/* Michaelis-Menten simulation */

dt = 1.0e-3
iterations = 10000
boxsize = 4.4964
partitions = 11

TIME_STEP = dt
ITERATIONS = iterations
INTERACTION_RADIUS = 0.003

NOTIFICATIONS {
	ALL_NOTIFICATIONS = ON
}

WARNINGS {
	ALL_WARNINGS = ERROR
}

PARTITION_X = [[0 TO boxsize STEP boxsize/partitions]]
PARTITION_Y = [[0 TO boxsize STEP boxsize/partitions]]
PARTITION_Z = [[0 TO boxsize STEP boxsize/partitions]]

DEFINE_MOLECULES
{
	E {DIFFUSION_CONSTANT_3D = 1e-7}
	S {DIFFUSION_CONSTANT_3D = 1e-7}
	ES {DIFFUSION_CONSTANT_3D = 1e-7}
	P {DIFFUSION_CONSTANT_3D = 1e-7}
}

DEFINE_REACTIONS
{
	E + S -> ES [5.88e6]:rxn_fwd
	ES -> E + S [1]:rxn_back
	ES -> E + P [1]:rxn_prod
}

INSTANTIATE world OBJECT 
{
	system BOX {
		CORNERS = [0,0,0],[boxsize,boxsize,boxsize]
		DEFINE_SURFACE_REGIONS {
			all {
				ELEMENT_LIST = [ALL_ELEMENTS]
			}
		}
	}

	E_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = E
		NUMBER_TO_RELEASE = 909
	}

	S_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = S
		NUMBER_TO_RELEASE = 9091
	}
}

REACTION_DATA_OUTPUT {
	STEP = dt * 10
	{COUNT[E,WORLD]}=>"./reaction_data/E.dat"
	{COUNT[S,WORLD]}=>"./reaction_data/S.dat"
	{COUNT[ES,WORLD]}=>"./reaction_data/ES.dat"
	{COUNT[P,WORLD]}=>"./reaction_data/P.dat"
}