/* explosion - molecular dynamics quasi-1D(3D) */
/* coded by Ikeuchi Mitsuru    */
/* ver 0.0.1   2005.11.05      */

import java.awt.*;
import java.awt.event.*;
import java.applet.*;

public class explosionMDQ1D extends Applet
  implements MouseListener, MouseMotionListener,
    ItemListener, ActionListener, AdjustmentListener, Runnable {

/*-------------------------------------- define gloval -----*/

  Choice ch_mat,ch_tempControl,ch_view;
  Button bt_reset, bt_startStop, bt_gogogo;
  Scrollbar sc_temp,sc_scale;
  Thread th = null;

  Dimension dim;
  Image imgOff;
  Graphics gOff;

  int sleepTime = 50;

  double t = 0.0;			    /* time (s)               */
  double dt = 5.0*1.0e-15;  /* time division (s)      */

  int Nsx = 200;
  int Nsy = 5;
  int Nsz = 5;

  double xMax = Nsx*1.0e-9; /* x-Box size in (m)      */
  double yMax = Nsy*1.0e-9; /* y-Box size in (m)      */
  double zMax = Nsz*1.0e-9; /* z-Box size in (m)      */

  double zDepth = 100.0*1.0e-9;
  int Nmt = 200*5*5;        /* number of molecules    */
  int NN = Nmt + 1;


  double dispWidth = 500.0;
  double dispScale = (dispWidth/xMax);
  double viewScale = 1.0;

  int resetSW = 0;
  int started = 1;
  int dispMode = 10;
  int tempMode = 0;
  double contTemp = 300.0;


  int dgX, dgY, dgXb,dgYb;
  double cx = 0.5*xMax;
  double cy = 0.5*yMax;
  double cz = 0.5*zMax;
  double theta = -20.0*3.14/180.0;
  double fai = -60.0*3.14/180.0;
  double dtheta = 0.0*3.14/180.0;
  double pai = 3.1415926536;

  double rc = 1.0e-9;
  double rc2 = rc*rc;

  double AU = 1.661e-27;
  double EE = 1.602e-19;
  double AA = 1.0e-10;
  double Morse[][] = {
  /*         0:mass		1:charge  2:D(eV)   3:A(A^-1)  4:r0(A)  5:color */
  /* 0 W */ {183.85 *AU, 0.0*EE, 0.9906*EE, 1.4116/AA, 3.032*AA, 0.30 },
  /* 1 Mo*/ { 95.94 *AU, 0.0*EE, 0.8032*EE, 1.5079/AA, 2.976*AA, 0.33 },
  /* 2 Cr*/ { 51.996*AU, 0.0*EE, 0.4414*EE, 1.5721/AA, 2.754*AA, 0.36 },
  /* 3 Fe*/ { 55.847*AU, 0.0*EE, 0.4174*EE, 1.3885/AA, 2.845*AA, 0.39 },
  /* 4 Ni*/ { 58.71 *AU, 0.0*EE, 0.4205*EE, 1.4199/AA, 2.780*AA, 0.42 },
  /* 5 Al*/ { 26.98 *AU, 0.0*EE, 0.2703*EE, 1.1646/AA, 3.253*AA, 0.45 },
  /* 6 Pb*/ {207.19 *AU, 0.0*EE, 0.2348*EE, 1.1836/AA, 3.733*AA, 0.48 },
  /* 7 Cu*/ { 63.54 *AU, 0.0*EE, 0.3429*EE, 1.3588/AA, 2.866*AA, 0.20 },
  /* 8 Ag*/ {107.87 *AU, 0.0*EE, 0.3323*EE, 1.3690/AA, 3.115*AA, 0.24 },
  /* 9 Ca*/ { 40.08 *AU, 0.0*EE, 0.1623*EE, 0.8054/AA, 4.569*AA, 0.13 },
  /*10 Sr*/ { 87.62 *AU, 0.0*EE, 0.1513*EE, 0.7878/AA, 4.988*AA, 0.16 },
  /*11 Ba*/ {137.34 *AU, 0.0*EE, 0.1416*EE, 0.6570/AA, 5.373*AA, 0.19 },
  /*12 Na*/ { 22.99 *AU, 0.0*EE, 0.0633*EE, 0.5900/AA, 5.336*AA, 0.01 },
  /*13 K */ { 39.102*AU, 0.0*EE, 0.0542*EE, 0.4977/AA, 6.369*AA, 0.04 },
  /*14 Rb*/ { 85.47 *AU, 0.0*EE, 0.0464*EE, 0.4298/AA, 7.207*AA, 0.07 },
  /*15 Cs*/ {132.905*AU, 0.0*EE, 0.0449*EE, 0.4157/AA, 7.557*AA, 0.10 },
  /*16 Ne*/ { 20.183*AU, 0.0*EE, 0.0031*EE, 1.6500/AA, 3.076*AA, 0.56 },
  /*17 Ar*/ { 39.948*AU, 0.0*EE, 0.0104*EE, 1.3400/AA, 3.816*AA, 0.60 },
  /*18 Kr*/ { 83.80 *AU, 0.0*EE, 0.0141*EE, 1.2500/AA, 4.097*AA, 0.64 },
  /*19 Xe*/ {131.30 *AU, 0.0*EE, 0.0200*EE, 1.2400/AA, 4.467*AA, 0.68 },
  /*20 Hg*/ {200.59 *AU, 0.0*EE, 0.0734*EE, 1.4900/AA, 3.255*AA, 0.72 }
  };

