; Title: Geomorphology ABM in CHANS
; Version 6.4
; Author: Li An
; Time of revision: March 16, 2016
; Purpose: For education and demonstration purpose. With initial input from the paper "Feedbacks in human-landscape systems: Lessons from the Waldo 
; Canyon Fire of Colorado, USA" by Chin, An, Florsheim et al.
;
; Major changes from the last version (Version 6.3)
; 1) This one shows the 3D landscape by adding the features in Jie's Geomorphology-3D-V3-Jie.nlogo model 
;    (saved under D:\1.Grants\5-CHES-ABMs\CHES-Models\River-Geomorphology-ABMs\Jie-2016-02-29\)

breed [households household]    ; Add on 02-19-2015 (v5.7)
breed [stayers stayer]          ; the acutral points of the landscape, added by Jie
breed [walkers walker]          ; turtles that move around the landscape, added by Jie
                                        
globals [  
  flow           ; This variable default to a number less than 65 cubic feet per second (cfs)
  storm?
  storm-duration ; How long the storm has lasted, which is a number between 1 and 96 units (one 
                 ; unit is 15 minutes
  change-rate    ; The change rate of sediment thickness, which is a function of flow.
  available-thick   
  rate-reduction ; The reduction % of change-rate (the change rate of sediment thickness), default to 0 for no reduction (add on 02-17-2015). 
  Total-sedi-chg ; Total change (often reduciton) of sediment for the entire river segments (add on 02-19-2015).
  PES            ; A variable for average PES-level of all the households --Add on 02-19-2015 (v5.6)
  PES-scores     ; An intermediate variable (v5.8)
  Tolerance      ; When the accumulated change/total possible change (27.685) ratio goes above this level, HHs increase PES by "PES-inflation"
  PES-inflation  ; New variable Add 02-25-2015: increment of PES at a qualified time (V6.1)
  degrade-level  ; A number between 0 (no degradation) and 1 (complete degradation). Add 02-25-2015 (V6.1)
  color-decider  ; Add on March 3, 2015.
  runtime        ; added by Jie, to record which run is it in
]

patches-own [    ; The elevation at the top of sediment, which is the sum of bedrock-elev and sediment-thick
 stream?         ; added by Jie
 elevation
 bedrock-elev    ; The elevation at the top of hardrock
 elevation-vis   ; elevation for landscape visulization purposes, added by Jie
 sediment-thick  ; The thickness of sediment that lies above hard rock
 patch-ID        ; ID of each cell or patch
 river-color     ; added by Jie
]

walkers-own [    ; added by Jie
  peak?          ; indicates whether a turtle has reached a "peak", that is, it can no longer go "uphill" from where it stands                 
]

households-own [ ; This procedure is new. Add on 02-19-2015 (v5.7)
  PES-level      ; The payment level for the PES program that may take 0 (no), 1 (low), 2 (moderate), and 3 (high) payment levels
]

to setup                 ; Set up both the environment (landscape) and agents. Only executed once each simulation
  clear-all  
  resize-world 0 39 0 39 0 9 ; added by Jie
  
  setup-patches          ; This procedure is defined below. It sets up the "world" or the landscape
  setup-landscape        ; added by Jie
  setup-household        ; Add on 02-19-2015 (v5.7)   It sets up households on the landscape
  set runtime 0          ; added by Jie
  reset-ticks
                         
  if (file-exists? "StreamDataOutput.csv") [
    file-delete "StreamDataOutput.csv" ; Version 3: Each run (instead of each tick), delete the file and whatever inside it.
  ]
end           

to setup-household       ; This procedure is new. Add on 02-19-2015 (v5.7, with changes in v5.8)
    
