# Test of diffusion on surfaces
# This requires Smoldyn version 2.01 to run

graphics opengl
random_seed 1

dim 2
species red

difc red(all) 3

color red(all) 1 0 0
display_size red(all) 5

time_start 0
time_stop 100
time_step 0.01

boundaries 0 0 100
boundaries 1 0 100
frame_thickness 0

start_surface surf1
color both black
neighbor_action hop

panel rect +0 20 20 20 r1
panel rect +1 20 30 30 r2
panel tri 40 20 60 40 t1
panel sphere 60 44 5 20 s1
neighbors r1 r2
neighbors r2 r1 t1
neighbors t1 r2 s1
neighbors s1 t1

panel cyl 20 60 30 60 5 c1
panel hemi 20 60 5 1 0 20 h1
panel hemi 30 60 5 -1 0 20 h2
panel disk 25 60 5 1 0 d1
panel disk 30 60 5 0 1 d2
neighbors c1 h1 h2 d1
neighbors h1 c1
neighbors h2 c1 d2
neighbors d1 h2 c1 d2
neighbors d2 d1 h2

#panel tri 20 10 30 10 t1
#panel tri 20 15 20 25 t2
#panel tri 25 15 35 25 t3
#panel sphere 70 20 10 20
#panel hemi 70 40 5 1 0 20
#panel hemi 75 40 5 -1 -1 20
#panel disk 75 60 5 1 0
#panel disk 85 60 5 -1 -1

end_surface

surface_mol 100 red(up) surf1 all all

text_display red(all)

ifdefine OUTFILE
  output_files OUTFILE
  cmd a listmols OUTFILE
endif

end_file

