/* gas Demixing - FM3D		       */
/* coded by Ikeuchi Mitsuru    */
/* ver 0.0.1   2004.04.03      */

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

public class gasDemixing3D extends Applet
  implements MouseListener, MouseMotionListener,
    ActionListener, ItemListener, AdjustmentListener, Runnable {

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

  Button bt_open;
  Choice cm1,cm2;
  Scrollbar scr,scs;
  Thread th = null;

  Dimension dim;
  Image imgOff;
  Graphics gOff;

  int sleepTime = 50;
  double dispScale = 5.0/3.4e-10;
  double sgm = 3.4e-10;         /* L-J sigma for Ar (m)   */

  double xMax0 = 40.0*sgm;      /* x-Box size in (m)      */
  double yMax0 = 40.0*sgm;      /* y-Box size in (m)      */
  double zMax0 = 40.0*sgm;      /* z-Box size in (m)      */
  double xMax = xMax0;
  double yMax = yMax0;
  double zMax = zMax0;


  int Nmt = 10*10*10;           /* number of molecules    */
  int NN = Nmt + 1;
  double t = 0.0;               /* time (s)               */
  double dt = 20.0*1.0e-15;     /* time division (s)      */

  int gate = 1;
  double volRatio = 1.0;
  double mol2Ratio = 0.5;
  int tempMode = 2;
  double contTemp = 300.0;
  double scale = 1.0;
  int dispMode = 3;

  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 = 10.0*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 rreg = 1.5e-9;
  double rreg2 = rreg*rreg;

  double AU = 1.661e-27;
  double EE = 1.602e-19;
  double AA = 1.0e-10;
  double Morse[][] = {
  /*         mass         charge   D(eV)     A(A^-1)    r0(A)   */
  /* 0 W */ {183.85 *AU,  0.0*EE, 0.9906*EE, 1.4116/AA, 3.032*AA},
  /* 1 Mo*/ { 95.94 *AU,  0.0*EE, 0.8032*EE, 1.5079/AA, 2.976*AA},
  /* 2 Cr*/ { 51.996*AU,  0.0*EE, 0.4414*EE, 1.5721/AA, 2.754*AA},
  /* 3 Fe*/ { 55.847*AU,  0.0*EE, 0.4174*EE, 1.3885/AA, 2.845*AA},
  /* 4 Ni*/ { 58.71 *AU,  0.0*EE, 0.4205*EE, 1.4199/AA, 2.780*AA},
  /* 5 Al*/ { 26.98 *AU,  0.0*EE, 0.2703*EE, 1.1646/AA, 3.253*AA},
  /* 6 Pb*/ {207.19 *AU,  0.0*EE, 0.2348*EE, 1.1836/AA, 3.733*AA},
  /* 7 Cu*/ { 63.54 *AU,  0.0*EE, 0.3429*EE, 1.3588/AA, 2.866*AA},
  /* 8 Ag*/ {107.87 *AU,  0.0*EE, 0.3323*EE, 1.3690/AA, 3.115*AA},
  /* 9 Ca*/ { 40.08 *AU,  0.0*EE, 0.1623*EE, 0.8054/AA, 4.569*AA},
  /*10 Sr*/ { 87.62 *AU,  0.0*EE, 0.1513*EE, 0.7878/AA, 4.988*AA},
  /*11 Ba*/ {137.34 *AU,  0.0*EE, 0.1416*EE, 0.6570/AA, 5.373*AA},
  /*12 Na*/ { 22.99 *AU,  0.0*EE, 0.0633*EE, 0.5900/AA, 5.336*AA},
  /*13 K */ { 39.102*AU,  0.0*EE, 0.0542*EE, 0.4977/AA, 6.369*AA},
  /*14 Rb*/ { 85.47 *AU,  0.0*EE, 0.0464*EE, 0.4298/AA, 7.207*AA},
  /*15 Cs*/ {132.905*AU,  0.0*EE, 0.0449*EE, 0.4157/AA, 7.557*AA},
  /*16 Ne*/ { 20.183*AU,  0.0*EE, 0.0031*EE, 1.6500/AA, 3.076*AA},
  /*17 Ar*/ { 39.948*AU,  0.0*EE, 0.0104*EE, 1.3400/AA, 3.816*AA},
  /*18 Kr*/ { 83.80 *AU,  0.0*EE, 0.0141*EE, 1.2500/AA, 4.097*AA},
  /*19 Xe*/ {131.30 *AU,  0.0*EE, 0.0200*EE, 1.2400/AA, 4.467*AA},
  /*20 Hg*/ {200.59 *AU,  0.0*EE, 0.0734*EE, 1.4900/AA, 3.255*AA}
  };
  int NmatKind = 21;