  String material[] = {
    "W" ,"Mo","Cr","Fe","Ni","Al","Pb","Cu","Ag","Ca",
    "Sr","Ba","Na","K" ,"Rb","Cs","Ne","Ar","Kr","Xe","Hg"
  };
  int NmatKind = 21;

  int MAT1 = 17;
  
  int kind[] = new int[NN];       /* i-th molec kind */
  double xx[] = new double[NN];   /* i-th x-position */
  double yy[] = new double[NN];   /* i-th y-position */
  double zz[] = new double[NN];   /* i-th z-position */
  double vx[] = new double[NN];   /* i-th x-velocity */
  double vy[] = new double[NN];   /* i-th y-velocity */
  double vz[] = new double[NN];   /* i-th z-velocity */
  double ffx[] = new double[NN];  /* i-th x-force    */
  double ffy[] = new double[NN];  /* i-th y-force    */
  double ffz[] = new double[NN];  /* i-th z-force    */

  int reg[][] = new int[NN][250];   /* registration */
  int section[][][][] = new int[Nsx][Nsy][Nsz][100];

  int srtz[][] = new int[2][NN];   /* z-sort work space */

  double forceTable[][][] = new double[NmatKind][NmatKind][1020];
  double dispColor[] = new double[NmatKind];

  double hh = 1.0e-12;

  double px[] = new double[NN]; 
  double py[] = new double[NN]; 
  double pz[] = new double[NN]; 

  double wkx[] = new double[8]; 
  double wky[] = new double[8]; 
  double wkz[] = new double[8]; 

  double pwkx[] = new double[8]; 
  double pwky[] = new double[8]; 
  double pwkz[] = new double[8]; 

  int boxp[][] = {
   {0,1},{0,2},{0,4},{1,3},{1,5},{2,3},{2,6},{4,5},{4,6},{3,7},{5,7},{6,7}
  };

  int rdf[] = new int[120];
  int vdf[] = new int[220];

  double virial[][] = new double[3][256];
  double memTemp[] = new double[256];
  int virialp = 0;

  int xpts[] = new int[200];
  int ypts[] = new int[200];
  double cpts[] = new double[200];

/*----------------------------- applet control functions -----*/

  public void init() {
    resize(630,400);
    setBackground(Color.white);

    dim = getSize();
    imgOff = createImage(dim.width,dim.height);
    gOff = imgOff.getGraphics();

    ch_mat = new Choice();
    ch_mat.addItem("W");  ch_mat.addItem("Mo"); ch_mat.addItem("Cr");
    ch_mat.addItem("Fe"); ch_mat.addItem("Ni"); ch_mat.addItem("Al");
    ch_mat.addItem("Pb"); ch_mat.addItem("Cu"); ch_mat.addItem("Ag"); 
    ch_mat.addItem("Ca"); ch_mat.addItem("Sr"); ch_mat.addItem("Ba");
    ch_mat.addItem("Na"); ch_mat.addItem("K");  ch_mat.addItem("Rb");
    ch_mat.addItem("Cs"); ch_mat.addItem("Ne"); ch_mat.addItem("Ar");
    ch_mat.addItem("Kr"); ch_mat.addItem("Xe"); ch_mat.addItem("Hg");
    ch_mat.addItemListener(this);
    ch_mat.select("Ar");

    ch_tempControl = new Choice();
    ch_tempControl.addItem("adiabatic");
    ch_tempControl.addItem("t scaling"); 
    ch_tempControl.addItem("wall cont.");
    ch_tempControl.addItemListener(this);
    ch_tempControl.select("adiabatic"); 

    ch_view = new Choice();
    ch_view.addItem("ball");
    ch_view.addItem("bond"); 
    ch_view.addItem("ball+bond");
    ch_view.addItem("real size");
    ch_view.addItem("temperature");
    ch_view.addItem("velocity");
    ch_view.addItem("momentum");
    ch_view.addItem("bond+rdf");
    ch_view.addItem("v+vdf");
    ch_view.addItem("1d mean n");
    ch_view.addItem("1d mean T");
    ch_view.addItem("1d coarse n");
    ch_view.addItem("1d coarse T");
    ch_view.addItemListener(this);
    ch_view.select("1d mean T");

    bt_reset= new Button("reset");
    bt_reset.addActionListener(this);

    bt_startStop= new Button("start/stop");
    bt_startStop.addActionListener(this); 

    bt_gogogo= new Button("go");
    bt_gogogo.addActionListener(this); 

    sc_temp= new Scrollbar(Scrollbar.HORIZONTAL,30,10,1,210);
    sc_temp.addAdjustmentListener(this);

    sc_scale= new Scrollbar(Scrollbar.HORIZONTAL,100,10,50,510);
    sc_scale.addAdjustmentListener(this);

    addMouseListener(this);  
    addMouseMotionListener(this);

    setLayout(new BorderLayout());
    Panel pnl = new Panel();
    pnl.setLayout(new GridLayout(1,6,5,0));
	/* pnl.add(new Label("  ")); */
    pnl.add(ch_mat);
    pnl.add(bt_gogogo);
    pnl.add(ch_tempControl);
    pnl.add(sc_temp);
    pnl.add(sc_scale);
    pnl.add(ch_view);
    add(pnl,"North");

    setInitialCondition();
  }

  public void start() {
    if (th == null) {
      th = new Thread(this);
      th.start();
    }
  }

  public void stop() {
    if (th != null) {
      th.stop();
      th = null;
    }
  }

  public void itemStateChanged(ItemEvent ev){
    if (ev.getSource() == ch_mat){
      MAT1 = ch_mat.getSelectedIndex();
	  resetSW = 1;
    } else if (ev.getSource() == ch_tempControl) {
      tempMode = ch_tempControl.getSelectedIndex();
    } else if (ev.getSource() == ch_view){
      dispMode = ch_view.getSelectedIndex();
    }
  }

