# Smoldyn configuration file to test wildcards in reactions
# This file simulates polymerization, one unit at a time
# This file uses a simple reaction rule, which gives a simple length distribution
# but ignores multiplicity in the monomer association reaction.

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 * + A <-> *A	FWDRATE REVRATE

expand_rules on-the-fly

# This reaction rule has the same reaction rate for all reactions.  This may be
# correct, depending on the model.  However, it is probably more accurate for the
# the monomer association reaction to be twice as fast, because its association can
# happen in either of two ways.  This change, in polymer_end2.txt, makes the model
# consistent with tbe BioNetGen model of essentially the same name.

# initial molecules
mol 20000 A u u u

cmd A diagnostics all

output_files polymer_end1out.txt stdout
output_format csv
cmd N 1000 molcount polymer_end1out.txt
cmd N 1000 molcount stdout

end_file