorial_mechanism", species=list(species.values()), phases=[gas], reactions=list(rxns.values()))
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