  public void actionPerformed(ActionEvent ev){
    if(ev.getSource() == bt_reset){ 
      resetSW = 1;
    } else if (ev.getSource() == bt_startStop){
      if (started==0) {
        started = 1;
      } else {
        started = 0;
      }
    } else if (ev.getSource() == bt_gogogo){
      gogogo(xMax/5.0, xMax/8.0, 3000.0);
    }
  }

  public void adjustmentValueChanged(AdjustmentEvent ev){
    if (ev.getSource() == sc_temp) { 
      contTemp = 10.0*(double)(sc_temp.getValue());
      vAjustment();
    } else if(ev.getSource() == sc_scale) { 
      viewScale = 0.01*(double)(sc_scale.getValue());
    }
  }

  public void mousePressed(MouseEvent ev){ }
  public void mouseReleased(MouseEvent ev){
    dgXb = 0; dgYb = 0;
    dgX = 0; dgY = 0;
  }
  public void mouseClicked(MouseEvent ev){ }
  public void mouseEntered(MouseEvent ev){ } 
  public void mouseExited (MouseEvent ev){ }

  public void mouseMoved  (MouseEvent ev){ }

  public void mouseDragged(MouseEvent ev){
    dgXb = dgX; dgYb = dgY;
    dgX=ev.getX();
    dgY=ev.getY();
    if (dgXb==0 && dgYb==0) {
      dgXb = dgX; dgYb = dgY;
    }
    theta += 0.5*3.14/180.0*(dgX-dgXb);
    fai += 0.5*3.14/180.0*(dgY-dgYb);
  }

  public void run() {
    while (th != null) {
      try {
        timeEvolution();
        offPaint();
        repaint();
        Thread.sleep(sleepTime);
      } catch (InterruptedException e) { }
    }
  }

  public void update(Graphics g) {
    paint(g);
  }

  public void paint(Graphics g) {
    g.drawImage(imgOff,0,0,this);
  }


/* ----------------------------- offPaint -------------------- */

  void offPaint() {
    int gbx,gby;
    double tmp;

    gOff.setColor(Color.white);
    gOff.fillRect(0,0,dim.width,dim.height);

    rotate(theta,fai);
    zSort();
    tmp = temperature();
    gbx = 20;
    gby = 100;

    if (dispMode==0) {
      ballPlot(gbx,gby, 0.6, 0);

    } else if (dispMode==1) {
      ballPlot(gbx,gby, 0.5, 1);

    } else if (dispMode==2) {
      ballPlot(gbx,gby, 0.5, 2);

    } else if (dispMode==3) {
      ballPlot(gbx,gby, 1.0, 0);

    } else if (dispMode==4) {
      ballPlot(gbx,gby, 0.6, 3);

    } else if (dispMode==5) {
      velocity3DPlot(gbx,gby, 10.0,0);

    } else if (dispMode==6) {
      velocity3DPlot(gbx,gby, 10.0,1);

    } else if (dispMode==7) {
	  ballPlot(gbx,gby, 0.5, 1);
      rdfPlot(400,140, 0.2);

    } else if (dispMode==8) {
	  velocity3DPlot(gbx,gby, 10.0,0);
      vdfPlot(400,140, 2.0,MAT1);

    } else if (dispMode==9) {
	  ballPlot(gbx,gby, 0.6, 0);
      meanPlot1D(gbx,gby+220, 1, 1000*1.0e-28, 0);

    } else if (dispMode==10) {
	  ballPlot(gbx,gby, 0.6, 3);
      meanPlot1D(gbx,gby+220, 1, 100/2000.0, 1);

    } else if (dispMode==11) {
	  ballPlot(gbx,gby, 0.6, 0);
      meanPlot1D(gbx,gby+220, 4, 1000*1.0e-28, 0);

    } else if (dispMode==12) {
	  ballPlot(gbx,gby, 0.6, 3);
      meanPlot1D(gbx,gby+220, 4, 100/2000.0, 1);

    } else if (dispMode==13) {
	  ;

    }


    gbx = dim.width/6;
    gOff.setColor(Color.black);
    gOff.drawString("t="+(int)(t*1.0e13+0.5)/10.0+" ps",gbx*0+10,40);

    gOff.drawString("temp control",gbx*2+10,40);
    gOff.drawString("cont T="+contTemp+"K",gbx*3+10,40);
    gOff.drawString("scale="+(int)(viewScale*100.0+0.499)+"%",gbx*4+10,40);
    gOff.drawString("view",gbx*5+10,40);

    gOff.setColor(Color.blue);
    gOff.drawString("T="+(int)(tmp*10+0.5)/10.0+" K",gbx*3+10,60);
    gOff.drawString("L="+(int)(xMax*1.0e10+0.5)/10.0+" nm",gbx*4+10,60);
    gOff.drawString("P="+(int)(pressure()/1.0e4+0.5)/100.0+"MPa",gbx*5+0,60);
    gOff.drawString("<P>="+(int)(meanPressure()/1.0e4+0.5)/100.0+"MPa",gbx*5+0,80);
    gOff.drawString("nkT="+(int)((Nmt/(xMax*yMax*zMax)*1.38e-23*tmp)/1.0e4+0.5)/100.0+"MPa",gbx*4+0,80);

    gOff.setColor(Color.black);
    gOff.drawString("regMax="+regMax()+"",gbx*5+10,100);
    gOff.drawString("secMax="+secMax()+"",gbx*5+10,120);

