/** applet No. 1178
 *
 * crystallization - kinetic Monte-Carlo Method 3D
 *
 * Created by Ikeuchi Mitsuru on June 03 2007.
 * Copyright (c) 2007 Ikeuchi Mitsuru. All rights reserved.
 *
 * ver 0.0.1   2007.06.03  created
 *
 */

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

public class crystallizationMtKMC3D extends Applet
  implements MouseListener, MouseMotionListener,
    ItemListener, ActionListener, AdjustmentListener, Runnable {

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

  Thread th = null; // for run()-paint() thread
  KMC3D kmc = null;

  // for event
  Choice ch_view;
  Button bt_reset, bt_startStop;
  Scrollbar sc_nn, sc_add, sc_qqhop, sc_qqnb, sc_kT;

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

  // KMC field variable copy
  int NNx = 36;
  int NNy = 36;
  int NNz = 36;
  int NNa = 0;
  double ddh = 1.0e-9;
  double xMax = ddh*NNx;
  double yMax = ddh*NNy;
  double zMax = ddh*NNz;

  // control 3D
  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;

  // display 3D
  int dispWidth = 630;
  int dispHeight = 420;
  int sleepTime = 50;
  int dispMode = 1;

  double dispScale = (240.0/xMax);
  double viewScale = 1.0;

  int NNN = 20000;
  int srtz[][] = new int[2][NNN];
  double px[] = new double[NNN]; 
  double py[] = new double[NNN]; 
  double pz[] = new double[NNN]; 
  double wkx[] = new double[8]; 
  double wky[] = new double[8]; 
  double wkz[] = new double[8]; 
  double pwkx[] = new double[8]; 
  double pwky[] = new double[8]; 
  double pwkz[] = new double[8]; 
  int boxp[][] = {
   {0,1},{0,2},{0,4},{1,3},{1,5},{2,3},{2,6},{4,5},{4,6},{3,7},{5,7},{6,7}
  };

  int thCount = 0;

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

  public void init() {

    resize(dispWidth,dispHeight);
    setBackground(Color.white);

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

    ch_view = new Choice();
    ch_view.add("0 yellow");
    ch_view.add("1 magenta");
    ch_view.add("2 green");
    ch_view.addItemListener(this);
    ch_view.select("1 magenta");

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

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

    sc_nn= new Scrollbar(Scrollbar.HORIZONTAL,100,10,1,210);
    sc_nn.addAdjustmentListener(this);

    sc_add= new Scrollbar(Scrollbar.HORIZONTAL,50,10,0,210);
    sc_add.addAdjustmentListener(this);

    sc_qqhop= new Scrollbar(Scrollbar.HORIZONTAL,20,10,0,110);
    sc_qqhop.addAdjustmentListener(this);

    sc_qqnb= new Scrollbar(Scrollbar.HORIZONTAL,30,10,0,110);
    sc_qqnb.addAdjustmentListener(this);

    sc_kT= new Scrollbar(Scrollbar.HORIZONTAL,60,10,25,210);
    sc_kT.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(sc_add);
    pnl.add(sc_qqhop);
    pnl.add(sc_qqnb);
    pnl.add(sc_kT);
    add(pnl,"North");
  }

  public void start() {
    if (kmc == null) {
      kmc = new KMC3D();
      kmc.start();
    }
    if (th == null) {
      th = new Thread(this);
      th.start();
    }
  }

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


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

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

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

  public void adjustmentValueChanged(AdjustmentEvent ev){
    if (ev.getSource() == sc_add) { 
      kmc.setAddingRate( 0.001*(double)(sc_add.getValue()) );
	  
    } else if (ev.getSource() == sc_qqhop) { 
      kmc.setQHopping( 0.01*(double)(sc_qqhop.getValue()) );

    } else if (ev.getSource() == sc_qqnb) { 
      kmc.setQNeighbor( 0.01*(double)(sc_qqnb.getValue()) );

    } else if (ev.getSource() == sc_kT) { 
      kmc.setKT( 0.001*(double)(sc_kT.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);
  }



