RMG Models & Mechanism Generation

This section will describe from a high level the basic procedure and major functions used by the Reaction Mechanism Generator (RMG) software to create chemistry models.

With many and complex functions composing the RMG software, it is useful to group the functions by their major purpose or the task which they accomplish within the overall model generation scheme. Nick Vandewiele suggested that the tasks required for model generation are...

1. Reaction generation
2. Synchronization
3. Thermodynamic and kinetic determination
4. ODE solving

RMG iteratively increases the size and complexity of the model completing each of these tasks for each incremental increase in complexity.

Bearing these major tasks and iterative nature of RMG in mind, the first function to consider would be execute function found on RMG-Py/rmgpy/rmg/main.py. This function contains