@fladdict さんの 「JSでアメーバのシミュレーション作ってみた (高速化編）」 http://fladdict.net/blog/2013/04/js-ameba-2.html のjavascriptソースコードをProcessing及びProcessing.jsで動くように修正してみた。動くように修正しただけなので、リファクタリングもかけてないですし、中のコメントも原則残したまんまです。 高速化前のソースhttps://gist.github.com/p5info/5343320

Ameba2.pde

import java.util.Date;
int numberOfNodes = 200;
Node[] nodes = new Node[numberOfNodes];

Edge[][] calcTable = new Edge[numberOfNodes][numberOfNodes];

class Edge{
  float distX;
  float distY;
  float distance;
  float angle;
}

void setup(){
  size(displayWidth, displayHeight); //Processing 2.x以降はdisplayWidth
  //size(screenWidth, screenHeight); //if Processing 1.5.1まではscreenWidth
  colorMode(RGB,255);
  noSmooth();
  strokeCap(SQUARE);
  background(0,0,0);
//@  //For FullScreen
//@  window.onresize = function()
//@  {
//@    size(window.innerWidth,window.innerHeight);
//@  };
  
  setup2();
}

void setup2(){
  //高速化テーブル  [NodeXId][NodeYId][dx,dy,dist];
  //あとで採用して最適化すること
  for(int yy=0; yy<numberOfNodes; yy++){
    for(int xx=0; xx<numberOfNodes; xx++){
      calcTable[yy][xx]=new Edge();
    }
  }
  
  for(int i=0; i<numberOfNodes; i++){
    Node nd = new Node();
    nd.index = i;
    nd.calcTable = calcTable;
    nd.x = (random(1f)*width-1)+1;
    nd.y = (random(1f)*height-1)+1;
    nd.maxVelocity=6;
    nd.friction = 0.9;
    nd.nodes = nodes;
    nd.nodeType = int(random(1f)*1.5 + random(1f)*1.2);
    nodes[i]= nd;;
  };
  
  
}

void draw(){
  background(0);
  
  //超高速化したので1回の描画に対して4回更新余裕っす
  int n = nodes.length;
  for(int h=0; h<4; h++){
    for(int i=0; i<n; i++)
    {
      for(int j=i+1; j<n; j++)
      {
        Node nd0 = nodes[i];
        Node nd1 = nodes[j];
        float dx = nd1.x - nd0.x;
        float dy = nd1.y - nd0.y;
        float dist = sqrt(dx*dx+dy*dy);
        calcTable[i][j].distX = dx;
        calcTable[i][j].distY = dy;
        calcTable[i][j].distance = dist;
        calcTable[i][j].angle = atan2(dy,dx);
        calcTable[j][i].distX = -dx;
        calcTable[j][i].distY = -dy;
        calcTable[j][i].distance = dist;
        calcTable[j][i].angle = atan2(-dy,-dx);
      }
    }
  
    for(int i=0; i<n; i++){
      Node nd = nodes[i];
      nd.resetForce();
      nd.update();
    
    };
  }
  
  /*
  
  //距離その他、必要な計算をあらかじめ一括で行う
  var n = nodes.length;
  for(var i=0; i<n; i++)
  {
    for(var j=i+1; j<n; j++)
    {
      var nd0 = nodes[i];
      var nd1 = nodes[j];
      var dx = nd1.x - nd0.x;
      var dy = nd1.y - nd0.y;
      var dist = sqrt(dx*dx+dy*dy);
      calcTable[i][j][0] = dx;
      calcTable[i][j][1] = dy;
      calcTable[i][j][2] = dist;
      calcTable[i][j][3] = atan2(dy,dx);
      calcTable[j][i][0] = -dx;
      calcTable[j][i][1] = -dy;
      calcTable[j][i][2] = dist;
      calcTable[j][i][3] = atan2(-dy,-dx);
    }
  }
  
  
  
  for(var i=0; i<n; i++){
    var nd = nodes[i];
    //超高速化したので1回の描画に対して3回更新しちゃおう
    for(var j=0; j<3; j++){
      nd.resetForce();
      nd.update();
    }
  };*/
  
  Date startDate = new Date();
  //noStroke();
  for(int i=0; i<n; i++)
  {
    for(int j=i; j<n-1; j++)
    {
      
