I am trying to code for a reverse reaction in biology - I have already done that by taking inspiration from a sample code pasted below. What I don't understand is how is the association rate constant (Kb in the code) and dissociation constant (Ku in the code) are affecting the forward and backward reactions in this code. Are they affecting the speed of movement of the products after they are formed? Are they affecting the speed with which they are formed? I want the Ku to affect affinity for substrates to form a product, and Ku to affect time to dissociate for products. The product is a complex formation of two substrates.
Also, why do they multiple Kb by 2? To slow the product complex down or speed it up? It should slow down due to increase in mass.
breed [reactants reactant] ;; reactants are green, products are red breed [products product]
to setup clear-all set-default-shape reactants "molecule1" set-default-shape products "molecule2" create-reactants number
[ set color green
setxy random-xcor random-ycor ] reset-ticks end
to go ask turtles
[ rt random-float 10 - random-float 10 ;; wander around randomly
fd 1 ] ask turtles
[ ifelse (breed = reactants)
[ react-forward ] ; reactants
[ react-backward ] ; products
] tick end
to react-forward if (any? other reactants-here) and
;; multiply Kb by 2 because 2 molecules are involved
random-float 1000 < (Kb * 2)
[ ask one-of other reactants-here
[ die ]
set breed products
set color red ] end
to react-backward if (random-float 1000) < Ku
[ set breed reactants ;; change back to reactant
set color green
;; then split into two reactants
hatch 1 [ set heading random 360 ] ] end
Related
I am a teacher of Primary Education and Early Childhood Education and I am trying to generate a simulator through NetLogo on how fertilization and pesticides are decimating the butterfly population. However, despite having read the manual, I am not managing to program the code to make it work.
My problem is that although I set the turtles I can't establish the following relationship between the variables/buttons:
If butterflies randomly touch a plant (which is fertilized with pesticide) its pollinating capacity is reduced by a certain percentage (depends on the amount of pesticide)
My problem is that I can't get the pollination capacity of the butterfly to be set to 100% initially and that the greater the amount of pesticide, the lower its pollination capacity is when touching a flower. Currently, although the amount of pesticide is the highest, there are peaks where its pollination capacity increases instead of being reduced.
breed [butterflies butterfly]
breed [flowers flower]
globals
[
butterfliesless-neighborhoods ;; how many patches have no butterflies in any neighboring patches?
pollinating-capacity ;; measures how well-bivouaced the butterflies are
]
patches-own
[
butterflies-nearby ;; how many butterflies in neighboring patches?
]
flowers-own
[
carried-butterflies ;; the butterflies I'm carrying (or nobody if I'm not carrying in)
found-bivouac? ;; becomes true when I find a bivouac to drop it in
]
to setup
clear-all
set-default-shape butterflies "butterflies"
set-default-shape flowers "flower"
ask patches
[ set pcolor green + (random-float 0.8) - 0.4] ;; varying the green just makes it look nicer
create-butterflies num-butterflies
[ set color white
set size 1.5 ;; easier to see
setxy random-xcor random-ycor ]
create-flowers num-flowers
[ set color brown
set size 1.5 ;; easier to see
set carried-butterflies nobody
set found-bivouac? false
setxy random-xcor random-ycor ]
reset-ticks
end
to update-butterflies-counts
ask patches
[ set butterflies-nearby (sum [count butterflies-here] of neighbors) ]
set butterfliesless-neighborhoods (count patches with [butterflies-nearby = 0])
end
to calculate-pollinating-capacity
set pollinating-capacity (butterfliesless-neighborhoods / (count patches with [not any? butterflies-here])) * 100
end
to go
ask flowers
[ ifelse carried-butterflies = nobody
[ search-for-butterflies ] ;; find a butterflies and pick it up
[ ifelse found-bivouac?
[ find-empty-spot ] ;; find an empty spot to drop the butterflies
[ find-new-bivouac ] ] ;; find a bivouac to drop the butterflies in
wiggle
fd 1
if carried-butterflies != nobody
;; bring my butterflies to where I just moved to
[ ask carried-butterflies [ move-to myself ] ] ]
ask butterflies with [not hidden?]
