/* Al fcc crystal - express embedded atom method */
/* Embedded-atom Potential: Mishin et.al., Phys. Rev. B65 224114 (2002) */
/* coded by Ikeuchi Mitsuru */
/* ver 0.0.1   2005.01.28   */
/* ver 0.0.2   2005.04.04 registration() code improved */

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

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

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

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

  Dimension dim;
  Image imgOff;
  Graphics gOff;

  int sleepTime = 50;
  double dispScale = 20.0/3.4e-10;

  double sgm = 3.4e-10;        /* L-J sigma for Ar (m)   */
  double xMax = 16.0*sgm;       /* x-Box size in (m)      */
  double yMax = 16.0*sgm;       /* y-Box size in (m)      */
  double zMax = 16.0*sgm;       /* z-Box size in (m)      */

  int Nbase = 20;
  int Nmt = Nbase*Nbase*Nbase/2;           /* number of molecules    */
  int NN = Nmt + 1;
  double t = 0.0;              /* time (s)               */
  double dt = 0.5*1.0e-15;     /* time division (s)      */

  int Nsx = 8; /* xMax/2.0sgm */
  int Nsy = 8; /* yMax/2.0sgm */
  int Nsz = 8; /* zMax/2.0sgm */

  int tempMode = 0;
  double contTemp = 100.0;
  double scale = 0.8;
  int dispMode = 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 = 10.0*3.14/180.0;
  double dtheta = 0.0*3.14/180.0;
  double pai = 3.1415926536;

  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 regNr[][] = new int[NN][100];   /* registration */
  int section[][][][] = new int[Nsx][Nsy][Nsz][50];

  int reg[][] = new int[NN][100];   /* registration */
  double rijReg[][] = new double[NN][100];   /* registration */


  double mass = 26.9815*1.661e-27;
  double latticeConstant = 4.05e-10;

  double rcut = 5.95414; /* A */
  double dr = 0.001; /* A */
  double droh = 0.001;

  double pair[] = new double[8000];
  double density[] = new double[8000];
  double embedded[] = new double[8000];

  int rdf[] = new int[120];


  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(630,380);
    setBackground(Color.white);

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

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

    scr= new Scrollbar(Scrollbar.HORIZONTAL,100,10,10,810);
    scr.addAdjustmentListener(this);

    scs= new Scrollbar(Scrollbar.HORIZONTAL,80,10,20,160);
    scs.addAdjustmentListener(this);

    addMouseListener(this);  
    addMouseMotionListener(this);

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

    setLayout(new BorderLayout());
    Panel pnl = new Panel();
    pnl.setLayout(new GridLayout(1,6,5,0));
    pnl.add(new Label("Al fcc(100)"));
    pnl.add(ctc);
    pnl.add(scr);
    pnl.add(new Label("  "));
    pnl.add(cvw);
    pnl.add(scs);
    add(pnl,"North");

    setEAM();
    setInitialPosition();
    setWaku();
    repaint();
  }

  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() == ctc){
      tempMode = ctc.getSelectedIndex();
    } else if (ev.getSource() == cvw){
      dispMode = cvw.getSelectedIndex();
    }
  }

  public void adjustmentValueChanged(AdjustmentEvent ev){
    if(ev.getSource() == scr) { 
      contTemp = 1.0*(double)(scr.getValue());
      if (tempMode==0) {
        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;
    double sc,sz,tmp,clr,tm;

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

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

    gbx = 70;
    gby = 80;
    sc = dispScale*scale;
    sz = 0.5*4.05e-10*0.707*sc;

    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) {

      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==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 (rijReg[j][k]<4.1e-10) {
            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)(sz*(0.4*pz[j]/zMax+0.6));

        for (k=1; k<reg[j][0]; k++) {
          jj = reg[j][k];
          if (rijReg[j][k]<4.1e-10) {
            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)(2.0*sz*(0.4*pz[j]/zMax+0.6)/0.8);

