# Hop diffusion simulation
# units are nm and us

graphics opengl_good
graphic_iter 100

dim 2
names red
max_mol 1000
#rand_seed 1
boxsize 50

difc red 8

color red 1 0 0

display_size red 5

time_start 0
time_stop 20000
time_step 0.1

boundaries 0 0 435
boundaries 1 0 435

max_surface 2

start_surface
name sides
action back red reflect
action front red jump
color both 0 0 0
max_panels rect 4
panel rect +0 0 0 435 r1
panel rect -0 435 0 435 r2
panel rect +1 0 0 435 r3
panel rect -1 0 435 435 r4
jump r1 front <-> r2 front
jump r3 front <-> r4 front
end_surface

start_surface
name lines
action both red m
rate red fsoln bsoln 0.000697
rate red bsoln fsoln 0.000697
color both 0 0 0
thickness 2
read_file MoroneData.txt
end_surface


mol 1 red 220 250
output_files hopdiffposout.txt
cmd n 100 molpos red hopdiffposout.txt


/*
mol 1000 red u u
output_files hopdiffout.txt
cmd n 10 meansqrdisp red all hopdiffout.txt
*/

end_file