  ask patches [ if (stream? = false and pzcor = 3 and (random-float 16) < 1.0) [sprout-households 1]] ; Households are placed on
  ask households [                                              ; non-water places randomly at a probability of 1/16.
    set shape "house" set size 1.2 
    set color-decider random-float 1    ; Add this line to fix a little bug on March 03, 2015.
    if (color-decider <= 0.25) [set PES-level 0 set color red]      ; Add on 02-20-2015 (v5.8). Add set color red 02-26-2015
    if (color-decider > 0.25 and color-decider <= 0.5) [set PES-level 1 set color brown]   ; Add on 02-20-2015 (v5.8)
    if (color-decider > 0.5 and color-decider <= 0.75) [set PES-level 2 set color yellow]  ; Add on 02-20-2015 (v5.8)
    if (color-decider > 0.75) [set PES-level 3 set color green]                            ; Add on 02-20-2015 (v5.8)
    ;show PES-level    
    ]
 ;show count households
 ;show count households with [PES-level = 0]
 ;show count households with [PES-level = 1]
 ;show count households with [PES-level = 2]
 ;show count households with [PES-level = 3]
  calculate-avg-PES  
  ;adopt-NBs-PES
end   

; Start of Jie's new 

to setup-patches
  
  ask patches [

    set stream? false   ; By default, the cells are not stream but dryland
    set elevation 2040  ; Default elevation, added by Jie
    ;set bedrock-elev 5000     ; Changed by Jie
    ;set sediment-thick 500    ; Changed by Jie
    set patch-ID 1200
    set river-color sky ; added by Jie. color code: blue 105; sky 95; cyan 85
    if (pxcor = 4 and pycor = 7) [
      set stream? true
      set bedrock-elev 2039.50
      set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 1]
    ]
    if (pxcor = 5 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.50       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 2]
    ]
    if (pxcor = 6 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.50       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 3]
    ]
    if (pxcor = 7 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.50       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 4]
    ]
    if (pxcor = 8 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.53       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 5]
     ]
    if (pxcor = 9 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.44       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 6]
     ]
    if (pxcor = 10 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.33       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 7]
     ]
    if (pxcor = 11 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.30       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 8]
     ]
    if (pxcor = 12 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.28       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 9]
     ]
    if (pxcor = 13 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.33       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 10]
     ]
    if (pxcor = 14 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.24       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 11]
     ]
    if (pxcor = 15 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.14       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 12]
     ]
    if (pxcor = 16 and pycor = 7) [
      set stream? true       set bedrock-elev 2039.09       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 13]
     ]
    if (pxcor = 17 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.94       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 14]
     ]
    if (pxcor = 18 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.90       set sediment-thick 0.30
      if pzcor = 0 [set patch-ID 15]
     ]
    if (pxcor = 19 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.82       set sediment-thick 0.40
      if pzcor = 0 [set patch-ID 16]
     ]
    if (pxcor = 20 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.71       set sediment-thick 0.50
      if pzcor = 0 [set patch-ID 17]
     ]
    if (pxcor = 21 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.60       set sediment-thick 0.60
      if pzcor = 0 [set patch-ID 18]
     ]
    if (pxcor = 22 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.49       set sediment-thick 0.70
      if pzcor = 0 [set patch-ID 19]
     ]
    if (pxcor = 23 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.37       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 20]
     ]
    if (pxcor = 24 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.38       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 21]
     ]
    if (pxcor = 25 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.37       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 22]
     ]
    if (pxcor = 26 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.34       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 23]
     ]
    if (pxcor = 27 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.30       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 24]
     ]
    if (pxcor = 28 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.26       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 25]
     ]
    if (pxcor = 29 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.23       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 26]
     ]
    if (pxcor = 30 and pycor = 7) [
      set stream? true       set bedrock-elev 2038.27       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 27]
     ]
    if (pxcor = 31 and pycor = 8) [
      set stream? true       set bedrock-elev 2038.06       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 28]
     ]
    if (pxcor = 32 and pycor = 9) [
      set stream? true       set bedrock-elev 2037.96       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 29]
     ]
    if (pxcor = 33 and pycor = 10) [
      set stream? true       set bedrock-elev 2037.93       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 30]
     ]
    if (pxcor = 34 and pycor = 11) [
      set stream? true       set bedrock-elev 2037.92       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 31]
