# Crowding test
# This file shows a combination of excluded volume and reactive interactions.

graphics opengl_good
#tiff_name crowdimages/image
#tiff_iter 5
#tiff_max 200

dim 2

boundaries x 0 20 r
boundaries y 0 20 r

time_start 0
time_stop 100
time_step 0.005

species red green

difc red(all) 1
difc green(all) 0.5

display_size red(all) 0.5
color red(all) red
display_size green(all) 1
color green(all) green

reaction rxn1 red + red -> red + red
binding_radius rxn1 1
product_placement rxn1 bounce

reaction rxn2 red + green -> red + green
binding_radius rxn2 1.5
product_placement rxn2 bounce
reaction_probability rxn2 0.99

reaction rxn2a red + green -> green + green
binding_radius rxn2a 1.5
product_placement rxn2a bounce 2
reaction_probability rxn2a 0.1    # this probability is used if rxn2 didn't happen
# note that the reaction rate has not been calibrated for this reaction

reaction rxn3 green + green -> green + green
binding_radius rxn3 2
product_placement rxn3 bounce

#mol 250 red u u
mol 5 green u u

text_display time red green

#output_files crowding3out.txt
cmd B gaussiansource red 250 10 5 10 5
#cmd B pause
#cmd A molcountspace2d red z 0 20  20  0 20  20  0 crowding3out.txt

end_file