# Crowding demo, for making a nice movie.


# Model parameters
define SYSLENGTH 50		# system length
define KRATE 25			# reaction rate
define MOL 1000


# Graphical output
graphics opengl_good		# level of graphics quality (or none)

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

time_start 0			# simulation starting time
time_stop 10			# simulation stopping time
time_step 0.0002		# simulation time step

boxsize 2

# Molecular species and their properties
species A B
difc A 10
difc B 10
color A red
color B green
display_size all(all) 0.5


# Surfaces in the system and their properties
start_surface walls
  action front all jump
  action back all reflect
  color both black
  thickness 1
  polygon both edge
  panel rect +0  0 0  SYSLENGTH rx1
  panel rect -0  SYSLENGTH 0  SYSLENGTH rx2
  panel rect +1  0 0 SYSLENGTH ry1
  panel rect -1  0 SYSLENGTH SYSLENGTH ry2
  jump rx1 front <-> rx2 front
  jump ry1 front <-> ry2 front
end_surface

read_file circles35.txt

surface smolcrowd2 polygon both none
surface smolcrowd polygon front face
surface smolcrowd color both black

# Chemical reactions
reaction fwd A + B -> 0 KRATE

# Place molecules for initial condition
mol MOL A u u
mol MOL B u u

# Output and other run-time commands
cmd B killmolinsphere all all
cmd B pause

tiff_name movie/crowdingdemo
tiff_iter 20
tiff_max 300


end_file

