/* periodic - homo Morse 3D   */
/* coded by Ikeuchi Mitsuru   */
/* ver 0.0.1   2004.02.07     */
/* ver 0.0.2   2004.06.10 improved velocity verlet code */

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

public class periodicHM3D extends Applet
  implements MouseListener, MouseMotionListener,
    ItemListener, AdjustmentListener, Runnable {

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

  Choice cm1,ctc,cvw;
  Scrollbar scr,scs;
  Thread th = null;

  Dimension dim;
  Image imgOff;
  Graphics gOff;

  int sleepTime = 50;
  double sgm = 3.4e-10;        /* L-J sigma for Ar (m)   */
  double dispScale = 10.0/sgm;

  double xMax = 20.0*sgm;      /* x-Box size in (m)      */
  double yMax = 20.0*sgm;      /* y-Box size in (m)      */
  double zMax = 20.0*sgm;      /* z-Box size in (m)      */


  int Nmt = 10*10*10;          /* number of molecules    */
  int NN = Nmt + 1;
  double t = 0.0;              /* time (s)               */
  double dt = 5.0*1.0e-15;     /* time division (s)      */


  int tempMode = 0;
  double contTemp = 1000.0;
  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 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 MAT1 = 0;

  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 Ntr = 16;
  int trp = 0;
  double trxx[][] = new double[NN][Ntr];
  double tryy[][] = new double[NN][Ntr];
  double trzz[][] = new double[NN][Ntr];

  double forceTable[] = new double[30000];

  double hh = 1.0e-13;
  double mas = 183.85*AU;
  double r0 = 3.032*AA;

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

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

  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}
  };

/*----------------------------- 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("W");  cm1.addItem("Mo"); cm1.addItem("Cr");
    cm1.addItem("Fe"); cm1.addItem("Ni"); cm1.addItem("Al");
    cm1.addItem("Pb"); cm1.addItem("Cu"); cm1.addItem("Ag"); 
    cm1.addItem("Ca"); cm1.addItem("Sr"); cm1.addItem("Ba");
    cm1.addItem("Na"); cm1.addItem("K");  cm1.addItem("Rb");
    cm1.addItem("Cs"); cm1.addItem("Ne"); cm1.addItem("Ar");
    cm1.addItem("Kr"); cm1.addItem("Xe"); cm1.addItem("Hg");
    cm1.addItemListener(this); 

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

    cvw = new Choice();
    cvw.addItem("ball"); cvw.addItem("line");
    cvw.addItem("both"); cvw.addItem("real");
    cvw.addItem("temp"); cvw.addItem("trace");
    cvw.addItemListener(this); 
    cvw.select("real"); 

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

    scs= new Scrollbar(Scrollbar.HORIZONTAL,100,10,20,210);
    scs.addAdjustmentListener(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(ctc);
    pnl.add(cvw);
    pnl.add(new Label("  "));
    pnl.add(scr);
    pnl.add(scs);
    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 itemStateChanged(ItemEvent ev){
    if (ev.getSource() == cm1){
      MAT1 = cm1.getSelectedIndex();
      t = 0.0;
      setInitialPosition();
    } else if (ev.getSource() == ctc) {
      tempMode = ctc.getSelectedIndex();
    } else if (ev.getSource() == cvw){
      dispMode = cvw.getSelectedIndex();
      if (dispMode==5) {
        traceInit();
      }
    }
  }

  public void adjustmentValueChanged(AdjustmentEvent ev){
    if (ev.getSource() == scr) { 
      contTemp = 10.0*(double)(scr.getValue());
      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,ip;
    int gx,gy,gz,g2x,g2y,gbx,gby,gbz,gb;
    double sc,sz,tmp,tm,clr;

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

    rotate(theta,fai);
    zSort();
    tmp = temperature();
    gbx = 60;
    gby = 80;
    sc = dispScale*scale;
    sz = 3.6*scale*Morse[MAT1][4]/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 (dispMode==0) {

      clr = 0.33;
      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*(0.4*(pz[j]/zMax)+0.6));
        gOff.setColor(Color.getHSBColor(0.33f,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)<1.2*Morse[MAT1][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*(0.4*(pz[j]/zMax)+0.6));

        for (k=1; k<reg[j][0]; k++) {
          jj = reg[j][k];
          if ( distance(j,jj)<1.2*Morse[MAT1][4] ) {
              g2x = (int)(sc*px[jj])+gbx;
              g2y = (int)(sc*py[jj])+gby;
              gOff.setColor(Color.gray);
              gOff.drawLine(gx,gy, g2x, g2y);
          }
        }
        gOff.setColor(Color.getHSBColor(0.33f,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*(0.4*(pz[j]/zMax)+0.6));
        gOff.setColor(Color.getHSBColor(0.33f,0.9f,(float)(0.4*pz[j]/zMax+0.4)));
        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*(0.4*(pz[j]/zMax)+0.6));
        tm = 0.5*Morse[MAT1][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( 0.33f, 0.99f, (float)tm ));
        gOff.fillOval(gx-gz/2,gy-gz/2, gz, gz);
      }

