Exercise 3 - Bryn Mawr Computer Science
Contents
1. these definitions are the first things to appear in a NetLogo program Also worthy of note is the text followed by double semi colons or comments Comments are annotations to source code that help explain the purpose and workings Anything followed by the to the end of the line is ignored when a program is built from code Let s look at the next code block to setup clear all set default shape turtles bug crt population set size 2 easier to see set color red J 7 red not carrying food setup patches do plotting end Here we see two more reserve words to and end These two words mark the start and end of a command procedure or function i e a block of code that performs a specific task In general the syntax for a command procedure is to procedure name do something do something else CMSC BIOL 361 Emergence Cellular Automata Introduction to NetLogo end The particular procedure illustrated on the previous page is standard and most NetLogo simulations will have one This is the setup procedure and is the list of commands that happen when the setup button is pressed on the interface This setup procedure does the following 1 Clears the display world of all patches and turtles clear al1 Establishes how turtles will be drawn set default shape turtles bug 3 Creates turtles which belong to the breed population crt The settings between the square braces following t2. library of all the pre existing simulations that have been written in NetLogo and incorporated in the software distribution As you can see there are quite a few and CMSC BIOL 361 Emergence Cellular Automata Introduction to NetLogo we will explore many of them over the next couple of weeks For now browse to the Biology folder and select the Ants simulation Then select Open to load the simulation into NetLogo When loaded NetLogo switches back to the Interface window which as you can see is now filled with stuff P ants NetLogo File Edit Tools Zoom Tabs Help normal speed on ticks Slider for setting initial conditions Buttons for controlling simulation Plot for presenting some data re the model Tools for creating new buttons sliders etc Window where CA world is visualized Shell for entering on the fly commands This stuff includes sliders for setting the initial conditions e g population size rate at which pheromones diffuse or evaporate and even an on off switch for the output plot buttons that allow you to setup or run the simulation and a plot that presents some data concerning the behavior of the simulation as well as the other aspects of the interface window tools for adding other controls and the interpreter for on the fly interaction Exercise 1 Play with Ants Press the setup button What happens Then press the go button What happen
3. we need to understand both the software and the language Let s start with the software First we should assume that NetLogo is installed on your machine However it may not be If not download an installer from the link provided on the class website and install it NetLogo will run on any platform Windows Mac Linux Good now launch the program Welcome to the NetLogo environment When you load the software it presents you with an interface screen i e Interface tab is selected and on top The interface screen allows you to 1 design and modify the interface for a simulation using a nice Graphical User Interface GUD 2 interact with a simulation that is already written and view it behavior and 3 use the interpreter aspect of NetLogo to run on the fly commands We will look at all of these options in a bit For now let s continue to see what else NetLogo has to offer Click on the Information tab Doing this brings the following to the front an editable help file If you are running a simulation written by someone else it should contain a description of the model and instructions on its use If you have written a simulation it is your responsibility to edit this file so that others are informed of the purpose and use of your simulation Now select the Procedures tab It is this window that you will write and edit NetLogo code Enough chit chat let s get started From the File Menu select Models Library This brings up a
4. CMSC BIOL 361 Emergence Cellular Automata Introduction to NetLogo Disclaimer To get you oriented to the NetLogo platform I ve put together an in depth step by step walkthrough of a NetLogo simulation and the development environment in which it is presented For those of you with significant programming experience under your belt this walkthrough may be a bit of overkill For those of you without significant programming experience it may still be a bit of overkill considering that StarLogo and NetLogo are frequently used by junior high school students i e the interface and language are very intuitive Nonetheless the detail is there for those who may need it For those of you who wish to read less carefully 1 e feel they can learn fine by exploring on their own I ve highlighted sections that you really should not skip in blue such as exercises that need to be answered Getting to Know NetLogo All About Ants NetLogo is a development environment For you non computer science people that means that it is a program that allows you to write code debug code translate that code into instructions the computer understands compile and interpret and run the instructions link and execute In other words it allows you to do all the steps necessary to write and execute a computer program in one convenient software package As already discussed it is also a programming language To use NetLogo effectively therefore