  int MAT0 = 20;
  int MAT1 = 16;
  int MAT2 = 19;
  int MAT3 = 9;
  int MAT4 = 20;

  int dom[] = new int[NN];
  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    */
  double fbx[] = new double[NN];  /* i-th x-force before dt */
  double fby[] = new double[NN];  /* i-th y-force before dt */
  double fbz[] = new double[NN];  /* i-th z-force before dt */

  int reg[][] = new int[NN][860];   /* registration */

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

  int kindT[] = new int[NmatKind];
  double forceTable[][][] = new double[5][5][10200];

  double hh = 1.0e-13;

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

  double wkx[] = new double[8+4]; 
  double wky[] = new double[8+4]; 
  double wkz[] = new double[8+4]; 

  double pwkx[] = new double[8+4]; 
  double pwky[] = new double[8+4]; 
  double pwkz[] = new double[8+4]; 

  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},
   {8,9},{8,10},{9,11},{10,11}
  };

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

  public void init() {
    resize(630,320);
    setBackground(Color.white);

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

    cm1 = new Choice();
    cm1.addItem("Ne"); cm1.addItem("Ar");
    cm1.addItem("Kr"); cm1.addItem("Xe"); 
    cm1.addItemListener(this);
    cm1.select("Ne");

    cm2 = new Choice();
    cm2.addItem("Ne"); cm2.addItem("Ar");
    cm2.addItem("Kr"); cm2.addItem("Xe"); 
    cm2.addItemListener(this);
    cm2.select("Xe"); 

    scr= new Scrollbar(Scrollbar.HORIZONTAL,300,10,10,510);
    scr.addAdjustmentListener(this);

    scs= new Scrollbar(Scrollbar.HORIZONTAL,100,10,50,210);
    scs.addAdjustmentListener(this);

    bt_open = new Button("open"); 
    bt_open.addActionListener(this);

    addMouseListener(this);  
    addMouseMotionListener(this);

    setLayout(new BorderLayout());
    Panel pnl=new Panel();
    pnl.setLayout(new GridLayout(1,6,5,0));
    pnl.add(cm1);
    pnl.add(cm2);
    pnl.add(new Label("  "));
    pnl.add(scr);
    pnl.add(scs);
    pnl.add(bt_open);
    add(pnl,"North");

    setInitialPosition();
    setWaku();
  }

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

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

  public void actionPerformed(ActionEvent ev){ 
     if(ev.getSource() == bt_open) {
       if (gate==1) {
         t = 0.0;
         gate = 0;
       }
     } 
  }

  public void itemStateChanged(ItemEvent ev){
    if (ev.getSource() == cm1){
      MAT1 = 16+cm1.getSelectedIndex();
      t = 0.0;
      setInitialPosition();
    } else if (ev.getSource() == cm2){
      MAT2 = 16+cm2.getSelectedIndex();
      t = 0.0;
      setInitialPosition();
    }
  }

  public void adjustmentValueChanged(AdjustmentEvent ev){
    if (ev.getSource() == scr) { 
      contTemp = 1.0*(double)(scr.getValue());
      if (tempMode==0 || tempMode==1) {
        vAjustment();
      }
    } else if(ev.getSource() == scs) { 
      scale = 0.01*(double)(scs.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 {
        calcposition();
        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 i,j,k,jj,farPoint;
    int gx,gy,gz,g2x,g2y,gbx,gby,gbz,gb;
    double sc,sz,tmp,tm,mtm,clr;

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

    setWaku();
    rotate(theta,fai);
    zSort();
    tmp = temperature();

    gbx = 60;
    gby = 80;
    sc = dispScale*scale;
    sz = 2.0*scale/AA;

