# Demonstration of using Smoldyn to analyze concentration fluctuations
# units are microns and seconds

define NMOL 20
define DIFC 20
define LENGTH 1

graphics opengl

dim 3

boundaries x -2 2
boundaries y -2 2
boundaries z -2 2
frame_thickness 0

species red

color red red
display_size red 3

difc red DIFC

time_start 0
time_stop 100
time_step 0.01

start_surface cell
  action red both reflect
  polygon both edge
  color both black
  panel cylinder -LENGTH 0 0  LENGTH 0 0  0.5  10 5
#  panel hemi  -1 0 0  0.5  1 0 0  10 3
#  panel hemi  1 0 0  0.5  -1 0 0  10 3
  panel disk  -LENGTH 0 0  0.5  1 0 0  10
  panel disk  LENGTH 0 0  0.5  -1 0 0  10
end_surface

start_compartment inside
  point 0 0 0
  surface cell
end_compartment

compartment_mol NMOL red inside


output_files FILEROOTout.txt
cmd E molcountspace red x -LENGTH LENGTH  2  -2 2  -2 2  0  FILEROOTout.txt

end_file



