Пример #1
0
  private void graphGrid(ArrayList<ArrayList<Position>> grid) throws InterruptedException {
    System.out.println(
        "Size of file by rows = " + grid.size() + ", columns = " + grid.get(0).size());
    final long current = System.currentTimeMillis();
    // System.out.println("Time for parsing file: " + ((current - startParseTime) / 1000) + " sec");
    // long afterEdge = 0;
    // long timeFindEdge = 0;

    ArrayList<Integer> ranges = findRanges();
    final Cell<Integer> threadsActive = new Cell<Integer>(threads);
    class EdgeThread extends Thread {

      int startRow = 0;
      int endRow = 0;

      public EdgeThread(int startRow, int endRow) {
        this.startRow = startRow;
        this.endRow = endRow;
      }

      public void run() {
        System.out.println("Thread: " + this.getId());
        findEdges(startRow, endRow);
        boolean lastThread;
        synchronized (threadsActive) {
          lastThread = --threadsActive.object == 0;
        }
        if (lastThread) {
          System.out.println("Last Thread: " + this.getId());
          long afterEdge = System.currentTimeMillis();
          long timeFindEdge = (afterEdge - current) / 1000;
          System.out.println("Time for findEdges: " + timeFindEdge + " sec");

          colorSCC();
          long afterColor = System.currentTimeMillis();
          long timeForColor = (afterColor - afterEdge) / 1000;
          System.out.println("Time for coloring and find CC: " + timeForColor + " sec");
          // findConnectedComponents();
          create();
          long timeForCreate = (System.currentTimeMillis() - afterColor) / 1000;
          System.out.println("Time for creating map: " + timeForCreate + " sec");
        }
      }
    }
    for (int i = 0; i < threads; i++) {
      EdgeThread thread = new EdgeThread(ranges.get(2 * i), ranges.get(2 * i + 1));
      thread.start();
    }

    Thread.currentThread().join();
  }
Пример #2
0
  public String toString(Molecule molecule) {
    // write header
    String returnString =
        String.format(
            "%%mem=%dGB\n%%nprocshared=%d\n#p geom=connect %s/genecp empiricaldispersion=gd3bj opt\n",
            mem, nprocshared, method);
    returnString += "\ntitle\n\n0 1\n";

    // write geometry
    returnString = returnString + molecule.getGJFstring() + "\n";

    // initialize some variables
    Atom fromAtom = null;
    Atom toAtom = null;
    Integer fromAtomNumber = 0;
    Integer toAtomNumber = 0;
    Double bondOrder = 0.0;
    DefaultWeightedEdge thisEdge = null;

    // read connectivity data into parallel arrays
    ArrayList<Integer> fromAtoms = new ArrayList<Integer>();
    ArrayList<Integer> toAtoms = new ArrayList<Integer>();
    ArrayList<Double> bondOrders = new ArrayList<Double>();
    ArrayList<Boolean> visited = new ArrayList<Boolean>();
    for (DefaultWeightedEdge e : molecule.connectivity.edgeSet()) {
      fromAtom = molecule.connectivity.getEdgeSource(e);
      fromAtomNumber = molecule.contents.indexOf(fromAtom) + 1;
      toAtom = molecule.connectivity.getEdgeTarget(e);
      toAtomNumber = molecule.contents.indexOf(toAtom) + 1;
      bondOrder = molecule.connectivity.getEdgeWeight(e);

      fromAtoms.add(fromAtomNumber);
      toAtoms.add(toAtomNumber);
      bondOrders.add(bondOrder);
      visited.add(false);
    }

    // write connectivity data
    for (int i = 0; i < molecule.contents.size(); i++) {
      returnString = returnString + (i + 1) + " ";
      for (int j = 0; j < fromAtoms.size(); j++) {
        if (fromAtoms.get(j) == i + 1 && visited.get(j) == false) {
          returnString =
              returnString + toAtoms.get(j) + " " + String.format("%.1f ", bondOrders.get(j));
          visited.set(j, true);
        }
        if (toAtoms.get(j) == i + 1 && visited.get(j) == false) {
          returnString =
              returnString + fromAtoms.get(j) + " " + String.format("%.1f ", bondOrders.get(j));
          visited.set(j, true);
        }
      }
      returnString = returnString + "\n";
    }

    // write footer
    returnString += String.format("\n@%s\n\n", basis);
    return returnString;
  }
Пример #3
0
 private ArrayList<Integer> findRanges() {
   int rowsPerRange = (int) Math.ceil((grid.size()) / (double) threads);
   ArrayList<Integer> ranges = new ArrayList<Integer>();
   int startRow = 0, endRow = rowsPerRange;
   for (int i = 0; i < threads; i++) {
     ranges.add(startRow);
     ranges.add(endRow);
     startRow = endRow;
     ;
     endRow += rowsPerRange;
   }
   ranges.set(ranges.size() - 1, Math.min(grid.size(), ranges.get(ranges.size() - 1)));
   System.out.println(ranges);
   return ranges;
 }
Пример #4
0
  private static <a> ArrayList<ArrayList<a>> transpose(ArrayList<ArrayList<a>> matrix) {
    ArrayList<ArrayList<a>> grid2 = new ArrayList<ArrayList<a>>();
    if (matrix.isEmpty()) return grid2;
    for (int i = 0; i < matrix.get(0).size(); i++) {

      grid2.add(new ArrayList<a>(matrix.size()));
    }
    System.out.println(grid2);
    for (int i = 0; i < matrix.size(); i++) {

      ArrayList<a> row = matrix.get(i);
      for (int j = 0; j < row.size(); j++) {

        grid2.get(j).add(row.get(j)); // .set(i, row.get(j));
      }
    }

    return grid2;
  }