ChemCell WWW Site - ChemCell Documentation - ChemCell
Commands

### run_style command

**Syntax:**

run_style style

- style =
*spatial* or *gillespie* or *ode* or *ode/rk*

**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).