Photosynthesis in Leaves

breed [co2s co2]
breed [o2s o2]
breed [h2os h2o]
breed [sugars sugar]
breed [photons photon]
breed [chloroplasts chloroplast]
breed [atps atp]
breed [panels panelp]
breed [carbon-complexes carbon-complex]
breed [flows flow]
breed [key-labels key-label]
breed [side-panels side-panel]

co2s-own [for-key]
o2s-own [for-key]
h2os-own [bound-to for-key]
photons-own [bound-to for-key]
atps-own [pair my-chloroplast state for-key]
sugars-own [for-key]
key-labels-own [for-key]


panels-own [pair my-chloroplast state age]
carbon-complexes-own [my-chloroplast ]
patches-own [region]


globals [
  #-co2-molecules
  #-o2-molecules
  #-glucose-molecules-produced
]

to start-up
  setup
end 

to setup
  clear-all
  ;import-world "Zoom.csv"
  ; import-drawing "Zoom.png"

  set #-co2-molecules initial-co2
  set #-o2-molecules 0
  set #-glucose-molecules-produced 0


  create-co2s initial-co2 [setxy (-10 + random-float 20) random 20  set-shape-size ]


  create-sugars 1      [setxy 15 -6.5 set-shape-size set for-key 1]
  create-key-labels 1  [setxy 18 -7.8 set shape "empty" set label "sugar (glucose) molecule"]
  create-co2s 1        [setxy 15 -3 set-shape-size set for-key 1]
  create-key-labels 1  [setxy 18 -3.7 set shape "empty" set label "carbon dioxide molecule"]
  create-o2s 1         [setxy 15 0.5 set-shape-size set for-key 1]
  create-key-labels 1  [setxy 16.8 -0.2 set shape "empty" set label "oxygen molecule"]

  create-h2os 1        [setxy 15 4 set-shape-size set for-key 1]
  create-key-labels 1  [setxy 16.5 3.5 set shape "empty" set label "water molecule"]

  create-photons 1 [setxy 15 7.5 set-shape-size set for-key 1]
  create-key-labels 1  [setxy 16.5 7 set shape "empty" set label "light (photon)"]
  make-initial-chloroplasts
  reset-ticks
end 

to set-shape-size
  if breed = sugars [set shape "sugar" set color black set size 2 ]
  if breed = chloroplasts [set color [0 200 0 150] set shape "circle" set size 4 ]
  if breed = h2os [set shape "h20"  set color black set size 2 ]
  if breed = co2s [set shape "co2" set color black set size 2 ]
  if breed = o2s [set shape "o2" set color black set size 2 ]
  if breed = photons [set color yellow + 3 set size 0.4 set heading 135 set shape "ray"]
end 

to make-initial-chloroplasts
  let angle-increment 0
  repeat initial-#-of-chloroplasts [
  create-chloroplasts 1 [

    set heading (angle-increment * 50 + random 20)
    fd (5.5 + random-float 3)
    set-shape-size
    ]
    set angle-increment angle-increment + 1
  ]
  create-flows 1 [set heading 90 set hidden? true]
  ask chloroplasts [
    let atp-count 0
    let atp-offset random 60
    let this-chloroplast self
    let this-pair 0
    set heading 0


    repeat 3 [
      repeat 2 [
        hatch 1 [set breed atps set heading (atp-offset + (atp-count * 60)) set my-chloroplast this-chloroplast set hidden? true set pair this-pair set state 0]
        set atp-count atp-count + 1
      ]

      set this-pair this-pair + 1
    ]
  ]
  ask patches [
    if ((pxcor < -10 or pxcor > 10) and (pycor = max-pycor or pycor = min-pycor)) or (pycor = max-pycor or pycor = min-pycor) or (pxcor = -10 or pxcor = 10 ) or (pycor = 0 and pxcor < -10 ) or (pxcor = min-pxcor or pxcor = max-pxcor) [
      sprout 1 [set breed side-panels set shape "square" set size 1.2 set color [180 180 180]]
    ]

    if ((pxcor = -10) or ((pxcor >= -10 and pxcor < 10) and pycor = max-pycor)) [set region 3]
    if (pxcor >  -10 and pxcor < 10 and pycor != max-pycor)    [set region 4]

    if ((pxcor = 10) or ((pxcor >= -10 and pxcor < 10) and pycor = min-pycor)) [set region 5]
    if (pxcor > 10)    [set region 6]


    if region = 4 [sprout 1  [set shape "square" set size 1.2 set color sky + 2 stamp die]]
    if region = 6 [sprout 1  [set shape "square" set size 1.2 set color gray stamp die]]

  ]
end 

to do-photon-flow

  if intensity-of-light > random 100 [
  ask n-of 1 patches with [region = 3] [
    sprout 1  [
      set breed photons
        set-shape-size
        set hidden? true
    ]

