cacatoo

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>Cacatoo manual</title><link rel="icon" type="image/png" href="images/favicon.png" /> <script src="scripts/prettify/prettify.js"> </script> <script src="scripts/prettify/lang-css.js"> </script> <link type="text/css" rel="stylesheet" href="styles/prettify-tomorrow.css"> <link type="text/css" rel="stylesheet" href="styles/menu.css"> <link type="text/css" rel="stylesheet" href="styles/jsdoc-default.css"> <link href='https://fonts.googleapis.com/icon?family=Material+Icons' rel='stylesheet'> <script src="scripts/jquery.js"></script> <script src="scripts/cacatoo.js"></script>  <script src="scripts/all.js"></script>  </head> <body>  <header class="header" id="btnNav"><buton class="header__button" id="btnNav" type="button"><i class="material-icons">menu</i></buton></header> <nav class="nav"><div class="nav__links"> <a href="#" class="nav__head"><i id="btnNavclose" class="material-icons" style="cursor:pointer"> menu </i> Cacatoo </a> <a href="index.html" id="nav__link" class="nav__link">Home</a> <a href="https://github.com/bramvandijk88/cacatoo" id="nav__link" target="_blank" class="nav__link"> Source code (Github)</a>  <a href="#" class="nav__head"><i class="material-icons"> play_circle_outline </i> Examples</a> <a href="example_predator_prey.html" id="nav__link" class="nav__link"> Predator prey</a> <a href="example_colony_growth.html" id="nav__link" class="nav__link"> Colony growth</a> <a href="example_pheromones.html" id="nav__link" class="nav__link"> Ant pheromones</a> <a href="example_aapjes.html" id="nav__link" class="nav__link"> Aapjes (monkeys)</a> <a href="example_mutational_jackpot.html" id="nav__link" class="nav__link"> Mutational jackpot</a> <a href="example_starlings.html" id="nav__link" class="nav__link"> Starlings</a> <a href="example_cooperation.html" id="nav__link" class="nav__link"> Cooperation</a> <a href="example_TEs.html" id="nav__link" class="nav__link"> Transposon evolution</a> <a href="examples_jsfiddle.html" id="nav__link" class="nav__link"> More examples (JSFiddle)</a> <a href="#" class="nav__head"><i class="material-icons"> grid_on </i> How to Cacatoo </a> <a href="overview.html" class="nav__link"> Tutorials (Blog style)</a> <a href="list_of_options.html" class="nav__link"> All configuration options</a> <a href="populating_the_simulation.html" class="nav__link"> Populating a simulation</a> <a href="display_and_colours.html" class="nav__link"> Display, colours, and UI</a> <a href="neighbourhood_retrieval.html" class="nav__link"> Neighbourhood retrieval</a> <a href="random_numbers.html" class="nav__link"> Using random numbers </a> <a href="grid_events.html" class="nav__link"> Grid events</a> <a href="working_with_odes.html" class="nav__link"> Working with ODEs</a> <a href="jsdocs/index.html" id="nav__headlink" target="_blank" class="nav__headlink"><i class="material-icons">data_object </i> Full JS-Docs</a> </div><div class="nav__overlay"></div></nav> <script> document.addEventListener("DOMContentLoaded", () => { const nav = document.querySelector(".nav"); document.querySelector("#btnNav").addEventListener("click", () => { nav.classList.add("nav--open"); }); document.querySelector(".nav__overlay").addEventListener("click", () => { nav.classList.remove("nav--open"); }); document.querySelector("#btnNavclose").addEventListener("click", () => { nav.classList.remove("nav--open"); }); var all_links = document.getElementsByClassName("nav__link"); var hide_menu = function() { nav.classList.remove("nav--open"); }; for (var i = 0; i < all_links.length; i++) { all_links[i].addEventListener('click', hide_menu, false); } }); </script>  <div id="main"> <h1 class="page-title">Mixing events</h1> <section> <header> </header> <article> <div class="container-overview"> Grid events are functions that can be called before or after updating the grid points. For example, after individuals have reproduced, you may want to apply some random mixing by using the Toffoli-Margolus diffusion algorithm:<br><br> <h5 style="margin-left:40px;" class="name"><span class="type-signature"></span>this.MargolusDiffusion<span class="signature">()</span><span class="type-signature"></span></h5> <br> Other available "mixing" functions are:<br> <h5 style="margin-left:40px;" class="name"><span class="type-signature"></span>this.perfectMix<span class="signature">()</span><span class="type-signature"></span></h5> <h5 style="margin-left:40px;" class="name"><span class="type-signature"></span>this.diffuseStates<span class="signature">(state,rate)</span><span class="type-signature"></span></h5> <h5 style="margin-left:40px;" class="name"><span class="type-signature"></span>this.diffuseODEstates<span class="signature">() // Uses diffusion rates as defined in ODE system </span><span class="type-signature"></span></h5> </article> </section> <h1 class="page-title">Custom events</h1> <section> <header> </header> <article> <div class="container-overview"> <br>Or you can define your own functions, for example a bottleneck where a fraction of the population dies: <br><br> <ul><h5 class="name"><span class="signature"> sim.model.bottleneck = function(fraction){ <div style="margin-left:40px;"> for (let i = 0; i < this.nc; i++) { <div style="margin-left:40px;"> for (let j = 0; j < this.nr; j++) { <div style="margin-left:40px;"> if(this.rng.genrand_real1() < fraction){ <div style="margin-left:40px;"> this.grid[i][j].alive = 0</div> <div style="margin-left:40px;"> this.grid[i][j].helping_rate = 0</div> }</div> }</div> } </div> } </span></ul> Which you can then call to kill 95% of the population within the "update" loop, every 100 time steps: <ul><h5 class="name"><span class="signature"> sim.model.update = function() { <div style="margin-left:40px;"> sim.model.synchronous()<br> if(sim.time%100==0) sim.model.bottleneck(0.95)</div> } </span></ul> </article> </section> </div> <div id="Navigator"></div> <br class="clear"> <script> prettyPrint();</script> <script src="scripts/linenumber.js"> </script> </body> </html>