# Smoldyn configuration file to test wildcards in reactions
# This file simulates polymerization, one unit at a time
# This file uses more complex reaction rules, which is slightly less simple to analyze
# but correctly accounts for multiplicity in the monomer reaction rate.

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 y 0 10 p

time_start 0
time_stop 4000
# polymers are longer here than in polymer_end1, so equilibration takes longer
time_step 0.01

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

# Reactions

reaction_rule rxn1 A + A <-> AA		2*FWDRATE REVRATE
reaction_rule rxn2 *AA + A <-> *AAA	FWDRATE REVRATE

expand_rules on-the-fly

# This could also be represented with the sole rule * + A <-> *A.  However, that has
# the same reaction rate for all reactions.  Here, the monomer association reaction
# is twice as fast, working on the assumption that its association can happen in either
# of two ways, which makes it consistent with tbe BioNetGen model of the same name.

# initial molecules
mol 20000 A u u u

cmd A diagnostics all

output_files polymer_end2out.txt stdout
output_format csv
cmd N 1000 molcount polymer_end2out.txt
cmd N 1000 molcount stdout

end_file