[ wiggle
fd pesticide-amount ]
tick
end
to wiggle ;; turtle procedure
rt random 50 - random 50
end
to search-for-butterflies ;; flowers procedure
set carried-butterflies one-of butterflies-here with [not hidden?]
if (carried-butterflies != nobody)
[ ask carried-butterflies
[ hide-turtle ] ;; make the butterflies invisible to other flowers
set color blue ;; turn flower blue while carrying butterflies
fd 1 ]
end
to find-new-bivouac ;; flowers procedure
if any? butterflies-here with [not hidden?]
[ set found-bivouac? true ]
end
to find-empty-spot ;; flowers procedure
if all? butterflies-here [hidden?]
[ ask carried-butterflies
[ show-turtle ] ;; make the butterflies visible again
set color brown ;; set my own color back to brown
set carried-butterflies nobody
set found-bivouac? false
rt random 360
fd 20 ]
end
Defined Buttons
Your screenshot is a nice start with sliders, buttons and plots. In the code tab consider making two breeds of turtles: butterflies and plants.
breed [butterflies butterfly]
butterflies-own [pollinatingCapacity]
breed [plants plant]
plants-own [pesticideAmount]
And then think about how you might decrease pollinatingCapacity of a butterfly when it is on the same patch as a plant. A butterfly can see if any plants are on the same patch using plants-here
In this model the boat moves diagonally across the world (which does not wrap, 00 bottom left, max-pycor & max-pxcor 49) and 20 fish move in the opposite diagonal. The model is set up so the boat counts the fish it encounters, and as a double-check each fish counts if it met the boat. It does not matter if the boat does not meet all the fish.
My problem is that on some (10-15%) of runs, although both agents appear to be on the same patch, the relevant record does not increase, i.e. times that f-count does not increase and other times the b-count might not increase. I have spent time watching the agents closely, and they appear to be on the same patch, but the record does not increase. As a beginner with NetLogo, is there something in the coding of "boats-here", "fish-here" or "neighbors" that I am overlooking that is related to the xcor/ycor of the agents? Or is the sequence of commands the source of the problem? Thanks for considering my question.
breed [boats boat]
breed [fish a-fish]
boats-own [b-count fuel]
fish-own [f-count]
to setup
clear-all
reset-ticks
create-boats 1
[apply-boat-properties]
create-fish 20
[apply-fish-properties]
end
to apply-boat-properties
ask boats
[
set color red
set size 0.3
set shape "star"
setxy min-pxcor max-pycor
set fuel 710
]
end
to apply-fish-properties
ask fish
[
set color blue
set size 0.3
set shape "star"
setxy random-xcor max-pycor
]
end
to go
if (any? boats with [fuel <= 0 ])
[ stop ]
ask boats
[
follow-route1
survey
]
ask fish
[
check-if-boat
move
]
tick
end
to follow-route1
ask boats
[
facexy 49 0
fd 0.05
pen-down
set fuel fuel - 1
]
end
to survey
ifelse any? fish-here ;; if boat on the same patch as a fish
[ask fish-here [ ;; ask the fish on this patch
if shape = "star"[ ;; with a "star" shape
set shape "circle" ;; change shape to "circle" shape
ask boats-here ;; ask boat on same patch to increase b-
count by 1
[set b-count b-count + 1]]
]
]
;; otherwise
[ask fish-on neighbors [ ;; ask fish on neighbouring 8 patches
if shape = "circle"[ ;; if the fish has a "circle" shape
set shape "star" ] ;; change that shape to "star" shape
]]
end
to move
ask fish
[
set heading 225
fd 0.0025
]
end
to check-if-boat
ifelse any? boats-here ;; if boats on same patch as the
fish
[
ask fish-here with [color = blue] ;; ask the blue fish to change
colour to yellow
[ set color yellow
set f-count f-count + 1] ;; and increase f-count by 1
]
[ask fish-here with [color = yellow] ;; otherwise ask fish with yellow
colour to change color to blue
[set color blue
] ]
end
to-report boat-b-count ;;Report count of boats with b-
count more than 1
report sum [b-count] of boats with [b-count > 0]
end
to-report fish-f-count ;;Report count of fish with f-
count more than 1
report sum [f-count] of fish with [f-count > 0]
end
to-report %fish-counted ;;Report count of fish with f-
count more than 1
report (sum [f-count] of fish / count fish) * 100
end
I am essentially trying to combine elements of the 'Segregation' model and 'Rebellion' model to form a model that is representative of alliance forming.
