/* irreversible bimolecular reactions */

/* long time step */
dt = 1.0e-7
iterations = 2000

/* short time step */
/* dt = 1.0e-8 */
/* iterations = 20000 */

TIME_STEP = dt
ITERATIONS = iterations
INTERACTION_RADIUS = 0.01

NOTIFICATIONS {
	ALL_NOTIFICATIONS = ON
}

WARNINGS {
	ALL_WARNINGS = ERROR
}


DEFINE_MOLECULES
{
	As {DIFFUSION_CONSTANT_3D = 1e-8}
	Bs {DIFFUSION_CONSTANT_3D = 1e-8}
	Cs {DIFFUSION_CONSTANT_3D = 1e-8}
	Am {DIFFUSION_CONSTANT_3D = 1e-8}
	Bm {DIFFUSION_CONSTANT_3D = 1e-8}
	Cm {DIFFUSION_CONSTANT_3D = 1e-8}
	Af {DIFFUSION_CONSTANT_3D = 1e-8}
	Bf {DIFFUSION_CONSTANT_3D = 1e-8}
	Cf {DIFFUSION_CONSTANT_3D = 1e-8}
}

DEFINE_REACTIONS
{
	As + Bs -> Cs [5.88e5]:rxn_s
	Am + Bm -> Cm [5.88e6]:rxn_m
	Af + Bf -> Cf [5.88e7]:rxn_f
}

INSTANTIATE world OBJECT 
{
	system BOX {
		CORNERS = [0,0,0],[0.2,0.2,0.2]
		DEFINE_SURFACE_REGIONS {
			all {
				ELEMENT_LIST = [ALL_ELEMENTS]
			}
		}
	}

	As_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = As
		NUMBER_TO_RELEASE = 8000
	}

	Bs_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = Bs
		NUMBER_TO_RELEASE = 8000
	}

	Am_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = Am
		NUMBER_TO_RELEASE = 8000
	}

	Bm_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = Bm
		NUMBER_TO_RELEASE = 8000
	}

	Af_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = Af
		NUMBER_TO_RELEASE = 8000
	}

	Bf_release_site RELEASE_SITE {
		SHAPE = world.system[all]
		MOLECULE = Bf
		NUMBER_TO_RELEASE = 8000
	}
}

REACTION_DATA_OUTPUT {
	STEP = dt * 1
	{COUNT[As,WORLD]}=>"./reaction_data/As.dat"
	{COUNT[Bs,WORLD]}=>"./reaction_data/Bs.dat"
	{COUNT[Cs,WORLD]}=>"./reaction_data/Cs.dat"
	{COUNT[Am,WORLD]}=>"./reaction_data/Am.dat"
	{COUNT[Bm,WORLD]}=>"./reaction_data/Bm.dat"
	{COUNT[Cm,WORLD]}=>"./reaction_data/Cm.dat"
	{COUNT[Af,WORLD]}=>"./reaction_data/Af.dat"
	{COUNT[Bf,WORLD]}=>"./reaction_data/Bf.dat"
	{COUNT[Cf,WORLD]}=>"./reaction_data/Cf.dat"
}