Yogogourt

;NetLogo Lab Project "Yogogourt" for LS_426 Winter 2013
; Copyright 2013 Bryan Guo & Tristan Sokol.


extensions [gogo]


globals [serial-port acidity temperature] 
breed [caseins casein]
breed [bacteria bacterium]
bacteria-own [bact-energy acid age bact-timer]  
caseins-own [destablized? cas-timer]

to add-milk
  create-caseins 100
[
  set color white 
  set size 2
  set cas-timer 6000
  set shape "dot"
  set destablized? false
  setxy random-xcor random-ycor
  ]
end 

to stir
  ifelse gogo:sensor 1 < 580 [
    gogo:talk-to-output-ports [ "b" ]
    gogo:output-port-on
    ]
  [
    gogo:talk-to-output-ports [ "a" ]
    gogo:output-port-off
    gogo:talk-to-output-ports [ "b" ]
    gogo:output-port-off
  ]
end 

to brownian  
ask caseins [
  ifelse count caseins-on neighbors >= 1 
  [
    rt random 360 fd 2]
  [lt random 360 fd 1 bk 1]
]
end 

to coagulate 
ask caseins [
    ifelse count caseins-on neighbors < 1
    [rt random 360 fd 1]
    [lt random 360 fd 1 bk 1
      if cas-timer = 0 [
      create-link-with one-of caseins-on neighbors]
      set cas-timer cas-timer - 1
      ] 
  ]
end 

to be-caseins 
    ask caseins [
      ifelse destablized? = 1
      [coagulate]
      [brownian]
    ]
end 

to setup
    ifelse length (gogo:ports) > 0
    [ set serial-port user-one-of "Select a port:" gogo:ports ]
    [ user-message "There is a problem with the connection. Check if the board is on, and if the cable is connected. Otherwise, try to quit NetLogo, power cycle the GoGo Board, and open NetLogo again. For more information on how to fix connection issues, refer to the NetLogo documentation or the info tab of this model"
      stop ]
  gogo:open serial-port
  repeat 5
  [ if not gogo:ping
    [ user-message "There is a problem with the connection. Check if the board is on, and if the cable is connected. Otherwise, try to quit NetLogo, power cycle the GoGo Board, and open NetLogo again. For more information on how to fix connection issues, refer to the NetLogo documentation or the info tab of this model"] ]
  gogo:talk-to-output-ports [ "a" "b" "c" "d"]
  set temperature gogo:sensor 1

  ca
  reset-ticks
  add-milk
end 

to go
  display
  ask caseins [be-caseins]
  ask bacteria [
    set acidity acidity + 1
    move
    reproduce
    ]
  if acidity > 1024 [
    ask caseins [set color yellow set destablized? 1]
    ]
  stir
  tick
end 

to move
  rt random 50
  lt random 50
  fd random 3
  set age age + 1 
  set acidity acidity + 1 
  if age > 12 [die]
end 

to add-bacteria
    create-bacteria 1 [
      set age 0
      set shape "dot" 
      set color red 
      set bact-timer temperature / 10 
      setxy random-xcor random-ycor
      set acidity 1
    ] 
end 

to reproduce 
ask bacteria [
if bact-timer = 0 [
  hatch 1 rt random 360 fd 1
;  set acidity acidity + 1
  ]
set bact-timer bact-timer - 1
]
end