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

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

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

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


  // --------------------------------------- off-paint -----------

  private void offPaint() {

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

    NNa = kmc.getNNa();
    NNx = kmc.getNNx();
    NNy = kmc.getNNy();
    NNz = kmc.getNNz();
    ddh = kmc.getddh();
    xMax = ddh*NNx;
    yMax = ddh*NNy;
    zMax = ddh*NNz;

    if (dispMode==0) {
      dispLattice(30, 80, 5);
      gOff.setColor(Color.black);
      gOff.drawRect(30,80,5*NNx,5*NNy);

    } else if (dispMode==1) {
      ball3dPlot(80, 100);

    } else if (dispMode==2) {
      ;

    }

    gOff.setColor(Color.black);
    gOff.drawString("t="+(int)(kmc.getTime()*1e14+0.5)/100.0+" ps",10,40);
    if (kmc.getStartSW()==0) {
      gOff.drawString("stopped",dispWidth/6*1+10,40);
    } else {
      gOff.drawString("started",dispWidth/6*1+10,40);
    }
    gOff.drawString("add rate="+(int)(kmc.getAddingRate()*1000.0+0.5)/1000.0+"",dispWidth/6*2,40);
    gOff.drawString("N="+NNa+"",dispWidth/6*2+10,60);
    gOff.drawString("Qhop="+(int)(kmc.getQHopping()*100.0+0.5)/100.0+" eV",dispWidth/6*3+10,40);
    gOff.drawString("Qnbr="+(int)(kmc.getQNeighbor()*100.0+0.5)/100.0+" eV",dispWidth/6*4+10,40);
    gOff.drawString("kT="+(int)(kmc.getKT()*1000+0.5)/1000.0+" eV",dispWidth/6*5+10,40);
    gOff.drawString("  ="+(int)(kmc.getKT()*11600+0.5)+" K",dispWidth/6*5+10,60);

    //gOff.setColor(Color.blue);
    //gOff.drawString("nn="+numberOfAdatom()+"",dispWidth/6*2+10,60);

    gOff.setColor(Color.black);
    gOff.drawString("thread KMC = "+kmc.getCount()+" ",400,380);
    gOff.drawString("thread disp = "+thCount+" ",400,400);
  }


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

  private void dispLattice(int gx, int gy, int span) {
    int i,j,ir, ia;
    double col;

    ir = span;
    for(i=0;i<NNx;i++) {
      for(j=0;j<NNy;j++) {
        ia = kmc.getLattice(i,j,18);
        if (ia>=0) {
          if (kmc.getKind(ia)==0) {
            gOff.setColor(Color.getHSBColor(0.1f,0.6f,0.8f));
          } else {
            gOff.setColor(Color.getHSBColor(0.05f,0.6f,0.8f));
          }
          gOff.fillRect(gx+span*i,gy+span*j, ir, ir);
        }
      }
    }
  }

  //

  private void ball3dPlot(int gbx, int gby) {
    int i,j,gx,gy,gz;
    double sc,sz;

    setWaku();
    rotate(theta,fai);
    zSort();

    drawWaku(gbx,gby,0);

    sc = dispScale*viewScale;

    for (i=0; i<NNa; i++) {
      j = srtz[0][i];
	  sz = 6;
      gx = (int)(sc*px[j])+gbx;
      gy = (int)(sc*py[j])+gby;
      gz = (int)(sz*(0.4*pz[j]/zMax+0.6));

      if (kmc.getKind(j)==0) {
        gOff.setColor(Color.getHSBColor(0.15f,0.6f,(float)(0.5*pz[j]/zMax+0.3)));
      } else {
        gOff.setColor(Color.getHSBColor(0.05f,0.6f,(float)(0.5*pz[j]/zMax+0.3)));
      }

      gOff.fillOval(gx-gz/2,gy-gz/2, gz, gz);
    }

    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.gray);
          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;

    i=0;
    sgm = ddh;

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

  //

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

    cosTh = Math.cos(th); sinTh = Math.sin(th);
    cosFi = Math.cos(fi); sinFi = Math.sin(fi);

    for (i=0; i<NNa; i++) {
      y = ddh*kmc.getAtom(i,1); z = ddh*kmc.getAtom(i,2);
      py[i] = cosFi*(y-cy)+sinFi*(z-cz) + cy; 
      pz[i] = -sinFi*(y-cy)+cosFi*(z-cz) + cz;
    } 
    for (i=0; i<NNa; i++) {
      x = ddh*kmc.getAtom(i,0);
      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;
    } 
    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;
    }  
  }