     ]
    if (pxcor = 35 and pycor = 12) [
      set stream? true       set bedrock-elev 2037.93       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 32]
     ]
    if (pxcor = 35 and pycor = 13) [
      set stream? true       set bedrock-elev 2038.04       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 33]
     ]
    if (pxcor = 35 and pycor = 14) [
      set stream? true       set bedrock-elev 2037.87       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 34]
     ]
    if (pxcor = 35 and pycor = 15) [
      set stream? true       set bedrock-elev 2037.81       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 35]
     ]
    if (pxcor = 35 and pycor = 16) [
      set stream? true       set bedrock-elev 2037.81       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 36]
     ]
    if (pxcor = 35 and pycor = 17) [
      set stream? true       set bedrock-elev 2037.77       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 37]
     ]
    if (pxcor = 35 and pycor = 18) [
      set stream? true       set bedrock-elev 2037.59       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 38]
     ]
    if (pxcor = 35 and pycor = 19) [
      set stream? true       set bedrock-elev 2037.45       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 39]
     ]
    if (pxcor = 35 and pycor = 20) [
      set stream? true       set bedrock-elev 2037.45       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 40]
     ]
    if (pxcor = 35 and pycor = 21) [
      set stream? true       set bedrock-elev 2037.45       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 41]
     ]
    if (pxcor = 35 and pycor = 22) [
      set stream? true       set bedrock-elev 2037.35       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 42]
     ]
    if (pxcor = 35 and pycor = 23) [
      set stream? true       set bedrock-elev 2037.29       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 43]
     ]
    if (pxcor = 35 and pycor = 24) [
      set stream? true       set bedrock-elev 2037.25       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 44]
     ]
    if (pxcor = 35 and pycor = 25) [
      set stream? true       set bedrock-elev 2037.11       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 45]
     ]
    if (pxcor = 35 and pycor = 26) [
      set stream? true       set bedrock-elev 2037.00       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 46]
     ]
    if (pxcor = 35 and pycor = 27) [
      set stream? true       set bedrock-elev 2036.97       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 47]
     ]
    if (pxcor = 35 and pycor = 28) [
      set stream? true       set bedrock-elev 2036.92       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 48]
     ]
    if (pxcor = 35 and pycor = 29) [
      set stream? true       set bedrock-elev 2036.88       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 49]
     ]
    if (pxcor = 35 and pycor = 30) [
      set stream? true       set bedrock-elev 2036.87       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 50]
     ]
    if (pxcor = 35 and pycor = 31) [
      set stream? true       set bedrock-elev 2036.95       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 51]
     ]
    if (pxcor = 35 and pycor = 32) [
      set stream? true       set bedrock-elev 2036.88       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 52]
     ]
    if (pxcor = 35 and pycor = 33) [
      set stream? true       set bedrock-elev 2036.83       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 53]
     ]
    if (pxcor = 35 and pycor = 34) [
      set stream? true       set bedrock-elev 2036.65       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 54]
     ]
    if (pxcor = 35 and pycor = 35) [
      set stream? true       set bedrock-elev 2036.52       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 55]
     ]
    if (pxcor = 21 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.45       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 70]
     ]
    if (pxcor = 22 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.35       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 69]
     ]
    if (pxcor = 23 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.30       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 68]
     ]
    if (pxcor = 24 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.40       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 67]
     ]
    if (pxcor = 25 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.55       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 66]
     ]
    if (pxcor = 26 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.60       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 65]
     ]
    if (pxcor = 27 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.53       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 64]
     ]
    if (pxcor = 28 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.46       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 63]
     ]
    if (pxcor = 29 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.44       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 62]
     ]
    if (pxcor = 30 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.45       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 61]
     ]
    if (pxcor = 31 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.48       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 60]
     ]
    if (pxcor = 32 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.54       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 59]
     ]
    if (pxcor = 33 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.60       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 58]
     ]
    if (pxcor = 34 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.63       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 57]
     ]
    if (pxcor = 35 and pycor = 36) [
      set stream? true       set bedrock-elev 2036.57       set sediment-thick 0.80
      if pzcor = 0 [set patch-ID 56]
    ]

