/** applet No. 1149
 *
 * smoothed sand - discrete element method 3D
 * - multi thread  DEM3D :: display - asynchronous
 *
 * Created by Ikeuchi Mitsuru on April 01 2007.
 * Copyright (c) 2007 Ikeuchi Mitsuru. All rights reserved.
 *
 * ver 0.0.1   2007.04.01  created
 * ver 0.0.2   2007.06.18  improved code
 *
 */

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

public class smoothedSandMtDEM3D extends Applet
  implements MouseListener, MouseMotionListener,
    ItemListener, ActionListener, AdjustmentListener, Runnable {

  // ------------------------------------ preset field -----------

  Thread th = null; // for run()-paint() thread
  Dynamics3D d3d = null;
  DisplayD3D dsp = new DisplayD3D();

  // for event
  Choice ch_mat,ch_view;
  Button bt_reset, bt_startStop, bt_step;
  Scrollbar sc_gravity, sc_depth, sc_scale;

  // for off-paint buffer
  Dimension dim;
  Image imgOff;
  Graphics gOff;

  int dgX, dgY, dgXb,dgYb; // mouse

  int sleepTime = 50;
  int dispMode = 2;
  int thCount = 0;


  // ------------------------------ applet main thread -----------

  public void init() {
    resize(630,420);
    setBackground(Color.white);

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

    ch_mat = new Choice();
    ch_mat.add("fixed");
    ch_mat.add("A");
    ch_mat.add("B");
    ch_mat.add("C");
    ch_mat.addItemListener(this);
    ch_mat.select("B");

    ch_view = new Choice();
    ch_view.add("ball");
    ch_view.add("line"); 
    ch_view.add("ball+line");
    ch_view.add("velocity");
    ch_view.addItemListener(this);
    ch_view.select("ball+line");

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

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

    bt_step = new Button("step");
    bt_step.addActionListener(this); 

    sc_gravity = new Scrollbar(Scrollbar.HORIZONTAL,98,10,0,510);
    sc_gravity.addAdjustmentListener(this);

    sc_depth = new Scrollbar(Scrollbar.HORIZONTAL,50,10,0,110);
    sc_depth.addAdjustmentListener(this);

    sc_scale = new Scrollbar(Scrollbar.HORIZONTAL,100,10,50,210);
    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(bt_reset);
    pnl.add(bt_startStop);
    pnl.add(new Label("  "));
    pnl.add(sc_gravity);
    pnl.add(sc_depth);
    pnl.add(ch_view);
    add(pnl,"North");

  }

  public void start() {
    if (d3d == null) {
      d3d = new Dynamics3D();
      d3d.start();
    }
    if (th == null) {
      th = new Thread(this);
      th.start();
    }
  }

  public void stop() {
    if (th != null) th = null;
    if (d3d != null) d3d = null;
  }


  // ---------------------------------- event listener -----------

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

  public void actionPerformed(ActionEvent ev){
    if(ev.getSource() == bt_reset){ 
      d3d.reset();
      thCount = 0;
    } else if (ev.getSource() == bt_startStop){
      if (d3d.getStartSW()==0) {
        d3d.setStartSW(1);
      } else {
        d3d.setStartSW(0);
      }
    } else if (ev.getSource() == bt_step){
      if (d3d.getStartSW()==0) {
        d3d.setStepSW();
      }
    }
  }

  public void adjustmentValueChanged(AdjustmentEvent ev){
    if (ev.getSource() == sc_gravity) { 
      d3d.setGravity( 0.1*(double)(sc_gravity.getValue()) );
    } else if (ev.getSource() == sc_depth) { 
      dsp.setDepth( 0.01*(double)(sc_depth.getValue()) );
    } else if (ev.getSource() == sc_scale) { 
      dsp.setViewScale( 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;
    }
	dsp.setViewDelta((dgX-dgXb), (dgY-dgYb));
  }



  // ========================= run() - paint() loop ==============

  public void run() {
    while (th != null) {
      try {
        Thread.sleep(sleepTime);
      } catch (InterruptedException e) { }
      thCount += 1;
      offPaint();
      repaint();
    }
  }

