# File to test species changes at surfaces

graphics opengl

dim 2
species red green
max_mol 500

difc red 5	# outside raft
difc green 1	# inside raft

color red 1 0 0
color green 0 1 0
display_size red 3
display_size green 3

time_start 0
time_stop 2000
time_step 0.01

boundaries 0 0 100
boundaries 1 0 100

mol 200 red u u

max_surface 2

start_surface walls
action both all reflect
color both 0 0 0
max_panels rect 4
panel rect +0 0 0 100
panel rect -0 100 0 100
panel rect +1 0 0 100
panel rect -1 0 100 100
end_surface

start_surface surf
rate red fsoln bsoln 5 green
rate green bsoln fsoln 1 red
# The concentration ratio equals the transmission coefficient ratio,
# so the latter must depend on the diffusion coefficients (i.e. the
# transmission coefficients differ because of different diffusion
# coefficients, not to make this active transport; this model is for
# passive transport).
color front 1 0.7 0
color back 0.6 0 0.6
thickness 2
max_panels sph 5
panel sph 80 20 10 50
panel sph 30 50 20 50
panel sph 70 70 15 50
end_surface

max_compartment 1
start_compartment raft
surface surf
point 80 20
point 30 50
point 70 70
end_compartment

cmd B killmolinsphere red surf

output_files stdout
cmd B molcountheader stdout
cmd N 10000 molcount stdout

end_file