    ; added by Jie
    if (pzcor = 0 and patch-ID < 71) [
      set elevation bedrock-elev + sediment-thick
      set pcolor river-color
    ]
  ]
end
   

to setup-landscape   ; added by Jie

  ; make a landscape with hills and valleys
  ask n-of 10 patches with [pzcor = 0 and stream? = false] [
    set elevation 5000
  ]

  ask patches [ set elevation-vis elevation]
  ; slightly smooth out the landscape
  repeat 10 [
    ; the terrain does not require use of the 3D patch grid just the 3D
    ; space to display the terrain so when we diffuse add anything
    ; diffusing up and down back to the first layer of patches.
    diffuse elevation-vis 1
    ask patches with [pzcor = 0 and stream? = true] [
      set elevation-vis 2040
    ]
  ]

  let max-elevation max [elevation-vis] of patches with [pzcor = 0]
  let min-elevation min [elevation-vis] of patches with [pzcor = 0]

  ; use turtles and links to display the landscape
  ; each patch has one stayer linking to neighboring stayers
  ask patches with [pzcor = 0] [
    sprout-stayers 1 [
      create-links-with turtles-on neighbors
      ht
    ]
  ]
  ; each stayer is set at a height proportional to the patch's elevation
  ask stayers [
    set zcor ((elevation-vis - min-elevation) / (max-elevation - min-elevation)) * max-pzcor
  ]

  ; put some turtles on patch centers in the landscape
  ;ask n-of 80 stayers [
      ;hatch-walkers 1 [
        ;st
        ;set peak? false
        ;set color red
        ;pd
        ;set pen-size 3
      ;]
   ;]
end


to flow-change
  
  ifelse (ticks = 27 or (ticks >= 60 and ticks <= 63)) [  ; Flow change reflects whether it rains & the river flow rises on some days
    set flow 70      ; Days 27 and 59, 60, 61, 62, and 63 are days with storms. The number 70 is just one between 65 and 310
    set storm? true
  ]
  [ set flow 40
    set storm? false
  ]
  
  ifelse (storm? = false)   ; The above ifelse clause sets what days would be storm days
  [set storm-duration 0]    ; On days without storms, the storm duration is zero
  [                         ; On days with a storm, the storm duration is set to different numbers according to Anne's data
    if (ticks = 27) [  ; 
      set storm-duration 3  ; Changed back from 1 to 3--did on 10/15/2014 evening based on Version 3.
    ]    
    if (ticks = 60) [       ; 
      set storm-duration 2  ;
    ]  

    if (ticks >= 61 and ticks <= 63 ) [
      set storm-duration 80 ; Used to be 96--change made on 10/15/2014.
    ]
  ]
end

to pave-channel
  ifelse (ticks = pave-time and build-pavement? = true)
    [
      let List_of_segments []  
        
      ask patches with [pcolor = blue] [       ; pavement only happen on stream patches (blue)   
        set List_of_segments  lput patch-ID List_of_segments   ; Put all stream patches into the above list    
      ]  ; The end 
     
      foreach sort List_of_segments [   
    
        ask patches with [patch-ID = ?] [
          if (patch-ID = 15) [
            set sediment-thick 0    set bedrock-elev bedrock-elev + 0.3
          ]        
          if (patch-ID = 16) [
            set sediment-thick 0    set bedrock-elev bedrock-elev + 0.4
          ]            
          if (patch-ID = 17) [
            set sediment-thick 0    set bedrock-elev bedrock-elev + 0.5
          ]                
          if (patch-ID = 18) [
            set sediment-thick 0    set bedrock-elev bedrock-elev + 0.6
          ]        
          if (patch-ID = 19) [
            set sediment-thick 0    set bedrock-elev bedrock-elev + 0.7
          ]            
          if (patch-ID <= 50 and patch-ID >= 20) [
            set sediment-thick 0    set bedrock-elev bedrock-elev + 0.8
          ]            
          set elevation bedrock-elev + sediment-thick   
        ]   ; End of ask patches
      ] ; End of foreach loop  
    ]  
    [] ;Otherwise do nothing
end

to calculate-avg-PES       ; Add on 02-20-2015 (v5.8)
  
