# Simulation file of basic diffusion and reaction
# This file is used to test and demonstrate the movesurfacemol command

graphics opengl_good
graphic_iter 1

dim 3
species red
max_mol 1000

time_start 0
time_stop 5000
time_step 0.1


difc red(all) 1
color red(all) 1 0 0
display_size all(all) 2

boundaries 0 0 100
boundaries 1 0 100
boundaries 2 0 100

max_surface 2
start_surface walls
action both all reflect
polygon both none
max_panels rect 6
panel rect +0 0 0 0 100 100
panel rect -0 100 0 0 100 100
panel rect +1 0 0 0 100 100
panel rect -1 0 100 0 100 100
panel rect +2 0 0 0 100 100
panel rect -2 0 0 100 100 100
end_surface

start_surface surf
action both all reflect
polygon both edge
max_panels sph 2
panel sph 30 30 30 20 10 10 sph1
panel sph 70 70 70 20 10 10 sph2
end_surface

surface_mol 20 red(front) surf sphere sph1

cmd E movesurfacemol red(front) 0.0002 surf:sph1 surf:sph2
cmd E movesurfacemol all(all) 0.00001 surf walls up

end_file