    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 (boxp[i][0]==farPoint || boxp[i][1]==farPoint) { 
        gOff.setColor(Color.lightGray);
        gOff.drawLine(gx,gy, g2x, g2y);
      } 
    }
	if (wkx[farPoint]>xMax/2.0) {
      for (i=12; i<16; 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 (gate==1) {
          gOff.setColor(Color.lightGray);
		} else {
		  if (tmp>contTemp) {
            gOff.setColor(Color.black); 
          } else {
            gOff.setColor(Color.red);
          }
		}
        gOff.drawLine(gx,gy, g2x, g2y);
      }
	}


    if (dispMode==0) {

      for (i=0; i<Nmt; i++) {
        j = srtz[0][i];
        gx = (int)(sc*px[j])+gbx;
        gy = (int)(sc*py[j])+gby;
        gz = (int)(0.6*sz*Morse[kind[j]][4]*(0.4*(pz[j]/zMax)+0.6));
        clr = ballColor(kind[j]);
        gOff.setColor(Color.getHSBColor(
          (float)clr,0.9f,(float)(0.4*pz[j]/zMax+0.4)));
        gOff.fillOval(gx-gz/2,gy-gz/2, gz, gz);
      }

    } else if (dispMode==1) {

      for (i=0; i<Nmt; i++) {
        j = srtz[0][i];
        gx = (int)(sc*px[j])+gbx;
        gy = (int)(sc*py[j])+gby;
        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)(sc*px[jj])+gbx;
              g2y = (int)(sc*py[jj])+gby;
              gOff.setColor(Color.gray);
              gOff.drawLine(gx,gy, g2x, g2y);
          }
        }
      }

    } else if (dispMode==2) {

      for (i=0; i<Nmt; i++) {
        j = srtz[0][i];
        gx = (int)(sc*px[j])+gbx;
        gy = (int)(sc*py[j])+gby;
        gz = (int)(0.6*sz*Morse[kind[j]][4]*(0.4*(pz[j]/zMax)+0.6));

        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)(sc*px[jj])+gbx;
              g2y = (int)(sc*py[jj])+gby;
              gOff.setColor(Color.gray);
              gOff.drawLine(gx,gy, g2x, g2y);
          }
        }
        clr = ballColor(kind[j]);
        gOff.setColor(Color.getHSBColor(
          (float)clr,0.9f,(float)(0.4*pz[j]/zMax+0.4)));
        gOff.fillOval(gx-gz/2,gy-gz/2, gz, gz);
      }

    } else if (dispMode==3) {

      for (i=0; i<Nmt; i++) {
        j = srtz[0][i];
        gx = (int)(sc*px[j])+gbx;
        gy = (int)(sc*py[j])+gby;
        gz = (int)(sz*Morse[kind[j]][4]*(0.4*(pz[j]/zMax)+0.6));
        clr = ballColor(kind[j]);
        if (dom[j]==0) {
          gOff.setColor(Color.getHSBColor(
            (float)clr,0.9f,(float)(0.4*pz[j]/zMax+0.4)));
		} else {
          gOff.setColor(Color.getHSBColor((float)clr,0.5f,0.5f));
		}
        gOff.fillOval(gx-gz/2,gy-gz/2, gz, gz);
      }

    } else if (dispMode==4) {

      for (i=0; i<Nmt; i++) {
        j = srtz[0][i];
        gx = (int)(sc*px[j])+gbx;
        gy = (int)(sc*py[j])+gby;
        gz = (int)(0.6*sz*Morse[kind[j]][4]*(0.4*(pz[j]/zMax)+0.6));
        clr = ballColor(kind[j]);
        tm = 0.5*Morse[kind[j]][0]*(vx[j]*vx[j]+vy[j]*vy[j]+vz[j]*vz[j])/(1.5*1.38e-23)/1000.0 + 0.3;
        if(tm>0.99) {
          tm = 0.99;
        }
        gOff.setColor(Color.getHSBColor( (float)clr, 0.99f, (float)tm ));
        gOff.fillOval(gx-gz/2,gy-gz/2, gz, gz);
      }

    }


    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 (boxp[i][0]!=farPoint && boxp[i][1]!=farPoint) { 
        gOff.setColor(Color.gray);
        if (tempMode==2) {
          if (tmp>contTemp) {
            gOff.setColor(Color.black); 
          } else {
            gOff.setColor(Color.red);
          }
        }
        gOff.drawLine(gx,gy, g2x, g2y);
      }
    }
    if (wkx[farPoint]<xMax/2.0) {
      for (i=12; i<16; 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 (gate==1) {
          gOff.setColor(Color.gray);
		} else {
		  if (tmp>contTemp) {
            gOff.setColor(Color.black); 
          } else {
            gOff.setColor(Color.red);
          }
		}
        gOff.drawLine(gx,gy, g2x, g2y);
      }
	}