        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)(sz*(0.4*pz[j]/zMax+0.6));

        tm = 0.5*mass*(vx[j]*vx[j]+vy[j]*vy[j]+vz[j]*vz[j])/(1.5*1.38e-23);
        tm = 0.66-tm/1000.0;
        if (tm<0.01) {
          tm = 0.01;
        }
        gOff.setColor(Color.getHSBColor((float)(tm),0.9f,0.7f));
        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);
      }
    }


    gbx = 500; gby = 100;
    gOff.setColor(Color.gray);
    for (i=0; i<100; i+=20) {
      gOff.drawLine(gbx+i,gby, gbx+i, gby+200);
    }
    gOff.drawLine(gbx,gby+100, gbx+100, gby+100);
    gOff.setColor(Color.black);
    gOff.drawRect(gbx,gby,100,200);
    gOff.drawString("0",gbx-5,gby+215);
    gOff.drawString("5 A",gbx+90,gby+215);
    gOff.setColor(Color.cyan);
    for (i=0; i<50; i++) {
      if (rdf[i]>0) {
        gOff.fillRect(gbx+i*2,gby+200-rdf[i]/40, 2, rdf[i]/40);
      }
    }

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

    gOff.drawString("box="+(int)(xMax*1.0e10+0.5)/10.0+" x "+(int)(yMax*1.0e10+0.5)/10.0+" x "+(int)(zMax*1.0e10+0.5)/10.0+" nm",630/6*4+10,60);

    gOff.setColor(Color.blue);
    gOff.drawString("t="+Math.floor(t*1.0e15+0.5)+"(fs)",630/6*0+10,40);
    gOff.drawString("T="+temperature()+" K",630/6*3+10,40);
/*
    gOff.drawString("reg max="+regMax()+" ",400,320);
    gOff.drawString("regNr max="+regNrMax()+" ",400,340);
    gOff.drawString("sec max="+secMax()+" ",400,360);
*/
  }


  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 regNrMax() {
    int i,m;

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

/*----------------------------------  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<Nmt/10; 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;
    }  
  }

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

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

  double temperature() {
    int i;
    double s;

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

/*-------------------- radial distribution function  ----------*/

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

    for (i=0; i<51; i++) {
      rdf[i]=0;
    }

    for (i=0; i<Nmt; i++) {
        for(k=1;k<reg[i][0];k++) {
        j = reg[i][k];
        rij=rijReg[i][k];
        if (rij<5.0e-10) {
          ir = (int)(Math.floor(rij*1.0e11+0.49999));
          rdf[ir] +=1;
        }
      }
    }
  }


/*-------------------------------------  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 EAM functions   -----------
*
*  pair[i]     : pair potential table  r = i*dr
*  density[i]  : electron density table  r = i*dr
*  embedded[i] : emdedded energy table  roh = i*droh
*
*  data for Aluminium  pair(r),density(r),embedded(roh) 
*  Mishin et.al., Phys. Rev. B65 224114 (2002)
*   "Embedded-atom Potential for B2-NiAl"
*
*--------------------------------------------------------------*/

  void setEAM() {
    int i;
    double rA, roh, ps, ms;

    double EAMdd = 2.22312;
    double EAMr0 = 3.21924;
    double EAMalp = 3.61338;
    double EAMq = 1.0881;
    double EAMdel = 0.00007600740772117544;
    double EAMs = 0.3984839;
    double EAMbet = 1.45222;
    double EAMeps = 0.0094920;
    double EAMa1 = -7.33;
    double EAMa2 = 9.5;
    double EAMa3 = -3.77;
    double EAMrc = 5.95414;
    double EAMh = 0.5002;

    for(i=0; i<8000; i++) {
      rA = dr*(double)(i);
      ps = EAMpsi( (rA - EAMrc)/EAMh );
      ms = Math.exp(-EAMq*EAMalp*(rA-EAMr0))-EAMq*Math.exp(-EAMalp*(rA-EAMr0));
      pair[i] = EAMdd*(ms + EAMdel)*ps;
      density[i] = EAMs*(rA*rA*Math.exp(-EAMbet*rA) + EAMeps)*ps;
    }
    for(i=0; i<8000; i++) {
      roh = droh*(double)(i);
      embedded[i] = EAMa1*roh + EAMa2*roh*roh + EAMa3*roh*roh*roh;
    }
  }

  double EAMpsi(double x) {
    double x4;

    if (x > 0.0) {
      return( 0.0 );
    } else {
      x4 = x*x*x*x;
      return( x4/(1 + x4) );
    }
  }


