# Crowded system simulation, two sizes
# Units are nm and us

define SEED 1
define NMOL1 6000
define NMOL2 500
define RADIUS1 2.2
define RADIUS2 4
#define BETTERGRAPHICS

ifdefine BETTERGRAPHICS
  graphics opengl_better
  light room ambient 0 0 0
  light 0 position -1 1 1 0
  light 0 diffuse 0.5 0.5 0.5
  light 0 ambient 0.5 0.5 0.5
  light 0 specular 0.5 0.5 0.5
else
  graphics opengl
  graphic_iter 1000
endif

#random_seed SEED

dim 3
boundaries x 0 100 p
boundaries y 0 100 p
boundaries z 0 100 p

species A1 A2

difc A1 65
difc A2 20

color A1 lightred
color A2 green
display_size A1 RADIUS1
display_size A2 RADIUS2

time_start 0
time_stop 10
time_step 0.0001

frame_thickness 2

mol NMOL1 A1 u u u
mol NMOL2 A2 u u u

reaction r1 A1 + A1 -> A1 + A1
binding_radius r1 2*RADIUS1
product_placement r1 bounce

reaction r2 A2 + A2 -> A2 + A2
binding_radius r2 2*RADIUS2
product_placement r2 bounce

reaction r3 A1 + A2 -> A1 + A2
binding_radius r3 RADIUS1+RADIUS2
product_placement r3 bounce

output_files crowding2sizeout.txt
output_format csv
cmd i 1 20 0.5 radialdistribution A2 A1 20 100 10 crowding2sizeout.txt
#cmd A radialdistribution A2 A1 20 100 0 crowding2sizeout.txt
#cmd A radialdistribution2 A2 A1 20 80 20 80 20 80 20 100 0 crowding2sizeout.txt

end_file