5. elsewhere in your code Once setup the next step is to actually run the simulation This is done with another standard user defined function go Below is the go procedure from the Ants simulation to go forever button ask turtles if who gt ticks stop delay initial departure ifelse color red look for food J 77 not carrying food look for it return to nest 7 Carrying food take it back to nest wiggle fd 1 diffuse chemical diffusion rate 100 ask patches set chemical chemical 100 evaporation rate 100 recolor patch tick do plotting end CMSC BIOL 361 Emergence Cellular Automata Introduction to NetLogo This go procedure does the following 1 Asks the turtles to perform all the commands in between the square braces that follow the ask turtles command including looking for food returning to the nest wiggling and moving forward one patch 2 Tells each patch to share some of its chemical see the patch definition with all eight of its neighboring patches diffuse 3 Asks all patches to update their amount of chemical 4 Update the tick counter tick a way of keeping track of time 5 Plot the change in the system on the plot After the go function is a whole bunch of other code all of which are additional procedures that accomplish or help accomplish the tasks outlined in the go procedure which is the meat of the simulation Now I could in excruciating deta
6. first place So let s explore a little further and look at the code for the Ant simulation by switching to the Procedures tab Below are segments from the code for the Ant simulation cut and paste directly from the original and then annotated to help you read through and understand what is going on The color scheme is also the same patches own chemical j amount of chemical on this patch food 77 amount of food on this patch 0 1 or 2 A comment nest 7 true on nest patches false elsewhere nest scent number that is higher closer to the nest food source number 7 number 1 2 or 3 to identify the food sources The ant program starts with a block of code that defines the variables that all patches can use In other words this code bit establishes the characteristics of a patch for the model where each variable saves an aspect of the patch s state e g a patch could have 5 g of chemical 1 food no nest 0 32 nest scent and a food source of 3 We know this because it begins with the word patches own This word is a reserve word or a phrase that is an integral part of the NetLogo programming language The reserve word is followed by square braces and any code statements in those braces are affiliated with the word There is also a reserve word turtles own that can be used to define any variables associated with turtles Both patches own and turtles own must be used first i e when necessary
7. he crt statement establish what population turtles look like 4 The setup function then calls two function written by the programmer one the sets up the patches and the other that does the plotting If you scroll down through the program you will see that these functions are defined in the same way as was the setup procedure This setup function has introduced us to many NetLogo commands Commands are words that perform specific tasks in NetLogo i e built in functions NetLogo commands appear in blue In addition to commands we can also see that there are other words that are colored These include values in red and standard NetLogo identifiers and operators in purple The standard setup procedure is followed by three more user defined setup functions setup patches setup nest and setup food If you look carefully you will see that setup patches initializes the world so that some patches are the ants nest and some their food It then recolors the patches using the user defined recolor patch function to reflect whether a patch contains food or is the nest All of this patch setting up happens in the setup function when the setup patch command is invoked Take home message you can define a procedure or function or block of code that completes a task using the keywords to and end and the syntax introduced earlier Once you define a procedure you can invoke it i e cause it to be executed by just typing the procedure name
8. il work through the remainder of the code for the Ant simulation but I am not going to Mainly because there are a lot of built in commands and a lot of details that can t be simply explained in one sitting Instead I suggest you read through the code on your own I think you will find it to be mostly intuitive Discuss it with your neighbor if you get confused After you are fairly comfortable or fairly frustrated by the Ant simulation I d like you to do the following Exercise 3 Familiarize yourself with NetLogo by doing Tutorial s 1 3 in the NetLogo User s Manual found through the Help Menu Exercise 4 Now that you are a NetLogo expert go back to the Ant simulation Let s go out on a limb and change the model Alter something it could be something big or something little Well not too little Changing the forward statement in the go procedure from fd 1 to fd 2 is TOO little The goal is to change the actual system being modeled by modifying one of the procedures that govern its behavior i e one of those functions following the go procedure Now run your newly adapted model Is the effect of your tampering visible How so Explain your modification and e mail me a copy of your program
9. s Given these initial conditions and the behavior of the system to which class of cellular automata do you think this model belongs Press the go button to stop the simulation Change the initial conditions by using the sliders Press the setup button to setup the model with the new conditions and then run again Do you still like your classification choice Exercise 2 So what is this a simulation of Press the Information tab to read a bit about the system this simulation is modeling Now that you understand the system go back to the Interface tab and play with the model some more Turn on the plot What insight does the plot give you into the behavior of the system Is this system emergent Why or why not Just from running this little simulation I hope you can see that NetLogo is a pretty cool development environment that lets you play with cellular automata models in a very sophisticated manner I mean there were actually ants running around on your computer screen Certainly this simulation is a lot more interesting than Conway s Game of Life And as you saw when you looked at the model s library there are many many simulations that we could happily spend hours playing with But we are here to learn some biology and some computer science which means we need to understand not only CMSC BIOL 361 Emergence Cellular Automata Introduction to NetLogo the output of the simulation but how the simulation was created in the
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