Write documentation of chemistry extension

At the moment, the amml documentation (docs/amml.md) only covers topics related to the atomistic simulation and modeling parts.

A section documenting the language's extension for properties of chemical species and reactions should be added. The chemistry extension/module can be used independently from the AMML. However it can benefit from the amml by accessing/re-using properties computed in the simulation steps. It could also be useful to include some examples of these amml-chemistry module connections.