# File to test species changes at surfaces

graphics opengl
random_seed 1

dim 3
boundaries x 0 100
boundaries y 0 100
boundaries z 0 20

species red green

difc red(all) 5		# outside raft
difc green(all) 1	# inside raft

color red(all) red
color green(all) green
display_size red(all) 3
display_size green(all) 3

time_start 0
time_stop 100
time_step 0.01

start_surface walls
polygon both edge
action all(all) both reflect
color both green
panel rect +x 0 0 0 100 20
panel rect -x 100 0 0 100 20
panel rect +y 0 0 0 100 20
panel rect -y 0 100 0 100 20
panel rect +z 0 0 0 100 100
panel rect -z 0 0 20 100 100
end_surface


start_surface membrane
color both grey 0.5
thickness 1
panel rect +z -5 -5 10 110 110 rect0
end_surface


start_surface raftedge
rate red(front) fsoln bsoln 5 green
rate green(front) 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 both cyan 0.5
polygon both face
thickness 1
panel cyl 50 50 0 50 50 20 25 20 10
end_surface

surface_mol 200 red(front) membrane rect rect0 90 50 10


ifdefine OUTFILE
  output_files OUTFILE
  cmd a listmols OUTFILE
endif


end_file