  //

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

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

}



// ================== kinetic Monte-Carlo Method 2D ==============

class KMC3D extends Thread {

  private double t = 0.0;
  private double dt = 1.0;
  private double ddh = 1.0e-9;

  private double qqHopping = 0.2;
  private double qqNeighbor = 0.3;
  private double kT = 0.06;
  private double addingRate = 0.05;
  private double totalRate = 1.0e15;

  private int NNx = 36;
  private int NNy = 36;
  private int NNz = 36;
  private int NNa = 0;
  private int maxNNa = 2000;

  private double xMax = ddh*NNx;
  private double yMax = ddh*NNy;
  private double zMax = ddh*NNz; 

  private int NNN = 20000;
  private int lattice[][][] = new int[NNx][NNy][NNz];
  private int atom[][] = new int[NNN][3];
  private int kind[] = new int[NNN];
  private double transition[] = new double[NNN*6];
  private double transitionAtom[] = new double[NNN];
  private double rate[] = new double[8];

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


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

  KMC3D() {
    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 ia;

    t = 0.0;
    count = 0;

    initLattice();
    //setCrystal(10, 10, 10, 15, 15, 15);
	NNa = 0;
    for(ia=0;ia<100;ia++) {
      addAnAtom(maxNNa);
    }

    setAllTransition();
    changeFlag = 0;
  }

  private void initLattice() {
    int i,j,k;

    for(i=0;i<NNx;i++) {
      for(j=0;j<NNy;j++) {
        for(k=0;k<NNz;k++) {
          lattice[i][j][k] = -1;
        }
      }
    }
  }

  private void setCrystal(int ix, int iy, int iz, int nx, int ny, int nz) {
    int i,j,k,ia;

    ia = 0;
    for(i=ix;i<ix+nx;i++) {
      for(j=iy;j<iy+ny;j++) {
        for(k=iz;k<iz+nz;k++) {
          kind[ia] = 0;
          atom[ia][0] = i; atom[ia][1] = j; atom[ia][2] = k;
          lattice[i][j][k] = ia;
          ia += 1;
        }
      }
    }
    NNa = ia;
  }


  private void setAtom(int ia) {
    int i,j,k;

    do {
      i = (int)(0.99999999*Math.random()*NNx);
      j = (int)(0.99999999*Math.random()*NNy);
      k = (int)(0.99999999*Math.random()*NNz);
    } while (lattice[i][j][k]>= 0);
	
    atom[ia][0] = i; atom[ia][1] = j; atom[ia][2] = k;
    lattice[i][j][k] = ia;
  }

  //

  private void addAnAtom(int mxNNa) {
    int ia;

    if (NNa<mxNNa) {
      ia = NNa;
      setAtom(ia);
      NNa += 1;

      kind[ia] = 1;
      totalRate = setAllTransition();
      changeFlag = 0;
    }
  }


  // ---------------------------------- 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,nn;
    double deltat;

    if (Math.random()<addingRate) addAnAtom(maxNNa);

    //nn = NNa/10+1; if (nn>1000) nn = 1000;
    nn=50;
    for(i=0;i<nn;i++) {
      deltat = kmcStep();
      t = t + deltat;
    }
    correctTotalRate();
  }

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

    s = 0.0;
    for(i=0;i<NNa;i++) {
      s += transitionAtom[i];
    }
    totalRate = s;
  }

  private double kmcStep() {
    int i,ip;
    double r;

    if (changeFlag==1) {
      totalRate = setAllTransition();
      changeFlag = 0;
    }

    ip = selectTransion(totalRate);
    move(ip);

    r = (1.0-1.0e-12)*Math.random()+1.0e-12;
    return(-Math.log(r)/totalRate);
  }


  // set transition , and calc. sum of transition

  private double setAllTransition() {
    int ia;
    double rsum;

    setRate();

    rsum = 0.0;
    for(ia=0;ia<NNa;ia++) {
      rsum += setTransition(ia);
    }
    return (rsum);
  }

  private double setTransition(int ia) {
    int i,j,k,nb,id;
    double s;

    i = atom[ia][0]; j = atom[ia][1]; k = atom[ia][2];
    nb = noOfNeighbor(i,j,k);