      Node nd0 = nodes[i];
      Node nd1 = nodes[j];
      Edge table = calcTable[i][j];
      float dx = table.distX;
      float dy = table.distY;
      float dist = table.distance;
      /*
      var rad = atan2(dy,dx);
      if(nd0.nodeType==nd1.nodeType && dist<150  && dist>2){
        var strokeCol = (150-dist)*1.5;
        fill(strokeCol, strokeCol,0);
        pushMatrix();
        translate(nd0.x, nd0.y);
        rotate(rad);
        scale(dist,1);
        
        rect(0,0,1,1);
        //line(nd0.x, nd0.y, nd1.x, nd1.y);
        popMatrix();

      }*/
      
      if(nd0.nodeType==nd1.nodeType && dist<150  && dist>10){
        
      
        float strokeCol = (150-dist)*1.5;
        stroke(strokeCol, strokeCol,0);
        line(nd0.x, nd0.y, nd1.x, nd1.y);
      }
      
    }
  }
  
  
  
  for(int i=0; i<n; i++){
    Node nd = nodes[i];
    //nd.draw();
  };
  
  Date endDate = new Date();
  println(endDate.getTime()-startDate.getTime());
}



class Node{
  int index = 0;
  float x =0;
  float y = 0;
  float vx = 0;
  float vy = 0;
  int maxVelocity = 2;
  float fx = 0;
  float fy = 0;
  int nodeType;
  float rotation = 0;
  Node[] nodes;
  float friction = 0.9;
  Edge[][] calcTable;
  void init()
  {
  }

  void update()
  {
    this.updateBoid();
    this.updateVelocity();
    this.updatePosition();
  }

  void resetForce()
  {
    this.fx = 0;
    this.fy = 0;
  }


  //ここでBoid計算
  void updateBoid()
  {
    int n = this.nodes.length;
    
    //Calc Position
    float fx = 0;
    float fy = 0;
    
    //仲間に近づく / 離れる
    for(int i=0; i<n; i++){
      Node nd = this.nodes[i];
      if(nd==this)
        continue;
      
      Edge table = this.calcTable[this.index][nd.index];
      float dx = table.distX;
      float dy = table.distY;
      float dist = table.distance;
      float rad = table.angle;
      float dist2 = dist*dist;
      
      
      //近づきすぎたら離れ、離れすぎたら近づく
      if(dist<50 && dist>1){
        float dist3 = dist*dist*dist;
        fx -= dx / dist3 * 40;
        fy -= dy / dist3 * 40;
      }else if(dist<200 && this.nodeType==nd.nodeType){
        float dist3 = dist*dist*dist;
        fx += dx / dist3 * 30;
        fy += dy / dist3 * 30;
      }
      
      //仲間と同じ方向に自走する
      if(dist>1){
        float rad2 = atan2(nd.vy,nd.vx);  //ここはテーブル化しちゃダメ！！（理由は考えよう！）
        fx += cos(rad2) /dist2;
        fy += sin(rad2) /dist2;
      }
    }
    
    //マウスから逃げる
    float mfx = mouseX - this.x;
    float mfy = mouseY - this.y;
    float mdistsq = mfx*mfx+mfy*mfy;
    float mrad = atan2(mfy,mfx);
    //console.log(mdist);
    if(mdistsq>1){
      fx -= cos(mrad)/mdistsq*300;
      fy -= sin(mrad)/mdistsq*300;
    }
    
  //@  //Normalize Speed
  //@  var d = dist(fx,fy);
  //@  if(d>1){
  //@    fx = fx / dist;
  //@    fy = fy / dist;
  //@  }
    
    //ブラウン運動
    this.fx += (random(1f)-0.5)*0.2;
    this.fy += (random(1f)-0.5)*0.2;
    
    this.fx += fx * 3;
    this.fy += fy * 3;
  }

  void updateVelocity()
  {
    this.vx = this.vx * this.friction + this.fx;
    this.vy = this.vy * this.friction + this.fy;
    float v = sqrt(this.vx*this.vx+this.vy*this.vy);
    
    if(v>this.maxVelocity){
      this.vx = this.vx / v * this.maxVelocity;
      this.vy = this.vy / v * this.maxVelocity;
    }
  }

  void updatePosition()
  {
    this.x += this.vx;
    this.y += this.vy;
    
    if(this.x<0){
      this.x =0;
      this.vx = abs(this.vx);
      this.fx = 0;
    }else if(this.x>width){
      this.x=width;
      this.vx = -abs(this.vx);
      this.fx = 0;
    }
    
    if(this.y<0){
      this.y=0;
      this.vy = abs(this.vy);
      this.fy = 0;
    }else if(this.y>height){
      this.y=height;
      this.vy = -abs(this.vy);
      this.fy = 0;
    }
  }

  void draw()
  {
    stroke(150,150,0);
    fill(0);
    ellipse(this.x, this.y, 10,10);
  }
}