    gOff.setColor(Color.black);
    gOff.drawString("orange",630/6*0+10,40);
    gOff.drawString("green",630/6*1+10,40);
    gOff.drawString("T cont="+(int)(contTemp+0.5)+" K",630/6*3+10,40);
    gOff.drawString("scale="+(int)(scale*100.0+0.5)+"%",630/6*4+10,40);
    if (gate==1) {
      gOff.drawString("door=closed",630/6*5+10,40);
	} else {
      gOff.drawString("door=open",630/6*5+10,40);
    }

    gOff.setColor(Color.blue);
    gOff.drawString("t="+(int)(t*1.0e13+0.5)/10.0+" ps",630/6*5,60);
    gOff.drawString("T="+(int)(tmp*10+0.5)/10.0+" K",630/6*3,60);
    gOff.drawString("L="+(int)(xMax*1.0e10+0.5)/10.0+" nm",630/6*4,60);
	
    gOff.setColor(Color.getHSBColor( 0.15f, 0.9f, 0.8f ));
    gOff.drawString("N(orange)="+nInBox(MAT1)+"",630/6*5,80);
    gOff.setColor(Color.getHSBColor( 0.33f, 0.9f, 0.8f ));
    gOff.drawString("N(green)="+nInBox(MAT2)+"",630/6*5,100);
  }

  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) );
  }

  double ballColor(int knd) {
    double c;

    c = 0.0;
    if (knd==MAT0) {
      c = 0.01;
    } else if (knd==MAT1) {
      c = 0.15;
    } else if (knd==MAT2) {
      c = 0.33;
    } else if (knd==MAT3) {
      c = 0.66;
    } else if (knd==MAT4) {
      c = 0.85;
    }
    return ( c );
  }

/*----------------------------------  findMin()  ----------*/

  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);
  }

/*-------------------------------------  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(th); sinTh = Math.sin(th);
    cosFi = Math.cos(fi); sinFi = Math.sin(fi);
    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<12; 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<12; i++) {
      pwkx[i] = cosTh*(wkx[i]-cx)+sinTh*(pwkz[i]-cz) + cx; 
      pwkz[i] = -sinTh*(wkx[i]-cx)+cosTh*(pwkz[i]-cz) + cz;
    }  
  }

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

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

    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;
        }
      }
    }

    ix=1;
    for (iy=0; iy<2; iy++) {
      for (iz=0; iz<2; iz++) {
        wkx[i] = -0.5*sgm+(xMax+sgm)*(double)(ix);
        wky[i] = 0.4*yMax-0.5*sgm+(0.2*yMax+sgm)*(double)(iy);
        wkz[i] = 0.4*zMax-0.5*sgm+(0.2*zMax+sgm)*(double)(iz);
        i += 1;
      }
    }
  }

/*-------------------------------------  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)*10.0)/10.0 );
  }

  int nInBox(int mat) {
    int i,n;

    n = 0; 
    for (i=0; i<Nmt; i++) {
	  if (kind[i]==mat && dom[i]==0) {
	    n += 1;
      }
    }
    return ( n );
  }

/*-------------------------------------  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];
    }
  }

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

  void setForceTable(){
    int i,j,ir,k0,k1; 
    double d,a,r0,y,r,sc;
    int kkk[] = {MAT0,MAT1,MAT2,MAT3,MAT4};

    kindT[MAT0] = 0; kindT[MAT1] = 1; kindT[MAT2] = 2;
    kindT[MAT3] = 3; kindT[MAT4] = 4;

    for (i=0; i<5; i++) {
      k0=kkk[i];
      for (j=0; j<5; j++) {
        k1=kkk[j];

        d = Math.sqrt(Morse[k0][2]*Morse[k1][2]);
        a = 0.5*(Morse[k0][3]+Morse[k1][3]);
        r0 = 0.5*(Morse[k0][4]+Morse[k1][4]);

        for (ir=100; ir<10000; ir++) {
          r = (double)ir*hh;
          y = Math.exp(-a*(r-r0));
          forceTable[i][j][ir]=2.0*d*a*y*(y-1.0);
        }
        for (ir=0; ir<100; ir++) {
          forceTable[i][j][ir]=forceTable[i][j][100];
        }

        for (ir=6000; ir<10000; ir++) {
          forceTable[i][j][ir] = cutoff(ir)*forceTable[i][j][ir];
        }
      }
    }
  }

  double cutoff(int ir) {
    double rt;

    rt = 0.0;
    if (ir<6000) {
      rt = 1.0;
    } else if (ir>=6000 && ir<10000) {
      rt = 0.5+0.5*Math.cos(3.1415926536*(((double)ir)/10000.0-0.6)/0.4);
    } else {
      rt = 0.0;
    }
    return( rt );
  }

