# Smoldyn configuration file to test wildcards in reactions
# This file simulates polymerization, where any two polymers can join end-to-end,
# or any polymer can divide at any place.

define FWDRATE	0.1
define REVRATE	0.1

# Graphical output
graphics opengl
graphic_iter 1000

# System space and time definitions
dim 3
boundaries x 0 10 p
boundaries y 0 10 p
boundaries z 0 10 p
time_start 0
time_stop 1000
time_step 0.01

# Molecular species and their properties
species A
difc A 1
color A red
display_size A(all) 2

# Reactions
reaction_rule rxn * + * <-> **	2*FWDRATE REVRATE

# the forward reaction rate is multiplied by 2 because the wildcards only consider a
# single possible bond with a reaction, whereas the reaction allows two possible bonds,
# which are on the left and right sides of the first reactant.

expand_rules on-the-fly

# initial molecules
mol 20000 A u u u

output_files polymer_midout.txt stdout
output_format csv
cmd N 1000 molcount polymer_midout.txt
cmd N 1000 molcount stdout

cmd A diagnostics all

end_file