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

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

  private void offPaint() {
    if (d3d != null) {
      dsp.plotGraph(gOff, d3d, dispMode, thCount);
    }
  }

}  



// ================================= display D3D class ===========

class DisplayD3D {

  Graphics gOff;
  Dynamics3D d3d;

  private int Nmt;

  private double xMax = Dynamics3D.xMax;
  private double yMax = Dynamics3D.yMax;
  private double zMax = Dynamics3D.zMax;
  private double AU = Dynamics3D.AU;
  private double AA = Dynamics3D.AA;

  private double zDepth = xMax;
  private double dispWidth = 250.0;
  private double dispScale = (dispWidth/xMax);
  private double viewScale = 1.0;
  private double depth = 0.5;

  private double cx = 0.5*xMax;
  private double cy = 0.5*yMax;
  private double cz = 0.5*zMax;
  private double theta = -20.0*3.14/180.0;
  private double fai = 10.0*3.14/180.0;

  private int NN = 10000;
  private int srtz[][] = new int[2][NN];

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

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

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

  private 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}
  };

  private int drawnCount = 0;


  // ------------------------------- class constructor -----------

  DisplayD3D() {
    setWaku();
  }


  // ----------------------------------- class methods -----------

  public void plotGraph(Graphics gg, Dynamics3D ad3d, int dispMode, int thCount) {
    int d3dCount, gbx, gby, gx;

    gOff = gg;
    d3d = ad3d;

    if (d3d==null) return;
    d3dCount = d3d.getCount();
    if (d3dCount==drawnCount) return;
    drawnCount = d3dCount;

    Nmt = d3d.getNmt();

    gOff.setColor(Color.white);
    gOff.fillRect(0,0,630,420);

    rotate(theta,fai);
    zSort();

    gbx = 70;
    gby = 90;

    if (dispMode==0) {
      ballPlot(gbx,gby, 1.2, 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) {
      velocity3DPlot(gbx,gby, 20.0,0);

    } else if (dispMode==4) {
      ;

    } else if (dispMode==5) {
      ;

    }

    gbx = 630/6;
    gOff.setColor(Color.black);
    gOff.drawString("t="+(int)(d3d.getTime()*10000.0+0.5)/10.0+" ms",gbx*0+10,40);
    if (d3d.getStartSW()==1) {
      gOff.drawString("started",630/6*1+10,40);
    } else {
      gOff.drawString("stop",630/6*1+10,40);
    }
    gOff.setColor(Color.black);

    gOff.drawString("gravity="+(int)(d3d.getGravity()/9.8*100.0+0.5)/100.0+" g",gbx*3+10,40);
    gOff.drawString("depth="+(int)(depth*100.0+0.5)+"%",gbx*4+10,40);
    gOff.drawString("view",gbx*5+10,40);

    gx = 450;
    gOff.setColor(Color.black);
    gOff.drawString("Box="+(int)(xMax*1000.0+0.5)/10.0+" x "+(int)(yMax*1000.0+0.5)/10.0+" x "+(int)(zMax*1000.0+0.5)/10.0+" cm",gx,60);

    gOff.drawString("regMax="+d3d.regMax()+"",530,80);
    gOff.drawString("secMax="+d3d.secMax()+"",530,100);

    gOff.setColor(Color.black);
    gOff.drawString("thread D3D = "+d3d.getCount()+" ",20,400);
    gOff.drawString("thread disp = "+thCount+" ",220,400);
  }