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

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

    a = 0.5*latticeConstant*1.12;
    i = 0;
    for (ix=0; ix<Nbase; ix++) {
      for (iy=0; iy<Nbase; iy++) {
        for (iz=0; iz<Nbase; iz++) {
          if ((ix+iy+iz)%2==0) {
            xx[i] = a*(double)(ix)+1.5*sgm;
            yy[i] = a*(double)(iy)+1.5*sgm;
            zz[i] = a*(double)(iz)+1.5*sgm;
            vx[i] = 100.0*Math.random()-50.0;
            vy[i] = 100.0*Math.random()-50.0;
            vz[i] = 100.0*Math.random()-50.0;
            ffx[i] = 0.0;
            ffy[i] = 0.0;
            ffz[i] = 0.0;
            i += 1;
          }
        }
      }
    }

    zSortInit();
  }



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

  void calcposition(){
    int i;
    
    if (tempMode==1 || t<200.0*dt) {
      vAjustment();
    }

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

  void timeEvolution(){
    int i; 
    double dtv2, a2, 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++) {
      a2 = dtv2/mass;
      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/mass;
      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] = 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];
      }
    }
  }

  void forceCalc() {
    int i,j,k;
    double fpi,rij,f,fxij,fyij,fzij;

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

    regProximity();
    for(i=0;i<Nmt;i++) {
      fpi = dFdroh(i);
      for(k=1;k<reg[i][0];k++) {
        j = reg[i][k];
        if (j>i) {
          rij = rij = rijReg[i][k];
          f = force(rij,fpi);
          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;
        }
      }
    }
  }

/*--------------------  registration of near atoms   ---*/

  void regNear() {
    int ip,jp,kp,iq;
    int i,j,k,i0,i1,j0,j1,k0,k1;
    double rrg,rrg2,r2;

    rrg = rcut*1.0e-10;
    rrg += 10000.0*dt*10;
    rrg2 = rrg*rrg;

    preRegistration();

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

      for(i=i0;i<=i1;i++) {
        for(j=j0;j<=j1;j++) {
          for(k=k0;k<=k1;k++) {
            for(iq=1;iq<=section[i][j][k][0];iq++) {
              jp = section[i][j][k][iq];
              if (jp!=ip) {
                r2=(xx[ip]-xx[jp])*(xx[ip]-xx[jp])+(yy[ip]-yy[jp])*(yy[ip]-yy[jp])+(zz[ip]-zz[jp])*(zz[ip]-zz[jp]);
                if (r2<rrg2) {
                  regNr[ip][kp]=jp;
                  kp += 1;
                }
              }
            }
          }
        }
      }
      regNr[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;
    }

  }

/*--------------------  embedded atom method calculation   ---*/

  double force(double r,double fpi) { 
    double ra,rt;

    ra = r*1.0e10;
    rt = -dpairdr(ra)-2.0*fpi*ddensdr(ra);

    return ( rt*1.6e-19/1.0e-10 );
  }

  void regProximity() {
    int i,j,k,jj;
    double rrg,rrg2,r2;

    rrg = rcut*1.0e-10;
    rrg2 = rrg*rrg;

    for(i=0;i<Nmt;i++) {
      k = 1;
      for(jj=1;jj<regNr[i][0];jj++) {
        j = regNr[i][jj];
        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<rrg2) {
          reg[i][k]=j;
          rijReg[i][k] = Math.sqrt(r2);
          k += 1;
        }
      }
      reg[i][0]=k;
    }
  }

  double dFdroh(int i) {
    int iroh;
    double rh,rt;

    rh = roh(i);
    iroh = (int)(rh/droh);
    rt = 0.0;
    if (rh>0.0) { 
      rt = 0.5*(embedded[iroh+1] - embedded[iroh-1])/droh;
    }
    return ( rt );
  }


  double roh(int i) {
    int j,k;
    double s;

    s = 0.0;
    for(k=1;k<reg[i][0];k++) {
      j = reg[i][k];
      s += density[ (int)(rijReg[i][k]*1.0e10/dr) ];
    }
    return(s);
  }

  double dpairdr(double r) {
    int ir;

    if (r<rcut) {
      ir = (int)(r/dr);
      return ( 0.5*(pair[ir+1] - pair[ir-1])/dr );
    } else {
      return ( 0.0 );
    }
  }

  double ddensdr(double r) {
    int ir;

    if (r<rcut) {
      ir = (int)(r/dr);
      return ( 0.5*(density[ir+1] - density[ir-1])/dr );
    } else {
      return ( 0.0 );
    }
  }

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

}  

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