RMG-Cat documentation

[mazeau]

this PR has cat documentation

[rwest]

Some things to consider including, based on queries from someone trying to use it:

Now i try to use RMG-Cat to construct kinetic model but SMILES from RMG output always show [Ni] (FIG 1,2) even I change in input database to Pt or another solid catalyst, but it still is Ni.

This is a known bug/feature. Because there is no real SMILES format for adsorbates and the software we use to do the SMILES translations (RDKit) is designed for single molecules, we were forced to hard-code a dummy atom. For now it is always [Ni]. We will probably make this configurable in future. Issue #53

Is it possible to use MOPAC to calculate thermodynamic properties of surface species such as C[Ni], (C[Ni])=CC[Ni],....etc?

No.

In a reaction system (surfaceReactor), what the model or calculation used to calculation? (batch, flow system or just Rate = dN/dt)

Not great for catalysis, and something we have plans to change, but for now it is an isothermal batch reactor with fixed volume and surface area.

[rwest]

Documentation has been moved across to the catmerge branch. Thanks