  set PES-scores  0    ; This procedure will be executed each step so we need to set it to zero at the beginning
  ask households [    
    set PES-scores PES-scores + PES-level    
  ]
  
  let PES-avg PES-scores / (count households) 
  set PES PES-avg ; Take out round on 02-23-2015 (v5.9)   
end

to increase-pay   ; Add on 02-25-2015 (v6.1)
  
  set Tolerance Allowed-degradation   ; To be determined and experimented by the user: 0 (do not allow any degradation)
                                      ; and 1 (all levels of degradation).
  ;print (word "****************Time****************" ticks word "Total degrade-level " degrade-level)
  set degrade-level Total-sedi-chg / 27.685    ; A measure of landscape degradation between 0 (best) and 1 (worst)
  
  ifelse (degrade-level > Tolerance and storm? = true) [set PES-inflation PES-increase] ; Only at times of storm,
  [set PES-inflation 0]               ; people would increase their PES at the magnitude of PES-inflation.
  
  ask households [ 
    ;if (ticks >= 60 and ticks <= 63) [
      ;show (word "Old " PES-level)
    ;]

    ifelse PES-level + PES-inflation < 3 [set PES-level PES-level + PES-inflation]
      [set PES-level 3]               ; Set a cap for PES at 3.
    
    ;if (ticks >= 60 and ticks <= 63) [
      ;show (word "New " PES-level)
    ;]   
  ]
  
end 

to adopt-NBs-PES       ; Each household looks at his neighbors and adopt their PES levels. Add on 02-20-2015 (v5.8)
  
  ask households [                        ; This loops through all household agents
    
    ;print (word "My household ID is "self word " with my earlier PES level = " PES-level " units")         ; Add 02-21-2015
        
    set PES-scores  0  ; These two variables need to be "emptied" as they are global variables
       
    ask other households in-radius Neighborhood-size  ; The neighborhood size (a radius) is set by the user (0 to 40)
      [set color white ; All households that are considered as neighbors are set to be white
        ;show (word "As a neighbor my ID is "self word " and My PES = " PES-level)      ; Add 02-21-2015
        set   PES-scores PES-scores + PES-level       ; Each neighbor's PES level is accumulated and assigned to PES-scores
      ]  
      
    ifelse ((count other households in-radius Neighborhood-size) != 0) ; If one or more households exist in my neighborhood
    [set PES-scores PES-scores / (count other households in-radius Neighborhood-size)] ; Calculate the average scores
    []   ; If my neighborhood is empty, do nothing
    
    ifelse ((count other households in-radius Neighborhood-size) != 0) ; If one or more households exist in my neighborhood
    [set PES-level PES-scores]                            ; Assign the average PES scores of my neighbors to me
    []                                                    ; Keep my earlier PES level if my neighborhood is empty
    
    ;show (word "For "self word ", my new PES level = " PES-level " units") ; Print the new PES level after considering my neighbors's
  ]
end

; Alternative 1: When storm comes, the sediments in all segments are removed to the same extent (not  very realistic)

to sediment-change-no-order                                        ; Changes made on 02-26-2015 (v6.2) 
  
  if (PES <= 1) [set rate-reduction 0.5 * PES]                        ; Add on 02-26-2015 (v6.2)   
  if (PES <= 2 and PES > 1) [set rate-reduction 0.2 * PES + 0.2]      ; Add on 02-26-2015 (v6.2)   
  if (PES <= 3 and PES > 2) [set rate-reduction 0.1 * PES + 0.6]      ; Add on 02-26-2015 (v6.2)   

  ask patches with [pcolor = blue] [
    
    ifelse (storm? = true)[
      set change-rate -0.113 * (1 - rate-reduction) * storm-duration ; add on 02-17-2015
    ]
    [set change-rate 0]
    
    ifelse (sediment-thick > 0 and storm? = true) [
    
      ifelse (sediment-thick > abs change-rate) [
        set sediment-thick sediment-thick + change-rate
        set Total-sedi-chg Total-sedi-chg + abs change-rate  ; Add 02-26-2015
      ]
      [
        set sediment-thick 0     
        set Total-sedi-chg Total-sedi-chg + sediment-thick
      ]
    ]
    []
    