  }

/*-------------------------------  plot methods  ----------*/

  void ballPlot(int gbx, int gby, double size, int imode) {
    int i,j,k,jj,gx,gy,g2x,g2y,gr;
	double sz,scl,tm;

    drawWaku(gbx,gby,0);

	scl = dispScale*viewScale;
    sz = size*viewScale/AA;
    for (i=0; i<Nmt; i++) {
      j = srtz[0][i];
      gx = (int)(scl*px[j])+gbx;
      gy = (int)(scl*py[j])+gby;
      gr = (int)(sz*Morse[kind[j]][4]*(0.2*(pz[j]/zDepth)+0.6));
	  if (gr<2) gr = 2;
	  if (imode==1 || imode==2) {
        for (k=1; k<reg[j][0]; k++) {
          jj = reg[j][k];
          if ( distance(j,jj)<0.6*(Morse[kind[j]][4]+Morse[kind[jj]][4]) ) {
            g2x = (int)(scl*px[jj])+gbx;
            g2y = (int)(scl*py[jj])+gby;
            gOff.setColor(Color.gray);
            gOff.drawLine(gx,gy, g2x, g2y);
          }
        }
	  }
	  if (imode==0 || imode==2) {
        gOff.setColor(Color.getHSBColor(
          (float)Morse[kind[j]][5],0.8f,(float)(0.2*pz[j]/zDepth+0.5)));
        gOff.fillOval(gx-gr/2,gy-gr/2, gr, gr);
      }
      if (imode==3) {
	    tm = Morse[kind[j]][0]*(vx[j]*vx[j]+vy[j]*vy[j]+vz[j]*vz[j])/(3.0*1.38e-23)/2000.0;
		if (tm>0.99) tm = 0.99;
        gOff.setColor(Color.getHSBColor(
          (float)Morse[kind[j]][5],0.8f,(float)(0.8*tm+0.2)));
        gOff.fillOval(gx-gr/2,gy-gr/2, gr, gr);
      }
	}
	drawWaku(gbx,gby,1);
  }

  double distance(int j, int jj) {
    double r2;

    r2 = (xx[j]-xx[jj])*(xx[j]-xx[jj])+(yy[j]-yy[jj])*(yy[j]-yy[jj])+(zz[j]-zz[jj])*(zz[j]-zz[jj]);
    return ( Math.sqrt(r2) );
  }


  void velocity3DPlot(int gbx, int gby, double mag, int imode) {
    int i,j,gx,gy,g2x,g2y;
    double sc,m,p2x,p2y,p2z,rotp2x,rotp2y,rotp2z;
    double cosTh,sinTh,cosFi,sinFi;

    cosTh = Math.cos(theta); sinTh = Math.sin(theta);
    cosFi = Math.cos(fai); sinFi = Math.sin(fai);

    drawWaku(gbx,gby,0);

    sc = dispScale*viewScale;

    for (i=0; i<Nmt; i++) {
      j = srtz[0][i];
      gx = (int)(sc*px[j])+gbx;
      gy = (int)(sc*py[j])+gby;

      if (imode==0) {
        p2x = xx[j]+mag*vx[j]*20*dt;
        p2y = yy[j]+mag*vy[j]*20*dt;
        p2z = zz[j]+mag*vz[j]*20*dt;
      } else {
	    m = mag*20*dt*0.01*Morse[kind[j]][0]/AU;
        p2x = xx[j]+m*vx[j];
        p2y = yy[j]+m*vy[j];
        p2z = zz[j]+m*vz[j];
	  }
      rotp2y = cosFi*(p2y-cy)+sinFi*(p2z-cz) + cy; 
      rotp2z = -sinFi*(p2y-cy)+cosFi*(p2z-cz) + cz;
      rotp2x = cosTh*(p2x-cx)+sinTh*(rotp2z-cz) + cx; 
      rotp2z = -sinTh*(p2x-cx)+cosTh*(rotp2z-cz) + cz;

      g2x = (int)(sc*rotp2x)+gbx;
      g2y = (int)(sc*rotp2y)+gby;
      gOff.setColor(Color.getHSBColor(
        (float)Morse[kind[j]][5],0.8f,(float)(0.2*pz[j]/zDepth+0.5)));
      gOff.drawLine(gx,gy, g2x,g2y);
    }
    drawWaku(gbx,gby,1);
  }


  void drawWaku(int gbx, int gby, int imode) {
    int i,gx,gy,g2x,g2y,farPoint;
    double sc,tmp;

	sc = dispScale*viewScale;
    farPoint = findMin();

    for (i=0; i<12; i++) {
      gx = (int)(sc*pwkx[boxp[i][0]])+gbx;
      gy = (int)(sc*pwky[boxp[i][0]])+gby;
      g2x = (int)(sc*pwkx[boxp[i][1]])+gbx;
      g2y = (int)(sc*pwky[boxp[i][1]])+gby;
	  if (imode==0) {
        if (boxp[i][0]==farPoint || boxp[i][1]==farPoint) { 
          gOff.setColor(Color.lightGray);
          gOff.drawLine(gx,gy, g2x, g2y);
        }
	  } else if (imode==1) {
        if (boxp[i][0]!=farPoint && boxp[i][1]!=farPoint) { 
          gOff.setColor(Color.gray);
          if (tempMode==2) {
		    tmp = temperature();
            if (tmp>contTemp) {
              gOff.setColor(Color.black); 
            } else {
              gOff.setColor(Color.red);
            }
          }
          gOff.drawLine(gx,gy, g2x, g2y);
		}
	  }
    }
  }

  int findMin() {
    int i,im;
    double m;

    im = 0; m = pwkz[im];
    for (i=0; i<8; i++) {
      if (pwkz[i]<m) {
        m = pwkz[i];
        im = i;
      }
    }
    return(im);
  }

