Reaction-diffusion simulations

strengths.simulate(system, t_sample, engine=None, print_progress=False, cgmap=None, **script_keyword_arguments)

Simulates the trajectory of a reaction diffusion system.

Parameters:

  • engine (RDSimulationEngineBase derived class) – the simulation engine that should handle the simulation. see the documentation or the engine_collection submodule for more information on the engines preinstalled with strengths. if None (default), engine_collection.default_engine() is used.

  • print_progress (bool) – if true, the progression of the simulation (percentage) is printed at frequently.

  • cgmap (array of int or None) – optionnal coarse graining index map.

Other parameters corresond to the remaining RDScript properties, and have the same default values :

  • time_step = 1e-3

  • sampling_policy = “on_t_sample”

  • sampling_interval = 1

  • t_max = “default”

  • rng_seed = None

  • units_system = UnitsSystem()

  • init_state_processing = “auto”

Returns:

system trajectory

Return type:

RDTrajectory

strengths.simulate_script(script, engine, print_progress=False, cgmap=None)

Simulates the trajectory of a reaction diffusion system, using a given engine.

Parameters:

  • script (RDScript) – the script of the simulation to be run.

  • engine (RDSimulationEngineBase derived class) – the simulation engine that should handle the simulation. see the documentation or the engine_collection submodule for more information on the engines preinstalled with strengths.

  • print_progress (bool) – if true, the progression of the simulation (percentage) is printed at frequently.

  • cgmap (array of int or None) – optionnal coarse graining index map.

Returns:

system trajectory.

Return type:

RDTrajectory