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

  private void ballPlot(int gbx, int gby, double size, int imode) {
    int i,j,k,jj,gx,gy,g2x,g2y,gr;
    double sz,scl,tm,r,r0,col;

    drawWaku(gbx,gby,0);

    scl = dispScale*viewScale;
    sz = size*viewScale/AA;

    for (i=0; i<Nmt; i++) {
      j = srtz[0][i];
	  if (d3d.getzz(j)/zMax>depth) continue;
      gx = (int)(scl*px[j])+gbx;
      gy = (int)(scl*py[j])+gby;
      gr = (int)(sz*d3d.getDia(j)*(0.3*(pz[j]/zDepth)+0.7));
      if (gr<2) gr = 2;
      if (imode==1 || imode==2) {
        for (k=1; k<d3d.getReg(j,0); k++) {
          jj = d3d.getReg(j,k);
          r = d3d.distance(j,jj);
          r0 = d3d.getDia(j,jj);
          if ( r<1.2*r0 ) {
            g2x = (int)(scl*px[jj])+gbx;
            g2y = (int)(scl*py[jj])+gby;
            if (d3d.bondQ(j,jj)==-1) {
              col = 0.33-50.0*(r/r0-1.0);if (col<0.01) col = 0.01;
              if (col>0.66) col = 0.66;
              gOff.setColor(Color.getHSBColor((float)(col),0.5f,0.8f));
            } else {
              gOff.setColor(Color.gray);
            }
            gOff.drawLine(gx,gy, g2x, g2y);
          }
        }
      }
      if (imode==0 || imode==2) {
        gOff.setColor(Color.getHSBColor(
          d3d.getCol(j),0.8f,(float)(0.4*pz[j]/zDepth+0.3)));
        gOff.fillOval(gx-gr/2,gy-gr/2, gr, gr);
      }
    }
    drawWaku(gbx,gby,1);
  }

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

    dt = d3d.getdt();
    drawWaku(gbx,gby,0);

    cosTh = Math.cos(theta); sinTh = Math.sin(theta);
    cosFi = Math.cos(fai); sinFi = Math.sin(fai);
    sc = dispScale*viewScale;
    sz = 0.3*viewScale/AA;

    for (i=0; i<Nmt; i++) {
      j = srtz[0][i];
      gx = (int)(sc*px[j])+gbx;
      gy = (int)(sc*py[j])+gby;
      gr = (int)(sz*d3d.getDia(j)*(0.3*(pz[j]/zDepth)+0.7));

      if (imode==0) {
        p2x = d3d.getxx(j)+mag*d3d.getvx(j)*20*dt;
        p2y = d3d.getyy(j)+mag*d3d.getvy(j)*20*dt;
        p2z = d3d.getzz(j)+mag*d3d.getvz(j)*20*dt;
      } else {
	    m = mag*20*dt*0.01*d3d.getMass(j)/AU;
        p2x = d3d.getxx(j)+m*d3d.getvx(j);
        p2y = d3d.getyy(j)+m*d3d.getvy(j);
        p2z = d3d.getzz(j)+m*d3d.getvz(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;
      if (d3d.getvx(j)>0) {
        gOff.setColor(Color.blue);
      } else {
        gOff.setColor(Color.red);
      }
      gOff.drawLine(gx,gy, g2x,g2y);
	  
      gOff.setColor(Color.getHSBColor(
        d3d.getCol(j),0.8f,(float)(0.4*pz[j]/zDepth+0.3)));
      gOff.fillOval(gx-gr/2,gy-gr/2, gr, gr);
    }

    drawWaku(gbx,gby,1);
  }


  private 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.black);
          gOff.drawLine(gx,gy, g2x, g2y);
        }
      }
    }
  }

  private 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);
  }

  //

  private 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

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

    for (i=0; i<Nmt; i++) {
      srtz[0][i] = i;
      srtz[1][i] = (int)(32767.0*pz[i]/zMax);
    }
    qSort(0,Nmt-1);    
  }

  private void qSort(int i,int j) {
    int k,p;

    if(i==j) return;
	p = i+1;
    while (p<=j && srtz[1][i]==srtz[1][p]) p++;
    if (p<=j) {
      if (srtz[1][i]>=srtz[1][p]) p = i;
      k = qSortPartition(i,j,srtz[1][p]);
      qSort(i,k-1);
      qSort(k,j);
    }
  }

  private int qSortPartition(int i,int j, int x) {
    int l,r,w;

    l = i; r = j;
    while (l<=r) {
      while (l<=j && srtz[1][l]<x) l++;
      while (r>=i && srtz[1][r]>=x) r--;
      if (l>r) break;
      w = srtz[0][l]; srtz[0][l] = srtz[0][r]; srtz[0][r] = w;
      w = srtz[1][l]; srtz[1][l] = srtz[1][r]; srtz[1][r] = w;
      l++; r--;
    }
    return ( l );
  }