    set elevation bedrock-elev + sediment-thick   
  ] 
end

; Alternative 2: When storm comes, the sediments in upstream segments are first removed:

to sediment-change-in-order 
  ;set PES 0                                  ; PES can take 0, 1, 2, or 3. To be linked to other variables (v5.6)
  if (PES <= 1) [set rate-reduction 0.5 * PES]               
  if (PES <= 2 and PES > 1) [set rate-reduction 0.2 * PES + 0.2]      ; Hypothetical relationship 02-23-2015 (v5.9)
  if (PES <= 3 and PES > 2) [set rate-reduction 0.1 * PES + 0.6]      ; Hypothetical relationship 02-23-2015 (v5.9)  
       
  let List_of_segments []                  ; Create a list as a container of stream patches
  
  ask patches with [pcolor = blue] [       ; Sediment change only happen on stream patches (blue)   
    
    set List_of_segments  lput patch-ID List_of_segments   ; Put all stream patches into the above list
    
    ifelse (storm? = true)[                ; Only for days with storm
      set change-rate -0.113 * (1.0 - rate-reduction) * storm-duration ; A negative number for sediment change per day. change on 02-17-2015
    ]
    [set change-rate 0]                    ; For days without storm, the change rate is zero  
      
  ]  ; The end of ask patches clause
  
  ifelse (storm? = false) [set available-thick 0]  ; Add on 02-25-2015
  [set available-thick 0.113 * (1.0 - rate-reduction) * storm-duration + available-thick] ; Note for days w/o storm, storm-duration =0. 
                                                      ; Change on 02-17-2015. Also + available-thick is added to make it carried over
                                                      ; to next step
  set Total-sedi-chg Total-sedi-chg + available-thick   ; Total amount of sediment change
   
  foreach sort List_of_segments [   
  
    ask patches with [patch-ID = ?] [ 
   
      if(storm? = true and available-thick > 0) [                   ; This "if" clause is added 02-19-2015
        ifelse (available-thick > sediment-thick) [                 ; This "if" condition limits to days with storm
          set available-thick available-thick - sediment-thick      ; The first available segment has its amount of sediment-thick removed
          set sediment-thick 0                                      ; As the result, its sediment is set to zero
        ]
        [
          set sediment-thick sediment-thick - available-thick
          set available-thick 0
        ]
      ]  ; End of the if(storm? = true and available-thick > 0) statement 
      set elevation bedrock-elev + sediment-thick        ; Finally, profile elevation is the sum of bedrock elevation     
    ]   ; End of ask patches
  ] ; End of foreach loop
  
end

to show-river-flow
  ; added by Jie
  set runtime runtime + 1
  ask patches with [patch-ID < 71] [
    set river-color (85 + 10 * ((runtime + patch-ID + 2) mod 3))
    set pcolor river-color
  ]
end

to do-plots

  set-current-plot "Profile elevations over segments"

  clear-plot
  
  let List_of_segments []
  let List_of_elev []
 
  ask patches with [patch-ID < 71] [ ; Changed by Jie

     set List_of_segments  lput patch-ID List_of_segments  
     set List_of_elev lput elevation List_of_elev
  ] 
  ;show sort List_of_segments   ; No need to print them except for code debugging 
  ;show sort List_of_segments
  ;show List_of_elev

  foreach sort List_of_segments [
    ask patches with [patch-ID = ?] [
      plotxy patch-ID elevation
    ]
  ]
  
  let mymean mean List_of_elev   
 
End 

; Note: remove the write-to-file part if it aims at creating a web-based Netlogo model.
to write-to-file   ; Added on Version 3.0, Oct 14, 2014  

  let List_of_segments []                  ; Create a list as a container of stream patches
  
  ask patches with [pcolor = blue] [       ; Only select stream patches   
    set List_of_segments  lput patch-ID List_of_segments   ; Put all stream patches into the list
  ]   

  file-open "StreamDataOutput.csv"
  