  ]
  ]
  ask photons [
    if for-key != 1 [fd 0.15 set bound-to 0]
    if for-key != 1 and region = 5 [die]
    if pxcor >= -9.6 [set hidden? false]
  ]
end 

to do-water-flow
  if water-flow-through-leaf > random 100 and random 3 = 0 [
    ask n-of 1 patches with [region = 3 and pycor < max-pycor]  [
      sprout 1 [
        set breed h2os
        set-shape-size
        set hidden? true
        create-link-from one-of flows [ tie set hidden? true ]
      ]
    ]
  ]
  ask h2os [
    if for-key != 1 [fd 0.01 rt random 10 lt random 10]
    if (pxcor >= 10 and for-key != 1 ) [die]
    if for-key = 1 [set hidden? false]
    if pxcor >= -9.6 [set hidden? false]
    if pycor > (max-pycor - .4) [set hidden? true]
    if pycor < (min-pycor + .4) [set hidden? true]
  ]
end 

to do-sugar-flow
    ask sugars [
    if for-key != 1 [fd 0.005 rt random 10 lt random 10]
    if (pxcor >= 10 and for-key != 1 )[die]
    if for-key = 1 [set hidden? false]
  ]
end 

to do-gas-flow
  ask co2s with [for-key != 1] [
    fd 0.08 rt random-float 0.005 lt random-float 0.005
    if xcor > 10 [set xcor -10]
    if xcor < -10 [set xcor 10]
  ]
  ask o2s with [for-key != 1]  [fd 0.05]
end 

to go

  ask turtles with [breed = co2s or breed = o2s or breed = h2os or breed = sugars or breed = photons] [
    ifelse region = 4 or for-key = 1 [set hidden? false][set hidden? true]
  ]
  do-photon-flow
  do-water-flow
  do-sugar-flow
  do-gas-flow
  ask flows [fd 0.05]
  ask side-panels [set hidden? false]




  ask atps with [state = 0] [
    let this-pair pair
    let this-chloroplasts my-chloroplast
    let h2os-near-me h2os in-radius 2
    let photons-near-me photons in-radius 2
    let total-atps atps with [pair = this-pair and my-chloroplast = this-chloroplasts  and state = 0]
    let other-charged-atps atps with [pair != this-pair and my-chloroplast = this-chloroplasts  and state = 1]
    if any? photons-near-me and any? h2os-near-me and not any? other-charged-atps  [
      if count h2os-near-me >= 2 and count total-atps = 2 [

        ask one-of h2os-near-me  [die]
        ask one-of other h2os-near-me [die]

        hatch 1 [set breed o2s set shape "o2" set size 2 set heading random 360]
        set hidden? false set state 1
        ask total-atps [set hidden? false set state 1]
    ]
    ]
  ]
  ask atps [ask photons in-radius 2 [die]]

  ask atps with [state = 1] [
    let this-pair pair
    let this-chloroplasts my-chloroplast
    let total-atps atps with [not hidden? and pair = this-pair and my-chloroplast = this-chloroplasts  and state = 1]

     ; show count total-atps
    if count total-atps = 2 [
      let co2s-near-me co2s in-radius 2
     ; show count co2s-near-me
      if count co2s-near-me >= 2 [

      let other-atps one-of other total-atps

      ask one-of co2s-near-me [
        set heading [heading] of myself
        setxy ([xcor] of myself) ([ycor] of myself)
        set breed carbon-complexes
        set my-chloroplast this-chloroplasts
        set shape "carbon-complexes"

        ask one-of other co2s-near-me [
          set heading [heading] of other-atps
          setxy ([xcor] of other-atps) ([ycor] of other-atps)
          set breed carbon-complexes
          set my-chloroplast this-chloroplasts
          set shape "carbon-complexes"
        ]
        hatch 1 [set breed o2s set shape "o2" set size 2 set heading random 360]
      ]
      ask total-atps [set state -1]

    ]

    ]
  ]
  ask atps with [state = 1] [set hidden? false set color (orange + 3 + random-float 1) set shape (word "electric-" random 10)]
  ask atps with [state != 1] [set hidden? true]

  ask chloroplasts [
    let this-chloroplast self
    let my-carbon-complexes carbon-complexes with [my-chloroplast = this-chloroplast]
    if count my-carbon-complexes = 6 [
      ask my-carbon-complexes with [my-chloroplast = this-chloroplast] [die]
      hatch 1 [set breed sugars set shape "sugar" set color black set heading random 360 set size 2 create-link-from one-of flows [ tie set hidden? true ]]
     set #-glucose-molecules-produced #-glucose-molecules-produced + 1
      ask atps with [my-chloroplast = this-chloroplast] [set hidden? true set state 0]
    ]

  ]
 update-counts
; wait delay

  tick
end 

to update-counts
  set #-co2-molecules count co2s with [for-key != 1]
 set #-o2-molecules count o2s  with [for-key != 1]
end