Defining chemical systems

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

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

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

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

• Mechanisms (see 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,Y,Z]

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

Reactions

Reactions are defined using rate-based classes such as musica:musica.mechanism_configuration.arrhenius.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=[X], products=[Y], gas_phase=gas)
arr2 = mc.Arrhenius(name="Y->Z", A=4.0e-3, C=50, reactants=[Y], products=[Z], gas_phase=gas)

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 mc: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="musica_example", species=species, phases=[gas], reactions=[arr1, arr2])