Preparing your simulation
The following diagram shows a general overview of the preparation steps when preparing a Graph Kinetic Monte Carlo simulation. This page contains full instructions and examples on how to do this.
graph LR
subgraph DFT[DFT software]
Opt([Geometry Optimization]) --> Freq([Frequency Analysis])
end
Freq --> RRKM[[RRKM tool]]
RRKM --> rates[(Reaction rates)]
script[["GraphML generator tool"]] --> GraphML[(GraphML molecule file)]
subgraph Input[Input file]
GraphML
rates
config[/Configuration/]
end
Input --> GKMC[[GKMC]]
Contents
Input file
Input files must use the input.schema.json schema. An example is available in examples/anthracene_input.json.
Reaction rates
Each referenced rate file must follow the ratefile.schema.json schema. The RRKM tool provides a Python-based command-line interface and API based on cclib that can produce these rate files based on computational chemistry calculations.