Hi,
You can attach the full mechanism file here if you like. What would be more useful to see is the code that sets up the reactor network, i.e. creating FlowReactor and ReactorSurface objects and adding them to a ReactorNet.
Usually, the surface mechanism itself includes a pseudo-species that represents and empty site. For example, in the case of ptcombust.yaml, this is the species PT(S), which appears as a “reactant” for any adsorption reaction and a “product” for any desorption reaction. There’s no need to represent the bulk phase at all unless you have non-catalytic reactions representing a deposition or ablation process. However, both catalytic and non-catalytic systems can be simulated using the FlowReactor class. See 1D_pfr_surfchem.py for an example.
Regards,
Ray