  // rotate 

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

    cosTh = Math.cos(th); sinTh = Math.sin(th);
    cosFi = Math.cos(fi); sinFi = Math.sin(fi);
    for (i=0; i<Nmt; i++) {
	  x = d3d.getxx(i); y = d3d.getyy(i); z = d3d.getzz(i);
      py[i] = cosFi*(y-cy)+sinFi*(z-cz) + cy; 
      pz[i] = -sinFi*(y-cy)+cosFi*(z-cz) + cz;
      px[i] = cosTh*(x-cx)+sinTh*(pz[i]-cz) + cx; 
      pz[i] = -sinTh*(x-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;
      pwkx[i] = cosTh*(wkx[i]-cx)+sinTh*(pwkz[i]-cz) + cx; 
      pwkz[i] = -sinTh*(wkx[i]-cx)+cosTh*(pwkz[i]-cz) + cz;
    }  
  }


  // ------------------------------------- I/O methods -----------

  public void setViewDelta(double xDisplacement, double yDisplacement) {
    theta += 0.5*3.14/180.0*xDisplacement;
    fai += 0.5*3.14/180.0*yDisplacement;
  }

  public void setDepth(double d) { depth = d; }
  public double getDepth() { return depth; }
  public void setViewScale(double s) { viewScale = s; }
  public double getViewScale() { return viewScale; }
}



// ================== discrete element method 3D class ===========

class Dynamics3D extends Thread {

  public static final double dt = 1.0e-4;
  public static final double xMax = 20.0*0.01;
  public static final double yMax = 20.0*0.01;
  public static final double zMax = 20.0*0.01;

  private double t = 0.0;

  private int Nmt = 10000;
  private int NN = Nmt + 1;

  private int Nsx = 20;
  private int Nsy = 20;
  private int Nsz = 20;

  private int incRate = 20;

  private double gravity = 9.8;
  private double spin = 2.0;
  private int MAT1 = 2;

  private double rc = 0.01;
  private double rc2 = rc*rc;
  private double hh = rc/1000.0;


  public static final double  AU = 1.0e-3;
  public static final double  EE = 0.0001;
  public static final double  AA = 0.001;

  private double material[][] = {
  // 0:mass(AU) 1:charge 2:D(EE) 3:A(/AA) 4:r0(AA) 5:damp 6:color
    { 10.0 *AU, 0.0*EE, 0.1*EE, 2.0/AA, 8.0*AA,100.0, 0.85 }, // fixed ball
    {  1.0 *AU, 0.0*EE, 0.5*EE, 2.0/AA, 8.0*AA, 50.0, 0.01 }, // 1 A
    {  5.0 *AU, 0.0*EE, 1.0*EE, 2.0/AA, 8.0*AA,100.0, 0.10 }, // 2 B
    { 10.0 *AU, 0.0*EE, 0.5*EE, 2.0/AA, 8.0*AA, 50.0, 0.20 }  // 3 C
  };

  private String materialStr[] = {
    "fixed", "A" ,"B","C" };
  private int NmatKind = 4;
  
  private int kind[] = new int[NN];
  private double xx[] = new double[NN];
  private double yy[] = new double[NN];
  private double zz[] = new double[NN];
  private double vx[] = new double[NN];
  private double vy[] = new double[NN];
  private double vz[] = new double[NN];
  private double ffx[] = new double[NN];
  private double ffy[] = new double[NN];
  private double ffz[] = new double[NN];

  private int bond[][] = new int[NN][20];
  private int reg[][] = new int[NN][100];
  private int section[][][][] = new int[Nsx][Nsy][Nsz][30];

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

  private int resetSW = 0;
  private int startSW = 1;
  private int stepSW = 1;
  private int sleepTime = 1;
  private int stopSleepTime = 100;
  private int count = 0;