/*-----  setWaku  -----*/

  void setWaku() {
    int i,ix,iy,iz;
    double sgm;

    sgm = 4.0e-10;
    i=0;
    for (ix=0; ix<2; ix++) {
      for (iy=0; iy<2; iy++) {
        for (iz=0; iz<2; iz++) {
          wkx[i] = -0.5*sgm+(xMax+sgm)*(double)(ix);
          wky[i] = -0.5*sgm+(yMax+sgm)*(double)(iy);
          wkz[i] = -0.5*sgm+(zMax+sgm)*(double)(iz);
          i += 1;
        }
      }
    }
  }

/*-------------------------------------  sort z  ----------*/

  void zSort() {
    int i,j,w;

    for (i=0; i<Nmt; i++) {
      j = srtz[0][i];
      srtz[1][i] = (int)(32767.0*pz[j]/zMax);
    } 
    for (i=0; i<100; i++) {
      for (j=0; j<Nmt-1; j++) {
        if (srtz[1][j]>srtz[1][j+1]) {
          w = srtz[0][j]; srtz[0][j]=srtz[0][j+1]; srtz[0][j+1]=w;
          w = srtz[1][j]; srtz[1][j]=srtz[1][j+1]; srtz[1][j+1]=w;
        }
      }
    }    
  }

  void zSortInit() {
    int i,j,w;

    for (i=0; i<Nmt; i++) {
      srtz[0][i] = i;
      srtz[1][i] = (int)(32767.0*pz[i]/zMax);
    } 
    for (i=0; i<Nmt; i++) {
      for (j=0; j<Nmt-1; j++) {
        if (srtz[1][j]>srtz[1][j+1]) {
          w = srtz[0][j]; srtz[0][j]=srtz[0][j+1]; srtz[0][j+1]=w;
          w = srtz[1][j]; srtz[1][j]=srtz[1][j+1]; srtz[1][j+1]=w;
        }
      }
    }    
  }

/*-------------------------------------  rotate  ----------*/

  void rotate(double th,double fi) {
    int i;
    double cosTh,sinTh,cosFi,sinFi;

    cosTh = Math.cos(theta); sinTh = Math.sin(theta);
    cosFi = Math.cos(fai); sinFi = Math.sin(fai);

    for (i=0; i<Nmt; i++) {
      py[i] = cosFi*(yy[i]-cy)+sinFi*(zz[i]-cz) + cy; 
      pz[i] = -sinFi*(yy[i]-cy)+cosFi*(zz[i]-cz) + cz;
    } 
    for (i=0; i<Nmt; i++) {
      px[i] = cosTh*(xx[i]-cx)+sinTh*(pz[i]-cz) + cx; 
      pz[i] = -sinTh*(xx[i]-cx)+cosTh*(pz[i]-cz) + cz;
    } 

    for (i=0; i<8; i++) {
      pwky[i] = cosFi*(wky[i]-cy)+sinFi*(wkz[i]-cz) + cy; 
      pwkz[i] = -sinFi*(wky[i]-cy)+cosFi*(wkz[i]-cz) + cz;
    } 
    for (i=0; i<8; i++) {
      pwkx[i] = cosTh*(wkx[i]-cx)+sinTh*(pwkz[i]-cz) + cx; 
      pwkz[i] = -sinTh*(wkx[i]-cx)+cosTh*(pwkz[i]-cz) + cz;
    }  
  }


/*-------------------- radial distribution set / plot  ----------*/

  void rdfPlot(int gx, int gy, double mag) {
    int i,iy,hoganWidth,hoganHight,xDiv,yDiv;

    setRadialDistribution();

    hoganWidth = 200; hoganHight = 200;
	xDiv = hoganWidth/5; yDiv = hoganHight/2;

    gOff.setColor(Color.cyan);
    for (i=0; i<100; i++) {
      iy = (int)(mag*rdf[i]);
	  if (iy>0) {
	    gOff.fillRect(gx+i*2,gy+hoganHight-iy,2,iy);
      }
    }

    drawHogan(gx, gy, hoganWidth, hoganHight, xDiv, yDiv);
    gOff.setColor(Color.black);
    gOff.drawString("0",gx-5,gy+hoganHight+20);
    gOff.drawString("1 (nm)",gx+hoganWidth-20,gy+hoganHight+20);
    gOff.drawString("radial distribution",gx+40,gy+hoganHight+40);
  }

  void drawHogan(int gx, int gy, int hoganWidth, int hoganHight, int xDiv, int yDiv) {
    int i;

    gOff.setColor(Color.gray);
    for (i=0; i<hoganWidth; i+=xDiv) {
      gOff.drawLine(gx+i,gy, gx+i, gy+hoganHight);
    }
    for (i=0; i<hoganHight; i+=yDiv) {
      gOff.drawLine(gx,gy+hoganHight-i, gx+hoganWidth, gy+hoganHight-i);
    }
    gOff.setColor(Color.black);
    gOff.drawRect(gx,gy,hoganWidth,hoganHight);
  }

  void setRadialDistribution() {
    int i,j,k,ir;
    double xi,xj,yi,yj,zi,zj;
    double r2,rij;

    for (i=0; i<120; i++) {
      rdf[i]=0;
    }

    for (i=0; i<Nmt; i++) {
      for(k=1;k<reg[i][0];k++) {
        j = reg[i][k];
        xi = xx[i]; xj = xx[j]; yi = yy[i]; yj = yy[j]; zi = zz[i]; zj = zz[j];
        if (yi-yj>0.5*yMax) { yj += yMax; };
        if (yi-yj<-0.5*yMax) { yj -= yMax; }; 
		if (zi-zj>0.5*zMax) { zj += zMax; };
        if (zi-zj<-0.5*zMax) { zj -= zMax; }; 
        r2 = (xi-xj)*(xi-xj)+(yi-yj)*(yi-yj)+(zi-zj)*(zi-zj);
        rij = Math.sqrt(r2);
        if (rij<10.0e-10) {
          ir = (int)(rij*1.0e11+0.49999);
          rdf[ir] +=1;
        }
      }
    }
  }