/*-------------------- set initial position  ----------*/

  void setInitialPosition(){
    int i; 
    double s;

    setForceTable();

    gate = 1;
    t = 0.0;
    xMax = xMax0;
    yMax = yMax0;
    zMax = zMax0;

    s = xMax/10.0;
    for (i=0; i<Nmt; i++) {
	  dom[i] = 0;
      kind[i] = MAT1;
      if (i%2==1) {
        kind[i] = MAT2;
      }
      xx[i] = s*(double)((i%100)%10)+0.5*s;
      yy[i] = s*(double)((i%100)/10)+0.5*s;
      zz[i] = s*(double)(i/100)+0.5*s;
      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;
      fbx[i] = 0.0;
      fby[i] = 0.0;
      fbz[i] = 0.0;
    }

    zSortInit();
  }

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

  void registration() {
    int i,j,k;
    double r2;

    for(i=0;i<Nmt;i++) {
      k = 1;
      for(j=i+1;j<Nmt;j++) {
        r2=(xx[i]-xx[j])*(xx[i]-xx[j])+(yy[i]-yy[j])*(yy[i]-yy[j])+(zz[i]-zz[j])*(zz[i]-zz[j]);
        if (r2<rreg2) {
          reg[i][k]=j;
          k += 1;
        }
      }
      reg[i][0]=k;
    }
  }

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

  void calcposition(){
    int i;

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

    registration();
    for (i=0; i<10; i++) {
      timeEvolution();
    }
  }

  void timeEvolution(){
    int i; 
    double rr, tmp;

    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++) {
      xx[i] += vx[i]*dt+0.5*dt*dt*ffx[i]/Morse[kind[i]][0];
      yy[i] += vy[i]*dt+0.5*dt*dt*ffy[i]/Morse[kind[i]][0];
      zz[i] += vz[i]*dt+0.5*dt*dt*ffz[i]/Morse[kind[i]][0];
      fbx[i] = ffx[i];
      fby[i] = ffy[i];
      fbz[i] = ffz[i];
    }
    forceCalc();
    for (i=0; i<Nmt; i++) {
      vx[i] += 0.5*dt*(ffx[i]+fbx[i])/Morse[kind[i]][0];
      vy[i] += 0.5*dt*(ffy[i]+fby[i])/Morse[kind[i]][0];
      vz[i] += 0.5*dt*(ffz[i]+fbz[i])/Morse[kind[i]][0];
    }

    for (i=0; i<Nmt; i++) {
	  if (dom[i]==0) {
        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) {
	      if (yy[i]>0.4*yMax && yy[i]<0.6*yMax && zz[i]>0.4*zMax && zz[i]<0.6*zMax && gate==0) {
		    dom[i] = 1;
		  } else {
            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] = 0.0; vx[i] = rr*vx[i]; vy[i] = -rr*vy[i]; vz[i] = rr*vz[i]; 
        }
        if (yy[i] > yMax) {
          yy[i] = yMax; vx[i] = rr*vx[i]; vy[i] = -rr*vy[i]; vz[i] = rr*vz[i];
        }
        if (zz[i] < 0.0) { 
          zz[i] = 0.0; vx[i] = rr*vx[i]; vy[i] = rr*vy[i]; vz[i] = -rr*vz[i]; 
        }
        if (zz[i] > zMax) {
          zz[i] = zMax; vx[i] = rr*vx[i]; vy[i] = rr*vy[i]; vz[i] = -rr*vz[i];
        }
      } else if (dom[i]==1) {
	    if (xx[i] < xMax) { 
          xx[i] = xMax; vx[i] = -rr*vx[i]; vy[i] = rr*vy[i];  vz[i] = rr*vz[i]; 
	    }
	  }
	}
  }

  void forceCalc() {
    int i,j,k;
    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];
        r2=(xx[i]-xx[j])*(xx[i]-xx[j])+(yy[i]-yy[j])*(yy[i]-yy[j])+(zz[i]-zz[j])*(zz[i]-zz[j]);
        if (r2<rc2) {
          rij = Math.sqrt(r2);
          f = force(rij,kind[i],kind[j]);
          fxij = f*(xx[i]-xx[j])/rij;
          fyij = f*(yy[i]-yy[j])/rij;
          fzij = f*(zz[i]-zz[j])/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[kindT[ki]][kindT[kj]][i] + 
      a*forceTable[kindT[ki]][kindT[kj]][i+1])/hh );
  }

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

}  

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