Here is what I have so far- when I attempt to run it I receive the error: THREATS breed does not own variable ACTIVE?
error while threat 0 running ACTIVE?
called by procedure GO
called by Button 'go'
breed [ agents an-agent]
breed [ threats threat ]
globals [
k ; factor for determining attack probability
threshold ; by how much must D - BS > A to make a state burden share
percent-similar ; on the average, what percent of a turtle's neighbors
; are the same color as that turtle? Likely to ally
percent-unhappy ; what percent of the turtles are unhappy? Or percieve threats?
visualization
]
agents-own [
allied-states ; R, fixed for the agent's lifetime, ranging from 0-1 (inclusive)- for each turtle, indicates whether at least %-similar-wanted percent of
; that turtle's neighbors are the same color as the turtle
perceived-threat ; T, also ranging from 0-1 (inclusive)- how many have a turtle of another color?
active? ; if true, then the agent is actively allied
; if false, then the agent is free-riding
conflict ; how many turns in conflict remain? (if 0, the agent is not in conflict)- sum of previous two variables
total-nearby ; sum of previous two variables
]
patches-own [
neighborhood ; surrounding patches within the vision radius
]
to setup
clear-all
; set globals
set k 2.3
set threshold 0.1
ask patches [
; make background a slightly dark gray
set pcolor gray - 1
; cache patch neighborhoods
set neighborhood patches in-radius vision
]
if initial-threats-density + initial-agent-density > 206 [
user-message (word
"The sum of INITIAL-THREATS-DENSITY and INITIAL-AGENT-DENSITY "
"should not be greater than 206.")
stop
]
; create threats
create-threats round (initial-threats-density * .01 * count patches) [
move-to one-of patches with [ not any? turtles-here ]
display-threats
]
; create agents
create-agents round (initial-agent-density * .01 * count patches) [
move-to one-of patches with [ not any? turtles-here ]
set heading 0
set allied-states random-float 1.0
set perceived-threat random-float 1.0
set active? false
set conflict 0
display-agent
]
; start clock and plot initial state of system
reset-ticks
end
to go
if all? turtles [ active? ] [ stop ]
move-unhappy-turtles
update-turtles
update-globals
tick
end
; unhappy turtles try a new spot
to move-unhappy-turtles
ask turtles with [ not active? ]
[ find-new-spot ]
end
; move until we find an unoccupied spot
to find-new-spot
rt random-float 360
fd random-float 10
if any? other turtles-here [ find-new-spot ] ; keep going until we find an unoccupied patch
move-to patch-here ; move to center of patch
end
to update-turtles
ask turtles [
; in next two lines, we use "neighbors" to test the eight patches
; surrounding the current patch
set allied-states count (turtles-on neighbors) with [ color = [ color ] of myself ]
set perceived-threat count (turtles-on neighbors) with [ color != [ color ] of myself ]
set total-nearby allied-states + perceived-threat
set active? allied-states >= (percent-similar * total-nearby / 100)
; add visualization here
if visualization = "old" [ set shape "default" set size 1.3 ]
if visualization = "square-x" [
ifelse active? [ set shape "square" ] [ set shape "X" ]
]
]
end
to update-globals
let similar-neighbors sum [ allied-states ] of turtles
let total-neighbors sum [ total-nearby ] of turtles
set percent-similar (similar-neighbors / total-neighbors) * 100
set percent-unhappy (count turtles with [ not active? ]) / (count turtles) * 100
; Agents engaged in conflict have the duration reduced at the end of each clock tick
ask agents [ if conflict > 0 [ set conflict conflict - 1 ] ]
; update agent display
ask agents [ display-agent ]
ask threats [ display-threats ]
; advance clock and update plots
tick
end
; AGENT AND THREAT BEHAVIOR
; move to an empty patch
to move ; turtle procedure