  foreach sort List_of_segments [
    ask patches with [patch-ID = ?] [
      file-type (word self ",")            ; This line print the patch coordinates
      file-type (word patch-ID ",")
      file-type (word ticks ",")
      file-type (word storm? ",")          ; Add on 02-19-2015
      file-type (word bedrock-elev ",")
      file-type (word sediment-thick ",")
      file-type (word elevation ",")
      file-type (word Total-sedi-chg ",")  ; Add on 02-19-2015
      file-type (word PES ",")             ; Add on 02-28-2015
      file-print "" ; This line is necessary; otherwise all data are written into one line
    ]
  ]
  file-close  
end

to show-data                   ; Add on 02-23-2015 (v5.9)
  
  if ticks = Simu-span - 1 [
    show word "The accumulated sediment = "Total-sedi-chg
    show word "The final Average PES level = " PES
    ]
end

to go
  if ticks >= Simu-span [ stop ]   

  flow-change
  ifelse (Sediment-chg-order? = true) [
    sediment-change-in-order
  ]
  [sediment-change-no-order]
  adopt-NBs-PES                ; Add on 02-20-2015 (v5.8)
  pave-channel
  show-river-flow              ; added by Jie
  increase-pay                 ; Add 02-25-2015 (V6.1)
  calculate-avg-PES            ; Add on 02-21-2015 (v5.8)
  do-plots
  write-to-file 
  show-data                    ; Add on 02-23-2015 (v5.9)
  tick
end
@#$#@#$#@
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Setup
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OBSERVER
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BUTTON
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Run
go
T
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OBSERVER
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"" ""
PENS
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PLOT
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Elevation of segments #1 ~ #10
Segment IDs
Profile elevation
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"" "clear-plot"
PENS
"default" 1.0 1 -5298144 true "" "plotxy 1 mean [elevation] of patches with [patch-ID = 1]"
"pen-1" 1.0 1 -7500403 true "" "plotxy 2 mean [elevation] of patches with [patch-ID = 2]"
"pen-2" 1.0 1 -2674135 true "" "plotxy 3 mean [elevation] of patches with [patch-ID = 3]"
"pen-3" 1.0 1 -955883 true "" "plotxy 4 mean [elevation] of patches with [patch-ID = 4]"
"pen-4" 1.0 1 -6459832 true "" "plotxy 5 mean [elevation] of patches with [patch-ID = 5]"
"pen-5" 1.0 1 -1184463 true "" "plotxy 6 mean [elevation] of patches with [patch-ID = 6]"
"pen-6" 1.0 1 -10899396 true "" "plotxy 7 mean [elevation] of patches with [patch-ID = 7]"
"pen-7" 1.0 1 -13840069 true "" "plotxy 8 mean [elevation] of patches with [patch-ID = 8]"
"pen-8" 1.0 1 -14835848 true "" "plotxy 9 mean [elevation] of patches with [patch-ID = 9]"
"pen-9" 1.0 1 -11221820 true "" "plotxy 10 mean [elevation] of patches with [patch-ID = 10]"

@#$#@#$#@
## WHAT IS IT?

(a general understanding of what the model is trying to show or explain)

## HOW IT WORKS

(what rules the agents use to create the overall behavior of the model)

## HOW TO USE IT

(how to use the model, including a description of each of the items in the Interface tab)

## THINGS TO NOTICE

(suggested things for the user to notice while running the model)

## THINGS TO TRY

(suggested things for the user to try to do (move sliders, switches, etc.) with the model)

## EXTENDING THE MODEL

(suggested things to add or change in the Code tab to make the model more complicated, detailed, accurate, etc.)

## NETLOGO FEATURES

(interesting or unusual features of NetLogo that the model uses, particularly in the Code tab; or where workarounds were needed for missing features)

## RELATED MODELS

(models in the NetLogo Models Library and elsewhere which are of related interest)

## CREDITS AND REFERENCES

(a reference to the model's URL on the web if it has one, as well as any other necessary credits, citations, and links)
@#$#@#$#@
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@#$#@#$#@
NetLogo 3D 5.1.0
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@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
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@#$#@#$#@
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