/*-------------------- verocity distribution set / plot  ----------*/

  void vdfPlot(int gx, int gy, double mag, int knd) {
    int hoganWidth,hoganHight,xDiv,yDiv;

    hoganWidth = 200; hoganHight = 200;
	xDiv = hoganWidth/4; yDiv = hoganHight/2;

    kindPlot(gx,gy+hoganHight, mag, -1);
    kindPlot(gx,gy+hoganHight, mag, knd);
    drawHogan(gx, gy, hoganWidth, hoganHight, xDiv, yDiv);

    gOff.setColor(Color.black);
    gOff.drawString("0",gx-5,gy+hoganHight+20);
    gOff.drawString("2000 m/s",gx+hoganWidth-30,gy+hoganHight+20);
    gOff.drawString("velocity distribution",gx+30,gy+hoganHight+40);
  }

  void kindPlot(int gx, int ghy, double mag, int knd) {
    int i,iy; 

    setVelocityDistribution(knd);

    gOff.setColor(Color.lightGray);
	if (knd>=0) {
      gOff.setColor(Color.getHSBColor((float)Morse[knd][5],0.8f,0.8f));
	}
    for (i=0; i<200; i++) {
      iy = (int)(mag*vdf[i]);
	  if (iy>0) {
	    gOff.drawLine(gx+i,ghy-iy,gx+i,ghy);
      }
    }
  }

  void setVelocityDistribution(int knd) {
    int i,iv;
    double v2,vv;

    for (i=0; i<220; i++) {
      vdf[i]=0;
    }

    for (i=0; i<Nmt; i++) {
      v2 = vx[i]*vx[i]+vy[i]*vy[i]+vz[i]*vz[i];
	  vv = Math.sqrt(v2);
        if (vv<2000.0) {
          iv = (int)(vv*0.1);
		  if (kind[i]==knd || knd==-1) {
            vdf[iv] +=1;
		  }
        }

    }
  }

/* -------------------------- grid plot 1D -------------- */

  void meanPlot1D(int gbx, int gby, int idiv, double weight, int imode) {
    int i,gx,gy,gdx;
    double sc,f;

    gdx = (int)(viewScale/Nsx*dispWidth*idiv);
	gOff.setColor(Color.getHSBColor(0.33f,0.9f,0.9f));

    for (i=0; i<=Nsx-idiv-idiv; i+=idiv) { 
	  f = weight*field1d(imode,i,idiv);
	  gx = (int)(viewScale*(i+idiv/2.0)/Nsx*dispWidth);
	  gy = (int)(viewScale*f);
      gOff.drawRect(gbx+gx,gby-gy,gdx,gy);
    }
  }


  double field1d(int imode, int ii, int idiv) {
    int i,j,k,ip,kp,n;
    double s;

    n = 0; s = 0.0;
    for(i=ii; i<ii+idiv; i++) {
      for (j=0; j<Nsy; j++) {
        for (k=0; k<Nsz; k++) {
		  n += section[i][j][k][0];
		  if (imode==1) {
            for (ip=1; ip<=section[i][j][k][0]; ip++) {
		      kp = section[i][j][k][ip];
			  s += Morse[kind[kp]][0]*(vx[kp]*vx[kp]+vy[kp]*vy[kp]+vz[kp]*vz[kp]);
			}
		  }
        }
      }
    }
	if (n==0) return ( 0.0 );
	if (imode==0) return( n/((xMax/Nsx*idiv)*yMax*zMax) );
	if (imode==1) return( s/n/(3.0*1.38e-23) );
    return( 0.0 );
  }

/*-------------------------------------  statictics  ----------------*/

  double temperature() {
    int i;
    double s;

    s = 0.0; 
    for (i=0; i<Nmt; i++) {
      s += 0.5*(Morse[kind[i]][0])*(vx[i]*vx[i] + vy[i]*vy[i] + vz[i]*vz[i]);
    }
    return ((double)Math.floor(s/((double)Nmt*1.5*1.38e-23)*100.0)/100.0 );
  }

  int regMax() {
    int i,m;

    m = 0;
    for(i=0;i<Nmt;i++) {
      if (reg[i][0]>m) {
        m = reg[i][0];
      }
    }
    return(m);
  }

  int secMax() {
    int i,j,k,m;

    m = 0;
    for(i=0;i<Nsx;i++) {
      for(j=0;j<Nsy;j++) {
        for(k=0;k<Nsz;k++) {
          if (section[i][j][k][0]>m) {
            m = section[i][j][k][0];
          }
        }
      }
    }
    return(m);
  }