  // ------------------------------- class constructor -----------

  Dynamics3D() {
    setInitialCondition();
  }


  // -------------------------------------- thread run -----------

  public void run() {
    while (true) {
      count += 1;
      timeEvolution();
      if (sleepTime>0) {
        try {
          Thread.sleep(sleepTime);
        } catch (InterruptedException e) { }
      }
    }
  }


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

  private void setInitialCondition() {
    int i; 
    double s;

    setForceTable();

    t = 0.0;
    count = 0;

    i = 0;
	i = setCloud(i, 2);
	i = setFloor(i, 0.7*yMax, 0);
    Nmt = i;

    //setBond();
  }

  private int setCloud(int ii, int mat) {
    int i,ix,iy,iz,nx,ny,nz;
    double a;

    i = ii;

    a = 1.4*material[mat][4];
    nx = (int)(xMax/a);
    ny = (int)(0.6*yMax/a);
    nz = (int)(zMax/a);

    for (ix=0; ix<nx; ix++) {
      for (iy=0; iy<ny; iy++) {
        for (iz=0; iz<nz; iz++) {
          kind[i] = mat;
          xx[i] = a*(ix+0.5);
          yy[i] = a*(iy+0.5);
		  zz[i] = a*(iz+0.5);
          vx[i] = 1.0*(Math.random()-0.5);
          vy[i] = 1.0*(Math.random()-0.5);
          vz[i] = 1.0*(Math.random()-0.5);
          ffx[i] = 0.0;
          ffy[i] = 0.0;
          ffz[i] = 0.0;
          i += 1;
        }
      }
    }
    return ( i );
  }

  private int setSand4Cloud(int ii,int mat) {
    int i,ix,iy,iz,nx,ny,nz;
    double a,aa;

    i = ii;

    a = 2.2*material[mat][4];
    nx = (int)(xMax/a);
    ny = (int)(0.65*yMax/a);
    nz = (int)(zMax/a);
    aa = xMax/nx;
    for (ix=0; ix<nx; ix++) {
      for (iy=0; iy<ny; iy++) {
        for (iz=0; iz<nz; iz++) {
          i = setSand4(i, ix*a+0.2*a, iy*a+0.2*a, iz*a+0.2*a, mat);
		}
      }
    }
    return ( i );
  }

  private int setSand4(int ii, double xPos, double yPos, double zPos, int mat) {
    int i;
    double a;

    i = ii;

    a = 1.0*material[mat][4];

    kind[ii] = mat;
    xx[ii] = xPos;
    yy[ii] = yPos;
    zz[ii] = zPos;
    vx[ii] = 1.0*(Math.random()-0.5);
    vy[ii] = 1.0*(Math.random()-0.5);
    vz[ii] = 1.0*(Math.random()-0.5);
    ffx[ii] = 0.0;
    ffy[ii] = 0.0;
    ffz[ii] = 0.0;
    i += 1;

    kind[ii+1] = mat;
    xx[ii+1] = xPos;
    yy[ii+1] = yPos+a;
    zz[ii+1] = zPos;
    vx[ii+1] = 1.0*(Math.random()-0.5);
    vy[ii+1] = 1.0*(Math.random()-0.5);
    vz[ii+1] = 1.0*(Math.random()-0.5);
    ffx[ii+1] = 0.0;
    ffy[ii+1] = 0.0;
    ffz[ii+1] = 0.0;
    i += 1;

    kind[ii+2] = mat;
    xx[ii+2] = xPos+0.866*a;
    yy[ii+2] = yPos+0.5*a;
    zz[ii+2] = zPos;
    vx[ii+2] = 1.0*(Math.random()-0.5);
    vy[ii+2] = 1.0*(Math.random()-0.5);
    vz[ii+2] = 1.0*(Math.random()-0.5);
    ffx[ii+2] = 0.0;
    ffy[ii+2] = 0.0;
    ffz[ii+2] = 0.0;
    i += 1;

