Syntax:
run_style style
Examples:
run_style spatial run_style gillespie
Description:
Set the style of simulation that will be run.
The spatial option runs a spatial reaction/diffusion model where particles diffuse volumetrially (3d) or on surfaces (2d) via Brownian motion with a diffusion coefficient defined by the diffusion command. Particles store coordinates (see the particles command) and geometric surfaces can be defined (see the triangles and region commands) for particles to interact with (see the permeable command).
In spatial simulations, pairs of particles react each timestep with a probability between 0.0 and 1.0 if they are within a cutoff distance of each other. Reactions and associated rates are set via the reaction command. The probability or react_modify commands are used to set the probability and cutoff distance for individual reactions. Setting the probability to 1.0 and the cutoff distance to the binding radius computed by the Smoldyn algorithms described in (Andrews) enables a Smoldyn-style spatial simulation to be run.
The gillespie option runs the "direct method" version of Gillespie's Stochastic Simulation Algorithm (SSA) as described in (Gillespie), with computational enhancements outlined in (Gibson/Bruck). Reactions and associated rates are set via the reaction command. The volume of the system is set via the volume command. Initial particle counts are set via the count command. This is a non-spatial simulation, so particle coordinates are not defined, nor is any geometric information.
The ode and ode/rk options solve the system of coupled reactions with a continuum ODE time integration scheme. For style ode a fixed-size timestep is used. For style ode/rk an adaptive timestep Runge-Kutta algorithm is used as described in (Shampine). Reactions and associated rates are set via the reaction command. The volume of the system is set via the volume command. Initial particle counts are set via the count command. This is a non-spatial simulation, so particle coordinates are not defined, nor is any geometric information.
Restrictions: none
Related commands: none
Default: none
(Andrews) Andrews and Bray, Phys Biol, 1, 137-151 (2004).
(Gibson/Bruck) Gibson and Bruck, J Phys Chem A, 104, 1876-1889 (2000).
(Gillespie) Gillespie, J Phys Chem, 81, 2340 (1977).
(Shampine) Shampine, Watts, and Davenport, SIAM Review, 18, 376-411 (1976).