    } else if (dispMode==5) {

      for (k=0; k<Ntr-1; k++) {
        ip = (trp+1+k)%Ntr;
        rotateTr(theta,fai,ip);
        zSort();
        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*(0.4*(pz[j]/zMax)+0.6));
          gOff.setColor(Color.getHSBColor( 0.33f, (float)(0.7/Ntr*k), 0.99f ));
          gOff.fillOval(gx-gz/2,gy-gz/2, gz, gz);
        }
      }

      rotate(theta,fai);
      zSort();
      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*(0.4*(pz[j]/zMax)+0.6));
        gOff.setColor(Color.getHSBColor(0.33f,0.9f,(float)(0.4*pz[j]/zMax+0.4)));
        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);
      }
    }

    gOff.setColor(Color.black);
    gOff.drawString("atom",630/6*0+10,40);
    gOff.drawString("temp control",630/6*1+10,40);
    gOff.drawString("view",630/6*2+10,40);
    gOff.drawString("cont T="+contTemp+"K",630/6*4+10,40);
    gOff.drawString("scale="+(int)(scale*100.0+0.499)+"%",630/6*5+10,40);

    gb = 630/6*5;
    gOff.setColor(Color.blue);
    gOff.drawString("t="+Math.floor(t*1.0e15+0.5)+" fs",gb,80);
    gOff.drawString("T="+(int)(tmp*10+0.5)/10.0+" K",gb,100);
    gOff.drawString("L="+(int)(xMax*1.0e10+0.5)/10.0+" nm",gb,120);

  }

  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) );
  }

/*----------------------------------  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<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;
    }  
  }

  void rotateTr(double th,double fi,int ip) {
    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*(tryy[i][ip]-cy)+sinFi*(trzz[i][ip]-cz) + cy; 
      pz[i] = -sinFi*(tryy[i][ip]-cy)+cosFi*(trzz[i][ip]-cz) + cz;
    }

    for (i=0; i<Nmt; i++) {
      px[i] = cosTh*(trxx[i][ip]-cx)+sinTh*(pz[i]-cz) + cx; 
      pz[i] = -sinTh*(trxx[i][ip]-cx)+cosTh*(pz[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;
        }
      }
    }
  }

/*-------------------------------------  trace  ----------*/

  void traceInit() {
    int i,j;

    for (i=0; i<Nmt; i++) {
      for (j=0; j<Ntr; j++) {
        trxx[i][j] = xx[i];
        tryy[i][j] = yy[i];
        trzz[i][j] = zz[i];
      }
    }
    trp = 0;

  }

  void traceSet() {
    int i,ip;

    ip = trp;
    for (i=0; i<Nmt; i++) {
      trxx[i][ip] = xx[i];
      tryy[i][ip] = yy[i];
      trzz[i][ip] = zz[i];
    }
    trp = (trp+1)%Ntr;

  }


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


  double rmsV() {
    int i;
    double s;

    s = 0.0; 
    for (i=0; i<Nmt; i++) {
      s += vx[i]*vx[i] + vy[i]*vy[i] + vz[i]*vz[i];
    }
    return ((double)Math.floor(Math.sqrt(s/(double)Nmt)*10.0)/10.0);
  }

  double temperature() {
    int i;
    double s;

    s = 0.0; 
    for (i=0; i<Nmt; i++) {
      s += 0.5*mas*(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 );
  }


/*-------------------------------------  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 knd) {
    int ir; 
    double d,a,r0,y,r;

    d = Morse[knd][2];
    a = Morse[knd][3];
    r0 = Morse[knd][4];

    for (ir=100; ir<30000; ir++) {
      r = (double)ir*hh;
      y = Math.exp(-a*(r-r0));
      forceTable[ir] = cutoff(r)*2.0*d*a*y*(y-1.0);
    }

    for (ir=0; ir<100; ir++) {
      forceTable[ir]=forceTable[100];
    }

  }

  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 );
  }

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

  void setInitialPosition(){
    int i; 
    double s;

    mas = Morse[MAT1][0];
    r0 = Morse[MAT1][4];
    rc = 2.4*r0;
    rc2 = rc*rc;
    setForceTable(MAT1);

    s = xMax/10.0;
    for (i=0; i<Nmt; i++) {
      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;
    }
    vAjustment();
    traceInit();
    zSortInit();
  }

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

  void registration() {
    int i,j,k;
    double xi,xj,yi,yj,zi,zj;
    double r2,rrg,rrg2;

    rrg = rc+3000.0*10*dt;
    rrg2 = rrg*rrg;
    for(i=0;i<Nmt;i++) {
      k = 1;
      for(j=i+1;j<Nmt;j++) {
        xi = xx[i]; xj = xx[j]; yi = yy[i]; yj = yy[j]; zi = zz[i]; zj = zz[j];
        if (xi-xj>0.5*xMax) { xj += xMax; };
        if (xi-xj<-0.5*xMax) { xj -= xMax; };  
        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<rrg2) {
          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();
    }
    if (dispMode==5) {
      traceSet();
    }
  }

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

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

    for (i=0; i<Nmt; i++) {
      if (xx[i] < 0.0) { 
        xx[i] += xMax; 
      }
      if (xx[i] > xMax) {
        xx[i] -= xMax; 
      }
      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 (xi-xj>0.5*xMax) { xj += xMax; };
        if (xi-xj<-0.5*xMax) { xj -= xMax; };  
        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);
          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 i;
    double a;

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

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

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

}  

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