Molecular Diffusion

globals[Difx Dify Dif step-size zoom]

breed[molecules molecule]

molecules-own[init-pos-x init-pos-y dist-x dist-y]

to setup
  ifelse any? patches with [pcolor = red] [clear-drawing clear-globals clear-ticks clear-turtles clear-all-plots][ca]
  set zoom 100
  set step-size sqrt (4 * free-diffusion-value * time-step)
  put-molecules
  reset-ticks
end 

to put-molecules
  create-molecules 1000 [
    ask patch 0 0 [set pcolor black]
    set shape "dot" set size 0.7 set color blue
    set init-pos-x 0 set init-pos-y 0
    if molecular-distribution = "uniform" [
      set init-pos-x random-xcor set init-pos-y random-ycor
      setxy init-pos-x init-pos-y
      while [[pcolor] of patch-here = red] [
        set init-pos-x random-xcor set init-pos-y random-ycor
        setxy init-pos-x init-pos-y
      ]
    ]
  ]
end 

to go
  ask molecules [move]
  tick
  update-vars
end 

to move
  let zoomed-step step-size * zoom
  while [patch-ahead zoomed-step = nobody or [pcolor] of patch-ahead zoomed-step = red][set heading random 360]
  fd zoomed-step
  set heading random 360
end 

to update-vars
  ask molecules [set dist-x xcor - init-pos-x set dist-y ycor - init-pos-y]
  set Difx (mean (map [ ?1 -> (?1 / zoom) ^ 2 ] ([dist-x] of molecules))) / (2 * ticks * time-step)
  set Dify (mean (map [ ?1 -> (?1 / zoom) ^ 2 ] ([dist-y] of molecules))) / (2 * ticks * time-step)
  set Dif ((Difx + Dify) / 2)
end