if movement? or breed = threats [
; move to a patch in vision; candidate patches are
; empty or contain only jailed agents
let targets neighborhood with [
not any? threats-here and all? agents-here [ conflict > 0 ]
]
if any? targets [ move-to one-of targets ]
]
end
; AGENT BEHAVIOR
to determine-behavior
set active? (burden-sharing - allied-states * estimated-conflict-probability > threshold)
end
to-report burden-sharing
report perceived-threat * (1 - alliance-protection)
end
to-report estimated-conflict-probability
let t count (threats-on neighborhood)
let a 1 + count (agents-on neighborhood) with [ active? ]
; See Info tab for a discussion of the following formula
report 1 - exp (- k * floor (t / a))
end
to alliance
if any? threats [attack]
set active? true
end
; THREAT BEHAVIOR
to attack
if any? (agents-on neighborhood) with [ active? ] [
; arrest suspect
let suspect one-of (agents-on neighborhood) with [ active? ]
move-to suspect ; move to patch of the jailed agent
ask suspect [
set active? false
set conflict random conflict-term
set color pink
]
]
end
; VISUALIZATION OF AGENTS AND COPS
to display-agent ; agent procedure
set color cyan
set shape "triangle"
end
to display-active?
set color pink
set shape "triangle"
end
to display-threats
set color red
set shape "circle 2"
end
The problem is that you have two breeds of turtles, agents and threats, and only agents "own" the variable active?. turtles is a superset of all breeds, so when the all? primitive tries to query the active? variable of literally all turtles, it tries to query active? for threats too, and can't find it. The line should be
if all? agents [ active? ] [ stop ]
I am new in using NetLogo, so I hope you can help me with this code.
I would like to build a network with two subnetwork, A and B, where A has N nodes and B beta*N nodes, where beta=0.5. Each network should be initialised with five fully connected nodes. I need to add a new node at a time, assuming that each has fixed out-degree k. Once a new node i comes into the network, it links to a randomly selected target node j. The other remaining k-1 nodes should be selected as following: with probability p, i should be linked to a random node of j's; with probability 1-p, i should be connected to another randomly selected node in A.
On the other hand, the nodes in B should be linked (directed link) to each node in A with probability P. P can vary from 0 to 1.
What I already tried is built the two networks with N and alpha*N nodes respectively. But, as I said, I am new in using NetLogo and I am finding many difficulties to build this network that should be really easy in a different programming language, I would be more familiar with.
; Global variables
breed [agents agent]
breed [bagents bagent]
to setup
clear-all
setup-agent
setup-bagent
end
; Defining agents
to setup-agent
set-default-shape turtles "person" ; agent shape
create-agents n-of-agents ; # of agents
[set size 2 ; agent size
set color white
setxy (random-xcor) (random-ycor)
]
; Random Network
ask agents [create-link-with one-of other agents with [not link-neighbor? myself]
ask links [set color white]
]
end
; Defining bagents
to setup-bagent
set-default-shape turtles "circle" ; bagents shape
set beta=0.5
let n-of-bagents beta*n-of-agents
create-bagents beta*n-of-agents ; # of bagents
[set size 2 ; bagent size
set color red
setxy (random-xcor) (random-ycor)
; Network
ask bagents [create-link-with one-of other bagents with [not link-neighbor? myself]
ask links [set color yellow]
]
end
to go
end
I hope you can help me to understand how to build such a network in NetLogo.
Many thanks
This does what you said. I don't think it's actually what you want as your algorithm is much better but still somewhat confused. But hopefully this gets you on the correct path.