    transition[ia*6+0] = dirRate((i+1)%NNx, j, k, nb);
    transition[ia*6+1] = dirRate((i-1+NNx)%NNx, j, k, nb);
    transition[ia*6+2] = dirRate(i, (j+1)%NNy, k, nb);
    transition[ia*6+3] = dirRate(i, (j-1+NNy)%NNy, k, nb);
    transition[ia*6+4] = dirRate(i, j, (k+1)%NNz, nb);
    transition[ia*6+5] = dirRate(i, j, (k-1+NNz)%NNz, nb);

    s = 0.0;
    for (id=0; id<6; id++) {
      s += transition[ia*6+id];
    }
    transitionAtom[ia] = s;
    return ( s );
  }

  private double dirRate(int ii, int jj, int kk, int nb) {
    int nb1;
    double rt;

    rt = 0.0;
    if (lattice[ii][jj][kk]>=0) {
      rt = 0.0;
    } else {
      nb1 = noOfNeighbor(ii,jj,kk)-1;
      if (nb<=nb1) {
        rt = rate[0];
      } else {
        rt = rate[nb-nb1];
      }
    }
    return(rt);
  }

  private int noOfNeighbor(int i, int j, int k) {
    int nb;

    nb = 0;
    if (lattice[(i+1)%NNx][j][k]>=0) nb += 1;
    if (lattice[(i-1+NNx)%NNx][j][k]>=0) nb += 1;
    if (lattice[i][(j+1)%NNy][k]>=0) nb += 1;
    if (lattice[i][(j-1+NNy)%NNy][k]>=0) nb += 1;
    if (lattice[i][j][(k+1)%NNz]>=0) nb += 1;
    if (lattice[i][j][(k-1+NNz)%NNz]>=0) nb += 1;
    return( nb );
  }

  private void setRate() {
    rate[0] = transitionRate(qqHopping);
    rate[1] = transitionRate(qqHopping + qqNeighbor);
    rate[2] = transitionRate(qqHopping + 2.0*qqNeighbor);
    rate[3] = transitionRate(qqHopping + 3.0*qqNeighbor);
    rate[4] = transitionRate(qqHopping + 4.0*qqNeighbor);
    rate[5] = transitionRate(qqHopping + 5.0*qqNeighbor);
    rate[6] = transitionRate(qqHopping + 6.0*qqNeighbor);
  }

  private double transitionRate(double energy) {
    double h,nue0;

    h = 6.626e-34;
    nue0 = kT*1.602e-19/h;

    return( nue0*Math.exp(-energy/kT) );
  }

  /* ----- hermonic transition state theory -----

  private double transitionRate(double energy) {
    double m,r,omega,nue,rate;

    m = 137.0*1.67e-27;
    r = 0.3*1.0e-9;
    omega = Math.sqrt(energy*1.6e-19/(m*r*r));
    nue = omega/(2.0*3.1416);//s

    rate = nue*Math.exp(-energy/kT);
    return( rate );
  }
  */

  // select transion

  private int selectTransion(double rsum) {
    int ia,iap;
    double rnd;

    rnd = rsum*Math.random();

    for (ia=0; ia<NNa; ia++) {
      rnd -= transitionAtom[ia];
      if (rnd<0.0) {
        rnd += transitionAtom[ia];
        for (iap=0; iap<6; iap++) {
          rnd -= transition[ia*6+iap];
          if (rnd<0.0) return (ia*6+iap);
        }
        return(ia*6+5);
      }
    }
    return((NNa-1)*6+5);
  }

  // move (update adatom[][],lattice[][])

  private void move(int ip) {
    int ia,id,i,j,k;
    double rs0,rs1;

    if (transition[ip]>0.0) {
      ia = ip/6;
      id = ip%6;
      i = atom[ia][0]; j = atom[ia][1]; k = atom[ia][2];

      lattice[i][j][k] = -1;
      if (id==0) i = (i+1)%NNx;
      if (id==1) i = (i-1+NNx)%NNx;
      if (id==2) j = (j+1)%NNy;
      if (id==3) j = (j-1+NNy)%NNy;
      if (id==4) k = (k+1)%NNz;
      if (id==5) k = (k-1+NNz)%NNz;
      atom[ia][0] = i; atom[ia][1] = j; atom[ia][2] = k;
      lattice[i][j][k] = ia;
	
      rs0 = rateAround(i,j,k);
      rs1 = setRateAround(i,j,k);
      totalRate = totalRate - rs0 + rs1;
    }
  }

