particles in a box Extent of Reaction

globals
[
  tick-Δ                          ;; how much we advance the tick counter this time through
  max-tick-Δ                      ;; the largest tick-Δ is allowed to be
  avg-speed-init avg-energy-init      ;; initial averages
  avg-speed avg-energy                ;; current averages
  fast medium slow lost-particles     ;; current counts
  percent-medium percent-slow         ;; percentage of current counts
  percent-fast percent-lost-particles ;; percentage of current counts
  box-edge1
  box-edge2
  leftbox-edge
  rightbox
  floor1
  floor2
 ; entropy1
  entropy2
 ; temperature
  R
  yboltz
  enthalpy1
 ; enthalpy2
 ; scale
  Eafloor
 ; initialstate ; particles in initially in state 1
  ΔG
  ΔG0
  ΔG0e
  -ΔG0e
  ΔS
  ΔH
  Kin1
  Kin2
  K
  tracer
  a
  cero
  cero1
  initialState
  avance1
  uA; potencial A
  uB; potencial B
  uAo; potencial A standard
  uBo; potencial B standard
  G
  G2
]

breed [ particles particle ]
breed [ flashes flash ]

flashes-own [birthday]

particles-own
[
  speed mass energy          ;; particle info
  last-collision
  state
]

to setup
  clear-all
  set-default-shape particles "circle"
  set-default-shape flashes "plane"
  set R 1.9858775 / 1000 ;constante de gases en kcal/mol/K
 ; set entropy1 0.3
  set entropy2 1 - entropy1
  set enthalpy1 0
  ifelse enthalpy1 <= enthalpy2
   [set floor1 0
     set floor2 enthalpy2 * scale] ; scale 1kcal= scale y coordenate
   [set floor2 0
     set floor1 -1 * scale * enthalpy2] ; scale 1kcal=scale y coordinate
  set Eafloor max (list floor1 floor2) + Ea * scale
 ; set initialstate 0.1
  set box-edge2 (max-pxcor)
  set box-edge1 min-pxcor + (entropy1 * max-pxcor * 2)
  set ΔH enthalpy2 - enthalpy1
  set ΔS  R * ln (entropy2 / entropy1) ;calculo entropía
  set ΔG0 ΔH - temperature * ΔS ;calculo Δ G cero teórica
  make-box
  ;make-particles
  ;update-variables
  reset-ticks
  set a 1
  set cero 0
  set avance1 avance
  set-plot-y-range 10000 10001
end 

to go
  set avance1 avance

  set initialState 1 - avance1

  while [initialState > 0.01]
  [
;        if avance1 > 0.5 [stop]
    clear-turtles
    make-particles
;  ask particles [ bounce ]
    update-variables
    update-plots
 ;   display
    set a a + 1
    set initialState  initialState - 0.001
    set avance1 1 - initialState

  if single = true [stop]
  ]
  if a > 1 [stop]
end 

to update-variables
  set uAo -1 * ΔG0
  set ΔG0 ΔH - temperature * ΔS ;calculo Δ G cero teórica
  set uBo 0
  set uAo -1 * ΔG0
  set Kin1 count turtles with [state = 1]
  set Kin2 count turtles with [state = 2]
  set K count turtles with [state = 2] / (count turtles with [state = 1] + 0.0000000000000001)
  set ΔG0e (- R * temperature * ln (K + 1E-10))
  set -ΔG0e -1 * ΔG0e
  set ΔG R * temperature * ln (K + 1E-10) + ΔG0
  set cero 0
  ; potenciales químicos
  set uA uAo + R * temperature * ln (Kin1 + 0.01)
  set uB uBo + R * temperature * ln (Kin2 + 0.01)
  set G (Kin1 * uA + Kin2 * uB)
  set G2 0 * uBo + 1 * uAo +
      avance1 * (uBo - uAo) +
      R * temperature * ( avance1 ) * ln ( avance1 + 1e-5 ) +
      R * temperature * (1 - avance1) * ln ( 1 - avance1)
  set G2 G2 * 5
end 

to bounce  ;; particle procedure

 ifelse state = 1
     [
     set yboltz floor1 - scale * ln (random-float 1) * R * temperature
     if yboltz >= Eafloor
     [set xcor min-pxcor + random (max-pxcor - min-pxcor)]
     ]
     [
     set yboltz floor2 - scale * ln (random-float 1) * R * temperature
     if yboltz >= Eafloor
     [set xcor min-pxcor + random (max-pxcor - min-pxcor)]
     ]

  ifelse yboltz > max-pycor
       [set ycor  max-pycor]
       [set ycor yboltz]

  ifelse (xcor >= min-pxcor and xcor < box-edge1)
   [set state 1
    set color green]
  [set state 2
    set color red]
end 

;;;
;;; drawing procedures

to make-box

     ; white the part of the  box that is inactive
     ifelse floor1 <= floor2
     [
       ask patches with [ (pxcor > box-edge1) and (pycor < floor2) ]
     [ set pcolor white ]
     ]
     [
       ask patches with [ (pxcor < box-edge1) and (pycor < floor1) ]
     [ set pcolor white ]
     ]

       ; limite superior
    ask patches with [ pycor > max-pycor - 5 ]
    [ set pcolor blue ]

    ; limite inferior
    ask patches with [ (pycor < floor1 + 5 and pycor > floor1 ) and (pxcor <= box-edge1) ]
    [ set pcolor yellow ]

    ask patches with [ (pycor < floor2 + 5 and pycor > floor2) and (pxcor >= box-edge1) ]
    [ set pcolor yellow ]
    ; limite izquierdo
    ask patches with [ (pxcor < min-pxcor + 5) and (pycor >= floor1) ]
    [ set pcolor yellow ]

    ; limite derecho
    ask patches with [ (pxcor > max-pxcor - 5) and (pycor >= floor2) ]
    [ set pcolor yellow ]

    ; limite central
    ask patches with [ (pxcor < box-edge1 + 3 and pxcor > box-edge1 - 3) and (pycor <= Eafloor) ]
    [ set pcolor yellow ]
end 
;;;


;; creates initial particles

to make-particles
  create-particles number-of-particles
  [

    set size 6
    ifelse random-float 1 < initialstate
    [
      set xcor min-pxcor + random (box-edge1 - min-pxcor)
      set yboltz floor1 - scale * ln (random-float 1) * R * temperature
;      set energy ln (random-float 1) * R * temperature
      ifelse yboltz > max-pycor
       [set ycor  max-pycor]
       [set ycor yboltz]
    ]

    [
      set xcor box-edge1 + random (box-edge2 - box-edge1)
      set yboltz floor2 - scale * ln (random-float 1) * R * temperature
;      set energy enthalpy2 + ln (random-float 1) * R * temperature
      ifelse yboltz > max-pycor
       [set ycor  max-pycor]
       [set ycor yboltz]
    ]


   ifelse (xcor >= min-pxcor and xcor < box-edge1)
  [set state 1
    set color green]
  [set state 2
    set color red]
    ;;random-position

  ]
  set K count turtles with [state = 2] / (count turtles with [state = 1] + 0.00000000000000000000001)
  set ΔG0e (- R * temperature * ln (K + 0.0000000000001))
  set ΔG R * temperature * ln (K + 0.0000000000001) + ΔG0
;  set avg-energy sum [energy] of particles
end 




; Copyright 1997 Uri Wilensky.
; See Info tab for full copyright and license.