UPDATED to make one node add each tick
globals
[ beta
prob
k
]
breed [A-agents A-agent]
breed [B-agents B-agent]
to setup
clear-all
set beta 0.5
set prob 0.2
set k 3
setup-A-seed
setup-B-seed
reset-ticks
end
to go
add-A-node
if random-float 1 < beta [add-B-node]
tick
end
; Defining A seed network
to setup-A-seed
create-A-agents 5
[ set shape "person"
set size 2
set color white
setxy random-xcor random-ycor
]
ask A-agents
[ create-links-to other A-agents
[ set color white ]
]
end
; Defining B seed network
to setup-B-seed
create-B-agents 5
[ set shape "circle"
set size 2
set color red
setxy random-xcor random-ycor
]
ask B-agents
[ create-links-to other B-agents
[ set color yellow ]
]
end
to add-A-node
create-A-agents 1
[ set shape "person"
set size 2
set color white
setxy random-xcor random-ycor
let target one-of other A-agents ; target is j in description
create-link-to target
repeat k - 1
[ let candidates (other [link-neighbors] of target) with [not link-neighbor? myself]
ifelse random-float 1 < prob or not any? candidates
[ create-link-to one-of other A-agents with [not link-neighbor? myself]
[ set color white ]
]
[ create-link-to one-of candidates
[ set color white ]
]
]
]
end
to add-B-node
create-B-agents 1
[ set shape "circle"
set size 2
set color red
setxy random-xcor random-ycor
let thisB self
ask A-agents
[ if random-float 1 < prob
[ create-link-from thisB
[ set color yellow
]
]
]
]
end
Some of the NetLogo issues I noticed in your code:
NetLogo does not use = for set
you must have space around mathematical operators (or NetLogo will think it's part of the name)
Some of the things you need to think about in your algorithm:
why do you have an initial B network if all Bs connect to each A with fixed probability?
what do you do if the selected A doesn't have any edges to follow?
As general advice, don't try writing something this complicated in one piece. Create your seed networks with 5 fully connected nodes. Make that work. Then do network A and make that work. Then bring in B. This iterative building is important for all programming languages. It is particularly important when using a new language so that you only have to debug one or two errors at a time and you know where the bugs are.
Sorry if this is obvious, I have searched everything I can think of and asked a colleague and we are both stuck.
I have some code (below - a slight twist on wolf sheep predation) that I want to run behaviorspace (input also below). However, it never runs to completion. It always seems to get stuck on step #0 of a run (the run # it gets stuck on varies). The runs that it sticks on work fine if they are run in isolation (so all the variables seem fine). It just seems to freeze (producing no error messages, nor does it crash).
Any ideas what is causing it?
Thanks,
Simon
Code:
globals [grass] ;; keep track of how much grass there is
;; Sheep and wolves are both breeds of turtle.
breed [sheep a-sheep] ;; sheep is its own plural, so we use "a-sheep" as the singular.
breed [wolves wolf]
turtles-own [energy] ;; both wolves and sheep have energy
patches-own [countdown]
to setup
clear-all
ask patches [ set pcolor green ]
;; check GRASS? switch.
;; if it is true, then grass grows and the sheep eat it
;; if it false, then the sheep don't need to eat
if grass? [
ask patches [
set countdown random grass-regrowth-time ;; initialize grass grow clocks randomly
set pcolor one-of [green brown]
]
]
if fences?[ ; this code adds in blue fences to create patches of various size (if fences are turned on). Turtles cannot pass over fences
ask patches with [pxcor mod connectivity2 = 0]
[ set pcolor blue ]
ask patches with [pycor mod connectivity = 0]
[ set pcolor blue ]
]
set-default-shape sheep "sheep"
create-sheep ((count patches - (count patches with [pcolor = blue])) / 25) ;; create the sheep, then initialize their variables. The starting density always remains constant despite a varying world size
[
set color white
set size 1.5 ;; easier to see
set label-color blue - 2
set energy random (2 * sheep-gain-from-food)
setxy random-xcor random-ycor
]
set-default-shape wolves "wolf"
create-wolves ((count patches - (count patches with [pcolor = blue])) / 50) ;; create the wolves, then initialize their variables. The starting density always remains constant despite a varying world size
[
set color black
set size 2 ;; easier to see
set energy random (2 * wolf-gain-from-food)
setxy random-xcor random-ycor
]
display-labels
set grass count patches with [pcolor = green]
reset-ticks
end
to go
if count wolves = 0 and count sheep = 0 and ((count patches with [pcolor = green]) = (count patches - (count patches with [pcolor = blue]))) [ stop ] ; stop model when the whole world has flipped to grass
ask sheep [
move
if grass? [
set energy energy - 1 ;; deduct energy for sheep only if grass? switch is on
eat-grass
]
death
reproduce-sheep
]
ask wolves [
move
set energy energy - 1 ;; wolves lose energy as they move
catch-sheep
death
reproduce-wolves
]
if grass? [ ask patches [ grow-grass ] ]
set grass count patches with [pcolor = green]
tick
display-labels
end
to move ;; turtle procedure
rt random 50
lt random 50
ifelse [pcolor] of patch-ahead 1 = blue
[ move] ;; If there is a blue patch ahead of you, choose another random direction
[ fd 1 ] ;; Otherwise, it is safe to move forward.
