Command Line Interface

A Command Line Interface (CLI) is also provided for running long simulations:


It can be used to simulate an existing model and save the resulting images:

./spatial-cli filename [simulator] [simulation_time] [image_interval] [max_cpu_threads]

Command line parameters

  • filename
    • the SBML file containing the model to be simulated
  • simulator
    • this can be dune or pixel
    • default: dune
  • simulation_time
    • the total length of the simulation (in model units of time)
    • default: 100
  • image_interval
    • the interval (in model units of time) at which concentration images should be saved
    • default: 10
  • max_cpu_threads
    • the maximum number of cpu threads that should be used
    • default: 0 (which means unlimitied / use all available threads)
    • note: this parameter only applies to the pixel simulator