# Quantitative test of diffusion on 3D surfaces
# units are nanometer and milliseconds

random_seed 1
define NMOL 2000

define VMOL 60 10 445
#define VMOL 0 0 450

graphics opengl_better
light room ambient 0 0 0
light 0 position -1 1 1 0
light 0 diffuse 0.5 0.5 0.5
light 0 ambient 0.5 0.5 0.5
light 0 specular 0.5 0.5 0.5

gauss_table_size 65536

dim 3
boundaries x -500 500
boundaries y -500 500
boundaries z -500 500

boxsize 1000

species red green

molecule_lists redlist greenlist
mol_list red(all) redlist
mol_list green(all) greenlist

difc red(all) 100	# 100 nm^2/ms = 0.1 um^2/s
difc green(all) 30000	# 300x faster than red to account for shorter time

color red(all) red
color green(all) green
display_size red(all) 5
display_size green(all) 4

time_start 0
time_stop 300
time_step 1

frame_thickness 0

start_surface surf1
color both lightgrey
polygon both fe
shininess both 10
thickness 2
panel hemisphere 0 0 0  450  0 0 -1  20 10 hemi1
#panel cylinder 0 0 0  0 0 -1  450  20 1 cyl1
panel hemisphere 0 0 0  450  0 0 1 20 10 hemi2
neighbors hemi1 hemi2
neighbors hemi2 hemi1

#neighbors hemi1 cyl1
#neighbors cyl1 hemi1 hemi2
#neighbors hemi2 cyl1
end_surface

surface_mol NMOL red(up) surf1 hemisphere hemi1  VMOL
surface_mol NMOL green(up) surf1 hemisphere hemi1  VMOL

cmd @ 1 set difc green(all) 0

ifdefine OUTFILE
  output_files OUTFILE
  cmd a listmols OUTFILE
endif


end_file

