Running JCompSim

Armed with a state and transition file, there are still some options available for running:

• --filename or -f: Output file name required
• --states: Path to states JSON file required
• --transitions: Path to transitions JSON file required
• --serialiser: Choice of serialiser. The following options are available:
  • full: Output written at each point that the system is solved for.
    For a deterministic solver, this is each point chosen by the solver.
    For a stochastic solver, this is at each event time.
  • final: Output the final state of the system only.
    N.B. If this is all you are interested in, it does provide some speed gain over outputting more often.
  • points: Output at equally spaced points. The spacing between points is provided by the argument --dt.
• --maxt: Maximum time to simulate for.
• --dt: Spacing between output points (only used if --serialiser points is used)
• --solver: Either stochastic for a stochastic solver (Gillespie algorithm) or deterministic for a deterministic solve (Runge-Kutta-Dopri5)

Example

./JCompSim -f sir_realisation_1.csv --states Models/SIR/states.json --transitions Models/SIR/transitions.json --maxt 300 --dt 1 --solver stochastic --serialiser points