# Simulation file of basic diffusion and reaction
# This file is used to test and demonstrate manipulation commands

graphics opengl_good
graphic_iter 1
graphic_delay 10
accuracy 5

dim 3
species red green blue black pink
max_mol 1000

time_start 0
time_stop 300
time_step 0.1

output_files stdout

cmd @ 10 pointsource red 100 30 50 50
cmd @ 20 pointsource green 100 60 60 50
cmd @ 30 volumesource blue 100 10 100 10 100 20 20
cmd @ 40 killmol red
cmd @ 50 pointsource black 1 50 50 50
cmd @ 60 killmolprob green 0.7
cmd @ 70 equilmol blue red 0.9
cmd @ 80 replacexyzmol pink 50 50 50
cmd @ 90 replacevolmol red black 0.9 0 100 50 100 0 100
cmd i 100 110 0.1 modulatemol black red 1 0
cmd @ 120 react1 red rxn
cmd @ 130 react1 black rxn
cmd @ 140 killmol all
cmd @ 150 volumesource red 200 0 100 0 100 0 100
cmd @ 160 fixmolcount red 250
cmd @ 170 fixmolcountonsurf blue(up) 50 sphere
cmd @ 180 fixmolcountonsurf blue(up) 20 sphere
cmd @ 190 settimestep 0.5

difc red 1
difc green 1
difc blue 1
color red(all) 1 0 0
color green 0 1 0
color blue(all) 0 0 1
color black 0 0 0
color pink 1 0.5 0.5
display_size all(all) 2
display_size black 5
display_size pink 5

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 sphere
action both all reflect
polygon both edge
max_panels sph 1
panel sph 30 30 30 20 10 10
end_surface

reaction rxn red -> 0 0.02

end_file