  private double setRateAround(int i0, int j0, int k0) {
    int i,j,k,ii,jj,kk;
    double srate;

    srate = 0.0;
    for (i=i0-2; i<=i0+2; i++) {
      ii = (i+NNx)%NNx;
      for (j=j0-2; j<=j0+2; j++) {
        jj =  (j+NNy)%NNy;
        for (k=k0-2; k<=k0+2; k++) {
          kk =  (k+NNz)%NNz;
          if (lattice[ii][jj][kk]>=0) {
            srate += setTransition(lattice[ii][jj][kk]);
          }
        }
      }
    }
    return ( srate );
  }

  private double rateAround(int i0, int j0, int k0) {
    int i,j,k,ii,jj,kk;
    double srate;

    srate = 0.0;
    for (i=i0-2; i<=i0+2; i++) {
      ii = (i+NNx)%NNx;
      for (j=j0-2; j<=j0+2; j++) {
        jj =  (j+NNy)%NNy;
        for (k=k0-2; k<=k0+2; k++) {
          kk =  (k+NNz)%NNz;
          if (lattice[ii][jj][kk]>=0) {
            srate += transitionAtom[lattice[ii][jj][kk]];
          }
        }
      }
    }
    return ( srate );
  }

  // --------------------------------------- utilities -----------

  private int numberOfAtom() {
    int i,j,k,n;

    n = 0;
    for(i=0;i<NNx;i++) {
      for(j=0;j<NNy;j++) {
        for(k=0;k<NNz;k++) {
          if (lattice[i][j][k]>=0) n += 1;
        }
      }
    }
    return(n);
  }


  // ------------------------------------- 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 setAddingRate(double ar) { addingRate = ar; changeFlag = 1; }
  public double getAddingRate() { return addingRate; }
  public void setQHopping(double qh) { qqHopping = qh; changeFlag = 1; }
  public double getQHopping() { return qqHopping; }
  public void setQNeighbor(double qn) { qqNeighbor = qn; changeFlag = 1; }
  public double getQNeighbor() { return qqNeighbor; }
  public void setKT(double ev) { kT = ev; changeFlag = 1; }
  public double getKT() { return kT; }

  // get data
  public int getNNa() { return NNa; }
  public int getNNx() { return NNx; }
  public int getNNy() { return NNy; }
  public int getNNz() { return NNz; }
  public double getddh() { return ddh; }

  public double getTime() { return t; }
  public int getNumberOfAtom() { return numberOfAtom(); }
  public int getLattice(int i, int j, int k) { return lattice[i][j][k]; }
  public int getAtom(int ia, int d) { return atom[ia][d]; }
  public int getKind(int ia) { return kind[ia]; }

}

/* ----- kinetic Monte-Carlo algorithm -----
 * ( or the Bortz-Kalos-Liebowitz (BKL) algorithm )
 *
 * i-th transition rate in the system : ri
 * total transition rate : RN = sum(ri, {i=1,2,...,N})
 *
 * 1) t = 0
 *
 * 2) select i : randomly (proportional to ri/RN)
 *  calculate R(i) = sum(rj, {j=1,2,...,i})
 *  get a uniform random number u in [0,1]
 *  find i  R(i-1) < u RN <= R(i)
 *
 * 3) execute i-th transition
 *
 * 4) update the time
 *  get a uniform random numner u in (0,1]
 *  dt = -log(u)/R
 *  t = t + dt
 *
 * 5) goto 2)
 *
 * ---------- transition state -----
 *
 * transion rate k
 *  k = nue0*exp(-dE/kT)
 *  nue0 = kT/h , h: Plank constant
 *
 *
 * ----- hermonic transition state theory -----
 *
 * oscillation in hermonic potential 
 *  U(x) = k x^2, k = V/r^2 (<- U(r) = V)
 *
 * motion equation m a = - kx 
 *   omega = sqrt(k/m) = sqrt( V/(m*r^2) )
 *
 * transion rate = (omega/(2 pai))*exp(-V/kT)
 *
 * m = 137*1.67e-27; // Ba
 * V = 0.3eV = 0.3*1.6e-19;
 * r = 0.3e-9;
 *
 * omega/(2 pai) = 2.4e11 (1/s)
 *
 *
 */