    kind[ii+3] = mat;
    xx[ii+3] = xPos+0.2887*a;
    yy[ii+3] = yPos+0.5*a;
    zz[ii+3] = zPos+0.8165*a;
    vx[ii+3] = 1.0*(Math.random()-0.5);
    vy[ii+3] = 1.0*(Math.random()-0.5);
    vz[ii+3] = 1.0*(Math.random()-0.5);
    ffx[ii+3] = 0.0;
    ffy[ii+3] = 0.0;
    ffz[ii+3] = 0.0;
    i += 1;

    bond[ii][0] = ii+1; bond[ii][1] = ii+2; bond[ii][2] = ii+3;
    bond[ii+1][0] = ii; bond[ii+1][1] = ii+2; bond[ii+1][2] = ii+3;
    bond[ii+2][0] = ii; bond[ii+2][1] = ii+1; bond[ii+2][2] = ii+3;
    bond[ii+3][0] = ii; bond[ii+3][1] = ii+1; bond[ii+3][2] = ii+2;

    return ( i );
  }


  int setFloor(int ii, double yPos, int mat) {
    int i,ix,iz,nx,nz;
    double a,ax,az,x,z;

    i = ii;

    a = material[mat][4];
    nx = 2*((int)(xMax/2.0/a+0.5)); ax = xMax/nx;
    nz = 2*((int)(zMax/2.0/a+0.5)); az = zMax/nz;

    for (ix=0; ix<nx; ix++) {
      for (iz=0; iz<nz; iz++) {
        x = ax*(ix+0.5); z = az*(iz+0.5);
        if ((x-0.5*xMax)*(x-0.5*xMax)+(z-0.5*zMax)*(z-0.5*zMax)>8.0*a*a) {
          kind[i] = mat;
          xx[i] = ax*(ix+0.5);
          yy[i] = yPos;
          zz[i] = az*(iz+0.5);
		  
          vx[i] = 0.0;
          vy[i] = 0.0;
          vz[i] = 0.0;
          ffx[i] = 0.0;
          ffy[i] = 0.0;
          ffz[i] = 0.0;
          i += 1;
        }
      }
    }
    return ( i );
  }

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

  private 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(material[i][2]*material[j][2]);
        a = 0.5*(material[i][3]+material[j][3]);
        r0 = 0.5*(material[i][4]+material[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];
        }
      }
    }
  }

  private 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 );
  }


  // ---------------------------------- time evolution -----------

  private void timeEvolution(){

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

    if (startSW==1) {
      timeStep();

    } else {
      if (stepSW==1) {
        timeStep();
        stepSW = 0;
      }
      try {
        Thread.sleep(stopSleepTime);
      } catch (InterruptedException e) { }
    }
  }

  private void timeStep() {
    int i;

    registration();
    for (i=0; i<incRate; i++) {
      timeStep1();
    }
  }

  private void timeStep1() {
    int i; 
    double dtv2, a2;

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

    for (i=0; i<Nmt; i++) {
      if (kind[i]>0) {
        a2 = dtv2/material[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++) {
      if (kind[i]>0) {
        a2 = dtv2/material[kind[i]][0];
        vx[i] += a2*ffx[i];
        vy[i] += a2*ffy[i];
        vz[i] += a2*ffz[i];
      }
    }

    setBoundary();
  }

  private void forceCalc() {
    int i,j,k,ki,kj;
    double xij,yij,zij,r2,rij,f,fxij,fyij,fzij;

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

    for(i=0;i<Nmt;i++) {
      for(k=1;k<reg[i][0];k++) {
        j = reg[i][k];
		xij = xx[i]-xx[j]; yij = yy[i]-yy[j]; zij = zz[i]-zz[j];
        r2 = xij*xij + yij*yij + zij*zij;
        if (r2<rc2) {
          rij = Math.sqrt(r2);
          ki = kind[i]; kj = kind[j];
          f = force(rij,ki,kj);
		  f += -0.5*(material[ki][5]+material[kj][5])*(xij*(vx[i]-vx[j])+yij*(vy[i]-vy[j])+zij*(vz[i]-vz[j]));
          fxij = f*xij/rij;
          fyij = f*yij/rij;
          fzij = f*zij/rij;

