# Smoldyn configuration file to test wildcards in reactions
# This file simulates polymerization, one unit at a time

define FWDRATE	20
define REVRATE	0.1

# Graphical output
graphics opengl_good

# System space and time definitions
dim 2
boundaries x 0 100 p
boundaries y 0 100 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 1

# Surfaces
start_surface walls
action all both reflect
color both black
panel rect +x 0 0 100
panel rect -x 100 0 100
panel rect +y 0 0 100
panel rect -y 0 100 100
end_surface

start_surface circle
action all both reflect
color both black
panel sphere 50 50 15 30
end_surface

# 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 1000 A u u

text_display time A

cmd B killmolinsphere all circle
cmd N 1000 molcountheader stdout
cmd N 1000 molcount stdout

cmd @ 100 diagnostics all

end_file