# Smoldyn configuration file template.
# Steve, Nov. 25, 2014
# units are nm, us

# This file fails because bounce reactions don't work with periodic boundaries.


# Model parameters
define SYSLENGTH 50		# system length
define KRATE 20			# reaction rate
define AMOL 2000
define BMOL 2000
define TMOL 1000
define CMOL 100
define CROWD 20
define ITER 1


# Graphical output
graphics opengl_good		# level of graphics quality (or none)
frame_thickness 0		# turns off display of the system boundaries

# System space and time definitions
dim 3				# 3D system
boundaries 0 0 SYSLENGTH p
boundaries 1 0 SYSLENGTH p
boundaries 2 0 1 p

time_start 0			# simulation starting time
time_stop 10			# simulation stopping time
time_step 0.01			# simulation time step

# Molecular species and their properties
#species A B T C
species C
#difc A 10
#difc B 10
#difc T 10
difc C 1
#color A red
#color B green
#color T blue
color C magenta
#display_size all(all) 0.1
display_size C 1


#molecule_lists Alist Blist Tlist Clist
#mol_list A Alist
#mol_list B Blist
#mol_list T Tlist
#mol_list C Clist

boxsize 50

# Chemical reactions
#reaction fwd A + B -> B KRATE
#reaction ac A + C -> A + C
#reaction bc B + C -> B + C
#reaction tc T + C -> T + C
reaction cc C + C -> C + C
#binding_radius ac 1
#binding_radius bc 1
#binding_radius tc 1
binding_radius cc 1
#product_placement ac bounce -1
#product_placement bc bounce -1
#product_placement tc bounce -1
product_placement cc bounce -1

# Place molecules for initial condition
#mol AMOL A u u u
#mol BMOL B u u u
#mol TMOL T u u u
mol 2 C u u u

# Output and other run-time commands
#text_display time A B C
#output_root bounce1/
#output_files reactionITER_CROWDout.txt msdITER_CROWDout.txt
#cmd B molcountheader reactionITER_CROWDout.txt
#cmd i 0 50 0.02 molcount reactionITER_CROWDout.txt
#cmd i 0 50 0.02 meansqrdisp T all msdITER_CROWDout.txt
output_files stdout
cmd E molcount stdout

end_file			# end of this file

