# Bimolecular reactions
# units are nm, us

define DT 0.1 		# time step; 0.1 is long step, 0.01 is short step

graphics none

dim 3
species As Bs Cs Am Bm Cm Af Bf Cf	# slow, medium, and fast reactions are run concurrently

molecule_lists slow med fast prod	# store molecules in separate lists for faster operation
mol_list As slow
mol_list Bs slow
mol_list Cs prod
mol_list Am med
mol_list Bm med
mol_list Cm prod
mol_list Af fast
mol_list Bf fast
mol_list Cf prod

difc all 1		# diffusion coefficients

time_start -DT		# run one step before simulation to remove initially overlapping molecules
time_stop 200
time_step DT

boundaries 0 0 200 p	# system boundaries
boundaries 1 0 200 p
boundaries 2 0 200 p

mol 8010 As u u u	# initial molecules; some spares are here due to initial overlaps
mol 8010 Bs u u u

mol 8100 Am u u u
mol 8100 Bm u u u

mol 12500 Af u u u
mol 12500 Bf u u u

reaction slow As + Bs -> Cs 1		# slow, medium, and fast reactions
reaction med  Am + Bm -> Cm 10
reaction fast Af + Bf -> Cf 100

output_files SmoldynBireact_outDT.txt
cmd @ 0 fixmolcount As 8000		# fix molecule counts at simulation start time
cmd @ 0 fixmolcount Bs 8000
cmd @ 0 fixmolcount Cs 0
cmd @ 0 fixmolcount Am 8000
cmd @ 0 fixmolcount Bm 8000
cmd @ 0 fixmolcount Cm 0
cmd @ 0 fixmolcount Af 8000
cmd @ 0 fixmolcount Bf 8000
cmd @ 0 fixmolcount Cf 0
cmd i 0 200 0.1 molcount SmoldynBireact_outDT.txt


end_file