/* ----- pressure ----- */

  void initVirial() {
    int i;

    for (i=0; i<256; i++) {
      virial[0][i] = 0.0;
      virial[1][i] = 0.0;
      virial[2][i] = 0.0;
      memTemp[i] = 0.0;
    }
    virialp = 0;
  }

  void setVirial() {
    int i;
    double xVir,yVir,zVir;

    xVir = 0.0; yVir = 0.0; zVir = 0.0;
    for (i=0; i<Nmt; i++) {
      xVir += ffx[i]*xx[i];
      yVir += ffy[i]*yy[i];
      zVir += ffz[i]*zz[i];
    }
    virial[0][virialp] = xVir;
    virial[1][virialp] = yVir;
    virial[2][virialp] = zVir;
    memTemp[virialp] = temperature();
    virialp = (virialp+1)%256;
  }

  double meanTemp() {
    int i;
    double st,tm;

    st = 0;
    for (i=0; i<256; i++) {
      st += memTemp[i];
    }
    tm = st/256.0;
    return( tm );
  }

  double meanPressure() {
    int i;
    double s,vir,tm,vol,p;

    s = 0.0;
    for (i=0; i<256; i++) {
      s += virial[0][i]+virial[1][i]+virial[2][i];
    }
    vir = s/256.0;
    tm = meanTemp();
    vol = xMax*yMax*zMax;
    p = (Nmt*1.38e-23*tm+vir/3.0)/vol;
    return( p );
  }

  double pressure() {
    int i,im;
    double vir,tm,vol,p;

    im = (virialp-1+256)%256;
    vir = virial[0][im]+virial[1][im]+virial[2][im];
    tm = temperature();
    vol = xMax*yMax*zMax;
    p = (Nmt*1.38e-23*tm+vir/3.0)/vol;
    return( p );
  }


/*-----------------------------  gogogo  --------------*/

  void gogogo(double x0, double r0, double temp) {
    int i;
    double r02,r2,v0;

    r02 = r0*r0;
    for (i=0; i<Nmt; i++) {
	  r2 = (xx[i]-x0)*(xx[i]-x0);
	  if (r2<=r02) {
	    v0 = Math.sqrt(1.38e-23*temp/Morse[kind[i]][0]);
        vx[i] = v0*(2.0*Math.random()-1.0)*2.0;
        vy[i] = v0*(2.0*Math.random()-1.0)*2.0;
        vz[i] = v0*(2.0*Math.random()-1.0)*2.0;
      }
    }
  }

/*-----------------------------  set initial condition  --------------*/

  void setInitialCondition() {
    int i,ix,iy,iz; 
    double a;

    setForceTable();
    setWaku();

    t = 0.0;

    a = xMax/100.0;
	i = 0;
    for (ix=0; ix<100; ix++) {
      for (iy=0; iy<5; iy++) {
        for (iz=0; iz<5; iz++) {
          xx[i] = a*(ix+0.5);
          yy[i] = a*(iy+0.5);
          zz[i] = a*(iz+0.5);

          kind[i] = MAT1;
          fillData(i);
          i += 1;
		}
	  }
    }
	Nmt = i;

    vAjustment();
    zSortInit();
    initVirial();
  }

  void fillData(int i) {
    vx[i] = 800.0*Math.random()-400.0;
    vy[i] = 800.0*Math.random()-400.0;
    vz[i] = 800.0*Math.random()-400.0;
    ffx[i] = 0.0;
    ffy[i] = 0.0;
    ffz[i] = 0.0;
  }

/*-------  set forceTable[i][j][ir]   -------*/

  void setForceTable(){
    int i,j,ir; 
    double d,a,r0,y,r,sc;

    for (i=0; i<NmatKind; i++) {
      for (j=0; j<NmatKind; j++) {

        d = Math.sqrt(Morse[i][2]*Morse[j][2]);
        a = 0.5*(Morse[i][3]+Morse[j][3]);
        r0 = 0.5*(Morse[i][4]+Morse[j][4]);

        for (ir=10; ir<1000; ir++) {
          r = (double)ir*hh;
          y = Math.exp(-a*(r-r0));
          forceTable[i][j][ir] = cutoff(r)*2.0*d*a*y*(y-1.0);
        }
        for (ir=0; ir<10; ir++) {
          forceTable[i][j][ir]=forceTable[i][j][10];
        }
      }
    }
  }

  double cutoff(double r) {
    double rt;

    rt = 0.0;
    if (r<0.8*rc) {
      rt = 1.0;
    } else if (r>=0.8*rc && r<rc) {
      rt = 0.5+0.5*Math.cos(3.1415926536*(r-0.8*rc)/(0.2*rc));
    } else {
      rt = 0.0;
    }
    return( rt );
  }

/*------------  v ajustment  ---------*/

  void vAjustment() {
    int i;
    double tmp, r;

    tmp = temperature();
    r = Math.sqrt(contTemp/tmp);
    for (i=0; i<Nmt; i++) {
      vx[i] = r*vx[i];
      vy[i] = r*vy[i];
      vz[i] = r*vz[i];
    }
  }


/*-------------------------------  molecules motion   --------------*/

  void timeEvolution() {
    int i;

    if (resetSW==1) {
      setInitialCondition();
      resetSW = 0;
      started = 1;
    }

    if (tempMode==1) {
      vAjustment();
    }

    registration();
    for (i=0; i<20; i++) {
      timeStep();
    }

    setVirial();
  }

  void timeStep() {
    int i; 
    double dtv2, a2, tmp, rr;

    dtv2 = dt/2.0;
    t = t + dt;

    rr = 1.0;
    if (tempMode==2) {
      tmp = temperature();
      rr = Math.sqrt(contTemp/tmp);
      if (rr<0.5) { rr = 0.5; } else if (rr>1.2){ rr=1.2; };
    }

    for (i=0; i<Nmt; i++) {
      a2 = dtv2/Morse[kind[i]][0];
      vx[i] += a2*ffx[i];
      vy[i] += a2*ffy[i];
      vz[i] += a2*ffz[i];
      xx[i] += vx[i]*dt;
      yy[i] += vy[i]*dt;
      zz[i] += vz[i]*dt;
    }
    forceCalc();
    for (i=0; i<Nmt; i++) {
      a2 = dtv2/Morse[kind[i]][0];
      vx[i] += a2*ffx[i];
      vy[i] += a2*ffy[i];
      vz[i] += a2*ffz[i];
    }