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

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

    for(i=0;i<Nmt;i++) {
      for(k=0;k<12;k++) {
        j = bond[i][k]; if (j<0) break;
        if (j>i) {
		  xij = xx[i]-xx[j]; yij = yy[i]-yy[j]; zij = zz[i]-zz[j];
          r2 = xij*xij + yij*yij + zij*zij;
          rij = Math.sqrt(r2);
	      ki = kind[i]; kj = kind[j];
          f = -100000000.0*(material[ki][2]+material[kj][2])*(rij-0.5*(material[ki][4]+material[kj][4]));
          fxij = f*xij/rij;
          fyij = f*yij/rij;
          fzij = f*zij/rij;

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

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

  }

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

    i = (int)(r/hh);
    a = r - i*hh;
    ret = ((hh-a)*forceTable[ki][kj][i] + a*forceTable[ki][kj][i+1])/hh;

    return( ret );
  }

  private void setBoundary() {
    int i; 
    double rr;

    rr = 0.9;
    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];
      }
    }
  }

  // registration

  private void registration() {
    int i,j,k,ip,jp,kp,i0,i1,j0,j1,k0,k1,iq;
    double r2,rreg,rreg2;
    double x,y,z;

    preRegistration();

    rreg = rc + 1.0*incRate*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); if (j0<0) j0 = 0;
      j1 = (int)(Nsy*(yy[ip]+rreg)/yMax); if (j1>=Nsy) j1 = Nsy-1;
      k0 = (int)(Nsz*(zz[ip]-rreg)/zMax); if (k0<0) k0 = 0;
      k1 = (int)(Nsz*(zz[ip]+rreg)/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<rreg2) {
                  reg[ip][kp]=jp;
                  kp += 1;
                }

              }
            }
          }
        }
      }
      reg[ip][0]=kp;
    }
  }

  private 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;
    }
  }


  // ----------------------------------------- utility -----------

  // bond manager

  private void clearBond() {
    int i,j,ip;
    double r,r0;

    for (i=0; i<Nmt; i++) {
      for (ip=0; ip<12; ip++) {
        bond[i][ip] = -1;
      }
    }
  }

  public int bondQ(int i, int j) {
    int ip;

    for (ip=0; ip<12; ip++) {
      if (bond[i][ip]==j) {
        return(-1);
      }
    }
    return(0);
  }

  public double distance(int i, int j) {
    double xij,yij,zij;

    xij = xx[i]-xx[j]; yij = yy[i]-yy[j]; zij = zz[i]-zz[j];
    return(Math.sqrt(xij*xij+yij*yij+zij*zij));
  }

  //

  public int regMax() {
    int i,m;

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

  public 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);
  }


  // ------------------------------------- I/O methods -----------

  // control
  public void reset() { resetSW = 1; }
  public void setStartSW(int sw) { startSW = sw; }
  public int getStartSW() { return startSW; }
  public void setStepSW() { stepSW = 1; }
  public int getCount() { return count; }

  public void setGravity(double g) { gravity = g; }
  public double getGravity() { return gravity; }
  public void setSpin(double s) { spin = s; }
  public double getSpin() { return spin; }

  // get data
  public double getTime() { return t; }
  public double getdt() { return dt; }
  public int getNmt() { return Nmt; }
  public double getxx(int i) { return xx[i]; }
  public double getyy(int i) { return yy[i]; }
  public double getzz(int i) { return zz[i]; }
  public double getvx(int i) { return vx[i]; }
  public double getvy(int i) { return vy[i]; }
  public double getvz(int i) { return vz[i]; }
  public double getMass(int i) { return material[kind[i]][0]; }
  //public double getPotentialD(int i) { return material[kind[i]][2]; }
  //public double getPotentialA(int i) { return material[kind[i]][3]; }
  public double getDia(int i) { return material[kind[i]][4]; }
  public double getDia(int i, int j) {
    return 0.5*(material[kind[i]][4]+material[kind[j]][4]); }
  public float getCol(int i) { return (float)material[kind[i]][6]; }
  public int getReg(int i, int j) { return reg[i][j]; }

}