end
to eat-grass ;; sheep procedure
;; sheep eat grass, turn the patch brown
if pcolor = green [
set pcolor brown
set energy energy + sheep-gain-from-food ;; sheep gain energy by eating
]
end
to reproduce-sheep ;; sheep procedure
if random-float 100 < sheep-reproduce [ ;; throw "dice" to see if you will reproduce
set energy (energy / 2) ;; divide energy between parent and offspring
hatch 1 [ ifelse [pcolor] of patch-ahead 1 = blue ;; hatch an offspring
[ move] ;; If there is a blue patch ahead of the offspring, it chooses another random direction
[ fd 1 ] ;;If not, offspring move forward 1 step
]]
end
to reproduce-wolves ;; wolf procedure
if random-float 100 < wolf-reproduce [ ;; throw "dice" to see if you will reproduce
set energy (energy / 2) ;; divide energy between parent and offspring
hatch 1 [ ifelse [pcolor] of patch-ahead 1 = blue ;; hatch an offspring
[ move ] ;; If there is a blue patch ahead of the offspring, it chooses another random direction
[ fd 1 ] ;;If not, offspring move forward 1 step
] ]
end
to catch-sheep ;; wolf procedure
let prey one-of sheep-here ;; grab a random sheep
if prey != nobody ;; did we get one? if so,
[ ask prey [ die ] ;; kill it
set energy energy + wolf-gain-from-food ] ;; get energy from eating
end
to death ;; turtle procedure
;; when energy dips below zero, die
if energy < 0 [ die ]
end
to grow-grass ;; patch procedure
;; countdown on brown patches: if reach 0, grow some grass
if pcolor = brown [
ifelse countdown <= 0
[ set pcolor green
set countdown grass-regrowth-time ]
[ set countdown countdown - 1 ]
]
end
to display-labels
ask turtles [ set label "" ]
if show-energy? [
ask wolves [ set label round energy ]
if grass? [ ask sheep [ set label round energy ] ]
]
end
; Copyright 1997 Uri Wilensky.
; See Info tab for full copyright and license.
behaviorspace input:
variables:
["world-width" 51]
["fences?" true]
["wolf-gain-from-food" 20]
["sheep-reproduce" 7]
["show-energy?" false]
["grass?" true]
["connectivity" 10 25 50]
["wolf-reproduce" 5]
["grass-regrowth-time" [1 1 100]]
["sheep-gain-from-food" 4]
repetitions: 1
reporters:
count wolves
count sheep
count patches with [pcolor = green]
measure runs at each step
setup: setup
Go: go
Stop (I have tried it with and without this): count wolves = 0 and count sheep = 0 and ((count patches with [pcolor = green]) = (count patches - (count patches with [pcolor = blue])))
Time limit: 5000
It's difficult for me to imagine this could be caused by anything other than running low on memory. Running very low on memory can cause the JVM to slow to a crawl.
What do the memory usage stats in the System tab of "About NetLogo" say? You can verify there that you're actually getting the heap size you asked for.