    for (i=0; i<Nmt; i++) {
      if (xx[i] < 0.0) { 
        xx[i] = 0.0; vx[i] = -rr*vx[i]; vy[i] = rr*vy[i];  vz[i] = rr*vz[i]; 
      }
      if (xx[i] > xMax) {
        xx[i] = xMax; vx[i] = -rr*vx[i]; vy[i] = rr*vy[i]; vz[i] = rr*vz[i];  
      }
      if (yy[i] < 0.0) { 
        yy[i] += yMax; 
      }
      if (yy[i] > yMax) {
        yy[i] -= yMax;
      }
      if (zz[i] < 0.0) { 
        zz[i] += zMax; 
      }
      if (zz[i] > zMax) {
        zz[i] -= zMax; 
      }
    }
  }

  void forceCalc() {
    int i,j,k;
    double xi,xj,yi,yj,zi,zj;
    double r2,rij,f,fxij,fyij,fzij;

    for(i=0;i<Nmt;i++) {
      ffx[i] = 0.0;
      ffy[i] = 0.0;
      ffz[i] = 0.0;
    }

    for(i=0;i<Nmt;i++) {
      for(k=1;k<reg[i][0];k++) {
        j = reg[i][k];
        xi = xx[i]; xj = xx[j]; yi = yy[i]; yj = yy[j]; zi = zz[i]; zj = zz[j];
        if (yi-yj>0.5*yMax) { yj += yMax; };
        if (yi-yj<-0.5*yMax) { yj -= yMax; }; 
		if (zi-zj>0.5*zMax) { zj += zMax; };
        if (zi-zj<-0.5*zMax) { zj -= zMax; }; 
        r2 = (xi-xj)*(xi-xj)+(yi-yj)*(yi-yj)+(zi-zj)*(zi-zj);
        if (r2<rc2) {
          rij = Math.sqrt(r2);
          f = force(rij,kind[i],kind[j]);
          fxij = f*(xi-xj)/rij;
          fyij = f*(yi-yj)/rij;
          fzij = f*(zi-zj)/rij;

          ffx[i] +=  fxij;
          ffy[i] +=  fyij;
          ffz[i] +=  fzij;

          ffx[j] += -fxij;
          ffy[j] += -fyij;
          ffz[j] += -fzij;
        }
      }
    }
  }

  double force(double r, int ki, int kj) {
    int i;
    double a;

    i = (int)(r/hh);
    a = r - i*hh;

    return ( ((hh-a)*forceTable[ki][kj][i] + 
      a*forceTable[ki][kj][i+1])/hh );
  }

/*-------------------------------  registration   -------------*/

  void registration() {
    int i,j,k,jj,kk,ip,jp,kp,i0,i1,j0,j1,k0,k1,iq;
    double r2,rreg,rreg2;
    double xi,xj,yi,yj,zi,zj;

    preRegistration();

    rreg = rc + 3000.0*20*dt;
    rreg2 = rreg*rreg;

    for(ip=0;ip<Nmt;ip++) {
      kp = 1;

      i0 = (int)(Nsx*(xx[ip]-rreg)/xMax); if (i0<0) i0 = 0;
      i1 = (int)(Nsx*(xx[ip]+rreg)/xMax); if (i1>=Nsx) i1 = Nsx-1;
      j0 = (int)(Nsy*(yy[ip]-rreg)/yMax+(double)Nsy)-Nsy;
      j1 = (int)(Nsy*(yy[ip]+rreg)/yMax);
      k0 = (int)(Nsz*(zz[ip]-rreg)/zMax+(double)Nsz)-Nsz;
      k1 = (int)(Nsz*(zz[ip]+rreg)/zMax);

      for(i=i0;i<=i1;i++) {
        for(j=j0;j<=j1;j++) {
          jj = (j+Nsy)%Nsy;
		  for(k=k0;k<=k1;k++) {
            kk = (k+Nsz)%Nsz;
	        for(iq=1;iq<=section[i][jj][kk][0];iq++) {
              jp = section[i][jj][kk][iq];
              if (jp>ip) {
                xi = xx[ip]; xj = xx[jp]; yi = yy[ip]; yj = yy[jp]; zi = zz[ip]; zj = zz[jp];
                if (yi-yj>0.5*yMax) yj += yMax;
                if (yi-yj<-0.5*yMax) yj -= yMax;
				if (zi-zj>0.5*zMax) zj += zMax;
                if (zi-zj<-0.5*zMax) zj -= zMax;
                r2=(xi-xj)*(xi-xj)+(yi-yj)*(yi-yj)+(zi-zj)*(zi-zj);
                if (r2<rreg2) {
                  reg[ip][kp]=jp;
                  kp += 1;
			    }
              }
            }
          }
        }
      }
      reg[ip][0]=kp;
    }
  }

  void preRegistration() {
    int i,j,k,ip,iq;

    for(i=0;i<Nsx;i++) {
      for(j=0;j<Nsy;j++) {
        for(k=0;k<Nsz;k++) {
          section[i][j][k][0] = 0;
        }
      }
    }

    for(ip=0;ip<Nmt;ip++) {
      i = (int)(Nsx*xx[ip]/xMax); if (i>=Nsx) i = Nsx-1;
      j = (int)(Nsy*yy[ip]/yMax); if (j>=Nsy) j = Nsy-1;
      k = (int)(Nsz*zz[ip]/zMax); if (k>=Nsz) k = Nsz-1;
      iq = section[i][j][k][0]+1;
      section[i][j][k][0] = iq;
      section[i][j][k][iq] = ip;
    }
  }

/*----- end of molecules motion -----*/

}  

/*----- end of applet -----*/